diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 00000000000..aae2702499b --- /dev/null +++ b/.editorconfig @@ -0,0 +1,16 @@ +# https://editorconfig.org/ +root = true + +# Default settings for all files. +[*] +end_of_line = lf +insert_final_newline = true +charset = utf-8 +indent_style = space +indent_size = 4 +trim_trailing_whitespace = true +max_line_length = 120 + +# Set indent size for json and YAML files. +[*.{json,yml,yaml}] +indent_size = 2 diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index ec9da68e969..a058bdaf38a 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -18,7 +18,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: "3.9" + python-version: '3.x' - name: Install dependencies run: | @@ -31,7 +31,7 @@ jobs: ruff format --check . - name: mypy - run: mypy ${{ github.event.repository.name }} + run: mypy src - name: pyright run: pyright diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 377fe28e21a..b6d5930dd17 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -35,11 +35,11 @@ jobs: resolution: highest extras: ci,optional - os: ubuntu-latest - python: "3.12" + python: '>3.9' resolution: lowest-direct extras: ci,optional - os: macos-latest - python: "3.10" + python: '3.10' resolution: lowest-direct extras: ci # test with only required dependencies installed @@ -77,7 +77,7 @@ jobs: micromamba activate pmg # TODO remove temporary fix. added since uv install torch is flaky. # track https://github.com/astral-sh/uv/issues/1921 for resolution - pip install torch + pip install torch --upgrade uv pip install numpy cython uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }} diff --git a/.gitignore b/.gitignore index 21e0621b8fb..2ac37aea6df 100644 --- a/.gitignore +++ b/.gitignore @@ -40,3 +40,4 @@ venv/ ENV/ env.bak/ venv.bak/ +.pdm-python diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0c66fbd86bf..bba0fa50a46 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,16 +2,16 @@ exclude: ^(docs|tests/files|tasks.py) ci: autoupdate_schedule: monthly - skip: [mypy, pyright] + skip: [ mypy, pyright ] autofix_commit_msg: pre-commit auto-fixes autoupdate_commit_msg: pre-commit autoupdate repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.8 + rev: v0.5.0 hooks: - id: ruff - args: [--fix, --unsafe-fixes] + args: [ --fix, --unsafe-fixes ] - id: ruff-format - repo: https://github.com/pre-commit/pre-commit-hooks @@ -22,7 +22,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.10.0 + rev: v1.10.1 hooks: - id: mypy @@ -30,19 +30,20 @@ repos: rev: v2.3.0 hooks: - id: codespell - stages: [commit, commit-msg] - exclude_types: [html] - additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11 + stages: [ commit, commit-msg ] + exclude_types: [ html ] + additional_dependencies: [ tomli ] # needed to read pyproject.toml below py3.11 + exclude: src/pymatgen/analysis/aflow_prototypes.json - repo: https://github.com/MarcoGorelli/cython-lint rev: v0.16.2 hooks: - id: cython-lint - args: [--no-pycodestyle] + args: [ --no-pycodestyle ] - id: double-quote-cython-strings - repo: https://github.com/adamchainz/blacken-docs - rev: 1.16.0 + rev: 1.18.0 hooks: - id: blacken-docs @@ -55,15 +56,15 @@ repos: # MD033: no inline HTML # MD041: first line in a file should be a top-level heading # MD025: single title - args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"] + args: [ --disable, MD013, MD024, MD025, MD033, MD041, "--" ] - repo: https://github.com/kynan/nbstripout rev: 0.7.1 hooks: - id: nbstripout - args: [--drop-empty-cells, --keep-output] + args: [ --drop-empty-cells, --keep-output ] - repo: https://github.com/RobertCraigie/pyright-python - rev: v1.1.366 + rev: v1.1.369 hooks: - id: pyright diff --git a/dev_scripts/chemenv/explicit_permutations.py b/dev_scripts/chemenv/explicit_permutations.py index f3225fa5293..097e80b25e0 100644 --- a/dev_scripts/chemenv/explicit_permutations.py +++ b/dev_scripts/chemenv/explicit_permutations.py @@ -10,7 +10,6 @@ import os import numpy as np - from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import ( AllCoordinationGeometries, ExplicitPermutationsAlgorithm, diff --git a/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py b/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py index bd71080c300..689ae58d86a 100644 --- a/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py +++ b/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py @@ -9,7 +9,6 @@ import json import numpy as np - from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import ( AbstractGeometry, diff --git a/dev_scripts/chemenv/get_plane_permutations_optimized.py b/dev_scripts/chemenv/get_plane_permutations_optimized.py index ef92a27e63e..127ca009f19 100644 --- a/dev_scripts/chemenv/get_plane_permutations_optimized.py +++ b/dev_scripts/chemenv/get_plane_permutations_optimized.py @@ -15,7 +15,6 @@ import numpy as np import tabulate - from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import ( AbstractGeometry, @@ -236,7 +235,7 @@ def random_permutations_iterator(initial_permutation, n_permutations): sym_measures = [c["symmetry_measure"] for c in csms] prt1(string="Continuous symmetry measures", printing_volume=printing_volume) prt1(string=sym_measures, printing_volume=printing_volume) - csms_with_recorded_permutation = [] # type: ignore + csms_with_recorded_permutation: list = [] explicit_permutations = [] for icsm, csm in enumerate(csms): found = False @@ -308,7 +307,6 @@ def random_permutations_iterator(initial_permutation, n_permutations): all_planes_point_indices += algo.other_plane_points # Setup of the permutations to be used for this algorithm - indices = list(range(cg.coordination_number)) if permutations_setup_type == "all": perms_iterator = itertools.permutations(indices) @@ -400,7 +398,8 @@ def random_permutations_iterator(initial_permutation, n_permutations): else: perms_used[some_perm] = 1 tcurrent = time.process_time() - time_left = (n_permutations - idx_perm) * (tcurrent - t0) / idx_perm # type: ignore + assert n_permutations is not None + time_left = (n_permutations - idx_perm) * (tcurrent - t0) / idx_perm time_left = f"{time_left:.1f}" idx_perm += 1 print( diff --git a/dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py b/dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py index 495a8bb668e..70449d924f8 100644 --- a/dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py +++ b/dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py @@ -8,7 +8,6 @@ import matplotlib.pyplot as plt import numpy as np - from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import ( AngleNbSetWeight, CNBiasNbSetWeight, diff --git a/dev_scripts/chemenv/test_algos.py b/dev_scripts/chemenv/test_algos.py index dbffdce27e5..17933a067a3 100644 --- a/dev_scripts/chemenv/test_algos.py +++ b/dev_scripts/chemenv/test_algos.py @@ -8,7 +8,6 @@ from random import shuffle import numpy as np - from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import ( AbstractGeometry, diff --git a/dev_scripts/chemenv/view_environment.py b/dev_scripts/chemenv/view_environment.py index 2caa22e9f34..69aa6adc42e 100644 --- a/dev_scripts/chemenv/view_environment.py +++ b/dev_scripts/chemenv/view_environment.py @@ -3,7 +3,6 @@ from __future__ import annotations import numpy as np - from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import ( SEPARATION_PLANE, AllCoordinationGeometries, diff --git a/dev_scripts/potcar_scrambler.py b/dev_scripts/potcar_scrambler.py index 0dd2b0190fa..c0793c713d9 100644 --- a/dev_scripts/potcar_scrambler.py +++ b/dev_scripts/potcar_scrambler.py @@ -9,7 +9,6 @@ import numpy as np from monty.os.path import zpath from monty.serialization import zopen - from pymatgen.core import SETTINGS from pymatgen.io.vasp import Potcar, PotcarSingle from pymatgen.io.vasp.sets import _load_yaml_config diff --git a/dev_scripts/update_pt_data.py b/dev_scripts/update_pt_data.py index 09dcad5dd44..ee7889c75ea 100644 --- a/dev_scripts/update_pt_data.py +++ b/dev_scripts/update_pt_data.py @@ -11,9 +11,8 @@ import requests from monty.dev import requires from monty.serialization import dumpfn, loadfn -from ruamel import yaml - from pymatgen.core import Element, get_el_sp +from ruamel import yaml try: from bs4 import BeautifulSoup @@ -30,8 +29,8 @@ def parse_oxi_state(): oxi_data = re.sub("[\n\r]", "", oxi_data) patt = re.compile("(.*?)", re.MULTILINE) - for m in patt.finditer(oxi_data): - line = m.group(1) + for match in patt.finditer(oxi_data): + line = match[1] line = re.sub("", "", line) line = re.sub("()+", "", line) line = re.sub("]*>", "", line) @@ -39,15 +38,15 @@ def parse_oxi_state(): oxi_states = [] common_oxi = [] for tok in re.split("", line.strip()): - m2 = re.match(r"([A-Z][a-z]*)", tok) - if m2: - el = m2.group(1) + match2 = re.match(r"([A-Z][a-z]*)", tok) + if match2: + el = match2[1] else: - m3 = re.match(r"()*([\+\-]\d)()*", tok) - if m3: - oxi_states += [int(m3.group(2))] - if m3.group(1): - common_oxi += [int(m3.group(2))] + match3 = re.match(r"()*([\+\-]\d)()*", tok) + if match3: + oxi_states += [int(match3[2])] + if match3[1]: + common_oxi += [int(match3[2])] if el in data: del data[el]["Max oxidation state"] del data[el]["Min oxidation state"] @@ -79,7 +78,7 @@ def parse_ionic_radii(): ionic_radii = {} for tok_idx in range(3, len(tokens)): if match := re.match(r"^\s*([0-9\.]+)", tokens[tok_idx]): - ionic_radii[int(header[tok_idx])] = float(match.group(1)) + ionic_radii[int(header[tok_idx])] = float(match[1]) if el in data: data[el][f"Ionic_radii{suffix}"] = ionic_radii diff --git a/dev_scripts/update_spacegroup_data.py b/dev_scripts/update_spacegroup_data.py new file mode 100644 index 00000000000..a4607cdbee7 --- /dev/null +++ b/dev_scripts/update_spacegroup_data.py @@ -0,0 +1,95 @@ +"""Script to update symm_ops.json and symm_data.yaml in symmetry module due to issues #3845 and #3862. +symm_ops.json: +- adds Hermann_mauguin point group key and short Hermann Mauguin space group symbol +- converts screw axis notation to symm_data standard +symm_data.json +- removes mapping of rhombohedral space group types onto symbol + appended H +- replaces I/P2_12_121 key with I/P2_12_12_1 +""" + +from __future__ import annotations + +import sys + +from monty.serialization import dumpfn, loadfn +from pymatgen.symmetry.groups import PointGroup + +__author__ = "Katharina Ueltzen @kaueltzen" +__date__ = "2024-06-06" + +SYMM_OPS = loadfn("../src/pymatgen/symmetry/symm_ops.json") +SYMM_DATA = loadfn("../src/pymatgen/symmetry/symm_data.json") + + +def convert_symmops_to_sg_encoding(symbol: str) -> str: + """ + Utility function to convert SYMMOPS space group type symbol notation + into SYMM_DATA["space_group_encoding"] key notation with underscores before + translational part of screw axes. + Args: + symbol (str): "hermann_mauguin" or "universal_h_m" key of symmops.json + Returns: + symbol in the format of SYMM_DATA["space_group_encoding"] keys + """ + symbol_representation = symbol.split(":") + representation = ":" + "".join(symbol_representation[1].split(" ")) if len(symbol_representation) > 1 else "" + + blickrichtungen = symbol_representation[0].split(" ") + blickrichtungen_new = [] + for br in blickrichtungen: + if len(br) > 1 and br[0].isdigit() and br[1].isdigit(): + blickrichtungen_new.append(br[0] + "_" + br[1:]) + else: + blickrichtungen_new.append(br) + return "".join(blickrichtungen_new) + representation + + +def remove_identity_from_full_hermann_mauguin(symbol: str) -> str: + """ + Utility function to remove identity along blickrichtung (except in P1). + Args: + symbol (str): "hermann_mauguin" key of symmops.json + Returns: + short "hermann_mauguin" key + """ + if symbol in ("P 1", "C 1", "P 1 "): + return symbol + blickrichtungen = symbol.split(" ") + blickrichtungen_new = [] + for br in blickrichtungen: + if br != "1": + blickrichtungen_new.append(br + " ") + return "".join(blickrichtungen_new) + + +new_symm_data = {} +for k, v in SYMM_DATA["space_group_encoding"].items(): + if k.endswith("H"): + new_symm_data[k.removesuffix("H")] = v + elif k == "I2_12_121": + new_symm_data["I2_12_12_1"] = v + elif k == "P2_12_121": + new_symm_data["P2_12_12_1"] = v + else: + new_symm_data[k] = v + +SYMM_DATA["space_group_encoding"] = new_symm_data + +for spg_idx, spg in enumerate(SYMM_OPS): + if "(" in spg["hermann_mauguin"]: + SYMM_OPS[spg_idx]["hermann_mauguin"] = spg["hermann_mauguin"].split("(")[0] + + short_h_m = remove_identity_from_full_hermann_mauguin(SYMM_OPS[spg_idx]["hermann_mauguin"]) + SYMM_OPS[spg_idx]["short_h_m"] = convert_symmops_to_sg_encoding(short_h_m) + SYMM_OPS[spg_idx]["hermann_mauguin_u"] = convert_symmops_to_sg_encoding(spg["hermann_mauguin"]) + +for spg_idx, spg in enumerate(SYMM_OPS): + try: + pg = PointGroup.from_space_group(spg["short_h_m"]) + except AssertionError as e: + print(spg, str(e)) + sys.exit(1) + SYMM_OPS[spg_idx]["point_group"] = pg.symbol + +dumpfn(SYMM_DATA, "../src/pymatgen/symmetry/symm_data.json") +dumpfn(SYMM_OPS, "../src/pymatgen/symmetry/symm_ops.json") diff --git a/docs/CHANGES.md b/docs/CHANGES.md index 6b162785e8e..b080903b763 100644 --- a/docs/CHANGES.md +++ b/docs/CHANGES.md @@ -6,6 +6,14 @@ nav_order: 4 # Changelog +## v2024.7.18 +- Fix `setuptools` for packaging (#3934) +- Improve Keep Redundant Spaces algorithm for PatchedPhaseDiagram (#3900) +- Add electronic structure methods for Species (#3902) +- Migrate `spglib` to new `SpglibDataset` format with version 2.5.0 (#3923) +- SpaceGroup changes (#3859) +- Add MD input set to FHI-aims (#3896) + ## v2024.6.10 * Fix bug in `update_charge_from_potcar` (#3866) * Fix bug in VASP parameter parsing (@mkhorton) diff --git a/docs/apidoc/conf.py b/docs/apidoc/conf.py index 9e5eb5577f1..fe33a4e80b8 100644 --- a/docs/apidoc/conf.py +++ b/docs/apidoc/conf.py @@ -19,7 +19,7 @@ from pymatgen.core import __author__, __file__, __version__ project = "pymatgen" -copyright = "2011, Materials Project" +copyright = "2011, Materials Project" # noqa: A001 author = __author__ @@ -64,7 +64,7 @@ # General information about the project. project = "pymatgen" -copyright = f"2011, {__author__}" +copyright = f"2011, {__author__}" # noqa: A001 # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the diff --git a/docs/compatibility.md b/docs/compatibility.md index 61bdee2354c..115ed7ebe7e 100644 --- a/docs/compatibility.md +++ b/docs/compatibility.md @@ -67,6 +67,24 @@ Windows and Linux. ## Recent Breaking Changes +### v2024.?.? + +The `symbol` attribute of `SpaceGroup` now always refers to its Hermann-Mauguin symbol +(see [#3859](https://github.com/materialsproject/pymatgen/pull/3859)). In order to replace +the old symbol, run + +```py +from pymatgen.symmetry.groups import SpaceGroup + +try: + new_symbol = SpaceGroup(old_symbol).symbol +except ValueError: + if old_symbol in ["P2_12_121", "I2_12_121"]: + new_symbol = SpaceGroup(old_symbol[:-1]+"_1").symbol + else: + new_symbol = SpaceGroup(old_symbol[:-1]).symbol +``` + ### v2024.5.31 * Update VASP sets to transition `atomate2` to use `pymatgen` input sets exclusively by @esoteric-ephemera in [#3835](https://github.com/materialsproject/pymatgen/pull/3835) diff --git a/docs/contributing.md b/docs/contributing.md index b568dacc247..3080cdb14d1 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -4,55 +4,91 @@ title: Contributing nav_order: 6 --- -# Collaborative Github Workflow +# Recommended developer workflow -For developers interested in expanding `pymatgen` for their own purposes, we recommend forking `pymatgen` directly from the [`pymatgen` GitHub repo](https://github.com/materialsproject/pymatgen). Here's a typical workflow: +For developers interested in expanding `pymatgen` for their own purposes, we recommend forking `pymatgen` directly from +the [`pymatgen` GitHub repo](https://github.com/materialsproject/pymatgen). Here's a recommended workflow (updated Jun +2024): -1. Create a free GitHub account (if you don't already have one) and perform the necessary setup (e.g., install SSH keys etc.). +1. Create a free GitHub account (if you don't already have one) and perform the necessary setup (e.g., install SSH keys + etc.). -1. Fork the `pymatgen` GitHub repo, i.e., go to the main [`pymatgen` GitHub repo](https://github.com/materialsproject/pymatgen) and click fork to create a copy of the `pymatgen` code base on your own GitHub account. +1. Fork the `pymatgen` GitHub repo, i.e., go to the + main [`pymatgen` GitHub repo](https://github.com/materialsproject/pymatgen) and click fork to create a copy of + the `pymatgen` code base on your own GitHub account. 1. Install `git` on your local machine (if you don't already have it). -1. Clone *your forked repo* to your local machine. You will work mostly with your local repo and only publish changes when they are ready to be merged: +1. Clone *your forked repo* to your local machine. You will work mostly with your local repo and only publish changes + when they are ready to be merged: ```sh git clone https://github.com//pymatgen + cd pymatgen # Go into pmg directory. ``` - Note that the entire Github repo is fairly large because of the presence of test files, but these are necessary for rigorous testing. + Note that the entire Github repo is fairly large because of the presence of test files, but these are necessary for + rigorous testing. + +1. Install the [uv package manager](https://github.com/astral-sh/uv): + + ```sh + pip install uv + ``` + +1. Create a virtual env for pymatgen. + + ```sh + uv create venv # A virtual env will be created in the .venv directory in the repo. + source .venv/bin/activate + ``` + +1. Install pymatgen in editable mode with dev and optional dependencies: + + ```sh + uv pip install -e '.[ci,optional]' + pre-commit install # Install pre-commit hook for linters. + ``` 1. Make a new branch for your contributions ```sh - git checkout -b my-new-fix-or-feature # should be run from up-to-date master + git checkout -b my-new-fix-or-feature # should be run from up-to-date master ``` -1. Code (see [Coding Guidelines](#coding-guidelines)). Commit early and commit often. Keep your code up to date. You need to add the main repository to the list of your remotes. +1. Code (see [Coding Guidelines](#coding-guidelines)). Commit early and commit often. Keep your code up to date. You + need to add the main repository to the list of your remotes. ```sh git remote add upstream https://github.com/materialsproject/pymatgen ``` - Make sure your repository is clean (no uncommitted changes) and is currently on the master branch. If not, commit or stash any changes and switch to the master. + Make sure your repository is clean (no uncommitted changes) and is currently on the master branch. If not, commit or + stash any changes and switch to the master. ```sh git checkout master ``` - Then you can pull all the new commits from the main line + Then you can pull all the new commits from the main line ```sh git pull upstream master ``` - Remember, pull is a combination of the commands fetch and merge, so there may be merge conflicts to be manually resolved. + Remember, pull is a combination of the commands fetch and merge, so there may be merge conflicts to be manually + resolved. -1. Publish your contributions. Assuming that you now have a couple of commits that you would like to contribute to the main repository. Please follow the following steps: +1. Publish your contributions. Assuming that you now have a couple of commits that you would like to contribute to the + main repository. Please follow the following steps: - 1. If your change is based on a relatively old state of the main repository, then you should probably bring your repository up-to-date first to see if the change is not creating any merge conflicts. + 1. If your change is based on a relatively old state of the main repository, then you should probably bring your + repository up-to-date first to see if the change is not creating any merge conflicts. - 1. Check that everything compiles cleanly and passes all tests. The `pymatgen` repo comes with a complete set of tests for all modules. If you have written new modules or methods, you must write tests for the new code as well (see [Coding Guidelines](#coding-guidelines)). Install and run `pytest` in your local repo directory and fix all errors before continuing further. + 1. Check that everything compiles cleanly and passes all tests. The `pymatgen` repo comes with a complete set of + tests for all modules. If you have written new modules or methods, you must write tests for the new code as + well (see [Coding Guidelines](#coding-guidelines)). Install and run `pytest` in your local repo directory and fix + all errors before continuing further. 1. If everything is ok, publish the commits to your GitHub repository. @@ -60,25 +96,38 @@ For developers interested in expanding `pymatgen` for their own purposes, we rec git push origin master ``` -1. Now that your commit is published, it doesn't mean that it has already been merged into the main repository. You should issue a merge request to `pymatgen` maintainers. They will pull your commits and run their own tests before releasing. +1. Now that your commit is published, it doesn't mean that it has already been merged into the main repository. You + should issue a merge request to `pymatgen` maintainers. They will pull your commits and run their own tests before + releasing. -"Work-in-progress" pull requests are encouraged, especially if this is your first time contributing to `pymatgen`, and the maintainers will be happy to help or provide code review as necessary. Put "\[WIP\]" in the title of your pull request to indicate it's not ready to be merged. +"Work-in-progress" pull requests are encouraged, especially if this is your first time contributing to `pymatgen`, and +the maintainers will be happy to help or provide code review as necessary. Put "\[WIP\]" in the title of your pull +request to indicate it's not ready to be merged. ## Coding Guidelines -Given that `pymatgen` is intended to be a long-term code base, we adopt very strict quality control and coding guidelines for all contributions to `pymatgen`. The following must be satisfied for your contributions to be accepted into `pymatgen`. +Given that `pymatgen` is intended to be a long-term code base, we adopt very strict quality control and coding +guidelines for all contributions to `pymatgen`. The following must be satisfied for your contributions to be accepted +into `pymatgen`. -1. **Unit tests** are required for all new modules and methods. The only way to minimize code regression is to ensure that all code is well tested. Untested contributions will not be accepted. -1. **Python PEP 8** [code style](https://python.org/dev/peps/pep-0008). We allow a few exceptions when they are well-justified (e.g., Element's atomic number is given a variable name of capital Z, in line with accepted scientific convention), but generally, PEP 8 must be observed. Code style will be automatically checked for all PRs and must pass before any PR is merged. To aid you, you can install and run the same set of formatters and linters that will run in CI using +1. **Unit tests** are required for all new modules and methods. The only way to minimize code regression is to ensure + that all code is well tested. Untested contributions will not be accepted. +1. **Python PEP 8** [code style](https://python.org/dev/peps/pep-0008). We allow a few exceptions when they are + well-justified (e.g., Element's atomic number is given a variable name of capital Z, in line with accepted scientific + convention), but generally, PEP 8 must be observed. Code style will be automatically checked for all PRs and must + pass before any PR is merged. To aid you, you can install and run the same set of formatters and linters that will + run in CI using ```sh pre-commit install # ensures linters are run prior to all future commits pre-commit run --files path/to/changed/files # ensure your current uncommitted changes don't offend linters # or - pre-commit run --all-files # ensure your entire codebase passes linters + pre-commit run --all-files # ensure your entire codebase passes linters ``` -1. **Python 3**. We only support Python 3.8+. -1. **Documentation** is required for all modules, classes and methods. In particular, the method doc strings should make clear the arguments expected and the return values. For complex algorithms (e.g., an Ewald summation), a summary of the algorithm should be provided and preferably with a link to a publication outlining the method in detail. +1. **Python 3**. Check the `pyproject.toml` for the supported Python versions. +1. **Documentation** is required for all modules, classes and methods. In particular, the method doc strings should make + clear the arguments expected and the return values. For complex algorithms (e.g., an Ewald summation), a summary of + the algorithm should be provided and preferably with a link to a publication outlining the method in detail. For the above, if in doubt, please refer to the core classes in `pymatgen` for examples of what is expected. diff --git a/docs/modules.html b/docs/modules.html index 9b2c893e40b..45c32066fbe 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -4,7 +4,7 @@ - pymatgen — pymatgen 2024.6.4 documentation + pymatgen — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -36,7 +36,7 @@
- 2024.6.4 + 2024.6.10
@@ -305,15 +305,7 @@

pymatgen
  • pymatgen.analysis.solar package
  • pymatgen.analysis.structure_prediction package
      diff --git a/docs/pymatgen.alchemy.html b/docs/pymatgen.alchemy.html index a27e5f00e16..98e821cb368 100644 --- a/docs/pymatgen.alchemy.html +++ b/docs/pymatgen.alchemy.html @@ -4,7 +4,7 @@ - pymatgen.alchemy package — pymatgen 2024.6.4 documentation + pymatgen.alchemy package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
      - 2024.6.4 + 2024.6.10
      @@ -173,13 +173,13 @@

      Submodules
      -class AbstractStructureFilter[source]
      +class AbstractStructureFilter[source]

      Bases: MSONable, ABC

      Structures that return True when passed to the test() method are retained during transmutation. Those that return False are removed.

      -abstract test(structure: Structure)[source]
      +abstract test(structure: Structure)[source]

      Structures that return true are kept in the Transmuter object during filtering.

      Parameters:
      @@ -198,7 +198,7 @@

      Submodules
      -class ChargeBalanceFilter[source]
      +class ChargeBalanceFilter[source]

      Bases: AbstractStructureFilter

      This filter removes structures that are not charge balanced from the transmuter. This only works if the structure is oxidation state @@ -207,7 +207,7 @@

      Submodules
      -test(structure: Structure)[source]
      +test(structure: Structure)[source]

      True if structure is neutral.

      @@ -215,7 +215,7 @@

      Submodules
      -class ContainsSpecieFilter(species, strict_compare=False, AND=True, exclude=False)[source]
      +class ContainsSpecieFilter(species, strict_compare=False, AND=True, exclude=False)[source]

      Bases: AbstractStructureFilter

      Filter for structures containing certain elements or species. By default compares by atomic number.

      @@ -233,13 +233,13 @@

      Submodules
      -as_dict() → dict[source]
      +as_dict() → dict[source]

      Get MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]
      Parameters:

      dct (dict) – Dict representation.

      @@ -252,7 +252,7 @@

      Submodules
      -test(structure: Structure)[source]
      +test(structure: Structure)[source]

      True if structure does not contain specified species.

      @@ -260,7 +260,7 @@

      Submodules
      -class RemoveDuplicatesFilter(structure_matcher: dict | StructureMatcher | None = None, symprec: float | None = None)[source]
      +class RemoveDuplicatesFilter(structure_matcher: dict | StructureMatcher | None = None, symprec: float | None = None)[source]

      Bases: AbstractStructureFilter

      This filter removes exact duplicate structures from the transmuter.

      Remove duplicate structures based on the structure matcher @@ -278,7 +278,7 @@

      Submodules
      -test(structure: Structure) → bool[source]
      +test(structure: Structure) → bool[source]
      Parameters:

      structure (Structure) – Input structure to test.

      @@ -296,7 +296,7 @@

      Submodules
      -class RemoveExistingFilter(existing_structures, structure_matcher=None, symprec=None)[source]
      +class RemoveExistingFilter(existing_structures, structure_matcher=None, symprec=None)[source]

      Bases: AbstractStructureFilter

      This filter removes structures existing in a given list from the transmuter.

      Remove existing structures based on the structure matcher @@ -315,13 +315,13 @@

      Submodules
      -as_dict()[source]
      +as_dict()[source]

      Get MSONable dict.

      -test(structure: Structure)[source]
      +test(structure: Structure)[source]

      True if structure is not in existing list.

      @@ -329,7 +329,7 @@

      Submodules
      -class SpecieProximityFilter(specie_and_min_dist_dict)[source]
      +class SpecieProximityFilter(specie_and_min_dist_dict)[source]

      Bases: AbstractStructureFilter

      This filter removes structures that have certain species that are too close together.

      @@ -344,13 +344,13 @@

      Submodules
      -as_dict()[source]
      +as_dict()[source]

      Get MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]
      Parameters:

      dct (dict) – Dict representation.

      @@ -363,7 +363,7 @@

      Submodules
      -test(structure: Structure)[source]
      +test(structure: Structure)[source]

      True if structure does not contain species within specified distances.

      @@ -371,7 +371,7 @@

      Submodules
      -class SpeciesMaxDistFilter(sp1, sp2, max_dist)[source]
      +class SpeciesMaxDistFilter(sp1, sp2, max_dist)[source]

      Bases: AbstractStructureFilter

      This filter removes structures that do have two particular species that are not nearest neighbors by a predefined max_dist. For instance, if you are @@ -391,7 +391,7 @@

      Submodules
      -test(structure: Structure)[source]
      +test(structure: Structure)[source]

      True if structure contains the two species but their distance is greater than max_dist.

      @@ -405,7 +405,7 @@

      Submodules
      -class TransformedStructure(structure: Structure, transformations: AbstractTransformation | Sequence[AbstractTransformation] | None = None, history: list[AbstractTransformation | dict[str, Any]] | None = None, other_parameters: dict[str, Any] | None = None)[source]
      +class TransformedStructure(structure: Structure, transformations: AbstractTransformation | Sequence[AbstractTransformation] | None = None, history: list[AbstractTransformation | dict[str, Any]] | None = None, other_parameters: dict[str, Any] | None = None)[source]

      Bases: MSONable

      Container for new structures that include history of transformations.

      Each transformed structure is made up of a sequence of structures with @@ -423,7 +423,7 @@

      Submodules
      -append_filter(structure_filter: AbstractStructureFilter) → None[source]
      +append_filter(structure_filter: AbstractStructureFilter) → None[source]

      Add a filter.

      Parameters:
      @@ -435,7 +435,7 @@

      Submodules
      -append_transformation(transformation, return_alternatives: bool = False, clear_redo: bool = True) → list[TransformedStructure] | None[source]
      +append_transformation(transformation, return_alternatives: bool = False, clear_redo: bool = True) → list[TransformedStructure] | None[source]

      Append a transformation to the TransformedStructure.

      Parameters:
      @@ -457,13 +457,13 @@

      Submodules
      -as_dict() → dict[str, Any][source]
      +as_dict() → dict[str, Any][source]

      Dict representation of the TransformedStructure.

      -extend_transformations(transformations: list[AbstractTransformation], return_alternatives: bool = False) → None[source]
      +extend_transformations(transformations: list[AbstractTransformation], return_alternatives: bool = False) → None[source]

      Extend a sequence of transformations to the TransformedStructure.

      Parameters:
      @@ -480,7 +480,7 @@

      Submodules
      -classmethod from_cif_str(cif_string: str, transformations: list[AbstractTransformation] | None = None, primitive: bool = True, occupancy_tolerance: float = 1.0) → Self[source]
      +classmethod from_cif_str(cif_string: str, transformations: list[AbstractTransformation] | None = None, primitive: bool = True, occupancy_tolerance: float = 1.0) → Self[source]

      Generate TransformedStructure from a cif string.

      Parameters:
      @@ -508,13 +508,13 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Create a TransformedStructure from a dict.

      -classmethod from_poscar_str(poscar_string: str, transformations: list[AbstractTransformation] | None = None) → Self[source]
      +classmethod from_poscar_str(poscar_string: str, transformations: list[AbstractTransformation] | None = None) → Self[source]

      Generate TransformedStructure from a poscar string.

      Parameters:
      @@ -529,7 +529,7 @@

      Submodules
      -classmethod from_snl(snl: StructureNL) → Self[source]
      +classmethod from_snl(snl: StructureNL) → Self[source]

      Create TransformedStructure from SNL.

      Parameters:
      @@ -543,7 +543,7 @@

      Submodules
      -get_vasp_input(vasp_input_set: type[VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, **kwargs) → dict[str, Any][source]
      +get_vasp_input(vasp_input_set: type[VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, **kwargs) → dict[str, Any][source]

      Get VASP input as a dict of VASP objects.

      Parameters:
      @@ -558,7 +558,7 @@

      Submodules
      -redo_next_change() → None[source]
      +redo_next_change() → None[source]

      Redo the last undone change in the TransformedStructure.

      Raises:
      @@ -569,7 +569,7 @@

      Submodules
      -set_parameter(key: str, value: Any) → TransformedStructure[source]
      +set_parameter(key: str, value: Any) → TransformedStructure[source]

      Set a parameter.

      Parameters:
      @@ -586,14 +586,14 @@

      Submodules
      -property structures: list[Structure][source]
      +property structures: list[Structure][source]

      Copy of all structures in the TransformedStructure. A structure is stored after every single transformation.

      -to_snl(authors: list[str], **kwargs) → StructureNL[source]
      +to_snl(authors: list[str], **kwargs) → StructureNL[source]

      Generate a StructureNL from TransformedStructure.

      Parameters:
      @@ -613,7 +613,7 @@

      Submodules
      -undo_last_change() → None[source]
      +undo_last_change() → None[source]

      Undo the last change in the TransformedStructure.

      Raises:
      @@ -624,7 +624,7 @@

      Submodules
      -property was_modified: bool[source]
      +property was_modified: bool[source]

      Boolean describing whether the last transformation on the structure made any alterations to it one example of when this would return false is in the case of performing a substitution transformation on the @@ -633,7 +633,7 @@

      Submodules
      -write_vasp_input(vasp_input_set: type[~pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, **kwargs) → None[source]
      +write_vasp_input(vasp_input_set: type[~pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, **kwargs) → None[source]

      Write VASP input to an output_dir.

      Parameters:
      @@ -662,7 +662,7 @@

      Submodules
      -class CifTransmuter(cif_string, transformations=None, primitive=True, extend_collection=False)[source]
      +class CifTransmuter(cif_string, transformations=None, primitive=True, extend_collection=False)[source]

      Bases: StandardTransmuter

      Generate a Transmuter from a cif string, possibly containing multiple structures.

      @@ -684,7 +684,7 @@

      Submodules
      -classmethod from_filenames(filenames, transformations=None, primitive=True, extend_collection=False) → Self[source]
      +classmethod from_filenames(filenames, transformations=None, primitive=True, extend_collection=False) → Self[source]

      Generate a TransformedStructureCollection from a cif, possibly containing multiple structures.

      @@ -704,7 +704,7 @@

      Submodules
      -class PoscarTransmuter(poscar_string, transformations=None, extend_collection=False)[source]
      +class PoscarTransmuter(poscar_string, transformations=None, extend_collection=False)[source]

      Bases: StandardTransmuter

      Generate a transmuter from a sequence of POSCARs.

      @@ -720,7 +720,7 @@

      Submodules
      -classmethod from_filenames(poscar_filenames, transformations=None, extend_collection=False) → StandardTransmuter[source]
      +classmethod from_filenames(poscar_filenames, transformations=None, extend_collection=False) → StandardTransmuter[source]

      Convenient constructor to generates a POSCAR transmuter from a list of POSCAR filenames.

      @@ -739,13 +739,13 @@

      Submodules
      -class StandardTransmuter(transformed_structures: list[TransformedStructure], transformations=None, extend_collection: int = 0, ncores: int | None = None)[source]
      +class StandardTransmuter(transformed_structures: list[TransformedStructure], transformations=None, extend_collection: int = 0, ncores: int | None = None)[source]

      Bases: object

      An example of a Transmuter object, which performs a sequence of transformations on many structures to generate TransformedStructures.

      -transformed_structures[source]
      +transformed_structures[source]

      List of all transformed structures.

      Type:
      @@ -775,7 +775,7 @@

      Submodules
      -add_tags(tags)[source]
      +add_tags(tags)[source]

      Add tags for the structures generated by the transmuter.

      Parameters:
      @@ -787,7 +787,7 @@

      Submodules
      -append_transformation(transformation, extend_collection=False, clear_redo=True)[source]
      +append_transformation(transformation, extend_collection=False, clear_redo=True)[source]

      Append a transformation to all TransformedStructures.

      Parameters:
      @@ -817,7 +817,7 @@

      Submodules
      -append_transformed_structures(trafo_structs_or_transmuter)[source]
      +append_transformed_structures(trafo_structs_or_transmuter)[source]

      Overloaded to accept either a list of transformed structures or transmuter, it which case it appends the second transmuter’s structures.

      @@ -829,7 +829,7 @@

      Submodules
      -apply_filter(structure_filter: AbstractStructureFilter)[source]
      +apply_filter(structure_filter: AbstractStructureFilter)[source]

      Apply a structure_filter to the list of TransformedStructures in the transmuter.

      @@ -841,7 +841,7 @@

      Submodules
      -extend_transformations(transformations)[source]
      +extend_transformations(transformations)[source]

      Extend a sequence of transformations to the TransformedStructure.

      Parameters:
      @@ -852,7 +852,7 @@

      Submodules
      -classmethod from_structures(structures, transformations=None, extend_collection=0) → Self[source]
      +classmethod from_structures(structures, transformations=None, extend_collection=0) → Self[source]

      Alternative constructor from structures rather than TransformedStructures.

      @@ -875,7 +875,7 @@

      Submodules
      -redo_next_change() → None[source]
      +redo_next_change() → None[source]

      Redo the last undone transformation in the TransformedStructure.

      Raises:
      @@ -886,7 +886,7 @@

      Submodules
      -set_parameter(key, value)[source]
      +set_parameter(key, value)[source]

      Add parameters to the transmuter. Additional parameters are stored in the as_dict() output.

      @@ -901,7 +901,7 @@

      Submodules
      -undo_last_change() → None[source]
      +undo_last_change() → None[source]

      Undo the last transformation in the TransformedStructure.

      Raises:
      @@ -912,7 +912,7 @@

      Submodules
      -write_vasp_input(**kwargs)[source]
      +write_vasp_input(**kwargs)[source]

      Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{formula}_{number}.

      @@ -926,7 +926,7 @@

      Submodules
      -batch_write_vasp_input(transformed_structures: Sequence[TransformedStructure], vasp_input_set: type[VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, subfolder: Callable[[TransformedStructure], str] | None = None, include_cif: bool = False, **kwargs)[source]
      +batch_write_vasp_input(transformed_structures: Sequence[TransformedStructure], vasp_input_set: type[VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, subfolder: Callable[[TransformedStructure], str] | None = None, include_cif: bool = False, **kwargs)[source]

      Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{group}/{formula}_{number}.

      diff --git a/docs/pymatgen.analysis.chemenv.connectivity.html b/docs/pymatgen.analysis.chemenv.connectivity.html index d15d305e286..1637c30333d 100644 --- a/docs/pymatgen.analysis.chemenv.connectivity.html +++ b/docs/pymatgen.analysis.chemenv.connectivity.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.connectivity package — pymatgen 2024.6.4 documentation + pymatgen.analysis.chemenv.connectivity package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
      - 2024.6.4 + 2024.6.10
      @@ -173,7 +173,7 @@

      Submodules
      -class ConnectedComponent(environments=None, links=None, environments_data=None, links_data=None, graph=None)[source]
      +class ConnectedComponent(environments=None, links=None, environments_data=None, links_data=None, graph=None)[source]

      Bases: MSONable

      Describe the connected components in a structure in terms of coordination environments.

      Constructor for the ConnectedComponent object.

      @@ -196,7 +196,7 @@

      Submodules
      -as_dict()[source]
      +as_dict()[source]

      Bson-serializable dict representation of the ConnectedComponent object.

      Returns:
      @@ -210,7 +210,7 @@

      Submodules
      -compute_periodicity(algorithm='all_simple_paths') → None[source]
      +compute_periodicity(algorithm='all_simple_paths') → None[source]
      Parameters:

      () (algorithm)

      @@ -220,19 +220,19 @@

      Submodules
      -compute_periodicity_all_simple_paths_algorithm()[source]
      +compute_periodicity_all_simple_paths_algorithm()[source]

      Get the periodicity vectors of the connected component.

      -compute_periodicity_cycle_basis() → None[source]
      +compute_periodicity_cycle_basis() → None[source]

      Compute periodicity vectors of the connected component.

      -coordination_sequence(source_node, path_size=5, coordination='number', include_source=False)[source]
      +coordination_sequence(source_node, path_size=5, coordination='number', include_source=False)[source]

      Get the coordination sequence for a given node.

      Parameters:
      @@ -282,7 +282,7 @@

      Submodules
      -description(full=False)[source]
      +description(full=False)[source]
      Parameters:

      full (bool) – Whether to return a short or full description.

      @@ -298,7 +298,7 @@

      Submodules
      -elastic_centered_graph(start_node=None)[source]
      +elastic_centered_graph(start_node=None)[source]
      Parameters:

      () (start_node)

      @@ -314,7 +314,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstructs the ConnectedComponent object from a dict representation of the ConnectedComponent object created using the as_dict method.

      @@ -332,7 +332,7 @@

      Submodules
      -classmethod from_graph(g) → Self[source]
      +classmethod from_graph(g) → Self[source]

      Constructor for the ConnectedComponent object from a graph of the connected component.

      Parameters:
      @@ -349,44 +349,44 @@

      Submodules
      -property graph[source]
      +property graph[source]

      The Networkx MultiGraph object of this connected component with environment as nodes and links between these nodes as edges with information about the image cell difference if any.

      -property is_0d: bool[source]
      +property is_0d: bool[source]

      Whether this connected component is 0-dimensional.

      -property is_1d: bool[source]
      +property is_1d: bool[source]

      Whether this connected component is 1-dimensional.

      -property is_2d: bool[source]
      +property is_2d: bool[source]

      Whether this connected component is 2-dimensional.

      -property is_3d: bool[source]
      +property is_3d: bool[source]

      Whether this connected component is 3-dimensional.

      -property is_periodic: bool[source]
      +property is_periodic: bool[source]

      Whether this connected component is periodic.

      -make_supergraph(multiplicity)[source]
      +make_supergraph(multiplicity)[source]
      Parameters:

      () (multiplicity)

      @@ -402,19 +402,19 @@

      Submodules
      -property periodicity[source]
      +property periodicity[source]

      Periodicity of this connected component.

      -property periodicity_vectors[source]
      +property periodicity_vectors[source]

      Periodicity vectors of this connected component.

      -show_graph(graph: MultiGraph | None = None, save_file: str | None = None, drawing_type: str = 'internal') → None[source]
      +show_graph(graph: MultiGraph | None = None, save_file: str | None = None, drawing_type: str = 'internal') → None[source]

      Displays the graph using the specified drawing type.

      Parameters:
      @@ -432,7 +432,7 @@

      Submodules
      -draw_network(env_graph, pos, ax, sg=None, periodicity_vectors=None)[source]
      +draw_network(env_graph, pos, ax, sg=None, periodicity_vectors=None)[source]

      Draw network of environments in a matplotlib figure axes.

      Parameters:
      @@ -449,7 +449,7 @@

      Submodules
      -make_supergraph(graph, multiplicity, periodicity_vectors)[source]
      +make_supergraph(graph, multiplicity, periodicity_vectors)[source]

      Make super graph from a graph of environments.

      Parameters:
      @@ -474,7 +474,7 @@

      Submodules
      -class ConnectivityFinder(multiple_environments_choice=None)[source]
      +class ConnectivityFinder(multiple_environments_choice=None)[source]

      Bases: object

      Main class used to find the structure connectivity of a structure.

      Constructor for the ConnectivityFinder.

      @@ -489,7 +489,7 @@

      Submodules
      -get_structure_connectivity(light_structure_environments)[source]
      +get_structure_connectivity(light_structure_environments)[source]

      Get the structure connectivity from the coordination environments provided as an input.

      @@ -508,7 +508,7 @@

      Submodules
      -setup_parameters(multiple_environments_choice)[source]
      +setup_parameters(multiple_environments_choice)[source]

      Setup of the parameters for the connectivity finder.

      @@ -520,7 +520,7 @@

      Submodules
      -class AbstractEnvironmentNode(central_site, i_central_site)[source]
      +class AbstractEnvironmentNode(central_site, i_central_site)[source]

      Bases: MSONable

      Abstract class used to define an environment as a node in a graph.

      Constructor for the AbstractEnvironmentNode object.

      @@ -535,104 +535,104 @@

      Submodules
      -ATOM = 6[source]
      +ATOM = 6[source]

      -CE_NNBCES_NBCES_LIGANDS = -1[source]
      +CE_NNBCES_NBCES_LIGANDS = -1[source]
      -COORDINATION_ENVIRONMENT = 0[source]
      +COORDINATION_ENVIRONMENT = 0[source]
      -DEFAULT_EXTENSIONS = (6, 0)[source]
      +DEFAULT_EXTENSIONS = (6, 0)[source]
      -LIGANDS_ARRANGEMENT = 4[source]
      +LIGANDS_ARRANGEMENT = 4[source]
      -NEIGHBORING_CES = 2[source]
      +NEIGHBORING_CES = 2[source]
      -NEIGHBORING_COORDINATION_ENVIRONMENTS = 2[source]
      +NEIGHBORING_COORDINATION_ENVIRONMENTS = 2[source]
      -NEIGHBORS_LIGANDS_ARRANGEMENT = 5[source]
      +NEIGHBORS_LIGANDS_ARRANGEMENT = 5[source]
      -NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE = 3[source]
      +NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE = 3[source]
      -NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT = 3[source]
      +NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT = 3[source]
      -NUMBER_OF_NEIGHBORING_CES = 1[source]
      +NUMBER_OF_NEIGHBORING_CES = 1[source]
      -NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS = 1[source]
      +NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS = 1[source]
      -property atom_symbol[source]
      +property atom_symbol[source]

      Symbol of the atom on the central site.

      -property ce[source]
      +property ce[source]

      Coordination environment of this node.

      -property ce_symbol[source]
      +property ce_symbol[source]

      Coordination environment of this node.

      -abstract property coordination_environment[source]
      +abstract property coordination_environment[source]

      Coordination environment of this node.

      -everything_equal(other)[source]
      +everything_equal(other)[source]

      Check equality with respect to another AbstractEnvironmentNode using the index of the central site as well as the central site itself.

      -property isite[source]
      +property isite[source]

      Index of the central site.

      -property mp_symbol[source]
      +property mp_symbol[source]

      Coordination environment of this node.

      @@ -640,7 +640,7 @@

      Submodules
      -class EnvironmentNode(central_site, i_central_site, ce_symbol)[source]
      +class EnvironmentNode(central_site, i_central_site, ce_symbol)[source]

      Bases: AbstractEnvironmentNode

      Define an environment as a node in a graph.

      Constructor for the EnvironmentNode object.

      @@ -656,13 +656,13 @@

      Submodules
      -property coordination_environment[source]
      +property coordination_environment[source]

      Coordination environment of this node.

      -everything_equal(other)[source]
      +everything_equal(other)[source]

      Compare with another environment node.

      Returns:
      @@ -678,7 +678,7 @@

      Submodules
      -get_environment_node(central_site, i_central_site, ce_symbol)[source]
      +get_environment_node(central_site, i_central_site, ce_symbol)[source]

      Get the EnvironmentNode class or subclass for the given site and symbol.

      Parameters:
      @@ -700,7 +700,7 @@

      Submodules
      -class StructureConnectivity(light_structure_environment, connectivity_graph=None, environment_subgraphs=None)[source]
      +class StructureConnectivity(light_structure_environment, connectivity_graph=None, environment_subgraphs=None)[source]

      Bases: MSONable

      Main class containing the connectivity of a structure.

      Constructor for the StructureConnectivity object.

      @@ -721,7 +721,7 @@

      Submodules
      -add_bonds(isite, site_neighbors_set)[source]
      +add_bonds(isite, site_neighbors_set)[source]

      Add the bonds for a given site index to the structure connectivity graph.

      Parameters:
      @@ -735,19 +735,19 @@

      Submodules
      -add_sites()[source]
      +add_sites()[source]

      Add the sites in the structure connectivity graph.

      -as_dict()[source]
      +as_dict()[source]

      Convert to MSONable dict.

      -environment_subgraph(environments_symbols=None, only_atoms=None)[source]
      +environment_subgraph(environments_symbols=None, only_atoms=None)[source]
      Parameters:
        @@ -766,7 +766,7 @@

        Submodules
        -classmethod from_dict(dct: dict) → Self[source]
        +classmethod from_dict(dct: dict) → Self[source]
        Parameters:

        dct (dict)

        @@ -779,33 +779,33 @@

        Submodules
        -get_connected_components(environments_symbols=None, only_atoms=None)[source]
        +get_connected_components(environments_symbols=None, only_atoms=None)[source]

        +print_links() → None[source]

        Print all links in the graph.

        -setup_atom_environment_subgraph(atom_environment)[source]
        +setup_atom_environment_subgraph(atom_environment)[source]
        -setup_atom_environments_subgraph(atoms_environments)[source]
        +setup_atom_environments_subgraph(atoms_environments)[source]
        -setup_connectivity_description()[source]
        +setup_connectivity_description()[source]
        -setup_environment_subgraph(environments_symbols, only_atoms=None)[source]
        +setup_environment_subgraph(environments_symbols, only_atoms=None)[source]

        Set up the graph for predefined environments and optionally atoms.

        Parameters:
        @@ -819,14 +819,14 @@

        Submodules
        -setup_environments_subgraph(environments_symbols)[source]
        +setup_environments_subgraph(environments_symbols)[source]

        -get_delta_image(isite1, isite2, data1, data2)[source]
        +get_delta_image(isite1, isite2, data1, data2)[source]

        Helper method to get the delta image between one environment and another from the ligand’s delta images.

        diff --git a/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files.html b/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files.html index 8108b82bb2b..baf9fc27fce 100644 --- a/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files.html +++ b/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files package — pymatgen 2024.6.4 documentation + pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
        - 2024.6.4 + 2024.6.10
        diff --git a/docs/pymatgen.analysis.chemenv.coordination_environments.html b/docs/pymatgen.analysis.chemenv.coordination_environments.html index 27f22d0cdc7..0cc1f18f6a8 100644 --- a/docs/pymatgen.analysis.chemenv.coordination_environments.html +++ b/docs/pymatgen.analysis.chemenv.coordination_environments.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.coordination_environments package — pymatgen 2024.6.4 documentation + pymatgen.analysis.chemenv.coordination_environments package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
        - 2024.6.4 + 2024.6.10
        @@ -555,7 +555,7 @@

        Submodules
        -class AbstractChemenvStrategy(structure_environments=None, symmetry_measure_type='csm_wcs_ctwcc')[source]
        +class AbstractChemenvStrategy(structure_environments=None, symmetry_measure_type='csm_wcs_ctwcc')[source]

        Bases: MSONable, ABC

        Base class to define a Chemenv strategy for the neighbors and coordination environment to be applied to a StructureEnvironments object.

        @@ -568,32 +568,32 @@

        Submodules
        -AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
        +AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]

      -DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
      +DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
      -STRATEGY_DESCRIPTION: str | None = None[source]
      +STRATEGY_DESCRIPTION: str | None = None[source]
      -STRATEGY_INFO_FIELDS: ClassVar[list] = [][source]
      +STRATEGY_INFO_FIELDS: ClassVar[list] = [][source]
      -STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = {}[source]
      +STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = {}[source]
      -abstract as_dict()[source]
      +abstract as_dict()[source]

      Bson-serializable dict representation of the SimplestChemenvStrategy object.

      Returns:
      @@ -604,7 +604,7 @@

      Submodules
      -equivalent_site_index_and_transform(psite)[source]
      +equivalent_site_index_and_transform(psite)[source]

      Get the equivalent site and corresponding symmetry+translation transformations.

      Parameters:
      @@ -618,7 +618,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstructs the SimpleAbundanceChemenvStrategy object from a dict representation of the SimpleAbundanceChemenvStrategy object created using the as_dict method.

      @@ -633,7 +633,7 @@

      Submodules
      -get_site_ce_fractions_and_neighbors(site, full_ce_info=False, strategy_info=False)[source]
      +get_site_ce_fractions_and_neighbors(site, full_ce_info=False, strategy_info=False)[source]

      Applies the strategy to the structure_environments object in order to get coordination environments, their fraction, csm, geometry_info, and neighbors

      @@ -649,7 +649,7 @@

      Submodules
      -abstract get_site_coordination_environment(site)[source]
      +abstract get_site_coordination_environment(site)[source]

      Applies the strategy to the structure_environments object in order to define the coordination environment of a given site.

      @@ -665,7 +665,7 @@

      Submodules
      -abstract get_site_coordination_environments(site)[source]
      +abstract get_site_coordination_environments(site)[source]

      Applies the strategy to the structure_environments object in order to define the coordination environment of a given site.

      @@ -681,7 +681,7 @@

      Submodules
      -abstract get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0, return_maps=True, return_strategy_dict_info=False)[source]
      +abstract get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0, return_maps=True, return_strategy_dict_info=False)[source]

      Applies the strategy to the structure_environments object in order to define the coordination environment of a given site.

      @@ -697,7 +697,7 @@

      Submodules
      -abstract get_site_neighbors(site)[source]
      +abstract get_site_neighbors(site)[source]

      Applies the strategy to the structure_environments object in order to get the neighbors of a given site.

      Parameters:
      @@ -716,13 +716,13 @@

      Submodules
      -prepare_symmetries()[source]
      +prepare_symmetries()[source]

      Prepare the symmetries for the structure contained in the structure environments.

      -set_option(option_name, option_value)[source]
      +set_option(option_name, option_value)[source]

      Set up a given option for this strategy.

      Parameters:
      @@ -736,7 +736,7 @@

      Submodules
      -set_structure_environments(structure_environments)[source]
      +set_structure_environments(structure_environments)[source]

      Set the structure environments to this strategy.

      Parameters:
      @@ -747,7 +747,7 @@

      Submodules
      -setup_options(all_options_dict)[source]
      +setup_options(all_options_dict)[source]

      Set up options for this strategy based on a dict.

      Parameters:
      @@ -758,13 +758,13 @@

      Submodules
      -property symmetry_measure_type[source]
      +property symmetry_measure_type[source]

      Type of symmetry measure.

      -property uniquely_determines_coordination_environments[source]
      +property uniquely_determines_coordination_environments[source]

      True if the strategy leads to a unique coordination environment.

      @@ -772,29 +772,29 @@

      Submodules
      -class AdditionalConditionInt(integer)[source]
      +class AdditionalConditionInt(integer)[source]

      Bases: int, StrategyOption

      Integer representing an additional condition in a strategy.

      Special int representing additional conditions.

      -allowed_values: str | None = "Integer amongst :\n - 0 for 'No additional condition'\n - 1 for 'Only anion-cation bonds'\n - 2 for 'No element-element bonds (same elements)'\n - 3 for 'Only anion-cation bonds and no element-element bonds (same elements)'\n - 4 for 'Only element-oxygen bonds'\n"[source]
      +allowed_values: str | None = "Integer amongst :\n - 0 for 'No additional condition'\n - 1 for 'Only anion-cation bonds'\n - 2 for 'No element-element bonds (same elements)'\n - 3 for 'Only anion-cation bonds and no element-element bonds (same elements)'\n - 4 for 'Only element-oxygen bonds'\n"[source]
      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -description = 'Only element-oxygen bonds'[source]
      +description = 'Only element-oxygen bonds'[source]
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize additional condition from dict.

      Parameters:
      @@ -805,14 +805,14 @@

      Submodules
      -integer = 4[source]
      +integer = 4[source]

      -class AngleCutoffFloat(cutoff)[source]
      +class AngleCutoffFloat(cutoff)[source]

      Bases: float, StrategyOption

      Angle cutoff in a strategy.

      Special float that should be between 0 and 1.

      @@ -823,18 +823,18 @@

      Submodules
      -allowed_values: str | None = 'Real number between 0 and 1'[source]
      +allowed_values: str | None = 'Real number between 0 and 1'[source]

      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize angle cutoff from dict.

      Parameters:
      @@ -847,7 +847,7 @@

      Submodules
      -class AngleNbSetWeight(aa=1)[source]
      +class AngleNbSetWeight(aa=1)[source]

      Bases: NbSetWeight

      Weight of neighbors set based on the angle.

      Initialize AngleNbSetWeight estimator.

      @@ -858,12 +858,12 @@

      Submodules
      -SHORT_NAME = 'AngleWeight'[source]
      +SHORT_NAME = 'AngleWeight'[source]

      -static angle_sum(nb_set)[source]
      +static angle_sum(nb_set)[source]

      Sum of all angles in a neighbors set.

      Parameters:
      @@ -877,7 +877,7 @@

      Submodules
      -angle_sumn(nb_set)[source]
      +angle_sumn(nb_set)[source]

      Sum of all angles to a given power in a neighbors set.

      Parameters:
      @@ -891,19 +891,19 @@

      Submodules
      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Construct AngleNbSetWeight from dict representation.

      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -927,7 +927,7 @@

      Submodules
      -class AnglePlateauNbSetWeight(angle_function=None, weight_function=None)[source]
      +class AnglePlateauNbSetWeight(angle_function=None, weight_function=None)[source]

      Bases: NbSetWeight

      Weight of neighbors set based on the angle.

      Initialize AnglePlateauNbSetWeight.

      @@ -941,18 +941,18 @@

      Submodules
      -SHORT_NAME = 'AnglePlateauWeight'[source]
      +SHORT_NAME = 'AnglePlateauWeight'[source]

      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize from dict.

      Parameters:
      @@ -966,7 +966,7 @@

      Submodules
      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -990,7 +990,7 @@

      Submodules
      -class CNBiasNbSetWeight(cn_weights, initialization_options)[source]
      +class CNBiasNbSetWeight(cn_weights, initialization_options)[source]

      Bases: NbSetWeight

      Weight of neighbors set based on specific biases towards specific coordination numbers.

      Initialize CNBiasNbSetWeight.

      @@ -1004,18 +1004,18 @@

      Submodules
      -SHORT_NAME = 'CNBiasWeight'[source]
      +SHORT_NAME = 'CNBiasWeight'[source]

      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod explicit(cn_weights)[source]
      +classmethod explicit(cn_weights)[source]

      Initialize weights explicitly for each coordination.

      Parameters:
      @@ -1029,7 +1029,7 @@

      Submodules
      -classmethod from_description(dct: dict) → Self[source]
      +classmethod from_description(dct: dict) → Self[source]

      Initialize weights from description.

      Parameters:
      @@ -1043,7 +1043,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize from dict.

      Parameters:
      @@ -1057,7 +1057,7 @@

      Submodules
      -classmethod geometrically_equidistant(weight_cn1, weight_cn13)[source]
      +classmethod geometrically_equidistant(weight_cn1, weight_cn13)[source]

      Initialize geometrically equidistant weights for each coordination.

      Arge:

      weight_cn1: Weight of coordination 1. @@ -1073,7 +1073,7 @@

      Submodules
      -classmethod linearly_equidistant(weight_cn1, weight_cn13)[source]
      +classmethod linearly_equidistant(weight_cn1, weight_cn13)[source]

      Initialize linearly equidistant weights for each coordination.

      Parameters:
      @@ -1090,7 +1090,7 @@

      Submodules
      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -1114,7 +1114,7 @@

      Submodules
      -class CSMFloat(cutoff)[source]
      +class CSMFloat(cutoff)[source]

      Bases: float, StrategyOption

      Real number representing a Continuous Symmetry Measure.

      Special float that should be between 0 and 100.

      @@ -1125,18 +1125,18 @@

      Submodules
      -allowed_values: str | None = 'Real number between 0 and 100'[source]
      +allowed_values: str | None = 'Real number between 0 and 100'[source]

      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize CSM from dict.

      Parameters:
      @@ -1149,7 +1149,7 @@

      Submodules
      -class DeltaCSMNbSetWeight(effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}, weight_estimator={'function': 'smootherstep', 'options': {'delta_csm_max': 3.0, 'delta_csm_min': 0.5}}, delta_cn_weight_estimators=None, symmetry_measure_type='csm_wcs_ctwcc')[source]
      +class DeltaCSMNbSetWeight(effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}, weight_estimator={'function': 'smootherstep', 'options': {'delta_csm_max': 3.0, 'delta_csm_min': 0.5}}, delta_cn_weight_estimators=None, symmetry_measure_type='csm_wcs_ctwcc')[source]

      Bases: NbSetWeight

      Weight of neighbors set based on the differences of CSM.

      Initialize DeltaCSMNbSetWeight.

      @@ -1165,33 +1165,33 @@

      Submodules
      -DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = {'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}[source]
      +DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = {'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}[source]

      -DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
      +DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
      -DEFAULT_WEIGHT_ESTIMATOR: ClassVar = {'function': 'smootherstep', 'options': {'delta_csm_max': 3.0, 'delta_csm_min': 0.5}}[source]
      +DEFAULT_WEIGHT_ESTIMATOR: ClassVar = {'function': 'smootherstep', 'options': {'delta_csm_max': 3.0, 'delta_csm_min': 0.5}}[source]
      -SHORT_NAME = 'DeltaCSMWeight'[source]
      +SHORT_NAME = 'DeltaCSMWeight'[source]
      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod delta_cn_specifics(delta_csm_mins=None, delta_csm_maxs=None, function='smootherstep', symmetry_measure_type='csm_wcs_ctwcc', effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}})[source]
      +classmethod delta_cn_specifics(delta_csm_mins=None, delta_csm_maxs=None, function='smootherstep', symmetry_measure_type='csm_wcs_ctwcc', effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}})[source]

      Initialize DeltaCSMNbSetWeight from specific coordination number differences.

      Parameters:
      @@ -1211,7 +1211,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize from dict.

      Parameters:
      @@ -1225,7 +1225,7 @@

      Submodules
      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -1249,7 +1249,7 @@

      Submodules
      -class DeltaDistanceNbSetWeight(weight_function=None, nbs_source='voronoi')[source]
      +class DeltaDistanceNbSetWeight(weight_function=None, nbs_source='voronoi')[source]

      Bases: NbSetWeight

      Weight of neighbors set based on the difference of distances.

      Initialize DeltaDistanceNbSetWeight.

      @@ -1263,18 +1263,18 @@

      Submodules
      -SHORT_NAME = 'DeltaDistanceNbSetWeight'[source]
      +SHORT_NAME = 'DeltaDistanceNbSetWeight'[source]

      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize from dict.

      Parameters:
      @@ -1288,7 +1288,7 @@

      Submodules
      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -1312,7 +1312,7 @@

      Submodules
      -class DistanceAngleAreaNbSetWeight(weight_type='has_intersection', surface_definition={'angle_bounds': {'lower': 0.1, 'upper': 0.8}, 'distance_bounds': {'lower': 1.2, 'upper': 1.8}, 'type': 'standard_elliptic'}, nb_sets_from_hints='fallback_to_source', other_nb_sets='0_weight', additional_condition=1, smoothstep_distance=None, smoothstep_angle=None)[source]
      +class DistanceAngleAreaNbSetWeight(weight_type='has_intersection', surface_definition={'angle_bounds': {'lower': 0.1, 'upper': 0.8}, 'distance_bounds': {'lower': 1.2, 'upper': 1.8}, 'type': 'standard_elliptic'}, nb_sets_from_hints='fallback_to_source', other_nb_sets='0_weight', additional_condition=1, smoothstep_distance=None, smoothstep_angle=None)[source]

      Bases: NbSetWeight

      Weight of neighbors set based on the area in the distance-angle space.

      Initialize CNBiasNbSetWeight.

      @@ -1331,28 +1331,28 @@

      Submodules
      -AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
      +AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]

      -DEFAULT_SURFACE_DEFINITION: ClassVar = {'angle_bounds': {'lower': 0.1, 'upper': 0.8}, 'distance_bounds': {'lower': 1.2, 'upper': 1.8}, 'type': 'standard_elliptic'}[source]
      +DEFAULT_SURFACE_DEFINITION: ClassVar = {'angle_bounds': {'lower': 0.1, 'upper': 0.8}, 'distance_bounds': {'lower': 1.2, 'upper': 1.8}, 'type': 'standard_elliptic'}[source]
      -SHORT_NAME = 'DistAngleAreaWeight'[source]
      +SHORT_NAME = 'DistAngleAreaWeight'[source]
      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize from dict.

      Parameters:
      @@ -1366,7 +1366,7 @@

      Submodules
      -rectangle_crosses_area(d1, d2, a1, a2)[source]
      +rectangle_crosses_area(d1, d2, a1, a2)[source]

      Whether a given rectangle crosses the area defined by the upper and lower curves.

      Parameters:
      @@ -1382,7 +1382,7 @@

      Submodules
      -w_area_has_intersection(nb_set, structure_environments, cn_map, additional_info)[source]
      +w_area_has_intersection(nb_set, structure_environments, cn_map, additional_info)[source]

      Get intersection of the neighbors set area with the surface.

      Parameters:
      @@ -1401,7 +1401,7 @@

      Submodules
      -w_area_intersection_nbsfh_fbs_onb0(nb_set, structure_environments, cn_map, additional_info)[source]
      +w_area_intersection_nbsfh_fbs_onb0(nb_set, structure_environments, cn_map, additional_info)[source]

      Get intersection of the neighbors set area with the surface.

      Parameters:
      @@ -1420,7 +1420,7 @@

      Submodules
      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -1444,7 +1444,7 @@

      Submodules
      -class DistanceCutoffFloat(cutoff)[source]
      +class DistanceCutoffFloat(cutoff)[source]

      Bases: float, StrategyOption

      Distance cutoff in a strategy.

      Special float that should be between 1 and infinity.

      @@ -1455,18 +1455,18 @@

      Submodules
      -allowed_values: str | None = 'Real number between 1 and +infinity'[source]
      +allowed_values: str | None = 'Real number between 1 and +infinity'[source]

      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize distance cutoff from dict.

      Parameters:
      @@ -1479,7 +1479,7 @@

      Submodules
      -class DistanceNbSetWeight(weight_function=None, nbs_source='voronoi')[source]
      +class DistanceNbSetWeight(weight_function=None, nbs_source='voronoi')[source]

      Bases: NbSetWeight

      Weight of neighbors set based on the distance.

      Initialize DistanceNbSetWeight.

      @@ -1493,18 +1493,18 @@

      Submodules
      -SHORT_NAME = 'DistanceNbSetWeight'[source]
      +SHORT_NAME = 'DistanceNbSetWeight'[source]

      -as_dict()[source]
      +as_dict()[source]

      MSOnable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize from dict.

      Parameters:
      @@ -1518,7 +1518,7 @@

      Submodules
      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -1542,7 +1542,7 @@

      Submodules
      -class DistancePlateauNbSetWeight(distance_function=None, weight_function=None)[source]
      +class DistancePlateauNbSetWeight(distance_function=None, weight_function=None)[source]

      Bases: NbSetWeight

      Weight of neighbors set based on the distance.

      Initialize DistancePlateauNbSetWeight.

      @@ -1556,18 +1556,18 @@

      Submodules
      -SHORT_NAME = 'DistancePlateauWeight'[source]
      +SHORT_NAME = 'DistancePlateauWeight'[source]

      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize from dict.

      Parameters:
      @@ -1581,7 +1581,7 @@

      Submodules
      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -1605,7 +1605,7 @@

      Submodules
      -class MultiWeightsChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc', dist_ang_area_weight=None, self_csm_weight=None, delta_csm_weight=None, cn_bias_weight=None, angle_weight=None, normalized_angle_distance_weight=None, ce_estimator={'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}})[source]
      +class MultiWeightsChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc', dist_ang_area_weight=None, self_csm_weight=None, delta_csm_weight=None, cn_bias_weight=None, angle_weight=None, normalized_angle_distance_weight=None, ce_estimator={'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}})[source]

      Bases: WeightedNbSetChemenvStrategy

      MultiWeightsChemenvStrategy.

      Constructor for the MultiWeightsChemenvStrategy.

      @@ -1617,17 +1617,17 @@

      Submodules
      -DEFAULT_CE_ESTIMATOR: ClassVar = {'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}}[source]
      +DEFAULT_CE_ESTIMATOR: ClassVar = {'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}}[source]

      -STRATEGY_DESCRIPTION: str | None = 'Multi Weights ChemenvStrategy'[source]
      +STRATEGY_DESCRIPTION: str | None = 'Multi Weights ChemenvStrategy'[source]
      -as_dict()[source]
      +as_dict()[source]
      Returns:

      Bson-serializable dict representation of the MultiWeightsChemenvStrategy object.

      @@ -1637,7 +1637,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstructs the MultiWeightsChemenvStrategy object from a dict representation of the MultipleAbundanceChemenvStrategy object created using the as_dict method.

      @@ -1652,13 +1652,13 @@

      Submodules
      -classmethod stats_article_weights_parameters()[source]
      +classmethod stats_article_weights_parameters()[source]

      Initialize strategy used in the statistics article.

      -property uniquely_determines_coordination_environments[source]
      +property uniquely_determines_coordination_environments[source]

      Whether this strategy uniquely determines coordination environments.

      @@ -1666,18 +1666,18 @@

      Submodules
      -class NbSetWeight[source]
      +class NbSetWeight[source]

      Bases: MSONable, ABC

      Abstract base class for neighbor set weight estimations.

      -abstract as_dict()[source]
      +abstract as_dict()[source]

      A JSON-serializable dict representation of this neighbors set weight.

      -abstract weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +abstract weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -1701,7 +1701,7 @@

      Submodules
      -class NormalizedAngleDistanceNbSetWeight(average_type, aa, bb)[source]
      +class NormalizedAngleDistanceNbSetWeight(average_type, aa, bb)[source]

      Bases: NbSetWeight

      Weight of neighbors set based on the normalized angle/distance.

      Initialize NormalizedAngleDistanceNbSetWeight.

      @@ -1716,12 +1716,12 @@

      Submodules
      -SHORT_NAME = 'NormAngleDistWeight'[source]
      +SHORT_NAME = 'NormAngleDistWeight'[source]

      -static ang(nb_set)[source]
      +static ang(nb_set)[source]

      Angle weight.

      Parameters:
      @@ -1735,7 +1735,7 @@

      Submodules
      -static anginvdist(nb_set)[source]
      +static anginvdist(nb_set)[source]

      Angle/distance weight.

      Parameters:
      @@ -1749,7 +1749,7 @@

      Submodules
      -anginvndist(nb_set)[source]
      +anginvndist(nb_set)[source]

      Angle/power distance weight.

      Parameters:
      @@ -1763,7 +1763,7 @@

      Submodules
      -angn(nb_set)[source]
      +angn(nb_set)[source]

      Power angle weight.

      Parameters:
      @@ -1777,7 +1777,7 @@

      Submodules
      -angninvdist(nb_set)[source]
      +angninvdist(nb_set)[source]

      Power angle/distance weight.

      Parameters:
      @@ -1791,7 +1791,7 @@

      Submodules
      -angninvndist(nb_set)[source]
      +angninvndist(nb_set)[source]

      Power angle/power distance weight.

      Parameters:
      @@ -1805,13 +1805,13 @@

      Submodules
      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -static aweight(fda_list)[source]
      +static aweight(fda_list)[source]

      Standard mean of the weights.

      Parameters:
      @@ -1825,7 +1825,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize from dict.

      Parameters:
      @@ -1839,7 +1839,7 @@

      Submodules
      -static gweight(fda_list)[source]
      +static gweight(fda_list)[source]

      Geometric mean of the weights.

      Parameters:
      @@ -1853,7 +1853,7 @@

      Submodules
      -static invdist(nb_set)[source]
      +static invdist(nb_set)[source]

      Inverse distance weight.

      Parameters:
      @@ -1867,7 +1867,7 @@

      Submodules
      -invndist(nb_set)[source]
      +invndist(nb_set)[source]

      Inverse power distance weight.

      Parameters:
      @@ -1881,7 +1881,7 @@

      Submodules
      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -1905,7 +1905,7 @@

      Submodules
      -class SelfCSMNbSetWeight(effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}, weight_estimator={'function': 'power2_decreasing_exp', 'options': {'alpha': 1, 'max_csm': 8.0}}, symmetry_measure_type='csm_wcs_ctwcc')[source]
      +class SelfCSMNbSetWeight(effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}, weight_estimator={'function': 'power2_decreasing_exp', 'options': {'alpha': 1, 'max_csm': 8.0}}, symmetry_measure_type='csm_wcs_ctwcc')[source]

      Bases: NbSetWeight

      Weight of neighbors set based on the Self CSM.

      Initialize SelfCSMNbSetWeight.

      @@ -1920,33 +1920,33 @@

      Submodules
      -DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = {'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}[source]
      +DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = {'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}[source]

      -DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
      +DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
      -DEFAULT_WEIGHT_ESTIMATOR: ClassVar = {'function': 'power2_decreasing_exp', 'options': {'alpha': 1, 'max_csm': 8.0}}[source]
      +DEFAULT_WEIGHT_ESTIMATOR: ClassVar = {'function': 'power2_decreasing_exp', 'options': {'alpha': 1, 'max_csm': 8.0}}[source]
      -SHORT_NAME = 'SelfCSMWeight'[source]
      +SHORT_NAME = 'SelfCSMWeight'[source]
      -as_dict()[source]
      +as_dict()[source]

      MSONable dict.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Initialize from dict.

      Parameters:
      @@ -1960,7 +1960,7 @@

      Submodules
      -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
      +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

      Get the weight of a given neighbors set.

      Parameters:
      @@ -1984,7 +1984,7 @@

      Submodules
      -class SimpleAbundanceChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc')[source]
      +class SimpleAbundanceChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc')[source]

      Bases: AbstractChemenvStrategy

      Simple ChemenvStrategy using the neighbors that are the most “abundant” in the grid of angle and distance parameters for the definition of neighbors in the Voronoi approach. @@ -1998,27 +1998,27 @@

      Submodules
      -DEFAULT_ADDITIONAL_CONDITION = 1[source]
      +DEFAULT_ADDITIONAL_CONDITION = 1[source]

      -DEFAULT_MAX_DIST = 2.0[source]
      +DEFAULT_MAX_DIST = 2.0[source]
      -STRATEGY_DESCRIPTION: str | None = 'Simple Abundance ChemenvStrategy using the most "abundant" neighbors map \nfor the definition of neighbors in the Voronoi approach. \nThe coordination environment is then given as the one with the \nlowest continuous symmetry measure.'[source]
      +STRATEGY_DESCRIPTION: str | None = 'Simple Abundance ChemenvStrategy using the most "abundant" neighbors map \nfor the definition of neighbors in the Voronoi approach. \nThe coordination environment is then given as the one with the \nlowest continuous symmetry measure.'[source]
      -STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = {'additional_condition': {'default': 1, 'internal': '_additional_condition', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt'>}, 'surface_calculation_type': {}}[source]
      +STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = {'additional_condition': {'default': 1, 'internal': '_additional_condition', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt'>}, 'surface_calculation_type': {}}[source]
      -as_dict()[source]
      +as_dict()[source]

      Bson-serializable dict representation of the SimpleAbundanceChemenvStrategy object.

      Returns:
      @@ -2029,7 +2029,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstructs the SimpleAbundanceChemenvStrategy object from a dict representation of the SimpleAbundanceChemenvStrategy object created using the as_dict method.

      @@ -2044,7 +2044,7 @@

      Submodules
      -get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]
      +get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]

      Get the coordination environment of a given site.

      Parameters:
      @@ -2065,7 +2065,7 @@

      Submodules
      -get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]
      +get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]

      Get the coordination environments of a given site.

      Parameters:
      @@ -2086,7 +2086,7 @@

      Submodules
      -get_site_neighbors(site)[source]
      +get_site_neighbors(site)[source]

      Get the neighbors of a given site with this strategy.

      Parameters:
      @@ -2100,7 +2100,7 @@

      Submodules
      -property uniquely_determines_coordination_environments[source]
      +property uniquely_determines_coordination_environments[source]

      Whether this strategy uniquely determines coordination environments.

      @@ -2108,7 +2108,7 @@

      Submodules
      -class SimplestChemenvStrategy(structure_environments=None, distance_cutoff=1.4, angle_cutoff=0.3, additional_condition=1, continuous_symmetry_measure_cutoff=10, symmetry_measure_type='csm_wcs_ctwcc')[source]
      +class SimplestChemenvStrategy(structure_environments=None, distance_cutoff=1.4, angle_cutoff=0.3, additional_condition=1, continuous_symmetry_measure_cutoff=10, symmetry_measure_type='csm_wcs_ctwcc')[source]

      Bases: AbstractChemenvStrategy

      Simplest ChemenvStrategy using fixed angle and distance parameters for the definition of neighbors in the Voronoi approach. The coordination environment is then given as the one with the lowest continuous symmetry measure.

      @@ -2123,37 +2123,37 @@

      Submodules
      -DEFAULT_ADDITIONAL_CONDITION = 1[source]
      +DEFAULT_ADDITIONAL_CONDITION = 1[source]

      -DEFAULT_ANGLE_CUTOFF = 0.3[source]
      +DEFAULT_ANGLE_CUTOFF = 0.3[source]
      -DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF = 10[source]
      +DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF = 10[source]
      -DEFAULT_DISTANCE_CUTOFF = 1.4[source]
      +DEFAULT_DISTANCE_CUTOFF = 1.4[source]
      -STRATEGY_DESCRIPTION: str | None = 'Simplest ChemenvStrategy using fixed angle and distance parameters \nfor the definition of neighbors in the Voronoi approach. \nThe coordination environment is then given as the one with the \nlowest continuous symmetry measure.'[source]
      +STRATEGY_DESCRIPTION: str | None = 'Simplest ChemenvStrategy using fixed angle and distance parameters \nfor the definition of neighbors in the Voronoi approach. \nThe coordination environment is then given as the one with the \nlowest continuous symmetry measure.'[source]
      -STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = {'additional_condition': {'default': 1, 'internal': '_additional_condition', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt'>}, 'angle_cutoff': {'default': 0.3, 'internal': '_angle_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat'>}, 'continuous_symmetry_measure_cutoff': {'default': 10, 'internal': '_continuous_symmetry_measure_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat'>}, 'distance_cutoff': {'default': 1.4, 'internal': '_distance_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceCutoffFloat'>}}[source]
      +STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = {'additional_condition': {'default': 1, 'internal': '_additional_condition', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt'>}, 'angle_cutoff': {'default': 0.3, 'internal': '_angle_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat'>}, 'continuous_symmetry_measure_cutoff': {'default': 10, 'internal': '_continuous_symmetry_measure_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat'>}, 'distance_cutoff': {'default': 1.4, 'internal': '_distance_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceCutoffFloat'>}}[source]
      -add_strategy_visualization_to_subplot(subplot, visualization_options=None, plot_type=None)[source]
      +add_strategy_visualization_to_subplot(subplot, visualization_options=None, plot_type=None)[source]

      Add a visual of the strategy on a distance-angle plot.

      Parameters:
      @@ -2168,19 +2168,19 @@

      Submodules
      -property additional_condition[source]
      +property additional_condition[source]

      Additional condition for this strategy.

      -property angle_cutoff[source]
      +property angle_cutoff[source]

      Angle cutoff used.

      -as_dict()[source]
      +as_dict()[source]

      Bson-serializable dict representation of the SimplestChemenvStrategy object.

      Returns:
      @@ -2191,19 +2191,19 @@

      Submodules
      -property continuous_symmetry_measure_cutoff[source]
      +property continuous_symmetry_measure_cutoff[source]

      CSM cutoff used.

      -property distance_cutoff[source]
      +property distance_cutoff[source]

      Distance cutoff used.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstructs the SimplestChemenvStrategy object from a dict representation of the SimplestChemenvStrategy object created using the as_dict method.

      @@ -2218,7 +2218,7 @@

      Submodules
      -get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]
      +get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]

      Get the coordination environment of a given site.

      Parameters:
      @@ -2239,7 +2239,7 @@

      Submodules
      -get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]
      +get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]

      Get the coordination environments of a given site.

      Parameters:
      @@ -2260,7 +2260,7 @@

      Submodules
      -get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0, return_maps=True, return_strategy_dict_info=False)[source]
      +get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0, return_maps=True, return_strategy_dict_info=False)[source]

      Get the coordination environments of a given site and additional information.

      Parameters:
      @@ -2284,7 +2284,7 @@

      Submodules
      -get_site_neighbors(site, isite=None, dequivsite=None, dthissite=None, mysym=None)[source]
      +get_site_neighbors(site, isite=None, dequivsite=None, dthissite=None, mysym=None)[source]

      Get the neighbors of a given site.

      Parameters:
      @@ -2304,7 +2304,7 @@

      Submodules
      -property uniquely_determines_coordination_environments[source]
      +property uniquely_determines_coordination_environments[source]

      Whether this strategy uniquely determines coordination environments.

      @@ -2312,17 +2312,17 @@

      Submodules
      -class StrategyOption[source]
      +class StrategyOption[source]

      Bases: MSONable, ABC

      Abstract class for the options of the chemenv strategies.

      -allowed_values: str | None = None[source]
      +allowed_values: str | None = None[source]
      -abstract as_dict()[source]
      +abstract as_dict()[source]

      A JSON-serializable dict representation of this strategy option.

      @@ -2330,7 +2330,7 @@

      Submodules
      -class TargetedPenaltiedAbundanceChemenvStrategy(structure_environments=None, truncate_dist_ang=True, additional_condition=1, max_nabundant=5, target_environments=('O:6',), target_penalty_type='max_csm', max_csm=5.0, symmetry_measure_type='csm_wcs_ctwcc')[source]
      +class TargetedPenaltiedAbundanceChemenvStrategy(structure_environments=None, truncate_dist_ang=True, additional_condition=1, max_nabundant=5, target_environments=('O:6',), target_penalty_type='max_csm', max_csm=5.0, symmetry_measure_type='csm_wcs_ctwcc')[source]

      Bases: SimpleAbundanceChemenvStrategy

      Simple ChemenvStrategy using the neighbors that are the most “abundant” in the grid of angle and distance parameters for the definition of neighbors in the Voronoi approach, with a bias for a given list of target @@ -2354,12 +2354,12 @@

      Submodules
      -DEFAULT_TARGET_ENVIRONMENTS = ('O:6',)[source]
      +DEFAULT_TARGET_ENVIRONMENTS = ('O:6',)[source]

      -as_dict()[source]
      +as_dict()[source]

      Bson-serializable dict representation of the TargetedPenaltiedAbundanceChemenvStrategy object.

      Returns:
      @@ -2370,7 +2370,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstructs the TargetedPenaltiedAbundanceChemenvStrategy object from a dict representation of the TargetedPenaltiedAbundanceChemenvStrategy object created using the as_dict method.

      @@ -2385,7 +2385,7 @@

      Submodules
      -get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]
      +get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]

      Get the coordination environment of a given site.

      Parameters:
      @@ -2406,7 +2406,7 @@

      Submodules
      -property uniquely_determines_coordination_environments[source]
      +property uniquely_determines_coordination_environments[source]

      Whether this strategy uniquely determines coordination environments.

      @@ -2414,7 +2414,7 @@

      Submodules
      -class WeightedNbSetChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc', nb_set_weights=None, ce_estimator={'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}})[source]
      +class WeightedNbSetChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc', nb_set_weights=None, ce_estimator={'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}})[source]

      Bases: AbstractChemenvStrategy

      WeightedNbSetChemenvStrategy.

      Constructor for the WeightedNbSetChemenvStrategy.

      @@ -2426,17 +2426,17 @@

      Submodules
      -DEFAULT_CE_ESTIMATOR: ClassVar = {'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}}[source]
      +DEFAULT_CE_ESTIMATOR: ClassVar = {'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}}[source]

      -STRATEGY_DESCRIPTION: str | None = '    WeightedNbSetChemenvStrategy'[source]
      +STRATEGY_DESCRIPTION: str | None = '    WeightedNbSetChemenvStrategy'[source]
      -as_dict()[source]
      +as_dict()[source]

      Bson-serializable dict representation of the WeightedNbSetChemenvStrategy object.

      Returns:
      @@ -2447,7 +2447,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstructs the WeightedNbSetChemenvStrategy object from a dict representation of the WeightedNbSetChemenvStrategy object created using the as_dict method.

      @@ -2462,14 +2462,14 @@

      Submodules
      -get_site_coordination_environment(site)[source]
      +get_site_coordination_environment(site)[source]

      Get the coordination environment of a given site.

      Not implemented for this strategy

      -get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]
      +get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]

      Get the coordination environments of a given site.

      Parameters:
      @@ -2490,7 +2490,7 @@

      Submodules
      -get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0, return_maps=True, return_strategy_dict_info=False, return_all=False)[source]
      +get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0, return_maps=True, return_strategy_dict_info=False, return_all=False)[source]

      Get the coordination environments of a given site and additional information.

      Parameters:
      @@ -2514,14 +2514,14 @@

      Submodules
      -get_site_neighbors(site)[source]
      +get_site_neighbors(site)[source]

      Get the neighbors of a given site.

      Not implemented for this strategy.

      -property uniquely_determines_coordination_environments[source]
      +property uniquely_determines_coordination_environments[source]

      Whether this strategy uniquely determines coordination environments.

      @@ -2529,7 +2529,7 @@

      Submodules
      -get_effective_csm(nb_set, cn_map, structure_environments, additional_info, symmetry_measure_type, max_effective_csm, effective_csm_estimator_ratio_function)[source]
      +get_effective_csm(nb_set, cn_map, structure_environments, additional_info, symmetry_measure_type, max_effective_csm, effective_csm_estimator_ratio_function)[source]

      Get the effective continuous symmetry measure of a given neighbors set.

      Parameters:
      @@ -2551,7 +2551,7 @@

      Submodules
      -set_info(additional_info, field, isite, cn_map, value) → None[source]
      +set_info(additional_info, field, isite, cn_map, value) → None[source]

      Set additional information for the weights.

      Parameters:
      @@ -2581,7 +2581,7 @@

      Submodules
      -class AbstractChemenvAlgorithm(algorithm_type)[source]
      +class AbstractChemenvAlgorithm(algorithm_type)[source]

      Bases: MSONable, ABC

      Base class used to define a Chemenv algorithm used to identify the correct permutation for the computation of the Continuous Symmetry Measure.

      @@ -2593,13 +2593,13 @@

      Submodules
      -property algorithm_type: str[source]
      +property algorithm_type: str[source]

      The type of algorithm.

      -abstract as_dict() → dict[str, Any][source]
      +abstract as_dict() → dict[str, Any][source]

      A JSON-serializable dict representation of the algorithm.

      @@ -2607,7 +2607,7 @@

      Submodules
      -class AllCoordinationGeometries(permutations_safe_override=False, only_symbols=None)[source]
      +class AllCoordinationGeometries(permutations_safe_override=False, only_symbols=None)[source]

      Bases: dict

      Store all the reference “coordination geometries” (list with instances of the CoordinationGeometry classes).

      @@ -2622,7 +2622,7 @@

      Submodules
      -get_geometries(coordination=None, returned='cg')[source]
      +get_geometries(coordination=None, returned='cg')[source]

      Get a list of coordination geometries with the given coordination number.

      Parameters:
      @@ -2636,7 +2636,7 @@

      Submodules
      -get_geometry_from_IUCr_symbol(IUCr_symbol: str) → CoordinationGeometry[source]
      +get_geometry_from_IUCr_symbol(IUCr_symbol: str) → CoordinationGeometry[source]

      Get the coordination geometry of the given IUCr symbol.

      Parameters:
      @@ -2647,7 +2647,7 @@

      Submodules
      -get_geometry_from_IUPAC_symbol(IUPAC_symbol: str) → CoordinationGeometry[source]
      +get_geometry_from_IUPAC_symbol(IUPAC_symbol: str) → CoordinationGeometry[source]

      Get the coordination geometry of the given IUPAC symbol.

      Parameters:
      @@ -2658,7 +2658,7 @@

      Submodules
      -get_geometry_from_mp_symbol(mp_symbol: str) → CoordinationGeometry[source]
      +get_geometry_from_mp_symbol(mp_symbol: str) → CoordinationGeometry[source]

      Get the coordination geometry of the given mp_symbol.

      Parameters:
      @@ -2669,7 +2669,7 @@

      Submodules
      -get_geometry_from_name(name: str) → CoordinationGeometry[source]
      +get_geometry_from_name(name: str) → CoordinationGeometry[source]

      Get the coordination geometry of the given name.

      Parameters:
      @@ -2680,7 +2680,7 @@

      Submodules
      -get_implemented_geometries(coordination=None, returned='cg', include_deactivated=False)[source]
      +get_implemented_geometries(coordination=None, returned='cg', include_deactivated=False)[source]

      Get a list of the implemented coordination geometries with the given coordination number.

      Parameters:
      @@ -2696,7 +2696,7 @@

      Submodules
      -get_not_implemented_geometries(coordination=None, returned='mp_symbol')[source]
      +get_not_implemented_geometries(coordination=None, returned='mp_symbol')[source]

      Get a list of the implemented coordination geometries with the given coordination number.

      Parameters:
      @@ -2711,7 +2711,7 @@

      Submodules
      -get_symbol_cn_mapping(coordination=None)[source]
      +get_symbol_cn_mapping(coordination=None)[source]

      Get a dictionary mapping the symbol of a CoordinationGeometry to its coordination.

      Parameters:
      @@ -2728,7 +2728,7 @@

      Submodules
      -get_symbol_name_mapping(coordination=None)[source]
      +get_symbol_name_mapping(coordination=None)[source]

      Get a dictionary mapping the symbol of a CoordinationGeometry to its name.

      Parameters:
      @@ -2745,7 +2745,7 @@

      Submodules
      -is_a_valid_coordination_geometry(mp_symbol=None, IUPAC_symbol=None, IUCr_symbol=None, name=None, cn=None) → bool[source]
      +is_a_valid_coordination_geometry(mp_symbol=None, IUPAC_symbol=None, IUCr_symbol=None, name=None, cn=None) → bool[source]

      Checks whether a given coordination geometry is valid (exists) and whether the parameters are coherent with each other.

      @@ -2763,7 +2763,7 @@

      Submodules
      -pretty_print(type='implemented_geometries', maxcn=8, additional_info=None)[source]
      +pretty_print(type='implemented_geometries', maxcn=8, additional_info=None)[source]

      Get a string with a list of the Coordination Geometries.

      Parameters:
      @@ -2787,7 +2787,7 @@

      Submodules
      -class CoordinationGeometry(mp_symbol, name, alternative_names=None, IUPAC_symbol=None, IUCr_symbol=None, coordination=None, central_site=None, points=None, solid_angles=None, permutations_safe_override=False, deactivate=False, faces=None, edges=None, algorithms=None, equivalent_indices=None, neighbors_sets_hints=None)[source]
      +class CoordinationGeometry(mp_symbol, name, alternative_names=None, IUPAC_symbol=None, IUCr_symbol=None, coordination=None, central_site=None, points=None, solid_angles=None, permutations_safe_override=False, deactivate=False, faces=None, edges=None, algorithms=None, equivalent_indices=None, neighbors_sets_hints=None)[source]

      Bases: object

      Store the ideal representation of a chemical environment or “coordination geometry”.

      Initialize one “coordination geometry” according to [Pure Appl. Chem., Vol. 79, No. 10, pp. 1779–1799, 2007] @@ -2819,36 +2819,36 @@

      Submodules
      -CSM_SKIP_SEPARATION_PLANE_ALGO = 10.0[source]
      +CSM_SKIP_SEPARATION_PLANE_ALGO = 10.0[source]

      -property IUCr_symbol: str[source]
      +property IUCr_symbol: str[source]

      The IUCr symbol of this coordination geometry.

      -property IUCr_symbol_str[source]
      +property IUCr_symbol_str[source]

      A string representation of the IUCr symbol of this coordination geometry.

      -property IUPAC_symbol: str[source]
      +property IUPAC_symbol: str[source]

      The IUPAC symbol of this coordination geometry.

      -property IUPAC_symbol_str: str[source]
      +property IUPAC_symbol_str: str[source]

      A string representation of the IUPAC symbol of this coordination geometry.

      -class NeighborsSetsHints(hints_type, options)[source]
      +class NeighborsSetsHints(hints_type, options)[source]

      Bases: object

      Class used to describe neighbors sets hints.

      This allows to possibly get a lower coordination from a capped-like model polyhedron.

      @@ -2864,18 +2864,18 @@

      Submodules
      -ALLOWED_HINTS_TYPES = ('single_cap', 'double_cap', 'triple_cap')[source]
      +ALLOWED_HINTS_TYPES = ('single_cap', 'double_cap', 'triple_cap')[source]

      -as_dict()[source]
      +as_dict()[source]

      A JSON-serializable dict representation of this NeighborsSetsHints.

      -double_cap_hints(hints_info)[source]
      +double_cap_hints(hints_info)[source]

      Return hints for an additional neighbors set, i.e. the voronoi indices that constitute this new neighbors set, in case of a “Double cap” hint.

      @@ -2893,13 +2893,13 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstruct the NeighborsSetsHints from a JSON-serializable dict.

      -hints(hints_info)[source]
      +hints(hints_info)[source]

      Return hints for an additional neighbors set, i.e. the voronoi indices that constitute this new neighbors set.

      @@ -2917,7 +2917,7 @@

      Submodules
      -single_cap_hints(hints_info)[source]
      +single_cap_hints(hints_info)[source]

      Return hints for an additional neighbors set, i.e. the voronoi indices that constitute this new neighbors set, in case of a “Single cap” hint.

      @@ -2935,7 +2935,7 @@

      Submodules
      -triple_cap_hints(hints_info)[source]
      +triple_cap_hints(hints_info)[source]

      Return hints for an additional neighbors set, i.e. the voronoi indices that constitute this new neighbors set, in case of a “Triple cap” hint.

      @@ -2955,51 +2955,51 @@

      Submodules
      -property algorithms[source]
      +property algorithms[source]

      The list of algorithms that are used to identify this coordination geometry.

      -as_dict()[source]
      +as_dict()[source]

      A JSON-serializable dict representation of this CoordinationGeometry.

      -property ce_symbol: str[source]
      +property ce_symbol: str[source]

      The symbol of this coordination geometry. Same as the MP symbol.

      -property coordination_number[source]
      +property coordination_number[source]

      The coordination number of this coordination geometry.

      -property distfactor_max[source]
      +property distfactor_max[source]

      The maximum distfactor for the perfect CoordinationGeometry (usually 1.0 for symmetric polyhedrons).

      -edges(sites, permutation=None, input='sites')[source]
      +edges(sites, permutation=None, input='sites')[source]

      Get the list of edges of this coordination geometry. Each edge is given as a list of its end vertices coordinates.

      -faces(sites, permutation=None)[source]
      +faces(sites, permutation=None)[source]

      Get the list of faces of this coordination geometry. Each face is given as a list of its vertices coordinates.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstructs the CoordinationGeometry from its JSON-serializable dict representation.

      Parameters:
      @@ -3013,55 +3013,55 @@

      Submodules
      -get_central_site()[source]
      +get_central_site()[source]

      Get the central site of this coordination geometry.

      -get_coordination_number() → int[source]
      +get_coordination_number() → int[source]

      Get the coordination number of this coordination geometry.

      -get_name() → str[source]
      +get_name() → str[source]

      Get the name of this coordination geometry.

      -get_pmeshes(sites, permutation=None)[source]
      +get_pmeshes(sites, permutation=None)[source]

      Get the pmesh strings used for jmol to show this geometry.

      -is_implemented() → bool[source]
      +is_implemented() → bool[source]

      Get True if this coordination geometry is implemented.

      -property mp_symbol: str[source]
      +property mp_symbol: str[source]

      The MP symbol of this coordination geometry.

      -property number_of_permutations[source]
      +property number_of_permutations[source]

      The number of permutations of this coordination geometry.

      -property pauling_stability_ratio[source]
      +property pauling_stability_ratio[source]

      The theoretical Pauling stability ratio (rC/rA) for this environment.

      -ref_permutation(permutation)[source]
      +ref_permutation(permutation)[source]

      Get the reference permutation for a set of equivalent permutations.

      Can be useful to skip permutations that have already been performed.

      @@ -3079,7 +3079,7 @@

      Submodules
      -solid_angles(permutation=None)[source]
      +solid_angles(permutation=None)[source]

      Get the list of “perfect” solid angles Each edge is given as a list of its end vertices coordinates.

      @@ -3088,7 +3088,7 @@

      Submodules
      -class ExplicitPermutationsAlgorithm(permutations)[source]
      +class ExplicitPermutationsAlgorithm(permutations)[source]

      Bases: AbstractChemenvAlgorithm

      Algorithm doing the explicit permutations for the calculation of the Continuous Symmetry Measure.

      @@ -3100,19 +3100,19 @@

      Submodules
      -as_dict()[source]
      +as_dict()[source]

      JSON-serializable representation of this ExplicitPermutationsAlgorithm.

      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstruct ExplicitPermutationsAlgorithm from its JSON-serializable dict representation.

      -property permutations: list[list[int]][source]
      +property permutations: list[list[int]][source]

      Permutations to be performed for this algorithm.

      @@ -3120,7 +3120,7 @@

      Submodules
      -class SeparationPlane(plane_points, mirror_plane=False, ordered_plane=False, point_groups=None, ordered_point_groups=None, explicit_permutations=None, minimum_number_of_points=None, explicit_optimized_permutations=None, multiplicity=None, other_plane_points=None)[source]
      +class SeparationPlane(plane_points, mirror_plane=False, ordered_plane=False, point_groups=None, ordered_point_groups=None, explicit_permutations=None, minimum_number_of_points=None, explicit_optimized_permutations=None, multiplicity=None, other_plane_points=None)[source]

      Bases: AbstractChemenvAlgorithm

      Algorithm using separation planes for the calculation of the Continuous Symmetry Measure.

      @@ -3151,14 +3151,14 @@

      Submodules
      -property argsorted_ref_separation_perm: list[int][source]
      +property argsorted_ref_separation_perm: list[int][source]

      “Arg sorted” ordered indices of the separation plane.

      This is used in the identification of the final permutation to be used.

      -as_dict()[source]
      +as_dict()[source]
      Returns:

      JSON-serializable dict representation of this SeparationPlane algorithm.

      @@ -3171,7 +3171,7 @@

      Submodules
      -classmethod from_dict(dct: dict) → Self[source]
      +classmethod from_dict(dct: dict) → Self[source]

      Reconstructs the SeparationPlane algorithm from its JSON-serializable dict representation.

      Parameters:
      @@ -3188,13 +3188,13 @@

      Submodules
      -property permutations: list[list[int]][source]
      +property permutations: list[list[int]][source]

      List of permutations to be performed for this separation plane algorithm.

      -property ref_separation_perm: list[int][source]
      +property ref_separation_perm: list[int][source]

      Ordered indices of the separation plane.

      Examples

      For a separation plane of type 2|4|3, with plane_points indices [0, 3, 5, 8] and @@ -3204,7 +3204,7 @@

      Submodules
      -safe_separation_permutations(ordered_plane=False, ordered_point_groups=None, add_opposite=False)[source]
      +safe_separation_permutations(ordered_plane=False, ordered_point_groups=None, add_opposite=False)[source]

      Simple and safe permutations for this separation plane.

      This is not meant to be used in production. Default configuration for ChemEnv does not use this method.

      @@ -3244,7 +3244,7 @@

      Submodules
      -class AbstractGeometry(central_site=None, bare_coords=None, centering_type='standard', include_central_site_in_centroid=False, optimization=None)[source]
      +class AbstractGeometry(central_site=None, bare_coords=None, centering_type='standard', include_central_site_in_centroid=False, optimization=None)[source]

      Bases: object

      Describe a geometry (perfect or distorted).

      Constructor for the abstract geometry

      @@ -3264,19 +3264,19 @@

      Submodules
      -property cn[source]
      +property cn[source]

      Coordination number

      -property coordination_number[source]
      +property coordination_number[source]

      Coordination number

      -classmethod from_cg(cg, centering_type='standard', include_central_site_in_centroid=False) → Self[source]
      +classmethod from_cg(cg, centering_type='standard', include_central_site_in_centroid=False) → Self[source]
      Parameters:
        @@ -3290,7 +3290,7 @@

        Submodules
        -points_wcs_csc(permutation=None)[source]
        +points_wcs_csc(permutation=None)[source]
        Parameters:

        permutation

        @@ -3300,7 +3300,7 @@

        Submodules
        -points_wcs_ctwcc(permutation=None)[source]
        +points_wcs_ctwcc(permutation=None)[source]
        Parameters:

        permutation

        @@ -3310,7 +3310,7 @@

        Submodules
        -points_wcs_ctwocc(permutation=None)[source]
        +points_wcs_ctwocc(permutation=None)[source]
        Parameters:

        permutation

        @@ -3320,7 +3320,7 @@

        Submodules
        -points_wocs_csc(permutation=None)[source]
        +points_wocs_csc(permutation=None)[source]
        Parameters:

        permutation

        @@ -3330,7 +3330,7 @@

        Submodules
        -points_wocs_ctwcc(permutation=None)[source]
        +points_wocs_ctwcc(permutation=None)[source]
        Parameters:

        permutation

        @@ -3340,7 +3340,7 @@

        Submodules
        -points_wocs_ctwocc(permutation=None)[source]
        +points_wocs_ctwocc(permutation=None)[source]
        Parameters:

        permutation

        @@ -3352,7 +3352,7 @@

        Submodules
        -class LocalGeometryFinder(permutations_safe_override: bool = False, plane_ordering_override: bool = True, plane_safe_permutations: bool = False, only_symbols=None)[source]
        +class LocalGeometryFinder(permutations_safe_override: bool = False, plane_ordering_override: bool = True, plane_safe_permutations: bool = False, only_symbols=None)[source]

        Bases: object

        Main class used to find the local environments in a structure.

        @@ -3368,47 +3368,47 @@

        Submodules
        -BVA_DISTANCE_SCALE_FACTORS: ClassVar = {'GGA_relaxed': 1.015, 'LDA_relaxed': 0.995, 'experimental': 1.0}[source]
        +BVA_DISTANCE_SCALE_FACTORS: ClassVar = {'GGA_relaxed': 1.015, 'LDA_relaxed': 0.995, 'experimental': 1.0}[source]

        -DEFAULT_BVA_DISTANCE_SCALE_FACTOR = 1.0[source]
        +DEFAULT_BVA_DISTANCE_SCALE_FACTOR = 1.0[source]
        -DEFAULT_SPG_ANALYZER_OPTIONS: ClassVar = {'angle_tolerance': 5, 'symprec': 0.001}[source]
        +DEFAULT_SPG_ANALYZER_OPTIONS: ClassVar = {'angle_tolerance': 5, 'symprec': 0.001}[source]
        -DEFAULT_STRATEGY = <pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object>[source]
        +DEFAULT_STRATEGY = <pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object>[source]
        -PRESETS: ClassVar = {'DEFAULT': {'maximum_distance_factor': 2.0, 'minimum_angle_factor': 0.05, 'optimization': 2, 'voronoi_normalized_angle_tolerance': 0.03, 'voronoi_normalized_distance_tolerance': 0.05}}[source]
        +PRESETS: ClassVar = {'DEFAULT': {'maximum_distance_factor': 2.0, 'minimum_angle_factor': 0.05, 'optimization': 2, 'voronoi_normalized_angle_tolerance': 0.03, 'voronoi_normalized_distance_tolerance': 0.05}}[source]
        -STRUCTURE_REFINEMENT_NONE = 'none'[source]
        +STRUCTURE_REFINEMENT_NONE = 'none'[source]
        -STRUCTURE_REFINEMENT_REFINED = 'refined'[source]
        +STRUCTURE_REFINEMENT_REFINED = 'refined'[source]
        -STRUCTURE_REFINEMENT_SYMMETRIZED = 'symmetrized'[source]
        +STRUCTURE_REFINEMENT_SYMMETRIZED = 'symmetrized'[source]
        -compute_coordination_environments(structure, indices=None, only_cations=True, strategy=<pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object>, valences='bond-valence-analysis', initial_structure_environments=None)[source]
        +compute_coordination_environments(structure, indices=None, only_cations=True, strategy=<pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object>, valences='bond-valence-analysis', initial_structure_environments=None)[source]
        Parameters:
          @@ -3425,7 +3425,7 @@

          Submodules
          -compute_structure_environments(excluded_atoms=None, only_atoms=None, only_cations=True, only_indices=None, maximum_distance_factor=2.0, minimum_angle_factor=0.05, max_cn=None, min_cn=None, only_symbols=None, valences='undefined', additional_conditions=None, info=None, timelimit=None, initial_structure_environments=None, get_from_hints=False, voronoi_normalized_distance_tolerance=0.05, voronoi_normalized_angle_tolerance=0.03, voronoi_distance_cutoff=None, recompute=None, optimization=2)[source]
          +compute_structure_environments(excluded_atoms=None, only_atoms=None, only_cations=True, only_indices=None, maximum_distance_factor=2.0, minimum_angle_factor=0.05, max_cn=None, min_cn=None, only_symbols=None, valences='undefined', additional_conditions=None, info=None, timelimit=None, initial_structure_environments=None, get_from_hints=False, voronoi_normalized_distance_tolerance=0.05, voronoi_normalized_angle_tolerance=0.03, voronoi_distance_cutoff=None, recompute=None, optimization=2)[source]

          Compute and returns the StructureEnvironments object containing all the information about the coordination environments in the structure

          @@ -3470,7 +3470,7 @@

          Submodules
          -coordination_geometry_symmetry_measures(coordination_geometry, tested_permutations=False, points_perfect=None, optimization=None)[source]
          +coordination_geometry_symmetry_measures(coordination_geometry, tested_permutations=False, points_perfect=None, optimization=None)[source]

          Get the symmetry measures of a given coordination_geometry for a set of permutations depending on the permutation setup. Depending on the parameters of the LocalGeometryFinder and on the coordination geometry, different methods are called.

          @@ -3489,7 +3489,7 @@

          Submodules
          -coordination_geometry_symmetry_measures_fallback_random(coordination_geometry, n_random=10, points_perfect=None, **kwargs)[source]
          +coordination_geometry_symmetry_measures_fallback_random(coordination_geometry, n_random=10, points_perfect=None, **kwargs)[source]

          Get the symmetry measures for a random set of permutations for the coordination geometry “coordination_geometry”. Fallback implementation for the plane separation algorithms measures of each permutation

          @@ -3508,7 +3508,7 @@

          Submodules
          -coordination_geometry_symmetry_measures_separation_plane(coordination_geometry, separation_plane_algo, testing=False, tested_permutations=False, points_perfect=None)[source]
          +coordination_geometry_symmetry_measures_separation_plane(coordination_geometry, separation_plane_algo, testing=False, tested_permutations=False, points_perfect=None)[source]

          Get the symmetry measures of the given coordination geometry “coordination_geometry” using separation facets to reduce the complexity of the system. Caller to the refined 2POINTS, 3POINTS and other …

          @@ -3523,7 +3523,7 @@

          Submodules
          -coordination_geometry_symmetry_measures_separation_plane_optim(coordination_geometry, separation_plane_algo, points_perfect=None, nb_set=None, optimization=None)[source]
          +coordination_geometry_symmetry_measures_separation_plane_optim(coordination_geometry, separation_plane_algo, points_perfect=None, nb_set=None, optimization=None)[source]

          Get the symmetry measures of the given coordination geometry “coordination_geometry” using separation facets to reduce the complexity of the system. Caller to the refined 2POINTS, 3POINTS and other …

          @@ -3553,7 +3553,7 @@

          Submodules
          -coordination_geometry_symmetry_measures_sepplane_optim(coordination_geometry, points_perfect=None, nb_set=None, optimization=None)[source]
          +coordination_geometry_symmetry_measures_sepplane_optim(coordination_geometry, points_perfect=None, nb_set=None, optimization=None)[source]

          Get the symmetry measures of a given coordination_geometry for a set of permutations depending on the permutation setup. Depending on the parameters of the LocalGeometryFinder and on the coordination geometry, different methods are called.

          @@ -3572,7 +3572,7 @@

          Submodules
          -coordination_geometry_symmetry_measures_standard(coordination_geometry, algo, points_perfect=None, optimization=None)[source]
          +coordination_geometry_symmetry_measures_standard(coordination_geometry, algo, points_perfect=None, optimization=None)[source]

          Get the symmetry measures for a set of permutations (whose setup depends on the coordination geometry) for the coordination geometry “coordination_geometry”. Standard implementation looking for the symmetry measures of each permutation

          @@ -3588,7 +3588,7 @@

          Submodules
          -get_coordination_symmetry_measures(only_minimum=True, all_csms=True, optimization=None)[source]
          +get_coordination_symmetry_measures(only_minimum=True, all_csms=True, optimization=None)[source]

          Get the continuous symmetry measures of the current local geometry in a dictionary.

          Returns:
          @@ -3599,7 +3599,7 @@

          Submodules
          -get_coordination_symmetry_measures_optim(only_minimum=True, all_csms=True, nb_set=None, optimization=None)[source]
          +get_coordination_symmetry_measures_optim(only_minimum=True, all_csms=True, nb_set=None, optimization=None)[source]

          Get the continuous symmetry measures of the current local geometry in a dictionary.

          Returns:
          @@ -3610,7 +3610,7 @@

          Submodules
          -get_structure()[source]
          +get_structure()[source]

          Get the pymatgen Structure that has been setup for the identification of geometries (the initial one might have been refined/symmetrized using the SpaceGroupAnalyzer).

          @@ -3623,7 +3623,7 @@

          Submodules
          -set_structure(lattice: Lattice, species, coords, coords_are_cartesian)[source]
          +set_structure(lattice: Lattice, species, coords, coords_are_cartesian)[source]

          Set up the pymatgen structure for which the coordination geometries have to be identified starting from the lattice, the species and the coordinates

          @@ -3640,7 +3640,7 @@

          Submodules
          -setup_explicit_indices_local_geometry(explicit_indices)[source]
          +setup_explicit_indices_local_geometry(explicit_indices)[source]

          Set up explicit indices for the local geometry, for testing purposes

          Parameters:
          @@ -3652,7 +3652,7 @@

          Submodules
          -setup_local_geometry(isite, coords, optimization=None)[source]
          +setup_local_geometry(isite, coords, optimization=None)[source]

          Set up the AbstractGeometry for the local geometry of site with index isite.

          Parameters:
          @@ -3666,7 +3666,7 @@

          Submodules
          -setup_ordered_indices_local_geometry(coordination)[source]
          +setup_ordered_indices_local_geometry(coordination)[source]

          Set up ordered indices for the local geometry, for testing purposes

          Parameters:
          @@ -3677,7 +3677,7 @@

          Submodules
          -setup_parameter(parameter, value)[source]
          +setup_parameter(parameter, value)[source]

          Setup of one specific parameter to the given value. The other parameters are unchanged. See setup_parameters method for the list of possible parameters

          @@ -3692,7 +3692,7 @@

          Submodules
          -setup_parameters(centering_type='standard', include_central_site_in_centroid=False, bva_distance_scale_factor=None, structure_refinement='refined', spg_analyzer_options=None)[source]
          +setup_parameters(centering_type='standard', include_central_site_in_centroid=False, bva_distance_scale_factor=None, structure_refinement='refined', spg_analyzer_options=None)[source]

          Setup of the parameters for the coordination geometry finder. A reference point for the geometries has to be chosen. This can be the centroid of the structure (including or excluding the atom for which the coordination geometry is looked for) or the atom itself. In the ‘standard’ centering_type, the reference point is the central @@ -3716,7 +3716,7 @@

          Submodules
          -setup_random_indices_local_geometry(coordination)[source]
          +setup_random_indices_local_geometry(coordination)[source]

          Set up random indices for the local geometry, for testing purposes

          Parameters:
          @@ -3727,7 +3727,7 @@

          Submodules
          -setup_random_structure(coordination)[source]
          +setup_random_structure(coordination)[source]

          Set up a purely random structure with a given coordination.

          Parameters:
          @@ -3738,7 +3738,7 @@

          Submodules
          -setup_structure(structure: Structure)[source]
          +setup_structure(structure: Structure)[source]

          Set up the structure for which the coordination geometries have to be identified. The structure is analyzed with the space group analyzer and a refined structure is used

          @@ -3750,7 +3750,7 @@

          Submodules
          -setup_test_perfect_environment(symbol, randomness=False, max_random_dist=0.1, symbol_type='mp_symbol', indices='RANDOM', random_translation='NONE', random_rotation='NONE', random_scale='NONE', points=None)[source]
          +setup_test_perfect_environment(symbol, randomness=False, max_random_dist=0.1, symbol_type='mp_symbol', indices='RANDOM', random_translation='NONE', random_rotation='NONE', random_scale='NONE', points=None)[source]
          Parameters:
            @@ -3770,7 +3770,7 @@

            Submodules
            -update_nb_set_environments(se, isite, cn, inb_set, nb_set, recompute=False, optimization=None)[source]
            +update_nb_set_environments(se, isite, cn, inb_set, nb_set, recompute=False, optimization=None)[source]
            Parameters:
              @@ -3790,7 +3790,7 @@

              Submodules
              -find_rotation(points_distorted, points_perfect)[source]
              +find_rotation(points_distorted, points_perfect)[source]

              This finds the rotation matrix that aligns the (distorted) set of points “points_distorted” with respect to the (perfect) set of points “points_perfect” in a least-square sense.

              @@ -3809,7 +3809,7 @@

              Submodules
              -find_scaling_factor(points_distorted, points_perfect, rot)[source]
              +find_scaling_factor(points_distorted, points_perfect, rot)[source]

              This finds the scaling factor between the (distorted) set of points “points_distorted” and the (perfect) set of points “points_perfect” in a least-square sense.

              @@ -3829,7 +3829,7 @@

              Submodules
              -symmetry_measure(points_distorted, points_perfect)[source]
              +symmetry_measure(points_distorted, points_perfect)[source]

              Computes the continuous symmetry measure of the (distorted) set of points “points_distorted” with respect to the (perfect) set of points “points_perfect”.

              @@ -3857,7 +3857,7 @@

              Submodules
              -class ChemicalEnvironments(coord_geoms=None)[source]
              +class ChemicalEnvironments(coord_geoms=None)[source]

              Bases: MSONable

              Store all the information about the chemical environment of a given site for a given list of coordinated neighbors (internally called “cn_map”).

              @@ -3870,7 +3870,7 @@

              Submodules
              -add_coord_geom(mp_symbol, symmetry_measure, algo='UNKNOWN', permutation=None, override=False, local2perfect_map=None, perfect2local_map=None, detailed_voronoi_index=None, other_symmetry_measures=None, rotation_matrix=None, scaling_factor=None)[source]
              +add_coord_geom(mp_symbol, symmetry_measure, algo='UNKNOWN', permutation=None, override=False, local2perfect_map=None, perfect2local_map=None, detailed_voronoi_index=None, other_symmetry_measures=None, rotation_matrix=None, scaling_factor=None)[source]

              Adds a coordination geometry to the ChemicalEnvironments object.

              Parameters:
              @@ -3897,7 +3897,7 @@

              Submodules
              -as_dict()[source]
              +as_dict()[source]

              Get a dictionary representation of the ChemicalEnvironments object.

              Returns:
              @@ -3908,7 +3908,7 @@

              Submodules
              -classmethod from_dict(dct: dict) → Self[source]
              +classmethod from_dict(dct: dict) → Self[source]

              Reconstructs the ChemicalEnvironments object from a dict representation of the ChemicalEnvironments created using the as_dict method.

              @@ -3923,7 +3923,7 @@

              Submodules
              -is_close_to(other, rtol=0.0, atol=1e-08) → bool[source]
              +is_close_to(other, rtol=0.0, atol=1e-08) → bool[source]

              Whether this ChemicalEnvironments object is close to another one.

              Parameters:
              @@ -3944,7 +3944,7 @@

              Submodules
              -minimum_geometries(n=None, symmetry_measure_type=None, max_csm=None)[source]
              +minimum_geometries(n=None, symmetry_measure_type=None, max_csm=None)[source]

              Get a list of geometries with increasing continuous symmetry measure in this ChemicalEnvironments object.

              Parameters:
              @@ -3961,7 +3961,7 @@

              Submodules
              -minimum_geometry(symmetry_measure_type=None, max_csm=None)[source]
              +minimum_geometry(symmetry_measure_type=None, max_csm=None)[source]

              Get the geometry with the minimum continuous symmetry measure of this ChemicalEnvironments.

              Returns:
              @@ -3978,7 +3978,7 @@

              Submodules
              -class LightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)[source]
              +class LightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)[source]

              Bases: MSONable

              Store the chemical environments of a given structure obtained from a given ChemenvStrategy. Currently, only strategies leading to the determination of a unique environment for each site is allowed @@ -4001,17 +4001,17 @@

              Submodules
              -DEFAULT_STATISTICS_FIELDS = ('anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present')[source]
              +DEFAULT_STATISTICS_FIELDS = ('anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present')[source]

              -DELTA_MAX_OXIDATION_STATE = 0.1[source]
              +DELTA_MAX_OXIDATION_STATE = 0.1[source]
              -class NeighborsSet(structure: Structure, isite, all_nbs_sites, all_nbs_sites_indices)[source]
              +class NeighborsSet(structure: Structure, isite, all_nbs_sites, all_nbs_sites_indices)[source]

              Bases: object

              Class used to store a given set of neighbors of a given site (based on a list of sites, the voronoi container is not part of the LightStructureEnvironments object).

              @@ -4028,13 +4028,13 @@

              Submodules
              -as_dict()[source]
              +as_dict()[source]

              A JSON-serializable dict representation of the NeighborsSet.

              -classmethod from_dict(dct, structure: Structure, all_nbs_sites) → Self[source]
              +classmethod from_dict(dct, structure: Structure, all_nbs_sites) → Self[source]

              Reconstructs the NeighborsSet algorithm from its JSON-serializable dict representation, together with the structure and all the possible neighbors sites.

              As an inner (nested) class, the NeighborsSet is not supposed to be used anywhere else that inside the @@ -4056,25 +4056,25 @@

              Submodules
              -property neighb_coords[source]
              +property neighb_coords[source]

              Coordinates of neighbors for this NeighborsSet.

              -property neighb_indices_and_images: list[dict[str, int]][source]
              +property neighb_indices_and_images: list[dict[str, int]][source]

              List of indices and images with respect to the original unit cell sites for this NeighborsSet.

              -property neighb_sites[source]
              +property neighb_sites[source]

              Neighbors for this NeighborsSet as pymatgen Sites.

              -property neighb_sites_and_indices[source]
              +property neighb_sites_and_indices[source]

              List of neighbors for this NeighborsSet as pymatgen Sites and their index in the original structure.

              @@ -4082,7 +4082,7 @@

              Submodules
              -as_dict()[source]
              +as_dict()[source]
              Returns:

              Bson-serializable representation of the LightStructureEnvironments object.

              @@ -4095,7 +4095,7 @@

              Submodules
              -clear_environments(conditions=None)[source]
              +clear_environments(conditions=None)[source]

              Get the clear environments in the structure.

              Parameters:
              @@ -4112,7 +4112,7 @@

              Submodules
              -contains_only_one_anion(anion)[source]
              +contains_only_one_anion(anion)[source]

              Whether this LightStructureEnvironments concerns a structure with only one given anion type.

              Parameters:
              @@ -4129,7 +4129,7 @@

              Submodules
              -contains_only_one_anion_atom(anion_atom)[source]
              +contains_only_one_anion_atom(anion_atom)[source]

              Whether this LightStructureEnvironments concerns a structure with only one given anion atom type.

              Parameters:
              @@ -4146,7 +4146,7 @@

              Submodules
              -environments_identified()[source]
              +environments_identified()[source]

              Get the set of environments identified in this structure.

              Returns:
              @@ -4160,7 +4160,7 @@

              Submodules
              -classmethod from_dict(dct: dict) → Self[source]
              +classmethod from_dict(dct: dict) → Self[source]

              Reconstructs the LightStructureEnvironments object from a dict representation of the LightStructureEnvironments created using the as_dict method.

              @@ -4175,7 +4175,7 @@

              Submodules
              -classmethod from_structure_environments(strategy, structure_environments, valences=None, valences_origin=None) → Self[source]
              +classmethod from_structure_environments(strategy, structure_environments, valences=None, valences_origin=None) → Self[source]

              Construct a LightStructureEnvironments object from a strategy and a StructureEnvironments object.

              Parameters:
              @@ -4195,7 +4195,7 @@

              Submodules
              -get_site_info_for_specie_allces(specie, min_fraction=0)[source]
              +get_site_info_for_specie_allces(specie, min_fraction=0)[source]

              Get list of indices that have the given specie.

              Parameters:
              @@ -4219,7 +4219,7 @@

              Submodules
              -get_site_info_for_specie_ce(specie, ce_symbol)[source]
              +get_site_info_for_specie_ce(specie, ce_symbol)[source]

              Get list of indices that have the given specie with a given Coordination environment.

              Parameters:
              @@ -4244,7 +4244,7 @@

              Submodules
              -get_statistics(statistics_fields=('anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present'), bson_compatible=False)[source]
              +get_statistics(statistics_fields=('anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present'), bson_compatible=False)[source]

              Get the statistics of environments for this structure.

              Parameters:
              @@ -4264,13 +4264,13 @@

              Submodules
              -setup_statistic_lists()[source]
              +setup_statistic_lists()[source]

              Set up the statistics of environments for this LightStructureEnvironments.

              -site_contains_environment(isite, ce_symbol)[source]
              +site_contains_environment(isite, ce_symbol)[source]

              Whether a given site contains a given coordination environment.

              Parameters:
              @@ -4290,7 +4290,7 @@

              Submodules
              -site_has_clear_environment(isite, conditions=None)[source]
              +site_has_clear_environment(isite, conditions=None)[source]

              Whether a given site has a “clear” environments.

              A “clear” environment is somewhat arbitrary. You can pass (multiple) conditions, e.g. the environment should have a continuous symmetry measure lower than this, a fraction higher than that, …

              @@ -4312,7 +4312,7 @@

              Submodules
              -structure_contains_atom_environment(atom_symbol, ce_symbol)[source]
              +structure_contains_atom_environment(atom_symbol, ce_symbol)[source]

              Checks whether the structure contains a given atom in a given environment.

              Parameters:
              @@ -4332,7 +4332,7 @@

              Submodules
              -structure_has_clear_environments(conditions=None, skip_none=True, skip_empty=False)[source]
              +structure_has_clear_environments(conditions=None, skip_none=True, skip_empty=False)[source]

              Whether all sites in a structure have “clear” environments.

              Parameters:
              @@ -4353,7 +4353,7 @@

              Submodules
              -property uniquely_determines_coordination_environments[source]
              +property uniquely_determines_coordination_environments[source]

              True if the coordination environments are uniquely determined.

              @@ -4361,7 +4361,7 @@

              Submodules
              -class StructureEnvironments(voronoi, valences, sites_map, equivalent_sites, ce_list, structure, neighbors_sets=None, info=None)[source]
              +class StructureEnvironments(voronoi, valences, sites_map, equivalent_sites, ce_list, structure, neighbors_sets=None, info=None)[source]

              Bases: MSONable

              Store the chemical environments of a given structure.

              Constructor for the StructureEnvironments object.

              @@ -4381,12 +4381,12 @@

              Submodules
              -AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
              +AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]

              -class NeighborsSet(structure: Structure, isite, detailed_voronoi, site_voronoi_indices, sources=None)[source]
              +class NeighborsSet(structure: Structure, isite, detailed_voronoi, site_voronoi_indices, sources=None)[source]

              Bases: object

              Store a given set of neighbors of a given site (based on the detailed_voronoi).

              Constructor for NeighborsSet.

              @@ -4405,7 +4405,7 @@

              Submodules
              -add_source(source)[source]
              +add_source(source)[source]

              Add a source to this NeighborsSet.

              Parameters:
              @@ -4416,43 +4416,43 @@

              Submodules
              -angle_plateau()[source]
              +angle_plateau()[source]

              Get the angles plateau’s for this NeighborsSet.

              -property angles[source]
              +property angles[source]

              Angles for each neighbor in this NeighborsSet.

              -as_dict()[source]
              +as_dict()[source]

              A JSON-serializable dict representation of the NeighborsSet.

              -property coords[source]
              +property coords[source]

              Coordinates of the current central atom and its neighbors for this NeighborsSet.

              -distance_plateau()[source]
              +distance_plateau()[source]

              Get the distances plateau’s for this NeighborsSet.

              -property distances[source]
              +property distances[source]

              Distances to each neighbor in this NeighborsSet.

              -classmethod from_dict(dct, structure: Structure, detailed_voronoi) → Self[source]
              +classmethod from_dict(dct, structure: Structure, detailed_voronoi) → Self[source]

              Reconstructs the NeighborsSet algorithm from its JSON-serializable dict representation, together with the structure and the DetailedVoronoiContainer.

              As an inner (nested) class, the NeighborsSet is not supposed to be used anywhere else that inside the @@ -4475,7 +4475,7 @@

              Submodules
              -get_neighb_voronoi_indices(permutation)[source]
              +get_neighb_voronoi_indices(permutation)[source]

              Get indices in the detailed_voronoi corresponding to the current permutation.

              Parameters:
              @@ -4492,56 +4492,56 @@

              Submodules
              -property info[source]
              +property info[source]

              Summarized information about this NeighborsSet.

              -property neighb_coords[source]
              +property neighb_coords[source]

              Coordinates of neighbors for this NeighborsSet.

              -property neighb_coordsOpt[source]
              +property neighb_coordsOpt[source]

              Optimized access to the coordinates of neighbors for this NeighborsSet.

              -property neighb_sites[source]
              +property neighb_sites[source]

              Neighbors for this NeighborsSet as pymatgen Sites.

              -property neighb_sites_and_indices[source]
              +property neighb_sites_and_indices[source]

              List of neighbors for this NeighborsSet as pymatgen Sites and their index in the original structure.

              -property normalized_angles[source]
              +property normalized_angles[source]

              Normalized angles for each neighbor in this NeighborsSet.

              -property normalized_distances[source]
              +property normalized_distances[source]

              Normalized distances to each neighbor in this NeighborsSet.

              -property source[source]
              +property source[source]

              Returns the source of this NeighborsSet (how it was generated, e.g. from which Voronoi cutoffs, or from hints).

              -voronoi_grid_surface_points(additional_condition=1, other_origins='DO_NOTHING')[source]
              +voronoi_grid_surface_points(additional_condition=1, other_origins='DO_NOTHING')[source]

              Get the surface points in the Voronoi grid for this neighbor from the sources. The general shape of the points should look like a staircase such as in the following figure :

              @@ -4590,7 +4590,7 @@

              Submodules
              -add_neighbors_set(isite, nb_set)[source]
              +add_neighbors_set(isite, nb_set)[source]

              Adds a neighbor set to the list of neighbors sets for this site.

              Parameters:
              @@ -4604,7 +4604,7 @@

              Submodules
              -as_dict()[source]
              +as_dict()[source]

              Bson-serializable dict representation of the StructureEnvironments object.

              Returns:
              @@ -4615,7 +4615,7 @@

              Submodules
              -differences_wrt(other)[source]
              +differences_wrt(other)[source]

              Get differences found in the current StructureEnvironments with respect to another StructureEnvironments.

              Parameters:
              @@ -4629,7 +4629,7 @@

              Submodules
              -classmethod from_dict(dct: dict) → Self[source]
              +classmethod from_dict(dct: dict) → Self[source]

              Reconstructs the StructureEnvironments object from a dict representation of the StructureEnvironments created using the as_dict method.

              @@ -4644,7 +4644,7 @@

              Submodules
              -get_coordination_environments(isite, cn, nb_set)[source]
              +get_coordination_environments(isite, cn, nb_set)[source]

              Get the ChemicalEnvironments for a given site, coordination and neighbors set.

              Parameters:
              @@ -4662,7 +4662,7 @@

              Submodules
              -get_csm(isite, mp_symbol)[source]
              +get_csm(isite, mp_symbol)[source]

              Get the continuous symmetry measure for a given site in the given coordination environment.

              Parameters:
              @@ -4679,7 +4679,7 @@

              Submodules
              -get_csm_and_maps(isite, max_csm=8.0, figsize=None, symmetry_measure_type=None) → tuple[Figure, Axes] | None[source]
              +get_csm_and_maps(isite, max_csm=8.0, figsize=None, symmetry_measure_type=None) → tuple[Figure, Axes] | None[source]

              Plotting of the coordination numbers of a given site for all the distfactor/angfactor parameters. If the chemical environments are given, a color map is added to the plot, with the lowest continuous symmetry measure as the value for the color of that distfactor/angfactor set.

              @@ -4700,7 +4700,7 @@

              Submodules
              -get_csms(isite, mp_symbol) → list[source]
              +get_csms(isite, mp_symbol) → list[source]

              Get the continuous symmetry measure(s) of site with index isite with respect to the perfect coordination environment with mp_symbol. For some environments, a given mp_symbol might not be available (if there is no voronoi parameters leading to a number of neighbors corresponding to @@ -4725,7 +4725,7 @@

              Submodules
              -get_environments_figure(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, colormap=None, figsize=None, strategy=None)[source]
              +get_environments_figure(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, colormap=None, figsize=None, strategy=None)[source]

              Plotting of the coordination environments of a given site for all the distfactor/angfactor regions. The chemical environments with the lowest continuous symmetry measure is shown for each distfactor/angfactor region as the value for the color of that distfactor/angfactor region (using a colormap).

              @@ -4755,7 +4755,7 @@

              Submodules
              -init_neighbors_sets(isite, additional_conditions=None, valences=None)[source]
              +init_neighbors_sets(isite, additional_conditions=None, valences=None)[source]

              Initialize the list of neighbors sets for the current site.

              Parameters:
              @@ -4772,7 +4772,7 @@

              Submodules
              -plot_csm_and_maps(isite, max_csm=8.0)[source]
              +plot_csm_and_maps(isite, max_csm=8.0)[source]

              Plotting of the coordination numbers of a given site for all the distfactor/angfactor parameters. If the chemical environments are given, a color map is added to the plot, with the lowest continuous symmetry measure as the value for the color of that distfactor/angfactor set.

              @@ -4788,7 +4788,7 @@

              Submodules
              -plot_environments(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None, strategy=None)[source]
              +plot_environments(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None, strategy=None)[source]

              Plotting of the coordination numbers of a given site for all the distfactor/angfactor parameters. If the chemical environments are given, a color map is added to the plot, with the lowest continuous symmetry measure as the value for the color of that distfactor/angfactor set.

              @@ -4811,7 +4811,7 @@

              Submodules
              -save_environments_figure(isite, imagename='image.png', plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None)[source]
              +save_environments_figure(isite, imagename='image.png', plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None)[source]

              Save the environments figure to a given file.

              Parameters:
              @@ -4832,7 +4832,7 @@

              Submodules
              -update_coordination_environments(isite, cn, nb_set, ce)[source]
              +update_coordination_environments(isite, cn, nb_set, ce)[source]

              Updates the coordination environment for this site, coordination and neighbor set.

              Parameters:
              @@ -4848,7 +4848,7 @@

              Submodules
              -update_site_info(isite, info_dict)[source]
              +update_site_info(isite, info_dict)[source]

              Update information about this site.

              Parameters:
              @@ -4868,7 +4868,7 @@

              Submodules
              -class DetailedVoronoiContainer(structure=None, voronoi_list2=None, voronoi_cutoff=10.0, isites=None, normalized_distance_tolerance=1e-05, normalized_angle_tolerance=0.001, additional_conditions=None, valences=None, maximum_distance_factor=None, minimum_angle_factor=None)[source]
              +class DetailedVoronoiContainer(structure=None, voronoi_list2=None, voronoi_cutoff=10.0, isites=None, normalized_distance_tolerance=1e-05, normalized_angle_tolerance=0.001, additional_conditions=None, valences=None, maximum_distance_factor=None, minimum_angle_factor=None)[source]

              Bases: MSONable

              Store the full Voronoi of a given structure.

              Constructor for the VoronoiContainer object. Either a structure is given, in which case the Voronoi is @@ -4894,12 +4894,12 @@

              Submodules
              -AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
              +AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]

              -as_dict()[source]
              +as_dict()[source]

              Bson-serializable dict representation of the VoronoiContainer.

              Returns:
              @@ -4910,22 +4910,22 @@

              Submodules
              -default_normalized_angle_tolerance = 0.001[source]
              +default_normalized_angle_tolerance = 0.001[source]

              -default_normalized_distance_tolerance = 1e-05[source]
              +default_normalized_distance_tolerance = 1e-05[source]
              -default_voronoi_cutoff = 10.0[source]
              +default_voronoi_cutoff = 10.0[source]
              -classmethod from_dict(dct: dict) → Self[source]
              +classmethod from_dict(dct: dict) → Self[source]

              Reconstructs the VoronoiContainer object from a dict representation of the VoronoiContainer created using the as_dict method.

              @@ -4940,7 +4940,7 @@

              Submodules
              -get_rdf_figure(isite, normalized=True, figsize=None, step_function=None)[source]
              +get_rdf_figure(isite, normalized=True, figsize=None, step_function=None)[source]

              Get the Radial Distribution Figure for a given site.

              Parameters:
              @@ -4962,7 +4962,7 @@

              Submodules
              -get_sadf_figure(isite, normalized=True, figsize=None, step_function=None)[source]
              +get_sadf_figure(isite, normalized=True, figsize=None, step_function=None)[source]

              Get the Solid Angle Distribution Figure for a given site.

              Parameters:
              @@ -4984,7 +4984,7 @@

              Submodules
              -is_close_to(other, rtol=0.0, atol=1e-08) → bool[source]
              +is_close_to(other, rtol=0.0, atol=1e-08) → bool[source]

              Whether two DetailedVoronoiContainer objects are close to each other.

              Parameters:
              @@ -5005,7 +5005,7 @@

              Submodules
              -maps_and_surfaces(isite, surface_calculation_type=None, max_dist=2.0, additional_conditions=None)[source]
              +maps_and_surfaces(isite, surface_calculation_type=None, max_dist=2.0, additional_conditions=None)[source]

              Get the different surfaces and their cn_map corresponding to the different distance-angle cutoffs for a given site.

              @@ -5025,7 +5025,7 @@

              Submodules
              -maps_and_surfaces_bounded(isite, surface_calculation_options=None, additional_conditions=None)[source]
              +maps_and_surfaces_bounded(isite, surface_calculation_options=None, additional_conditions=None)[source]

              Get the different surfaces (using boundaries) and their cn_map corresponding to the different distance-angle cutoffs for a given site.

              @@ -5044,7 +5044,7 @@

              Submodules
              -neighbors(isite, distfactor, angfactor, additional_condition=None)[source]
              +neighbors(isite, distfactor, angfactor, additional_condition=None)[source]

              Get the neighbors of a given site corresponding to a given distance and angle factor.

              Parameters:
              @@ -5063,7 +5063,7 @@

              Submodules
              -neighbors_surfaces(isite, surface_calculation_type=None, max_dist=2.0)[source]
              +neighbors_surfaces(isite, surface_calculation_type=None, max_dist=2.0)[source]

              Get the different surfaces corresponding to the different distance-angle cutoffs for a given site.

              Parameters:
              @@ -5081,7 +5081,7 @@

              Submodules
              -neighbors_surfaces_bounded(isite, surface_calculation_options=None)[source]
              +neighbors_surfaces_bounded(isite, surface_calculation_options=None)[source]

              Get the different surfaces (using boundaries) corresponding to the different distance-angle cutoffs for a given site.

              @@ -5099,7 +5099,7 @@

              Submodules
              -setup_neighbors_distances_and_angles(indices)[source]
              +setup_neighbors_distances_and_angles(indices)[source]

              Initialize the angle and distance separations.

              Parameters:
              @@ -5110,7 +5110,7 @@

              Submodules
              -setup_voronoi_list(indices, voronoi_cutoff)[source]
              +setup_voronoi_list(indices, voronoi_cutoff)[source]

              Set up of the voronoi list of neighbors by calling qhull.

              Parameters:
              @@ -5127,7 +5127,7 @@

              Submodules
              -to_bson_voronoi_list2()[source]
              +to_bson_voronoi_list2()[source]

              Transforms the voronoi_list into a vlist + bson_nb_voro_list, that are BSON-encodable.

              Returns:
              @@ -5138,7 +5138,7 @@

              Submodules
              -voronoi_parameters_bounds_and_limits(isite, plot_type, max_dist)[source]
              +voronoi_parameters_bounds_and_limits(isite, plot_type, max_dist)[source]

              Get the different boundaries and limits of the distance and angle factors for the given site.

              Parameters:
              @@ -5158,7 +5158,7 @@

              Submodules
              -from_bson_voronoi_list2(bson_nb_voro_list2: list[PeriodicSite], structure: Structure)[source]
              +from_bson_voronoi_list2(bson_nb_voro_list2: list[PeriodicSite], structure: Structure)[source]

              Get the voronoi_list needed for the VoronoiContainer object from a BSON-encoded voronoi_list.

              Parameters:
              diff --git a/docs/pymatgen.analysis.chemenv.html b/docs/pymatgen.analysis.chemenv.html index bdc9d269227..5afb5b316e3 100644 --- a/docs/pymatgen.analysis.chemenv.html +++ b/docs/pymatgen.analysis.chemenv.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv package — pymatgen 2024.6.4 documentation + pymatgen.analysis.chemenv package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
              - 2024.6.4 + 2024.6.10
              diff --git a/docs/pymatgen.analysis.chemenv.utils.html b/docs/pymatgen.analysis.chemenv.utils.html index ef0e186303a..7f76b9a6d4f 100644 --- a/docs/pymatgen.analysis.chemenv.utils.html +++ b/docs/pymatgen.analysis.chemenv.utils.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils package — pymatgen 2024.6.4 documentation + pymatgen.analysis.chemenv.utils package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
              - 2024.6.4 + 2024.6.10
              @@ -276,7 +276,7 @@

              Submodules
              -class ChemEnvConfig(package_options=None)[source]
              +class ChemEnvConfig(package_options=None)[source]

              Bases: object

              Store the configuration of the chemenv package: - Materials project access @@ -289,12 +289,12 @@

              Submodules
              -DEFAULT_PACKAGE_OPTIONS: ClassVar = {'default_max_distance_factor': 1.5, 'default_strategy': {'strategy': 'SimplestChemenvStrategy', 'strategy_options': {'additional_condition': 1, 'angle_cutoff': 0.3, 'continuous_symmetry_measure_cutoff': 10, 'distance_cutoff': 1.4}}}[source]
              +DEFAULT_PACKAGE_OPTIONS: ClassVar = {'default_max_distance_factor': 1.5, 'default_strategy': {'strategy': 'SimplestChemenvStrategy', 'strategy_options': {'additional_condition': 1, 'angle_cutoff': 0.3, 'continuous_symmetry_measure_cutoff': 10, 'distance_cutoff': 1.4}}}[source]

              -classmethod auto_load(root_dir=None)[source]
              +classmethod auto_load(root_dir=None)[source]

              Autoload options.

              Parameters:
              @@ -305,19 +305,19 @@

              Submodules
              -property has_materials_project_access[source]
              +property has_materials_project_access[source]

              Whether MP access is enabled.

              -package_options_description()[source]
              +package_options_description()[source]

              Describe package options.

              -save(root_dir=None)[source]
              +save(root_dir=None)[source]

              Save the options.

              Parameters:
              @@ -328,13 +328,13 @@

              Submodules
              -setup()[source]
              +setup()[source]

              Setup the class.

              -setup_package_options()[source]
              +setup_package_options()[source]

              Setup the package options.

              @@ -346,7 +346,7 @@

              Submodules
              -exception AbstractChemenvError(cls, method, msg)[source]
              +exception AbstractChemenvError(cls, method, msg)[source]

              Bases: Exception

              Abstract class for Chemenv errors.

              @@ -362,7 +362,7 @@

              Submodules
              -exception ChemenvError(cls: str, method: str, msg: str)[source]
              +exception ChemenvError(cls: str, method: str, msg: str)[source]

              Bases: Exception

              Chemenv error.

              @@ -378,7 +378,7 @@

              Submodules
              -exception EquivalentSiteSearchError(site)[source]
              +exception EquivalentSiteSearchError(site)[source]

              Bases: AbstractChemenvError

              Equivalent site search error.

              @@ -390,7 +390,7 @@

              Submodules
              -exception NeighborsNotComputedChemenvError(site)[source]
              +exception NeighborsNotComputedChemenvError(site)[source]

              Bases: AbstractChemenvError

              Neighbors not computed error.

              @@ -402,7 +402,7 @@

              Submodules
              -exception SolidAngleError(cosinus)[source]
              +exception SolidAngleError(cosinus)[source]

              Bases: AbstractChemenvError

              Solid angle error.

              @@ -418,7 +418,7 @@

              Submodules
              -class Plane(coefficients, p1=None, p2=None, p3=None)[source]
              +class Plane(coefficients, p1=None, p2=None, p3=None)[source]

              Bases: object

              Describe a plane.

              Initialize a plane from the 4 coefficients a, b, c and d of ax + by + cz + d = 0

              @@ -429,60 +429,60 @@

              Submodules
              -TEST_2D_POINTS = (array([0., 0.]), array([1., 0.]), array([0., 1.]), array([-1.,  0.]), array([ 0., -1.]), array([0., 2.]), array([2., 0.]), array([ 0., -2.]), array([-2.,  0.]), array([1., 1.]), array([2., 2.]), array([-1., -1.]), array([-2., -2.]), array([1., 2.]), array([ 1., -2.]), array([-1.,  2.]), array([-1., -2.]), array([2., 1.]), array([ 2., -1.]), array([-2.,  1.]), array([-2., -1.]))[source]
              +TEST_2D_POINTS = (array([0., 0.]), array([1., 0.]), array([0., 1.]), array([-1.,  0.]), array([ 0., -1.]), array([0., 2.]), array([2., 0.]), array([ 0., -2.]), array([-2.,  0.]), array([1., 1.]), array([2., 2.]), array([-1., -1.]), array([-2., -2.]), array([1., 2.]), array([ 1., -2.]), array([-1.,  2.]), array([-1., -2.]), array([2., 1.]), array([ 2., -1.]), array([-2.,  1.]), array([-2., -1.]))[source]

              -property a[source]
              +property a[source]

              Coefficient a of the plane.

              -property abcd[source]
              +property abcd[source]

              A tuple with the plane coefficients.

              -property b[source]
              +property b[source]

              Coefficient b of the plane.

              -property c[source]
              +property c[source]

              Coefficient c of the plane.

              -property coefficients[source]
              +property coefficients[source]

              A copy of the plane coefficients as a numpy array.

              -property crosses_origin[source]
              +property crosses_origin[source]

              Whether this plane crosses the origin (i.e. coefficient d is 0.0).

              -property d[source]
              +property d[source]

              Coefficient d of the plane.

              -property distance_to_origin[source]
              +property distance_to_origin[source]

              Distance of the plane to the origin.

              -distance_to_point(point)[source]
              +distance_to_point(point)[source]

              Compute the absolute distance from the plane to the point

              Parameters:
              @@ -496,7 +496,7 @@

              Submodules
              -distances(points)[source]
              +distances(points)[source]

              Compute the distances from the plane to each of the points. Positive distances are on the side of the normal of the plane while negative distances are on the other side.

              @@ -512,7 +512,7 @@

              Submodules
              -distances_indices_groups(points, delta=None, delta_factor=0.05, sign=False)[source]
              +distances_indices_groups(points, delta=None, delta_factor=0.05, sign=False)[source]

              Compute the distances from the plane to each of the points. Positive distances are on the side of the normal of the plane while negative distances are on the other side. Indices sorting the points from closest to furthest is also computed. Grouped indices are also given, for which indices of the distances that are @@ -539,7 +539,7 @@

              Submodules
              -distances_indices_sorted(points, sign=False)[source]
              +distances_indices_sorted(points, sign=False)[source]

              Compute the distances from the plane to each of the points. Positive distances are on the side of the normal of the plane while negative distances are on the other side. Indices sorting the points from closest to furthest is also computed.

              @@ -560,7 +560,7 @@

              Submodules
              -fit_error(points, fit='least_square_distance')[source]
              +fit_error(points, fit='least_square_distance')[source]

              Evaluate the error for a list of points with respect to this plane.

              Parameters:
              @@ -577,7 +577,7 @@

              Submodules
              -fit_least_square_distance_error(points)[source]
              +fit_least_square_distance_error(points)[source]

              Evaluate the sum of squared distances error for a list of points with respect to this plane.

              Parameters:
              @@ -591,7 +591,7 @@

              Submodules
              -fit_maximum_distance_error(points)[source]
              +fit_maximum_distance_error(points)[source]

              Evaluate the max distance error for a list of points with respect to this plane.

              Parameters:
              @@ -605,7 +605,7 @@

              Submodules
              -classmethod from_2points_and_origin(p1, p2) → Self[source]
              +classmethod from_2points_and_origin(p1, p2) → Self[source]

              Initialize plane from two points and the origin.

              Parameters:
              @@ -622,7 +622,7 @@

              Submodules
              -classmethod from_3points(p1, p2, p3) → Self[source]
              +classmethod from_3points(p1, p2, p3) → Self[source]

              Initialize plane from three points.

              Parameters:
              @@ -640,7 +640,7 @@

              Submodules
              -classmethod from_coefficients(a, b, c, d) → Self[source]
              +classmethod from_coefficients(a, b, c, d) → Self[source]

              Initialize plane from its coefficients.

              Parameters:
              @@ -659,7 +659,7 @@

              Submodules
              -classmethod from_npoints(points, best_fit='least_square_distance') → Self[source]
              +classmethod from_npoints(points, best_fit='least_square_distance') → Self[source]

              Initialize plane from a list of points.

              If the number of points is larger than 3, will use a least square fitting or max distance fitting.

              @@ -677,7 +677,7 @@

              Submodules
              -classmethod from_npoints_least_square_distance(points) → Self[source]
              +classmethod from_npoints_least_square_distance(points) → Self[source]

              Initialize plane from a list of points using a least square fitting procedure.

              Parameters:
              @@ -691,7 +691,7 @@

              Submodules
              -classmethod from_npoints_maximum_distance(points) → Self[source]
              +classmethod from_npoints_maximum_distance(points) → Self[source]

              Initialize plane from a list of points using a max distance fitting procedure.

              Parameters:
              @@ -705,7 +705,7 @@

              Submodules
              -indices_separate(points, dist_tolerance)[source]
              +indices_separate(points, dist_tolerance)[source]

              Get three lists containing the indices of the points lying on one side of the plane, on the plane and on the other side of the plane. The dist_tolerance parameter controls the tolerance to which a point is considered to lie on the plane or not (distance to the plane)

              @@ -726,7 +726,7 @@

              Submodules
              -init_3points(non_zeros, zeros)[source]
              +init_3points(non_zeros, zeros)[source]

              Initialize three random points on this plane.

              Parameters:
              @@ -740,7 +740,7 @@

              Submodules
              -is_in_list(plane_list) → bool[source]
              +is_in_list(plane_list) → bool[source]

              Checks whether the plane is identical to one of the Planes in the plane_list list of Planes

              Parameters:
              @@ -757,7 +757,7 @@

              Submodules
              -is_in_plane(pp, dist_tolerance) → bool[source]
              +is_in_plane(pp, dist_tolerance) → bool[source]

              Determines if point pp is in the plane within the tolerance dist_tolerance

              Parameters:
              @@ -777,7 +777,7 @@

              Submodules
              -is_same_plane_as(plane) → bool[source]
              +is_same_plane_as(plane) → bool[source]

              Checks whether the plane is identical to another Plane “plane”

              Parameters:
              @@ -794,7 +794,7 @@

              Submodules
              -orthonormal_vectors()[source]
              +orthonormal_vectors()[source]

              Get a list of three orthogonal vectors, the two first being parallel to the plane and the third one is the normal vector of the plane

              @@ -809,7 +809,7 @@

              Submodules
              -classmethod perpendicular_bisector(p1, p2) → Self[source]
              +classmethod perpendicular_bisector(p1, p2) → Self[source]

              Initialize a plane from the perpendicular bisector of two points.

              The perpendicular bisector of two points is the plane perpendicular to the vector joining these two points and passing through the middle of the segment joining the two points.

              @@ -828,7 +828,7 @@

              Submodules
              -project_and_to2dim(pps, plane_center)[source]
              +project_and_to2dim(pps, plane_center)[source]

              Projects the list of points pps to the plane and changes the basis from 3D to the 2D basis of the plane

              Parameters:
              @@ -842,7 +842,7 @@

              Submodules
              -project_and_to2dim_ordered_indices(pps, plane_center='mean')[source]
              +project_and_to2dim_ordered_indices(pps, plane_center='mean')[source]

              Projects each points in the point list pps on plane and returns the indices that would sort the list of projected points in anticlockwise order

              @@ -857,7 +857,7 @@

              Submodules
              -projectionpoints(pps)[source]
              +projectionpoints(pps)[source]

              Projects each points in the point list pps on plane and returns the list of projected points

              Parameters:
              @@ -873,7 +873,7 @@

              Submodules
              -anticlockwise_sort(pps)[source]
              +anticlockwise_sort(pps)[source]

              Sort a list of 2D points in anticlockwise order

              Parameters:
              @@ -887,7 +887,7 @@

              Submodules
              -anticlockwise_sort_indices(pps)[source]
              +anticlockwise_sort_indices(pps)[source]

              Get the indices that would sort a list of 2D points in anticlockwise order

              Parameters:
              @@ -901,7 +901,7 @@

              Submodules
              -changebasis(uu, vv, nn, pps)[source]
              +changebasis(uu, vv, nn, pps)[source]

              For a list of points given in standard coordinates (in terms of e1, e2 and e3), returns the same list expressed in the basis (uu, vv, nn), which is supposed to be orthonormal.

              @@ -921,7 +921,7 @@

              Submodules
              -collinear(p1, p2, p3=None, tolerance=0.25)[source]
              +collinear(p1, p2, p3=None, tolerance=0.25)[source]

              Checks if the three points p1, p2 and p3 are collinear or not within a given tolerance. The collinearity is checked by computing the area of the triangle defined by the three points p1, p2 and p3. If the area of this triangle is less than (tolerance x largest_triangle), then the three points are considered collinear. The @@ -949,7 +949,7 @@

              Submodules
              -diamond_functions(xx, yy, y_x0, x_y0)[source]
              +diamond_functions(xx, yy, y_x0, x_y0)[source]

              Method that creates two upper and lower functions based on points xx and yy as well as intercepts defined by y_x0 and x_y0. The resulting functions form kind of a distorted diamond-like structure aligned from @@ -999,7 +999,7 @@

              Submodules
              -function_comparison(f1, f2, x1, x2, numpoints_check=500)[source]
              +function_comparison(f1, f2, x1, x2, numpoints_check=500)[source]

              Method that compares two functions.

              Parameters:
              @@ -1028,7 +1028,7 @@

              Submodules
              -get_lower_and_upper_f(surface_calculation_options)[source]
              +get_lower_and_upper_f(surface_calculation_options)[source]

              Get the lower and upper functions defining a surface in the distance-angle space of neighbors.

              Parameters:
              @@ -1042,7 +1042,7 @@

              Submodules
              -is_anion_cation_bond(valences, ii, jj) → bool[source]
              +is_anion_cation_bond(valences, ii, jj) → bool[source]

              Checks if two given sites are an anion and a cation.

              Parameters:
              @@ -1063,7 +1063,7 @@

              Submodules
              -matrixTimesVector(MM, aa)[source]
              +matrixTimesVector(MM, aa)[source]
              Parameters:
                @@ -1079,7 +1079,7 @@

                Submodules
                -quarter_ellipsis_functions(xx: ArrayLike, yy: ArrayLike) → dict[str, Callable][source]
                +quarter_ellipsis_functions(xx: ArrayLike, yy: ArrayLike) → dict[str, Callable][source]

                Method that creates two quarter-ellipse functions based on points xx and yy. The ellipsis is supposed to be aligned with the axes. The two ellipsis pass through the two points xx and yy.

                @@ -1097,7 +1097,7 @@

                Submodules
                -rectangle_surface_intersection(rectangle, f_lower, f_upper, bounds_lower=None, bounds_upper=None, check=True, numpoints_check=500)[source]
                +rectangle_surface_intersection(rectangle, f_lower, f_upper, bounds_lower=None, bounds_upper=None, check=True, numpoints_check=500)[source]

                Method to calculate the surface of the intersection of a rectangle (aligned with axes) and another surface defined by two functions f_lower and f_upper.

                @@ -1120,7 +1120,7 @@

                Submodules
                -rotateCoords(coords, R)[source]
                +rotateCoords(coords, R)[source]

                Rotate the list of points using rotation matrix R

                Parameters:
                @@ -1137,7 +1137,7 @@

                Submodules
                -rotateCoordsOpt(coords, R)[source]
                +rotateCoordsOpt(coords, R)[source]

                Rotate the list of points using rotation matrix R

                Parameters:
                @@ -1154,7 +1154,7 @@

                Submodules
                -separation_in_list(separation_indices, separation_indices_list)[source]
                +separation_in_list(separation_indices, separation_indices_list)[source]

                Checks if the separation indices of a plane are already in the list

                Parameters:
                @@ -1174,7 +1174,7 @@

                Submodules
                -solid_angle(center, coords)[source]
                +solid_angle(center, coords)[source]

                Helper method to calculate the solid angle of a set of coords from the center.

                Parameters:
                @@ -1191,7 +1191,7 @@

                Submodules
                -sort_separation(separation)[source]
                +sort_separation(separation)[source]

                Sort a separation.

                Parameters:
                @@ -1205,7 +1205,7 @@

                Submodules
                -sort_separation_tuple(separation)[source]
                +sort_separation_tuple(separation)[source]

                Sort a separation.

                Parameters:
                @@ -1219,7 +1219,7 @@

                Submodules
                -spline_functions(lower_points, upper_points, degree=3)[source]
                +spline_functions(lower_points, upper_points, degree=3)[source]

                Method that creates two (upper and lower) spline functions based on points lower_points and upper_points.

                Parameters:
                @@ -1237,7 +1237,7 @@

                Submodules
                -vectorsToMatrix(aa, bb)[source]
                +vectorsToMatrix(aa, bb)[source]

                Performs the vector multiplication of the elements of two vectors, constructing the 3x3 matrix.

                Parameters:
                @@ -1261,77 +1261,77 @@

                Submodules
                -class AdditionalConditions[source]
                +class AdditionalConditions[source]

                Bases: object

                Additional conditions that can be used to filter coordination environments.

                -ALL = (0, 1, 2, 3, 4)[source]
                +ALL = (0, 1, 2, 3, 4)[source]
                -CONDITION_DESCRIPTION: ClassVar = {0: 'No additional condition', 1: 'Only anion-cation bonds', 2: 'No element-element bonds (same elements)', 3: 'Only anion-cation bonds and no element-element bonds (same elements)', 4: 'Only element-oxygen bonds'}[source]
                +CONDITION_DESCRIPTION: ClassVar = {0: 'No additional condition', 1: 'Only anion-cation bonds', 2: 'No element-element bonds (same elements)', 3: 'Only anion-cation bonds and no element-element bonds (same elements)', 4: 'Only element-oxygen bonds'}[source]
                -NONE = 0[source]
                +NONE = 0[source]
                -NO_AC = 0[source]
                +NO_AC = 0[source]
                -NO_ADDITIONAL_CONDITION = 0[source]
                +NO_ADDITIONAL_CONDITION = 0[source]
                -NO_E2SEB = 2[source]
                +NO_E2SEB = 2[source]
                -NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 2[source]
                +NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 2[source]
                -ONLY_ACB = 1[source]
                +ONLY_ACB = 1[source]
                -ONLY_ACB_AND_NO_E2SEB = 3[source]
                +ONLY_ACB_AND_NO_E2SEB = 3[source]
                -ONLY_ANION_CATION_BONDS = 1[source]
                +ONLY_ANION_CATION_BONDS = 1[source]
                -ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 3[source]
                +ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 3[source]
                -ONLY_E2OB = 4[source]
                +ONLY_E2OB = 4[source]
                -ONLY_ELEMENT_TO_OXYGEN_BONDS = 4[source]
                +ONLY_ELEMENT_TO_OXYGEN_BONDS = 4[source]
                -check_condition(condition, structure: Structure, parameters)[source]
                +check_condition(condition, structure: Structure, parameters)[source]
                Parameters:
                -evaluate(value)[source]
                +evaluate(value)[source]

                Evaluate the ratio function for the given value.

                Parameters:
                @@ -1384,7 +1384,7 @@

                Submodules
                -classmethod from_dict(dct: dict) → Self[source]
                +classmethod from_dict(dct: dict) → Self[source]

                Construct ratio function from dict.

                Parameters:
                @@ -1395,7 +1395,7 @@

                Submodules
                -setup_parameters(options_dict)[source]
                +setup_parameters(options_dict)[source]

                Set up the parameters for this ratio function.

                Parameters:
                @@ -1408,7 +1408,7 @@

                Submodules
                -class CSMFiniteRatioFunction(function, options_dict=None)[source]
                +class CSMFiniteRatioFunction(function, options_dict=None)[source]

                Bases: AbstractRatioFunction

                Concrete implementation of a series of ratio functions applied to the continuous symmetry measure (CSM).

                Uses “finite” ratio functions.

                @@ -1426,12 +1426,12 @@

                Submodules
                -ALLOWED_FUNCTIONS: ClassVar = {'power2_decreasing_exp': ['max_csm', 'alpha'], 'smootherstep': ['lower_csm', 'upper_csm'], 'smoothstep': ['lower_csm', 'upper_csm']}[source]
                +ALLOWED_FUNCTIONS: ClassVar = {'power2_decreasing_exp': ['max_csm', 'alpha'], 'smootherstep': ['lower_csm', 'upper_csm'], 'smoothstep': ['lower_csm', 'upper_csm']}[source]

                -fractions(data)[source]
                +fractions(data)[source]

                Get the fractions from the CSM ratio function applied to the data.

                Parameters:
                @@ -1445,7 +1445,7 @@

                Submodules
                -mean_estimator(data)[source]
                +mean_estimator(data)[source]

                Get the weighted CSM using this CSM ratio function applied to the data.

                Parameters:
                @@ -1459,7 +1459,7 @@

                Submodules
                -power2_decreasing_exp(vals)[source]
                +power2_decreasing_exp(vals)[source]

                Get the evaluation of the ratio function f(x)=exp(-a*x)*(x-1)^2.

                The CSM values (i.e. “x”), are scaled to the “max_csm” parameter. The “a” constant correspond to the “alpha” parameter.

                @@ -1475,7 +1475,7 @@

                Submodules
                -ratios(data)[source]
                +ratios(data)[source]

                Get the fractions from the CSM ratio function applied to the data.

                Parameters:
                @@ -1489,7 +1489,7 @@

                Submodules
                -smootherstep(vals)[source]
                +smootherstep(vals)[source]

                Get the evaluation of the smootherstep ratio function: f(x)=6*x^5-15*x^4+10*x^3.

                The CSM values (i.e. “x”), are scaled between the “lower_csm” and “upper_csm” parameters.

                @@ -1504,7 +1504,7 @@

                Submodules
                -smoothstep(vals)[source]
                +smoothstep(vals)[source]

                Get the evaluation of the smoothstep ratio function: f(x)=3*x^2-2*x^3.

                The CSM values (i.e. “x”), are scaled between the “lower_csm” and “upper_csm” parameters.

                @@ -1521,7 +1521,7 @@

                Submodules
                -class CSMInfiniteRatioFunction(function, options_dict=None)[source]
                +class CSMInfiniteRatioFunction(function, options_dict=None)[source]

                Bases: AbstractRatioFunction

                Concrete implementation of a series of ratio functions applied to the continuous symmetry measure (CSM).

                Uses “infinite” ratio functions.

                @@ -1539,12 +1539,12 @@

                Submodules
                -ALLOWED_FUNCTIONS: ClassVar = {'power2_inverse_decreasing': ['max_csm'], 'power2_inverse_power2_decreasing': ['max_csm']}[source]
                +ALLOWED_FUNCTIONS: ClassVar = {'power2_inverse_decreasing': ['max_csm'], 'power2_inverse_power2_decreasing': ['max_csm']}[source]

                -fractions(data)[source]
                +fractions(data)[source]

                Get the fractions from the CSM ratio function applied to the data.

                Parameters:
                @@ -1558,7 +1558,7 @@

                Submodules
                -mean_estimator(data)[source]
                +mean_estimator(data)[source]

                Get the weighted CSM using this CSM ratio function applied to the data.

                Parameters:
                @@ -1572,7 +1572,7 @@

                Submodules
                -power2_inverse_decreasing(vals)[source]
                +power2_inverse_decreasing(vals)[source]

                Get the evaluation of the ratio function f(x)=(x-1)^2 / x.

                The CSM values (i.e. “x”), are scaled to the “max_csm” parameter. The “a” constant correspond to the “alpha” parameter.

                @@ -1588,7 +1588,7 @@

                Submodules
                -power2_inverse_power2_decreasing(vals)[source]
                +power2_inverse_power2_decreasing(vals)[source]

                Get the evaluation of the ratio function f(x)=(x-1)^2 / x^2.

                The CSM values (i.e. “x”), are scaled to the “max_csm” parameter. The “a” constant correspond to the “alpha” parameter.

                @@ -1604,7 +1604,7 @@

                Submodules
                -ratios(data)[source]
                +ratios(data)[source]

                Get the fractions from the CSM ratio function applied to the data.

                Parameters:
                @@ -1620,7 +1620,7 @@

                Submodules
                -class DeltaCSMRatioFunction(function, options_dict=None)[source]
                +class DeltaCSMRatioFunction(function, options_dict=None)[source]

                Bases: AbstractRatioFunction

                Concrete implementation of a series of ratio functions applied to differences of continuous symmetry measures (DeltaCSM).

                @@ -1639,12 +1639,12 @@

                Submodules
                -ALLOWED_FUNCTIONS: ClassVar = {'smootherstep': ['delta_csm_min', 'delta_csm_max']}[source]
                +ALLOWED_FUNCTIONS: ClassVar = {'smootherstep': ['delta_csm_min', 'delta_csm_max']}[source]

                -smootherstep(vals)[source]
                +smootherstep(vals)[source]

                Get the evaluation of the smootherstep ratio function: f(x)=6*x^5-15*x^4+10*x^3.

                The DeltaCSM values (i.e. “x”), are scaled between the “delta_csm_min” and “delta_csm_max” parameters.

                @@ -1661,7 +1661,7 @@

                Submodules
                -class RatioFunction(function, options_dict=None)[source]
                +class RatioFunction(function, options_dict=None)[source]

                Bases: AbstractRatioFunction

                Concrete implementation of a series of ratio functions.

                Constructor for AbstractRatioFunction.

                @@ -1675,12 +1675,12 @@

                Submodules
                -ALLOWED_FUNCTIONS: ClassVar = {'inverse_smootherstep': ['lower', 'upper'], 'inverse_smoothstep': ['lower', 'upper'], 'power2_decreasing_exp': ['max', 'alpha'], 'power2_inverse_decreasing': ['max'], 'power2_inverse_power2_decreasing': ['max'], 'smootherstep': ['lower', 'upper'], 'smoothstep': ['lower', 'upper']}[source]
                +ALLOWED_FUNCTIONS: ClassVar = {'inverse_smootherstep': ['lower', 'upper'], 'inverse_smoothstep': ['lower', 'upper'], 'power2_decreasing_exp': ['max', 'alpha'], 'power2_inverse_decreasing': ['max'], 'power2_inverse_power2_decreasing': ['max'], 'smootherstep': ['lower', 'upper'], 'smoothstep': ['lower', 'upper']}[source]

                -inverse_smootherstep(vals)[source]
                +inverse_smootherstep(vals)[source]

                Get the evaluation of the “inverse” smootherstep ratio function: f(x)=1-(6*x^5-15*x^4+10*x^3).

                The values (i.e. “x”), are scaled between the “lower” and “upper” parameters.

                @@ -1695,7 +1695,7 @@

                Submodules
                -inverse_smoothstep(vals)[source]
                +inverse_smoothstep(vals)[source]

                Get the evaluation of the “inverse” smoothstep ratio function: f(x)=1-(3*x^2-2*x^3).

                The values (i.e. “x”), are scaled between the “lower” and “upper” parameters.

                @@ -1710,7 +1710,7 @@

                Submodules
                -power2_decreasing_exp(vals)[source]
                +power2_decreasing_exp(vals)[source]

                Get the evaluation of the ratio function f(x)=exp(-a*x)*(x-1)^2.

                The values (i.e. “x”), are scaled to the “max” parameter. The “a” constant correspond to the “alpha” parameter.

                @@ -1726,7 +1726,7 @@

                Submodules
                -power2_inverse_decreasing(vals)[source]
                +power2_inverse_decreasing(vals)[source]

                Get the evaluation of the ratio function f(x)=(x-1)^2 / x.

                The values (i.e. “x”), are scaled to the “max” parameter.

                @@ -1741,7 +1741,7 @@

                Submodules
                -power2_inverse_power2_decreasing(vals)[source]
                +power2_inverse_power2_decreasing(vals)[source]

                Get the evaluation of the ratio function f(x)=(x-1)^2 / x^2.

                The values (i.e. “x”), are scaled to the “max” parameter.

                @@ -1756,7 +1756,7 @@

                Submodules
                -smootherstep(vals)[source]
                +smootherstep(vals)[source]

                Get the evaluation of the smootherstep ratio function: f(x)=6*x^5-15*x^4+10*x^3.

                The values (i.e. “x”), are scaled between the “lower” and “upper” parameters.

                @@ -1771,7 +1771,7 @@

                Submodules
                -smoothstep(vals)[source]
                +smoothstep(vals)[source]

                Get the evaluation of the smoothstep ratio function: f(x)=3*x^2-2*x^3.

                The values (i.e. “x”), are scaled between the “lower” and “upper” parameters.

                @@ -1792,7 +1792,7 @@

                Submodules
                -class MultiGraphCycle(nodes, edge_indices, validate=True, ordered=None)[source]
                +class MultiGraphCycle(nodes, edge_indices, validate=True, ordered=None)[source]

                Bases: MSONable

                Describe a cycle in a multigraph.

                nodes are the nodes of the cycle and edge_indices are the indices of the edges in the cycle. @@ -1816,7 +1816,7 @@

                Submodules
                -order(raise_on_fail: bool = True)[source]
                +order(raise_on_fail: bool = True)[source]

                Orders the SimpleGraphCycle.

                The ordering is performed such that the first node is the “lowest” one and the second node is the lowest one of the two neighbor nodes of the @@ -1831,7 +1831,7 @@

                Submodules
                -validate(check_strict_ordering=False)[source]
                +validate(check_strict_ordering=False)[source]
                Parameters:

                check_strict_ordering

                @@ -1843,7 +1843,7 @@

                Submodules
                -class SimpleGraphCycle(nodes, validate=True, ordered=None)[source]
                +class SimpleGraphCycle(nodes, validate=True, ordered=None)[source]

                Bases: MSONable

                Describe a cycle in a simple graph (graph without multiple edges).

                Note that the convention used here is the networkx convention for which simple graphs allow @@ -1863,13 +1863,13 @@

                Submodules
                -as_dict() → dict[source]
                +as_dict() → dict[source]

                MSONable dict

                -classmethod from_dict(dct: dict, validate: bool = False) → Self[source]
                +classmethod from_dict(dct: dict, validate: bool = False) → Self[source]

                Serialize from dict.

                Parameters:
                @@ -1883,7 +1883,7 @@

                Submodules
                -classmethod from_edges(edges, edges_are_ordered: bool = True) → Self[source]
                +classmethod from_edges(edges, edges_are_ordered: bool = True) → Self[source]

                Construct SimpleGraphCycle from a list edges.

                By default, the edges list is supposed to be ordered as it will be much faster to construct the cycle. If edges_are_ordered is set to @@ -1893,7 +1893,7 @@

                Submodules
                -order(raise_on_fail=True)[source]
                +order(raise_on_fail=True)[source]

                Orders the SimpleGraphCycle.

                The ordering is performed such that the first node is the “lowest” one and the second node is the lowest one of the two neighbor nodes of the first node. If @@ -1907,7 +1907,7 @@

                Submodules
                -validate(check_strict_ordering=False)[source]
                +validate(check_strict_ordering=False)[source]
                Parameters:

                check_strict_ordering

                @@ -1919,7 +1919,7 @@

                Submodules
                -get_all_elementary_cycles(graph)[source]
                +get_all_elementary_cycles(graph)[source]
                Parameters:

                graph

                @@ -1929,7 +1929,7 @@

                Submodules
                -get_all_simple_paths_edges(graph, source, target, cutoff=None, data=True)[source]
                +get_all_simple_paths_edges(graph, source, target, cutoff=None, data=True)[source]

                Get all the simple path and edges.

                Parameters:
                @@ -1946,7 +1946,7 @@

                Submodules
                -get_delta(node1, node2, edge_data)[source]
                +get_delta(node1, node2, edge_data)[source]

                Get the delta.

                Parameters:
                @@ -1965,7 +1965,7 @@

                Submodules
                -cosinus_step(xx, edges=None, inverse=False)[source]
                +cosinus_step(xx, edges=None, inverse=False)[source]
                Parameters:
                  @@ -1979,7 +1979,7 @@

                  Submodules
                  -divisors(n)[source]
                  +divisors(n)[source]

                  From a given natural integer, returns the list of divisors in ascending order

                  Parameters:
                  @@ -1993,7 +1993,7 @@

                  Submodules
                  -get_center_of_arc(p1, p2, radius)[source]
                  +get_center_of_arc(p1, p2, radius)[source]
                  Parameters:
                    @@ -2007,7 +2007,7 @@

                    Submodules
                    -get_linearly_independent_vectors(vectors: list[ArrayLike]) → list[np.ndarray][source]
                    +get_linearly_independent_vectors(vectors: list[ArrayLike]) → list[np.ndarray][source]
                    Parameters:

                    vectors (list[ArrayLike]) – List of vectors

                    @@ -2017,7 +2017,7 @@

                    Submodules
                    -normal_cdf_step(xx, mean, scale)[source]
                    +normal_cdf_step(xx, mean, scale)[source]
                    Parameters:
                      @@ -2031,7 +2031,7 @@

                      Submodules
                      -power2_decreasing_exp(xx, edges=None, alpha=1.0)[source]
                      +power2_decreasing_exp(xx, edges=None, alpha=1.0)[source]
                      Parameters:
                        @@ -2045,7 +2045,7 @@

                        Submodules
                        -power2_inverse_decreasing(xx, edges=None, prefactor=None)[source]
                        +power2_inverse_decreasing(xx, edges=None, prefactor=None)[source]
                        Parameters:
                          @@ -2059,7 +2059,7 @@

                          Submodules
                          -power2_inverse_power2_decreasing(xx, edges=None, prefactor=None)[source]
                          +power2_inverse_power2_decreasing(xx, edges=None, prefactor=None)[source]
                          Parameters:
                            @@ -2073,7 +2073,7 @@

                            Submodules
                            -power2_inverse_powern_decreasing(xx, edges=None, prefactor=None, powern=2.0)[source]
                            +power2_inverse_powern_decreasing(xx, edges=None, prefactor=None, powern=2.0)[source]
                            Parameters:
                              @@ -2088,7 +2088,7 @@

                              Submodules
                              -power2_tangent_decreasing(xx, edges=None, prefactor=None)[source]
                              +power2_tangent_decreasing(xx, edges=None, prefactor=None)[source]
                              Parameters:
                                @@ -2102,7 +2102,7 @@

                                Submodules
                                -power3_step(xx, edges=None, inverse=False)[source]
                                +power3_step(xx, edges=None, inverse=False)[source]
                                Parameters:
                                  @@ -2116,7 +2116,7 @@

                                  Submodules
                                  -powern_decreasing(xx, edges=None, nn=2)[source]
                                  +powern_decreasing(xx, edges=None, nn=2)[source]
                                  Parameters:
                                    @@ -2130,7 +2130,7 @@

                                    Submodules
                                    -powern_parts_step(xx, edges=None, inverse=False, nn=2)[source]
                                    +powern_parts_step(xx, edges=None, inverse=False, nn=2)[source]
                                    Parameters:
                                      @@ -2145,7 +2145,7 @@

                                      Submodules
                                      -prime_factors(n: int) → list[int][source]
                                      +prime_factors(n: int) → list[int][source]

                                      Lists prime factors of a given natural integer, from greatest to smallest

                                      Parameters:
                                      @@ -2159,7 +2159,7 @@

                                      Submodules
                                      -scale_and_clamp(xx, edge0, edge1, clamp0, clamp1)[source]
                                      +scale_and_clamp(xx, edge0, edge1, clamp0, clamp1)[source]
                                      Parameters:
                                        @@ -2175,7 +2175,7 @@

                                        Submodules
                                        -smootherstep(xx, edges=None, inverse=False)[source]
                                        +smootherstep(xx, edges=None, inverse=False)[source]
                                        Parameters:
                                          @@ -2189,7 +2189,7 @@

                                          Submodules
                                          -smoothstep(xx, edges=None, inverse=False)[source]
                                          +smoothstep(xx, edges=None, inverse=False)[source]
                                          Parameters:
                                            @@ -2207,7 +2207,7 @@

                                            Submodules
                                            -compute_environments(chemenv_configuration)[source]
                                            +compute_environments(chemenv_configuration)[source]

                                            Compute the environments.

                                            Parameters:
                                            @@ -2218,7 +2218,7 @@

                                            Submodules
                                            -draw_cg(vis, site, neighbors, cg=None, perm=None, perfect2local_map=None, show_perfect=False, csm_info=None, symmetry_measure_type='csm_wcs_ctwcc', perfect_radius=0.1, show_distorted=True, faces_color_override=None)[source]
                                            +draw_cg(vis, site, neighbors, cg=None, perm=None, perfect2local_map=None, show_perfect=False, csm_info=None, symmetry_measure_type='csm_wcs_ctwcc', perfect_radius=0.1, show_distorted=True, faces_color_override=None)[source]

                                            Draw cg.

                                            Parameters:
                                            @@ -2242,7 +2242,7 @@

                                            Submodules
                                            -visualize(cg, zoom=None, vis=None, factor=1.0, view_index=True, faces_color_override=None)[source]
                                            +visualize(cg, zoom=None, vis=None, factor=1.0, view_index=True, faces_color_override=None)[source]

                                            Visualizing a coordination geometry :param cg: :param zoom: diff --git a/docs/pymatgen.analysis.diffraction.html b/docs/pymatgen.analysis.diffraction.html index e0f70e14ec6..e7b37750d3b 100644 --- a/docs/pymatgen.analysis.diffraction.html +++ b/docs/pymatgen.analysis.diffraction.html @@ -4,7 +4,7 @@ - pymatgen.analysis.diffraction package — pymatgen 2024.6.4 documentation + pymatgen.analysis.diffraction package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@

                                            - 2024.6.4 + 2024.6.10
                                            @@ -147,22 +147,22 @@

                                            Submodules
                                            -class AbstractDiffractionPatternCalculator[source]
                                            +class AbstractDiffractionPatternCalculator[source]

                                            Bases: ABC

                                            Abstract base class for computing the diffraction pattern of a crystal.

                                            -SCALED_INTENSITY_TOL = 0.001[source]
                                            +SCALED_INTENSITY_TOL = 0.001[source]
                                            -TWO_THETA_TOL = 1e-05[source]
                                            +TWO_THETA_TOL = 1e-05[source]
                                            -abstract get_pattern(structure: Structure, scaled=True, two_theta_range=(0, 90))[source]
                                            +abstract get_pattern(structure: Structure, scaled=True, two_theta_range=(0, 90))[source]

                                            Calculates the diffraction pattern for a structure.

                                            Parameters:
                                            @@ -185,7 +185,7 @@

                                            Submodules
                                            -get_plot(structure: Structure, two_theta_range: tuple[float, float] = (0, 90), annotate_peaks='compact', ax: plt.Axes = None, with_labels=True, fontsize=16) → plt.Axes[source]
                                            +get_plot(structure: Structure, two_theta_range: tuple[float, float] = (0, 90), annotate_peaks='compact', ax: plt.Axes = None, with_labels=True, fontsize=16) → plt.Axes[source]

                                            Get the diffraction plot as a matplotlib Axes.

                                            Parameters:
                                            @@ -215,7 +215,7 @@

                                            Submodules
                                            -plot_structures(structures, fontsize=6, **kwargs)[source]
                                            +plot_structures(structures, fontsize=6, **kwargs)[source]

                                            Plot diffraction patterns for multiple structures on the same figure.

                                            Parameters:
                                            @@ -274,7 +274,7 @@

                                            Submodules
                                            -show_plot(structure: Structure, **kwargs)[source]
                                            +show_plot(structure: Structure, **kwargs)[source]

                                            Show the diffraction plot.

                                            Parameters:
                                            @@ -297,7 +297,7 @@

                                            Submodules
                                            -class DiffractionPattern(x, y, hkls, d_hkls)[source]
                                            +class DiffractionPattern(x, y, hkls, d_hkls)[source]

                                            Bases: Spectrum

                                            A representation of a diffraction pattern.

                                            @@ -316,19 +316,19 @@

                                            Submodules
                                            -XLABEL = '$2\\Theta$'[source]
                                            +XLABEL = '$2\\Theta$'[source]

                                            -YLABEL = 'Intensity'[source]
                                            +YLABEL = 'Intensity'[source]

                                            -get_unique_families(hkls)[source]
                                            +get_unique_families(hkls)[source]

                                            Get unique families of Miller indices. Families must be permutations of each other.

                                            @@ -350,7 +350,7 @@

                                            Submodules
                                            -class NDCalculator(wavelength=1.54184, symprec: float = 0, debye_waller_factors=None)[source]
                                            +class NDCalculator(wavelength=1.54184, symprec: float = 0, debye_waller_factors=None)[source]

                                            Bases: AbstractDiffractionPatternCalculator

                                            Computes the powder neutron diffraction pattern of a crystal structure. This code is a slight modification of XRDCalculator in @@ -380,7 +380,7 @@

                                            Submodules
                                            -get_pattern(structure: Structure, scaled=True, two_theta_range=(0, 90))[source]
                                            +get_pattern(structure: Structure, scaled=True, two_theta_range=(0, 90))[source]

                                            Calculates the powder neutron diffraction pattern for a structure.

                                            Parameters:
                                            @@ -412,7 +412,7 @@

                                            Submodules
                                            -class TEMCalculator(symprec: float | None = None, voltage: float = 200, beam_direction: tuple[int, int, int] = (0, 0, 1), camera_length: int = 160, debye_waller_factors: dict[str, float] | None = None, cs: float = 1)[source]
                                            +class TEMCalculator(symprec: float | None = None, voltage: float = 200, beam_direction: tuple[int, int, int] = (0, 0, 1), camera_length: int = 160, debye_waller_factors: dict[str, float] | None = None, cs: float = 1)[source]

                                            Bases: AbstractDiffractionPatternCalculator

                                            Compute the TEM pattern of a crystal structure for multiple Laue zones. Code partially inspired from XRD calculation implementation. X-ray factor to electron factor

                                            @@ -445,7 +445,7 @@

                                            Submodules
                                            -bragg_angles(interplanar_spacings: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]
                                            +bragg_angles(interplanar_spacings: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]

                                            Get the Bragg angles for every hkl point passed in (where n = 1).

                                            Parameters:
                                            @@ -462,7 +462,7 @@

                                            Submodules
                                            -cell_intensity(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[Tuple3Ints, float][source]
                                            +cell_intensity(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[Tuple3Ints, float][source]

                                            Calculates cell intensity for each hkl plane. For simplicity’s sake, take I = |F|**2.

                                            Parameters:
                                            @@ -479,7 +479,7 @@

                                            Submodules
                                            -cell_scattering_factors(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[Tuple3Ints, int][source]
                                            +cell_scattering_factors(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[Tuple3Ints, int][source]

                                            Calculates the scattering factor for the whole cell.

                                            Parameters:
                                            @@ -496,7 +496,7 @@

                                            Submodules
                                            -electron_scattering_factors(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[str, dict[Tuple3Ints, float]][source]
                                            +electron_scattering_factors(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[str, dict[Tuple3Ints, float]][source]

                                            Calculates atomic scattering factors for electrons using the Mott-Bethe formula (1st order Born approximation).

                                            Parameters:
                                            @@ -513,7 +513,7 @@

                                            Submodules
                                            -static generate_points(coord_left: int = -10, coord_right: int = 10) → ndarray[source]
                                            +static generate_points(coord_left: int = -10, coord_right: int = 10) → ndarray[source]

                                            Generate a bunch of 3D points that span a cube.

                                            Parameters:
                                            @@ -533,7 +533,7 @@

                                            Submodules
                                            -get_first_point(structure: Structure, points: list) → dict[Tuple3Ints, float][source]
                                            +get_first_point(structure: Structure, points: list) → dict[Tuple3Ints, float][source]

                                            Get the first point to be plotted in the 2D DP, corresponding to maximum d/minimum R.

                                            Parameters:
                                            @@ -550,7 +550,7 @@

                                            Submodules
                                            -static get_interplanar_angle(structure: Structure, p1: Tuple3Ints, p2: Tuple3Ints) → float[source]
                                            +static get_interplanar_angle(structure: Structure, p1: Tuple3Ints, p2: Tuple3Ints) → float[source]

                                            Get the interplanar angle (in degrees) between the normal of two crystal planes. Formulas from International Tables for Crystallography Volume C pp. 2-9.

                                            @@ -569,7 +569,7 @@

                                            Submodules
                                            -get_interplanar_spacings(structure: Structure, points: list[Tuple3Ints] | np.ndarray) → dict[Tuple3Ints, float][source]
                                            +get_interplanar_spacings(structure: Structure, points: list[Tuple3Ints] | np.ndarray) → dict[Tuple3Ints, float][source]
                                            Parameters:
                                              @@ -592,7 +592,7 @@

                                              Submodules
                                              -get_pattern(structure: Structure, scaled: bool | None = None, two_theta_range: tuple[float, float] | None = None) → pd.DataFrame[source]
                                              +get_pattern(structure: Structure, scaled: bool | None = None, two_theta_range: tuple[float, float] | None = None) → pd.DataFrame[source]

                                              Get all relevant TEM DP info in a pandas dataframe.

                                              Parameters:
                                              @@ -610,7 +610,7 @@

                                              Submodules
                                              -get_plot_2d(structure: Structure) → go.Figure[source]
                                              +get_plot_2d(structure: Structure) → go.Figure[source]

                                              Generate the 2D diffraction pattern of the input structure.

                                              Parameters:
                                              @@ -624,7 +624,7 @@

                                              Submodules
                                              -get_plot_2d_concise(structure: Structure) → go.Figure[source]
                                              +get_plot_2d_concise(structure: Structure) → go.Figure[source]

                                              Generate the concise 2D diffraction pattern of the input structure of a smaller size and without layout. Does not display.

                                              @@ -639,7 +639,7 @@

                                              Submodules
                                              -static get_plot_coeffs(p1: tuple[int, int, int], p2: tuple[int, int, int], p3: tuple[int, int, int]) → ndarray[source]
                                              +static get_plot_coeffs(p1: tuple[int, int, int], p2: tuple[int, int, int], p3: tuple[int, int, int]) → ndarray[source]

                                              Calculates coefficients of the vector addition required to generate positions for each DP point by the Moore-Penrose inverse method.

                                              @@ -658,7 +658,7 @@

                                              Submodules
                                              -get_positions(structure: Structure, points: list) → dict[Tuple3Ints, np.ndarray][source]
                                              +get_positions(structure: Structure, points: list) → dict[Tuple3Ints, np.ndarray][source]

                                              Calculates all the positions of each hkl point in the 2D diffraction pattern by vector addition. Distance in centimeters.

                                              @@ -676,7 +676,7 @@

                                              Submodules
                                              -get_s2(bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]
                                              +get_s2(bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]

                                              Calculates the s squared parameter (= square of sin theta over lambda) for each hkl plane.

                                              Parameters:
                                              @@ -694,7 +694,7 @@

                                              Submodules
                                              -is_parallel(structure: Structure, plane: Tuple3Ints, other_plane: Tuple3Ints) → bool[source]
                                              +is_parallel(structure: Structure, plane: Tuple3Ints, other_plane: Tuple3Ints) → bool[source]

                                              Checks if two hkl planes are parallel in reciprocal space.

                                              Parameters:
                                              @@ -712,7 +712,7 @@

                                              Submodules
                                              -normalized_cell_intensity(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[Tuple3Ints, float][source]
                                              +normalized_cell_intensity(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[Tuple3Ints, float][source]

                                              Normalizes the cell_intensity dict to 1, for use in plotting.

                                              Parameters:
                                              @@ -729,7 +729,7 @@

                                              Submodules
                                              -tem_dots(structure: Structure, points) → list[source]
                                              +tem_dots(structure: Structure, points) → list[source]

                                              Generate all TEM_dot as named tuples that will appear on the 2D diffraction pattern.

                                              Parameters:
                                              @@ -746,7 +746,7 @@

                                              Submodules
                                              -wavelength_rel() → float[source]
                                              +wavelength_rel() → float[source]
                                              Calculates the wavelength of the electron beam with relativistic kinematic effects taken

                                              into account.

                                              @@ -763,7 +763,7 @@

                                              Submodules
                                              -x_ray_factors(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[str, dict[Tuple3Ints, float]][source]
                                              +x_ray_factors(structure: Structure, bragg_angles: dict[Tuple3Ints, float]) → dict[str, dict[Tuple3Ints, float]][source]

                                              Calculates x-ray factors, which are required to calculate atomic scattering factors. Method partially inspired by the equivalent process in the xrd module.

                                              @@ -781,7 +781,7 @@

                                              Submodules
                                              -zone_axis_filter(points: list[tuple[int, int, int]] | ndarray, laue_zone: int = 0) → list[tuple[int, int, int]][source]
                                              +zone_axis_filter(points: list[tuple[int, int, int]] | ndarray, laue_zone: int = 0) → list[tuple[int, int, int]][source]

                                              Filter out all points that exist within the specified Laue zone according to the zone axis rule.

                                              Parameters:
                                              @@ -804,7 +804,7 @@

                                              Submodules
                                              -class XRDCalculator(wavelength='CuKa', symprec: float = 0, debye_waller_factors=None)[source]
                                              +class XRDCalculator(wavelength='CuKa', symprec: float = 0, debye_waller_factors=None)[source]

                                              Bases: AbstractDiffractionPatternCalculator

                                              Computes the XRD pattern of a crystal structure.

                                              This code is implemented by Shyue Ping Ong as part of UCSD’s NANO106 - @@ -868,12 +868,12 @@

                                              Submodules
                                              -AVAILABLE_RADIATION = ('CuKa', 'CuKa2', 'CuKa1', 'CuKb1', 'MoKa', 'MoKa2', 'MoKa1', 'MoKb1', 'CrKa', 'CrKa2', 'CrKa1', 'CrKb1', 'FeKa', 'FeKa2', 'FeKa1', 'FeKb1', 'CoKa', 'CoKa2', 'CoKa1', 'CoKb1', 'AgKa', 'AgKa2', 'AgKa1', 'AgKb1')[source]
                                              +AVAILABLE_RADIATION = ('CuKa', 'CuKa2', 'CuKa1', 'CuKb1', 'MoKa', 'MoKa2', 'MoKa1', 'MoKb1', 'CrKa', 'CrKa2', 'CrKa1', 'CrKb1', 'FeKa', 'FeKa2', 'FeKa1', 'FeKb1', 'CoKa', 'CoKa2', 'CoKa1', 'CoKb1', 'AgKa', 'AgKa2', 'AgKa1', 'AgKb1')[source]

                                              -get_pattern(structure: Structure, scaled=True, two_theta_range=(0, 90))[source]
                                              +get_pattern(structure: Structure, scaled=True, two_theta_range=(0, 90))[source]

                                              Calculates the diffraction pattern for a structure.

                                              Parameters:
                                              diff --git a/docs/pymatgen.analysis.elasticity.html b/docs/pymatgen.analysis.elasticity.html index d979aad5c97..947a46c4288 100644 --- a/docs/pymatgen.analysis.elasticity.html +++ b/docs/pymatgen.analysis.elasticity.html @@ -4,7 +4,7 @@ - pymatgen.analysis.elasticity package — pymatgen 2024.6.4 documentation + pymatgen.analysis.elasticity package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                              - 2024.6.4 + 2024.6.10
                                              @@ -195,7 +195,7 @@

                                              Submodules
                                              -class ComplianceTensor(s_array)[source]
                                              +class ComplianceTensor(s_array)[source]

                                              Bases: Tensor

                                              This class represents the compliance tensor, and exists primarily to keep the voigt-conversion scheme consistent @@ -209,7 +209,7 @@

                                              Submodules
                                              -class ElasticTensor(input_array, tol: float = 0.0001)[source]
                                              +class ElasticTensor(input_array, tol: float = 0.0001)[source]

                                              Bases: NthOrderElasticTensor

                                              This class extends Tensor to describe the 3x3x3x3 second-order elastic tensor, C_{ijkl}, with various methods for estimating other properties derived from the second @@ -230,40 +230,40 @@

                                              Submodules
                                              -agne_diffusive_thermalcond(*args, **kwargs)[source]
                                              +agne_diffusive_thermalcond(*args, **kwargs)[source]

                                              -cahill_thermalcond(*args, **kwargs)[source]
                                              +cahill_thermalcond(*args, **kwargs)[source]
                                              -clarke_thermalcond(*args, **kwargs)[source]
                                              +clarke_thermalcond(*args, **kwargs)[source]
                                              -property compliance_tensor[source]
                                              +property compliance_tensor[source]

                                              The Voigt notation compliance tensor, which is the matrix inverse of the Voigt notation elastic tensor.

                                              -debye_temperature(*args, **kwargs)[source]
                                              +debye_temperature(*args, **kwargs)[source]
                                              -directional_elastic_mod(n) → float[source]
                                              +directional_elastic_mod(n) → float[source]

                                              Calculate directional elastic modulus for a specific vector.

                                              -directional_poisson_ratio(n: ArrayLike, m: ArrayLike, tol: float = 1e-08) → float[source]
                                              +directional_poisson_ratio(n: ArrayLike, m: ArrayLike, tol: float = 1e-08) → float[source]

                                              Calculates the poisson ratio for a specific direction relative to a second, orthogonal direction.

                                              @@ -279,7 +279,7 @@

                                              Submodules
                                              -classmethod from_independent_strains(strains, stresses, eq_stress=None, vasp=False, tol: float = 1e-10) → Self[source]
                                              +classmethod from_independent_strains(strains, stresses, eq_stress=None, vasp=False, tol: float = 1e-10) → Self[source]

                                              Constructs the elastic tensor least-squares fit of independent strains

                                              Parameters:
                                              @@ -299,7 +299,7 @@

                                              Submodules
                                              -classmethod from_pseudoinverse(strains, stresses) → Self[source]
                                              +classmethod from_pseudoinverse(strains, stresses) → Self[source]

                                              Class method to fit an elastic tensor from stress/strain data. Method uses Moore-Penrose pseudo-inverse to invert the s = C*e equation with elastic tensor, stress, and @@ -316,25 +316,25 @@

                                              Submodules
                                              -property g_reuss: float[source]
                                              +property g_reuss: float[source]

                                              The G_r shear modulus (in eV/A^3).

                                              -property g_voigt: float[source]
                                              +property g_voigt: float[source]

                                              The G_v shear modulus (in eV/A^3).

                                              -property g_vrh: float[source]
                                              +property g_vrh: float[source]

                                              The G_vrh (Voigt-Reuss-Hill) average shear modulus (in eV/A^3).

                                              -get_structure_property_dict(structure: Structure, include_base_props: bool = True, ignore_errors: bool = False) → dict[str, float | Structure | None][source]
                                              +get_structure_property_dict(structure: Structure, include_base_props: bool = True, ignore_errors: bool = False) → dict[str, float | Structure | None][source]

                                              Get a dictionary of properties derived from the elastic tensor and an associated structure.

                                              @@ -353,74 +353,74 @@

                                              Submodules
                                              -green_kristoffel(u) → float[source]
                                              +green_kristoffel(u) → float[source]

                                              Get the Green-Kristoffel tensor for a second-order tensor.

                                              -property homogeneous_poisson: float[source]
                                              +property homogeneous_poisson: float[source]

                                              The homogeneous poisson ratio.

                                              -property k_reuss: float[source]
                                              +property k_reuss: float[source]

                                              The K_r bulk modulus (in eV/A^3).

                                              -property k_voigt: float[source]
                                              +property k_voigt: float[source]

                                              The K_v bulk modulus (in eV/A^3).

                                              -property k_vrh: float[source]
                                              +property k_vrh: float[source]

                                              The K_vrh (Voigt-Reuss-Hill) average bulk modulus (in eV/A^3).

                                              -long_v(*args, **kwargs)[source]
                                              +long_v(*args, **kwargs)[source]
                                              -property property_dict[source]
                                              +property property_dict[source]

                                              A dictionary of properties derived from the elastic tensor.

                                              -snyder_ac(*args, **kwargs)[source]
                                              +snyder_ac(*args, **kwargs)[source]
                                              -snyder_opt(*args, **kwargs)[source]
                                              +snyder_opt(*args, **kwargs)[source]
                                              -snyder_total(*args, **kwargs)[source]
                                              +snyder_total(*args, **kwargs)[source]
                                              -trans_v(*args, **kwargs)[source]
                                              +trans_v(*args, **kwargs)[source]
                                              -property universal_anisotropy: float[source]
                                              +property universal_anisotropy: float[source]

                                              The universal anisotropy value.

                                              -property y_mod: float[source]
                                              +property y_mod: float[source]

                                              Calculates Young’s modulus (in SI units) using the Voigt-Reuss-Hill averages of bulk and shear moduli.

                                              @@ -429,7 +429,7 @@

                                              Submodules
                                              -class ElasticTensorExpansion(c_list: Sequence)[source]
                                              +class ElasticTensorExpansion(c_list: Sequence)[source]

                                              Bases: TensorCollection

                                              This class is a sequence of elastic tensors corresponding to an elastic tensor expansion, which can be used to @@ -445,34 +445,34 @@

                                              Submodules
                                              -calculate_stress(strain) → float[source]
                                              +calculate_stress(strain) → float[source]

                                              Calculate’s a given elastic tensor’s contribution to the stress using Einstein summation.

                                              -energy_density(strain, convert_GPa_to_eV=True)[source]
                                              +energy_density(strain, convert_GPa_to_eV=True)[source]

                                              Calculate the elastic energy density due to a strain in eV/A^3 or GPa.

                                              -classmethod from_diff_fit(strains, stresses, eq_stress=None, tol: float = 1e-10, order=3) → Self[source]
                                              +classmethod from_diff_fit(strains, stresses, eq_stress=None, tol: float = 1e-10, order=3) → Self[source]

                                              Generate an elastic tensor expansion via the fitting function defined below in diff_fit.

                                              -get_compliance_expansion()[source]
                                              +get_compliance_expansion()[source]

                                              Get a compliance tensor expansion from the elastic tensor expansion.

                                              -get_effective_ecs(strain, order=2)[source]
                                              +get_effective_ecs(strain, order=2)[source]

                                              Get the effective elastic constants from the elastic tensor expansion.

                                              @@ -488,7 +488,7 @@

                                              Submodules
                                              -get_ggt(n, u)[source]
                                              +get_ggt(n, u)[source]

                                              Get the Generalized Gruneisen tensor for a given third-order elastic tensor expansion.

                                              @@ -503,7 +503,7 @@

                                              Submodules
                                              -get_gruneisen_parameter(temperature=None, structure=None, quad=None)[source]
                                              +get_gruneisen_parameter(temperature=None, structure=None, quad=None)[source]

                                              Get the single average gruneisen parameter from the TGT.

                                              Parameters:
                                              @@ -523,7 +523,7 @@

                                              Submodules
                                              -get_heat_capacity(temperature, structure: Structure, n, u, cutoff=100.0)[source]
                                              +get_heat_capacity(temperature, structure: Structure, n, u, cutoff=100.0)[source]

                                              Get the directional heat capacity for a higher order tensor expansion as a function of direction and polarization.

                                              @@ -544,7 +544,7 @@

                                              Submodules
                                              -get_stability_criteria(s, n)[source]
                                              +get_stability_criteria(s, n)[source]

                                              Get the stability criteria from the symmetric Wallace tensor from an input vector and stress value.

                                              @@ -562,14 +562,14 @@

                                              Submodules
                                              -get_strain_from_stress(stress) → float[source]
                                              +get_strain_from_stress(stress) → float[source]

                                              Get the strain from a stress state according to the compliance expansion corresponding to the tensor expansion.

                                              -get_symmetric_wallace_tensor(tau)[source]
                                              +get_symmetric_wallace_tensor(tau)[source]

                                              Get the symmetrized wallace tensor for determining yield strength criteria.

                                              @@ -582,7 +582,7 @@

                                              Submodules
                                              -get_tgt(temperature: float | None = None, structure: Structure = None, quad=None)[source]
                                              +get_tgt(temperature: float | None = None, structure: Structure = None, quad=None)[source]

                                              Get the thermodynamic Gruneisen tensor (TGT) by via an integration of the GGT weighted by the directional heat capacity.

                                              @@ -609,7 +609,7 @@

                                              Submodules
                                              -get_wallace_tensor(tau)[source]
                                              +get_wallace_tensor(tau)[source]

                                              Get the Wallace Tensor for determining yield strength criteria.

                                              @@ -622,7 +622,7 @@

                                              Submodules
                                              -get_yield_stress(n)[source]
                                              +get_yield_stress(n)[source]

                                              Get the yield stress for a given direction.

                                              Parameters:
                                              @@ -634,7 +634,7 @@

                                              Submodules
                                              -omega(structure: Structure, n, u)[source]
                                              +omega(structure: Structure, n, u)[source]

                                              Find directional frequency contribution to the heat capacity from direction and polarization.

                                              @@ -652,14 +652,14 @@

                                              Submodules
                                              -property order: int[source]
                                              +property order: int[source]

                                              Order of the elastic tensor expansion, i. e. the order of the highest included set of elastic constants.

                                              -thermal_expansion_coeff(structure: Structure, temperature: float, mode: Literal['dulong - petit', 'debye'] = 'debye')[source]
                                              +thermal_expansion_coeff(structure: Structure, temperature: float, mode: Literal['dulong - petit', 'debye'] = 'debye')[source]

                                              Get thermal expansion coefficient from third-order constants.

                                              Parameters:
                                              @@ -680,7 +680,7 @@

                                              Submodules
                                              -class NthOrderElasticTensor(input_array, check_rank=None, tol: float = 0.0001)[source]
                                              +class NthOrderElasticTensor(input_array, check_rank=None, tol: float = 0.0001)[source]

                                              Bases: Tensor

                                              An object representing an nth-order tensor expansion of the stress-strain constitutive equations.

                                              @@ -695,12 +695,12 @@

                                              Submodules
                                              -GPa_to_eV_A3 = 0.006241509074460764[source]
                                              +GPa_to_eV_A3 = 0.006241509074460764[source]

                                              -calculate_stress(strain)[source]
                                              +calculate_stress(strain)[source]

                                              Calculate’s a given elastic tensor’s contribution to the stress using Einstein summation.

                                              @@ -712,13 +712,13 @@

                                              Submodules
                                              -energy_density(strain, convert_GPa_to_eV=True)[source]
                                              +energy_density(strain, convert_GPa_to_eV=True)[source]

                                              Calculate the elastic energy density due to a strain.

                                              -classmethod from_diff_fit(strains, stresses, eq_stress=None, order=2, tol: float = 1e-10) → Self[source]
                                              +classmethod from_diff_fit(strains, stresses, eq_stress=None, order=2, tol: float = 1e-10) → Self[source]

                                              Takes a list of strains and stresses, and returns a list of coefficients for a polynomial fit of the given order.

                                              @@ -742,20 +742,20 @@

                                              Submodules
                                              -property order[source]
                                              +property order[source]

                                              Order of the elastic tensor.

                                              -symbol = 'C'[source]
                                              +symbol = 'C'[source]
                                              -diff_fit(strains, stresses, eq_stress=None, order=2, tol: float = 1e-10)[source]
                                              +diff_fit(strains, stresses, eq_stress=None, order=2, tol: float = 1e-10)[source]

                                              nth order elastic constant fitting function based on central-difference derivatives with respect to distinct strain states. The algorithm is summarized as follows:

                                              @@ -802,7 +802,7 @@

                                              Submodules
                                              -find_eq_stress(strains, stresses, tol: float = 1e-10)[source]
                                              +find_eq_stress(strains, stresses, tol: float = 1e-10)[source]

                                              Find stress corresponding to zero strain state in stress-strain list.

                                              Parameters:
                                              @@ -817,7 +817,7 @@

                                              Submodules
                                              -generate_pseudo(strain_states, order=3)[source]
                                              +generate_pseudo(strain_states, order=3)[source]

                                              Generate the pseudo-inverse for a given set of strains.

                                              Parameters:
                                              @@ -844,7 +844,7 @@

                                              Submodules
                                              -get_diff_coeff(hvec, n=1)[source]
                                              +get_diff_coeff(hvec, n=1)[source]

                                              Helper function to find difference coefficients of an derivative on an arbitrary mesh.

                                              @@ -859,7 +859,7 @@

                                              Submodules
                                              -get_strain_state_dict(strains, stresses, eq_stress=None, tol: float = 1e-10, add_eq=True, sort=True)[source]
                                              +get_strain_state_dict(strains, stresses, eq_stress=None, tol: float = 1e-10, add_eq=True, sort=True)[source]

                                              Create a dictionary of voigt notation stress-strain sets keyed by “strain state”, i. e. a tuple corresponding to the non-zero entries in ratios to the lowest nonzero value, @@ -889,7 +889,7 @@

                                              Submodules
                                              -get_symbol_list(rank, dim=6)[source]
                                              +get_symbol_list(rank, dim=6)[source]

                                              Get a symbolic representation of the Voigt-notation tensor that places identical symbols for entries related by index transposition, i. e. C_1121 = C_1211 etc.

                                              @@ -916,14 +916,14 @@

                                              Submodules
                                              -raise_if_unphysical(func)[source]
                                              +raise_if_unphysical(func)[source]

                                              Wrapper for functions or properties that should raise an error if tensor is unphysical.

                                              -subs(entry, cmap)[source]
                                              +subs(entry, cmap)[source]

                                              Sympy substitution function, primarily for the purposes of numpy vectorization.

                                              @@ -947,7 +947,7 @@

                                              Submodules
                                              -class Deformation(deformation_gradient)[source]
                                              +class Deformation(deformation_gradient)[source]

                                              Bases: SquareTensor

                                              Subclass of SquareTensor that describes the deformation gradient tensor.

                                              Create a Deformation object. Note that the constructor uses __new__ rather than @@ -960,7 +960,7 @@

                                              Submodules
                                              -apply_to_structure(structure: Structure)[source]
                                              +apply_to_structure(structure: Structure)[source]

                                              Apply the deformation gradient to a structure.

                                              Parameters:
                                              @@ -972,7 +972,7 @@

                                              Submodules
                                              -classmethod from_index_amount(matrix_pos, amt) → Self[source]
                                              +classmethod from_index_amount(matrix_pos, amt) → Self[source]

                                              Factory method for constructing a Deformation object from a matrix position and amount.

                                              @@ -989,33 +989,33 @@

                                              Submodules
                                              -get_perturbed_indices(tol: float = 1e-08)[source]
                                              +get_perturbed_indices(tol: float = 1e-08)[source]

                                              Get indices of perturbed elements of the deformation gradient, i. e. those that differ from the identity.

                                              -property green_lagrange_strain[source]
                                              +property green_lagrange_strain[source]

                                              Calculate the Euler-Lagrange strain from the deformation gradient.

                                              -is_independent(tol: float = 1e-08)[source]
                                              +is_independent(tol: float = 1e-08)[source]

                                              Check to determine whether the deformation is independent.

                                              -symbol = 'd'[source]
                                              +symbol = 'd'[source]

                                              -class DeformedStructureSet(structure: Structure, norm_strains: Sequence[float] = (-0.01, -0.005, 0.005, 0.01), shear_strains: Sequence[float] = (-0.06, -0.03, 0.03, 0.06), symmetry=False)[source]
                                              +class DeformedStructureSet(structure: Structure, norm_strains: Sequence[float] = (-0.01, -0.005, 0.005, 0.01), shear_strains: Sequence[float] = (-0.06, -0.03, 0.03, 0.06), symmetry=False)[source]

                                              Bases: Sequence

                                              class that generates a set of independently deformed structures that can be used to calculate linear stress-strain response.

                                              @@ -1037,7 +1037,7 @@

                                              Submodules
                                              -class Strain(strain_matrix)[source]
                                              +class Strain(strain_matrix)[source]

                                              Bases: SquareTensor

                                              Subclass of SquareTensor that describes the Green-Lagrange strain tensor.

                                              Create a Strain object. Note that the constructor uses __new__ @@ -1052,7 +1052,7 @@

                                              Submodules
                                              -classmethod from_deformation(deformation: ArrayLike) → Self[source]
                                              +classmethod from_deformation(deformation: ArrayLike) → Self[source]

                                              Factory method that returns a Strain object from a deformation gradient.

                                              @@ -1064,7 +1064,7 @@

                                              Submodules
                                              -classmethod from_index_amount(idx: tuple | int, amount: float) → Self[source]
                                              +classmethod from_index_amount(idx: tuple | int, amount: float) → Self[source]

                                              Like Deformation.from_index_amount, except generates a strain from the zero 3x3 tensor or Voigt vector with the amount specified in the index location. Ensures @@ -1081,7 +1081,7 @@

                                              Submodules
                                              -get_deformation_matrix(shape: Literal['upper', 'lower', 'symmetric'] = 'upper')[source]
                                              +get_deformation_matrix(shape: Literal['upper', 'lower', 'symmetric'] = 'upper')[source]

                                              Get the deformation matrix.

                                              Parameters:
                                              @@ -1095,12 +1095,12 @@

                                              Submodules
                                              -symbol = 'e'[source]
                                              +symbol = 'e'[source]

                                              -property von_mises_strain[source]
                                              +property von_mises_strain[source]

                                              Equivalent strain to Von Mises Stress.

                                              @@ -1108,7 +1108,7 @@

                                              Submodules
                                              -convert_strain_to_deformation(strain, shape: Literal['upper', 'lower', 'symmetric'])[source]
                                              +convert_strain_to_deformation(strain, shape: Literal['upper', 'lower', 'symmetric'])[source]

                                              This function converts a strain to a deformation gradient that will produce that strain. Supports three methods:

                                              @@ -1131,7 +1131,7 @@

                                              Submodules
                                              -class Stress(stress_matrix)[source]
                                              +class Stress(stress_matrix)[source]

                                              Bases: SquareTensor

                                              This class extends SquareTensor as a representation of the stress.

                                              @@ -1146,7 +1146,7 @@

                                              Submodules
                                              -property dev_principal_invariants[source]
                                              +property dev_principal_invariants[source]

                                              The principal invariants of the deviatoric stress tensor, which is calculated by finding the coefficients of the characteristic polynomial of the stress tensor minus the identity times the mean @@ -1155,19 +1155,19 @@

                                              Submodules
                                              -property deviator_stress[source]
                                              +property deviator_stress[source]

                                              The deviatoric component of the stress.

                                              -property mean_stress[source]
                                              +property mean_stress[source]

                                              The mean stress.

                                              -piola_kirchoff_1(def_grad)[source]
                                              +piola_kirchoff_1(def_grad)[source]

                                              Calculates the first Piola-Kirchoff stress.

                                              Parameters:
                                              @@ -1178,7 +1178,7 @@

                                              Submodules
                                              -piola_kirchoff_2(def_grad)[source]
                                              +piola_kirchoff_2(def_grad)[source]

                                              Calculates the second Piola-Kirchoff stress.

                                              Parameters:
                                              @@ -1189,12 +1189,12 @@

                                              Submodules
                                              -symbol = 's'[source]
                                              +symbol = 's'[source]

                                              -property von_mises[source]
                                              +property von_mises[source]

                                              The von Mises stress.

                                              diff --git a/docs/pymatgen.analysis.ferroelectricity.html b/docs/pymatgen.analysis.ferroelectricity.html index 7916ba08357..f5f247517a8 100644 --- a/docs/pymatgen.analysis.ferroelectricity.html +++ b/docs/pymatgen.analysis.ferroelectricity.html @@ -4,7 +4,7 @@ - pymatgen.analysis.ferroelectricity package — pymatgen 2024.6.4 documentation + pymatgen.analysis.ferroelectricity package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                              - 2024.6.4 + 2024.6.10
                                              @@ -150,7 +150,7 @@

                                              Submodules
                                              -class EnergyTrend(energies)[source]
                                              +class EnergyTrend(energies)[source]

                                              Bases: object

                                              Analyze the trend in energy across a distortion path.

                                              @@ -160,25 +160,25 @@

                                              Submodules
                                              -endpoints_minima(slope_cutoff=0.005)[source]
                                              +endpoints_minima(slope_cutoff=0.005)[source]

                                              Test if spline endpoints are at minima for a given slope cutoff.

                                              -max_spline_jump()[source]
                                              +max_spline_jump()[source]

                                              Get maximum difference between spline and energy trend.

                                              -smoothness()[source]
                                              +smoothness()[source]

                                              Get rms average difference between spline and energy trend.

                                              -spline()[source]
                                              +spline()[source]

                                              Fit spline to energy trend data.

                                              @@ -186,7 +186,7 @@

                                              Submodules
                                              -class Polarization(p_elecs, p_ions, structures: Sequence[Structure], p_elecs_in_cartesian=True, p_ions_in_cartesian=False)[source]
                                              +class Polarization(p_elecs, p_ions, structures: Sequence[Structure], p_elecs_in_cartesian=True, p_ions_in_cartesian=False)[source]

                                              Bases: object

                                              Recover the same branch polarization for a set of polarization calculations along the nonpolar - polar distortion path of a ferroelectric.

                                              @@ -211,7 +211,7 @@

                                              Submodules
                                              -classmethod from_outcars_and_structures(outcars, structures, calc_ionic_from_zval=False) → Self[source]
                                              +classmethod from_outcars_and_structures(outcars, structures, calc_ionic_from_zval=False) → Self[source]

                                              Create Polarization object from list of Outcars and Structures in order of nonpolar to polar.

                                              Note, we recommend calculating the ionic dipole moment using calc_ionic @@ -221,14 +221,14 @@

                                              Submodules
                                              -get_lattice_quanta(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                              +get_lattice_quanta(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                              Get the dipole / polarization quanta along a, b, and c for all structures.

                                              -get_pelecs_and_pions(convert_to_muC_per_cm2=False)[source]
                                              +get_pelecs_and_pions(convert_to_muC_per_cm2=False)[source]

                                              Get the electronic and ionic dipole moments / polarizations.

                                              convert_to_muC_per_cm2: Convert from electron * Angstroms to microCoulomb

                                              per centimeter**2

                                              @@ -238,20 +238,20 @@

                                              Submodules
                                              -get_polarization_change(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                              +get_polarization_change(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                              Get difference between nonpolar and polar same branch polarization.

                                              -get_polarization_change_norm(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                              +get_polarization_change_norm(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                              Get magnitude of difference between nonpolar and polar same branch polarization.

                                              -get_same_branch_polarization_data(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                              +get_same_branch_polarization_data(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                              Get same branch dipole moment (convert_to_muC_per_cm2=False) or polarization for given polarization data (convert_to_muC_per_cm2=True).

                                              Polarization is a lattice vector, meaning it is only defined modulo the @@ -288,20 +288,20 @@

                                              Submodules
                                              -max_spline_jumps(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                              +max_spline_jumps(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                              Get maximum difference between spline and same branch polarization data.

                                              -same_branch_splines(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                              +same_branch_splines(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                              Fit splines to same branch polarization. This is used to assess any jumps in the same branch polarization.

                                              -smoothness(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                              +smoothness(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                              Get rms average difference between spline and same branch polarization data.

                                              @@ -309,7 +309,7 @@

                                              Submodules
                                              -calc_ionic(site: PeriodicSite, structure: Structure, zval: float) → np.ndarray[source]
                                              +calc_ionic(site: PeriodicSite, structure: Structure, zval: float) → np.ndarray[source]

                                              Calculate the ionic dipole moment using ZVAL from pseudopotential.

                                              site: PeriodicSite structure: Structure @@ -319,7 +319,7 @@

                                              Submodules
                                              -get_nearest_site(struct: Structure, coords: Sequence[float], site: PeriodicSite, r: float | None = None)[source]
                                              +get_nearest_site(struct: Structure, coords: Sequence[float], site: PeriodicSite, r: float | None = None)[source]

                                              Given coords and a site, find closet site to coords.

                                              Parameters:
                                              @@ -337,7 +337,7 @@

                                              Submodules
                                              -get_total_ionic_dipole(structure, zval_dict)[source]
                                              +get_total_ionic_dipole(structure, zval_dict)[source]

                                              Get the total ionic dipole moment for a structure.

                                              structure: pymatgen Structure zval_dict: specie, zval dictionary pairs @@ -347,7 +347,7 @@

                                              Submodules
                                              -zval_dict_from_potcar(potcar) → dict[str, float][source]
                                              +zval_dict_from_potcar(potcar) → dict[str, float][source]

                                              Create zval_dictionary for calculating the ionic polarization from Potcar object.

                                              potcar: Potcar object

                                              diff --git a/docs/pymatgen.analysis.gb.html b/docs/pymatgen.analysis.gb.html index c0cdc49c060..9fbb860332c 100644 --- a/docs/pymatgen.analysis.gb.html +++ b/docs/pymatgen.analysis.gb.html @@ -4,7 +4,7 @@ - pymatgen.analysis.gb package — pymatgen 2024.6.4 documentation + pymatgen.analysis.gb package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                              - 2024.6.4 + 2024.6.10
                                              diff --git a/docs/pymatgen.analysis.html b/docs/pymatgen.analysis.html index 60ddd18a948..d78fc3640ec 100644 --- a/docs/pymatgen.analysis.html +++ b/docs/pymatgen.analysis.html @@ -4,7 +4,7 @@ - pymatgen.analysis namespace — pymatgen 2024.6.4 documentation + pymatgen.analysis namespace — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                              - 2024.6.4 + 2024.6.10
                                              @@ -2330,15 +2330,7 @@

                                              Subpackagespymatgen.analysis.solar package
                                            • pymatgen.analysis.structure_prediction package
                                                @@ -2430,7 +2422,7 @@

                                                Submodules
                                                -class AdsorbateSiteFinder(slab: Slab, selective_dynamics: bool = False, height: float = 0.9, mi_vec: ArrayLike | None = None)[source]
                                                +class AdsorbateSiteFinder(slab: Slab, selective_dynamics: bool = False, height: float = 0.9, mi_vec: ArrayLike | None = None)[source]

                                                Bases: object

                                                This class finds adsorbate sites on slabs and generates adsorbate structures according to user-defined criteria.

                                                @@ -2478,7 +2470,7 @@

                                                Submodules
                                                -add_adsorbate(molecule: Molecule, ads_coord, repeat=None, translate=True, reorient=True)[source]
                                                +add_adsorbate(molecule: Molecule, ads_coord, repeat=None, translate=True, reorient=True)[source]

                                                Add an adsorbate at a particular coordinate. Adsorbate represented by a Molecule object and is translated to (0, 0, 0) if translate is True, or positioned relative to the input adsorbate coordinate if @@ -2501,7 +2493,7 @@

                                                Submodules
                                                -adsorb_both_surfaces(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]
                                                +adsorb_both_surfaces(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]

                                                Generate all adsorption structures for a given molecular adsorbate on both surfaces of a slab. This is useful for calculating surface energy where both surfaces need to be equivalent or @@ -2524,7 +2516,7 @@

                                                Submodules
                                                -classmethod assign_selective_dynamics(slab)[source]
                                                +classmethod assign_selective_dynamics(slab)[source]

                                                Helper function to assign selective dynamics site_properties based on surface, subsurface site properties.

                                                @@ -2536,13 +2528,13 @@

                                                Submodules
                                                -assign_site_properties(slab: Slab, height=0.9)[source]
                                                +assign_site_properties(slab: Slab, height=0.9)[source]

                                                Assign site properties.

                                                -classmethod ensemble_center(site_list, indices, cartesian=True)[source]
                                                +classmethod ensemble_center(site_list, indices, cartesian=True)[source]

                                                Find the center of an ensemble of sites selected from a list of sites. Helper method for the find_adsorption_sites algorithm.

                                                @@ -2560,7 +2552,7 @@

                                                Submodules
                                                -find_adsorption_sites(distance=2.0, put_inside=True, symm_reduce=0.01, near_reduce=0.01, positions=('ontop', 'bridge', 'hollow'), no_obtuse_hollow=True)[source]
                                                +find_adsorption_sites(distance=2.0, put_inside=True, symm_reduce=0.01, near_reduce=0.01, positions=('ontop', 'bridge', 'hollow'), no_obtuse_hollow=True)[source]

                                                Find surface sites according to the above algorithm. Returns a list of corresponding Cartesian coordinates.

                                                @@ -2590,7 +2582,7 @@

                                                Submodules
                                                -find_surface_sites_by_height(slab: Slab, height=0.9, xy_tol=0.05)[source]
                                                +find_surface_sites_by_height(slab: Slab, height=0.9, xy_tol=0.05)[source]

                                                Find surface sites by determining which sites are within a threshold value in height from the topmost site in a list of sites.

                                                @@ -2613,7 +2605,7 @@

                                                Submodules
                                                -classmethod from_bulk_and_miller(structure, miller_index, min_slab_size=8.0, min_vacuum_size=10.0, max_normal_search=None, center_slab=True, selective_dynamics=False, undercoord_threshold=0.09) → Self[source]
                                                +classmethod from_bulk_and_miller(structure, miller_index, min_slab_size=8.0, min_vacuum_size=10.0, max_normal_search=None, center_slab=True, selective_dynamics=False, undercoord_threshold=0.09) → Self[source]

                                                Construct the adsorbate site finder from a bulk structure and a miller index, which allows the surface sites to be determined from the difference in bulk and slab coordination, as @@ -2641,7 +2633,7 @@

                                                Submodules
                                                -generate_adsorption_structures(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]
                                                +generate_adsorption_structures(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]

                                                Generate all adsorption structures for a given molecular adsorbate. Can take repeat argument or minimum length/width of precursor slab as an input.

                                                @@ -2665,7 +2657,7 @@

                                                Submodules
                                                -generate_substitution_structures(atom, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)[source]
                                                +generate_substitution_structures(atom, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)[source]

                                                Perform substitution-type doping on the surface and returns all possible configurations where one dopant is substituted per surface. Can substitute one surface or both.

                                                @@ -2687,7 +2679,7 @@

                                                Submodules
                                                -get_extended_surface_mesh(repeat=(5, 5, 1))[source]
                                                +get_extended_surface_mesh(repeat=(5, 5, 1))[source]

                                                Get an extended surface mesh for to use for adsorption site finding by constructing supercell of surface sites.

                                                @@ -2699,7 +2691,7 @@

                                                Submodules
                                                -near_reduce(coords_set, threshold=0.0001)[source]
                                                +near_reduce(coords_set, threshold=0.0001)[source]

                                                Prune coordinate set for coordinates that are within threshold.

                                                Parameters:
                                                @@ -2713,19 +2705,19 @@

                                                Submodules
                                                -subsurface_sites()[source]
                                                +subsurface_sites()[source]

                                                Convenience method to return list of subsurface sites.

                                                -property surface_sites[source]
                                                +property surface_sites[source]

                                                Convenience method to return a list of surface sites.

                                                -symm_reduce(coords_set, threshold=1e-06)[source]
                                                +symm_reduce(coords_set, threshold=1e-06)[source]

                                                Reduce the set of adsorbate sites by finding removing symmetrically equivalent duplicates.

                                                @@ -2743,20 +2735,20 @@

                                                Submodules
                                                -get_mi_vec(slab)[source]
                                                +get_mi_vec(slab)[source]

                                                Convenience function which returns the unit vector aligned with the miller index.

                                                -get_rot(slab: Slab) → SymmOp[source]
                                                +get_rot(slab: Slab) → SymmOp[source]

                                                Get the transformation to rotate the z axis into the miller index.

                                                -plot_slab(slab: Slab, ax: plt.Axes, scale=0.8, repeat=5, window=1.5, draw_unit_cell=True, decay=0.2, adsorption_sites=True, inverse=False)[source]
                                                +plot_slab(slab: Slab, ax: plt.Axes, scale=0.8, repeat=5, window=1.5, draw_unit_cell=True, decay=0.2, adsorption_sites=True, inverse=False)[source]

                                                Help visualize the slab in a 2-D plot, for convenient viewing of output of AdsorbateSiteFinder.

                                                Parameters:
                                                @@ -2777,13 +2769,13 @@

                                                Submodules
                                                -put_coord_inside(lattice, cart_coordinate)[source]
                                                +put_coord_inside(lattice, cart_coordinate)[source]

                                                Convert a Cartesian coordinate such that it is inside the unit cell.

                                                -reorient_z(structure)[source]
                                                +reorient_z(structure)[source]

                                                Reorient a structure such that the z axis is concurrent with the normal to the A-B plane.

                                                @@ -2794,7 +2786,7 @@

                                                Submodules
                                                -class BondDissociationEnergies(molecule_entry: dict[str, str | dict[str, str | int]], fragment_entries: list[dict[str, str | dict[str, str | int]]], allow_additional_charge_separation: bool = False, multibreak: bool = False)[source]
                                                +class BondDissociationEnergies(molecule_entry: dict[str, str | dict[str, str | int]], fragment_entries: list[dict[str, str | dict[str, str | int]]], allow_additional_charge_separation: bool = False, multibreak: bool = False)[source]

                                                Bases: MSONable

                                                Standard constructor for bond dissociation energies. All bonds in the principle molecule are looped through and their dissociation energies are calculated given the energies of the resulting @@ -2819,7 +2811,7 @@

                                                Submodules
                                                -build_new_entry(frags: list, bonds: list) → list[source]
                                                +build_new_entry(frags: list, bonds: list) → list[source]

                                                Build a new entry for bond dissociation that will be returned to the user.

                                                Parameters:
                                                @@ -2839,7 +2831,7 @@

                                                Submodules
                                                -filter_fragment_entries(fragment_entries: list) → None[source]
                                                +filter_fragment_entries(fragment_entries: list) → None[source]

                                                Filter the fragment entries.

                                                Parameters:
                                                @@ -2850,7 +2842,7 @@

                                                Submodules
                                                -fragment_and_process(bonds)[source]
                                                +fragment_and_process(bonds)[source]

                                                Fragment and process bonds.

                                                Parameters:
                                                @@ -2861,7 +2853,7 @@

                                                Submodules
                                                -search_fragment_entries(frag) → list[source]
                                                +search_fragment_entries(frag) → list[source]

                                                Search all fragment entries for those isomorphic to the given fragment. We distinguish between entries where both initial and final MoleculeGraphs are isomorphic to the given fragment (entries) vs those where only the initial MoleculeGraph is isomorphic to the given @@ -2881,7 +2873,7 @@

                                                Submodules
                                                -class BVAnalyzer(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015, charge_neutrality_tolerance=1e-05, forbidden_species=None)[source]
                                                +class BVAnalyzer(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015, charge_neutrality_tolerance=1e-05, forbidden_species=None)[source]

                                                Bases: object

                                                This class implements a maximum a posteriori (MAP) estimation method to determine oxidation states in a structure. The algorithm is as follows: @@ -2921,12 +2913,12 @@

                                                Submodules
                                                -CHARGE_NEUTRALITY_TOLERANCE = 1e-05[source]
                                                +CHARGE_NEUTRALITY_TOLERANCE = 1e-05[source]

                                                -get_oxi_state_decorated_structure(structure: Structure)[source]
                                                +get_oxi_state_decorated_structure(structure: Structure)[source]

                                                Get an oxidation state decorated structure. This currently works only for ordered structures only.

                                                @@ -2944,7 +2936,7 @@

                                                Submodules
                                                -get_valences(structure: Structure)[source]
                                                +get_valences(structure: Structure)[source]

                                                Get a list of valences for each site in the structure.

                                                Parameters:
                                                @@ -2966,7 +2958,7 @@

                                                Submodules
                                                -add_oxidation_state_by_site_fraction(structure, oxidation_states)[source]
                                                +add_oxidation_state_by_site_fraction(structure, oxidation_states)[source]

                                                Add oxidation states to a structure by fractional site.

                                                Parameters:
                                                @@ -2979,7 +2971,7 @@

                                                Submodules
                                                -calculate_bv_sum(site, nn_list, scale_factor=1.0)[source]
                                                +calculate_bv_sum(site, nn_list, scale_factor=1.0)[source]

                                                Calculate the BV sum of a site.

                                                Parameters:
                                                @@ -2997,7 +2989,7 @@

                                                Submodules
                                                -calculate_bv_sum_unordered(site, nn_list, scale_factor=1)[source]
                                                +calculate_bv_sum_unordered(site, nn_list, scale_factor=1)[source]

                                                Calculate the BV sum of a site for unordered structures.

                                                Parameters:
                                                @@ -3015,7 +3007,7 @@

                                                Submodules
                                                -get_z_ordered_elmap(comp)[source]
                                                +get_z_ordered_elmap(comp)[source]

                                                Arbitrary ordered element map on the elements/species of a composition of a given site in an unordered structure. Returns a list of tuples ( element_or_specie: occupation) in the arbitrary order.

                                                @@ -3051,7 +3043,7 @@

                                                Submodules
                                                -class ChemicalPotentialDiagram(entries: list[PDEntry], limits: dict[Element, tuple[float, float]] | None = None, default_min_limit: float = -50.0, formal_chempots: bool = True)[source]
                                                +class ChemicalPotentialDiagram(entries: list[PDEntry], limits: dict[Element, tuple[float, float]] | None = None, default_min_limit: float = -50.0, formal_chempots: bool = True)[source]

                                                Bases: MSONable

                                                The chemical potential diagram is the mathematical dual to the compositional phase diagram. To create the diagram, convex minimization is @@ -3089,37 +3081,37 @@

                                                Submodules
                                                -property border_hyperplanes: ndarray[source]
                                                +property border_hyperplanes: ndarray[source]

                                                Bordering hyperplanes.

                                                -property chemical_system: str[source]
                                                +property chemical_system: str[source]

                                                The chemical system (A-B-C-…) of diagram object.

                                                -property domains: dict[str, ndarray][source]
                                                +property domains: dict[str, ndarray][source]

                                                Mapping of formulas to array of domain boundary points.

                                                -property el_refs: dict[Element, PDEntry][source]
                                                +property el_refs: dict[Element, PDEntry][source]

                                                A dictionary of elements and reference entries.

                                                -property entry_dict: dict[str, ComputedEntry][source]
                                                +property entry_dict: dict[str, ComputedEntry][source]

                                                Mapping between reduced formula and ComputedEntry.

                                                -get_plot(elements: list[Element | str] | None = None, label_stable: bool | None = True, formulas_to_draw: list[str] | None = None, draw_formula_meshes: bool | None = True, draw_formula_lines: bool | None = True, formula_colors: list[str] = ['rgb(27,158,119)', 'rgb(217,95,2)', 'rgb(117,112,179)', 'rgb(231,41,138)', 'rgb(102,166,30)', 'rgb(230,171,2)', 'rgb(166,118,29)', 'rgb(102,102,102)'], element_padding: float | None = 1.0) → Figure[source]
                                                +get_plot(elements: list[Element | str] | None = None, label_stable: bool | None = True, formulas_to_draw: list[str] | None = None, draw_formula_meshes: bool | None = True, draw_formula_lines: bool | None = True, formula_colors: list[str] = ['rgb(27,158,119)', 'rgb(217,95,2)', 'rgb(117,112,179)', 'rgb(231,41,138)', 'rgb(102,166,30)', 'rgb(230,171,2)', 'rgb(166,118,29)', 'rgb(102,102,102)'], element_padding: float | None = 1.0) → Figure[source]

                                                Plot the 2-dimensional or 3-dimensional chemical potential diagram using an interactive Plotly interface.

                                                Elemental axes can be specified; if none provided, will automatically default @@ -3158,19 +3150,19 @@

                                                Submodules
                                                -property hyperplane_entries: list[PDEntry][source]
                                                +property hyperplane_entries: list[PDEntry][source]

                                                List of entries corresponding to hyperplanes.

                                                -property hyperplanes: ndarray[source]
                                                +property hyperplanes: ndarray[source]

                                                Array of hyperplane data.

                                                -property lims: ndarray[source]
                                                +property lims: ndarray[source]

                                                Array of limits used in constructing hyperplanes.

                                                @@ -3178,7 +3170,7 @@

                                                Submodules
                                                -get_2d_orthonormal_vector(line_pts: ndarray) → ndarray[source]
                                                +get_2d_orthonormal_vector(line_pts: ndarray) → ndarray[source]

                                                Calculates a vector that is orthonormal to a line given by a set of points. Used for determining the location of an annotation on a 2-d chemical potential diagram.

                                                @@ -3197,7 +3189,7 @@

                                                Submodules
                                                -get_centroid_2d(vertices: ndarray) → ndarray[source]
                                                +get_centroid_2d(vertices: ndarray) → ndarray[source]

                                                A bare-bones implementation of the formula for calculating the centroid of a 2D polygon. Useful for calculating the location of an annotation on a chemical potential domain within a 3D chemical potential diagram.

                                                @@ -3218,7 +3210,7 @@

                                                Submodules
                                                -simple_pca(data: ndarray, k: int = 2) → tuple[ndarray, ndarray, ndarray][source]
                                                +simple_pca(data: ndarray, k: int = 2) → tuple[ndarray, ndarray, ndarray][source]

                                                A bare-bones implementation of principal component analysis (PCA) used in the ChemicalPotentialDiagram class for plotting.

                                                @@ -3247,7 +3239,7 @@

                                                Submodules
                                                -class CostAnalyzer(costdb)[source]
                                                +class CostAnalyzer(costdb)[source]

                                                Bases: object

                                                Given a CostDB, figures out the minimum cost solutions via convex hull.

                                                @@ -3257,7 +3249,7 @@

                                                Submodules
                                                -get_cost_per_kg(comp)[source]
                                                +get_cost_per_kg(comp)[source]

                                                Get best estimate of minimum cost/kg based on known data.

                                                Parameters:
                                                @@ -3274,7 +3266,7 @@

                                                Submodules
                                                -get_cost_per_mol(comp: CompositionLike) → float[source]
                                                +get_cost_per_mol(comp: CompositionLike) → float[source]

                                                Get best estimate of minimum cost/mol based on known data.

                                                Parameters:
                                                @@ -3291,7 +3283,7 @@

                                                Submodules
                                                -get_lowest_decomposition(composition)[source]
                                                +get_lowest_decomposition(composition)[source]

                                                Get the decomposition leading to lowest cost.

                                                Parameters:
                                                @@ -3310,13 +3302,13 @@

                                                Submodules
                                                -class CostDB[source]
                                                +class CostDB[source]

                                                Bases: ABC

                                                Abstract class for representing a Cost database. Can be extended, e.g. for file-based or REST-based databases.

                                                -abstract get_entries(chemsys)[source]
                                                +abstract get_entries(chemsys)[source]

                                                For a given chemical system, return an array of CostEntries.

                                                Parameters:
                                                @@ -3332,7 +3324,7 @@

                                                Submodules
                                                -class CostDBCSV(filename)[source]
                                                +class CostDBCSV(filename)[source]

                                                Bases: CostDB

                                                Read a CSV file to get costs. Format is formula,cost_per_kg,name,BibTeX.

                                                @@ -3342,7 +3334,7 @@

                                                Submodules
                                                -get_entries(chemsys)[source]
                                                +get_entries(chemsys)[source]

                                                For a given chemical system, return an array of CostEntries.

                                                Parameters:
                                                @@ -3358,7 +3350,7 @@

                                                Submodules
                                                -class CostEntry(composition, cost, name, reference)[source]
                                                +class CostEntry(composition, cost, name, reference)[source]

                                                Bases: PDEntry

                                                Extends PDEntry to include a BibTeX reference and include language about cost.

                                                @@ -3402,7 +3394,7 @@

                                                Submodules
                                                -calculate_dimensionality_of_site(bonded_structure, site_index, inc_vertices=False)[source]
                                                +calculate_dimensionality_of_site(bonded_structure, site_index, inc_vertices=False)[source]

                                                Calculate the dimensionality of the component containing the given site.

                                                Implements directly the modified breadth-first-search algorithm described in Algorithm 1 of:

                                                @@ -3437,7 +3429,7 @@

                                                Submodules
                                                -find_clusters(struct, connected_matrix)[source]
                                                +find_clusters(struct, connected_matrix)[source]

                                                Find bonded clusters of atoms in the structure with periodic boundary conditions.

                                                If there are atoms that are not bonded to anything, returns [0,1,0]. (For @@ -3466,7 +3458,7 @@

                                                Submodules
                                                -find_connected_atoms(struct, tolerance=0.45, ldict=None)[source]
                                                +find_connected_atoms(struct, tolerance=0.45, ldict=None)[source]

                                                Find bonded atoms and returns a adjacency matrix of bonded atoms.

                                                Author: “Gowoon Cheon” Email: “gcheon@stanford.edu”

                                                @@ -3498,7 +3490,7 @@

                                                Submodules
                                                -get_dimensionality_cheon(structure_raw, tolerance=0.45, ldict=None, standardize=True, larger_cell=False)[source]
                                                +get_dimensionality_cheon(structure_raw, tolerance=0.45, ldict=None, standardize=True, larger_cell=False)[source]

                                                Algorithm for finding the dimensions of connected subunits in a structure. This method finds the dimensionality of the material even when the material is not layered along low-index planes, or does not have flat @@ -3544,7 +3536,7 @@

                                                Submodules
                                                -get_dimensionality_gorai(structure, max_hkl=2, el_radius_updates=None, min_slab_size=5, min_vacuum_size=5, standardize=True, bonds=None)[source]
                                                +get_dimensionality_gorai(structure, max_hkl=2, el_radius_updates=None, min_slab_size=5, min_vacuum_size=5, standardize=True, bonds=None)[source]

                                                This method returns whether a structure is 3D, 2D (layered), or 1D (linear chains or molecules) according to the algorithm published in Gorai, P., Toberer, E. & Stevanovic, V. Computational Identification of Promising @@ -3587,7 +3579,7 @@

                                                Submodules
                                                -get_dimensionality_larsen(bonded_structure)[source]
                                                +get_dimensionality_larsen(bonded_structure)[source]

                                                Gets the dimensionality of a bonded structure.

                                                The dimensionality of the structure is the highest dimensionality of all structure components. This method is very robust and can handle @@ -3619,7 +3611,7 @@

                                                Submodules
                                                -get_structure_components(bonded_structure, inc_orientation=False, inc_site_ids=False, inc_molecule_graph=False)[source]
                                                +get_structure_components(bonded_structure, inc_orientation=False, inc_site_ids=False, inc_molecule_graph=False)[source]

                                                Gets information on the components in a bonded structure.

                                                Correctly determines the dimensionality of all structures, regardless of structure type or improper connections due to periodic boundary conditions.

                                                @@ -3689,7 +3681,7 @@

                                                Submodules
                                                -zero_d_graph_to_molecule_graph(bonded_structure, graph)[source]
                                                +zero_d_graph_to_molecule_graph(bonded_structure, graph)[source]

                                                Converts a zero-dimensional networkx Graph object into a MoleculeGraph.

                                                Implements a similar breadth-first search to that in calculate_dimensionality_of_site().

                                                @@ -3718,7 +3710,7 @@

                                                Submodules
                                                -get_warren_cowley_parameters(structure: Structure, r: float, dr: float) → dict[tuple, float][source]
                                                +get_warren_cowley_parameters(structure: Structure, r: float, dr: float) → dict[tuple, float][source]

                                                Warren-Crowley parameters.

                                                Parameters:
                                                @@ -3745,12 +3737,12 @@

                                                Submodules
                                                -class EnergyModel[source]
                                                +class EnergyModel[source]

                                                Bases: MSONable, ABC

                                                Abstract structure filter class.

                                                -classmethod from_dict(dct: dict) → Self[source]
                                                +classmethod from_dict(dct: dict) → Self[source]
                                                Parameters:

                                                dct (dict) – Dict representation.

                                                @@ -3763,7 +3755,7 @@

                                                Submodules
                                                -abstract get_energy(structure) → float[source]
                                                +abstract get_energy(structure) → float[source]
                                                Parameters:

                                                structure – Structure

                                                @@ -3778,7 +3770,7 @@

                                                Submodules
                                                -class EwaldElectrostaticModel(real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=8.0)[source]
                                                +class EwaldElectrostaticModel(real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=8.0)[source]

                                                Bases: EnergyModel

                                                Wrapper around EwaldSum to calculate the electrostatic energy.

                                                Initialize the model. Args have the same definitions as in @@ -3802,13 +3794,13 @@

                                                Submodules
                                                -as_dict()[source]
                                                +as_dict()[source]

                                                MSONable dict

                                                -get_energy(structure: Structure)[source]
                                                +get_energy(structure: Structure)[source]
                                                Parameters:

                                                structure – Structure

                                                @@ -3823,7 +3815,7 @@

                                                Submodules
                                                -class IsingModel(j, max_radius)[source]
                                                +class IsingModel(j, max_radius)[source]

                                                Bases: EnergyModel

                                                A very simple Ising model, with r^2 decay.

                                                @@ -3836,13 +3828,13 @@

                                                Submodules
                                                -as_dict()[source]
                                                +as_dict()[source]

                                                MSONable dict

                                                -get_energy(structure: Structure)[source]
                                                +get_energy(structure: Structure)[source]
                                                Parameters:

                                                structure – Structure

                                                @@ -3857,20 +3849,20 @@

                                                Submodules
                                                -class NsitesModel[source]
                                                +class NsitesModel[source]

                                                Bases: EnergyModel

                                                Sets the energy to the number of sites. More sites => higher “energy”. Used to rank structures from smallest number of sites to largest number of sites after enumeration.

                                                -as_dict()[source]
                                                +as_dict()[source]

                                                MSONable dict

                                                -get_energy(structure: Structure)[source]
                                                +get_energy(structure: Structure)[source]
                                                Parameters:

                                                structure – Structure

                                                @@ -3885,7 +3877,7 @@

                                                Submodules
                                                -class SymmetryModel(symprec: float = 0.1, angle_tolerance=5)[source]
                                                +class SymmetryModel(symprec: float = 0.1, angle_tolerance=5)[source]

                                                Bases: EnergyModel

                                                Sets the energy to the negative of the spacegroup number. Higher symmetry => lower “energy”.

                                                @@ -3900,13 +3892,13 @@

                                                Submodules
                                                -as_dict()[source]
                                                +as_dict()[source]

                                                MSONable dict

                                                -get_energy(structure: Structure)[source]
                                                +get_energy(structure: Structure)[source]
                                                Parameters:

                                                structure – Structure

                                                @@ -3927,7 +3919,7 @@

                                                Submodules
                                                -class Birch(volumes, energies)[source]
                                                +class Birch(volumes, energies)[source]

                                                Bases: EOSBase

                                                Birch EOS.

                                                @@ -3942,7 +3934,7 @@

                                                Submodules
                                                -class BirchMurnaghan(volumes, energies)[source]
                                                +class BirchMurnaghan(volumes, energies)[source]

                                                Bases: EOSBase

                                                BirchMurnaghan EOS.

                                                @@ -3957,7 +3949,7 @@

                                                Submodules
                                                -class DeltaFactor(volumes, energies)[source]
                                                +class DeltaFactor(volumes, energies)[source]

                                                Bases: PolynomialEOS

                                                Fitting a polynomial EOS using delta factor.

                                                @@ -3970,7 +3962,7 @@

                                                Submodules
                                                -fit(order=3)[source]
                                                +fit(order=3)[source]

                                                Overridden since this eos works with volume**(2/3) instead of volume.

                                                @@ -3978,7 +3970,7 @@

                                                Submodules
                                                -class EOS(eos_name='murnaghan')[source]
                                                +class EOS(eos_name='murnaghan')[source]

                                                Bases: object

                                                Convenient wrapper. Retained in its original state to ensure backward compatibility.

                                                @@ -4009,12 +4001,12 @@

                                                Submodules
                                                -MODELS: ClassVar = {'birch': <class 'pymatgen.analysis.eos.Birch'>, 'birch_murnaghan': <class 'pymatgen.analysis.eos.BirchMurnaghan'>, 'deltafactor': <class 'pymatgen.analysis.eos.DeltaFactor'>, 'murnaghan': <class 'pymatgen.analysis.eos.Murnaghan'>, 'numerical_eos': <class 'pymatgen.analysis.eos.NumericalEOS'>, 'pourier_tarantola': <class 'pymatgen.analysis.eos.PourierTarantola'>, 'vinet': <class 'pymatgen.analysis.eos.Vinet'>}[source]
                                                +MODELS: ClassVar = {'birch': <class 'pymatgen.analysis.eos.Birch'>, 'birch_murnaghan': <class 'pymatgen.analysis.eos.BirchMurnaghan'>, 'deltafactor': <class 'pymatgen.analysis.eos.DeltaFactor'>, 'murnaghan': <class 'pymatgen.analysis.eos.Murnaghan'>, 'numerical_eos': <class 'pymatgen.analysis.eos.NumericalEOS'>, 'pourier_tarantola': <class 'pymatgen.analysis.eos.PourierTarantola'>, 'vinet': <class 'pymatgen.analysis.eos.Vinet'>}[source]

                                                -fit(volumes, energies)[source]
                                                +fit(volumes, energies)[source]

                                                Fit energies as function of volumes.

                                                Parameters:
                                                @@ -4036,7 +4028,7 @@

                                                Submodules
                                                -class EOSBase(volumes, energies)[source]
                                                +class EOSBase(volumes, energies)[source]

                                                Bases: ABC

                                                Abstract class that must be subclassed by all equation of state implementations.

                                                @@ -4050,38 +4042,38 @@

                                                Submodules
                                                -property b0: float[source]
                                                +property b0: float[source]

                                                The bulk modulus in units of energy/unit of volume^3.

                                                -property b0_GPa: FloatWithUnit[source]
                                                +property b0_GPa: FloatWithUnit[source]

                                                The bulk modulus in GPa. This assumes the energy and volumes are in eV and Ang^3.

                                                -property b1[source]
                                                +property b1[source]

                                                The derivative of bulk modulus w.r.t. pressure(dimensionless).

                                                -property e0: float[source]
                                                +property e0: float[source]

                                                The min energy.

                                                -fit()[source]
                                                +fit()[source]

                                                Do the fitting. Does least square fitting. If you want to use custom fitting, must override this.

                                                -func(volume)[source]
                                                +func(volume)[source]

                                                The equation of state function with the parameters other than volume set to the ones obtained from fitting.

                                                @@ -4096,7 +4088,7 @@

                                                Submodules
                                                -plot(width=8, height=None, ax: plt.Axes = None, dpi=None, **kwargs)[source]
                                                +plot(width=8, height=None, ax: plt.Axes = None, dpi=None, **kwargs)[source]

                                                Plot the equation of state.

                                                Parameters:
                                                @@ -4122,7 +4114,7 @@

                                                Submodules
                                                -plot_ax(ax: plt.Axes = None, fontsize=12, **kwargs)[source]
                                                +plot_ax(ax: plt.Axes = None, fontsize=12, **kwargs)[source]

                                                Plot the equation of state on axis ax.

                                                Parameters:
                                                @@ -4182,13 +4174,13 @@

                                                Submodules
                                                -property results[source]
                                                +property results[source]

                                                A summary dict.

                                                -property v0[source]
                                                +property v0[source]

                                                The minimum or the reference volume in Ang^3.

                                                @@ -4196,14 +4188,14 @@

                                                Submodules
                                                -exception EOSError[source]
                                                +exception EOSError[source]

                                                Bases: Exception

                                                Error class for EOS fitting.

                                                -class Murnaghan(volumes, energies)[source]
                                                +class Murnaghan(volumes, energies)[source]

                                                Bases: EOSBase

                                                Murnaghan EOS.

                                                @@ -4218,7 +4210,7 @@

                                                Submodules
                                                -class NumericalEOS(volumes, energies)[source]
                                                +class NumericalEOS(volumes, energies)[source]

                                                Bases: PolynomialEOS

                                                A numerical EOS.

                                                @@ -4231,7 +4223,7 @@

                                                Submodules
                                                -fit(min_ndata_factor=3, max_poly_order_factor=5, min_poly_order=2)[source]
                                                +fit(min_ndata_factor=3, max_poly_order_factor=5, min_poly_order=2)[source]

                                                Fit the input data to the ‘numerical eos’, the equation of state employed in the quasiharmonic Debye model described in the paper: 10.1103/PhysRevB.90.174107.

                                                @@ -4257,7 +4249,7 @@

                                                Submodules
                                                -class PolynomialEOS(volumes, energies)[source]
                                                +class PolynomialEOS(volumes, energies)[source]

                                                Bases: EOSBase

                                                Derives from EOSBase. Polynomial based equations of states must subclass this.

                                                @@ -4271,7 +4263,7 @@

                                                Submodules
                                                -fit(order)[source]
                                                +fit(order)[source]

                                                Do polynomial fitting and set the parameters. Uses numpy polyfit.

                                                Parameters:
                                                @@ -4284,7 +4276,7 @@

                                                Submodules
                                                -class PourierTarantola(volumes, energies)[source]
                                                +class PourierTarantola(volumes, energies)[source]

                                                Bases: EOSBase

                                                Pourier-Tarantola EOS.

                                                @@ -4299,7 +4291,7 @@

                                                Submodules
                                                -class Vinet(volumes, energies)[source]
                                                +class Vinet(volumes, energies)[source]

                                                Bases: EOSBase

                                                Vinet EOS.

                                                @@ -4318,7 +4310,7 @@

                                                Submodules
                                                -class EwaldMinimizer(matrix, m_list, num_to_return=1, algo=0)[source]
                                                +class EwaldMinimizer(matrix, m_list, num_to_return=1, algo=0)[source]

                                                Bases: object

                                                This class determines the manipulations that will minimize an Ewald matrix, given a list of possible manipulations. This class does not perform the @@ -4353,34 +4345,34 @@

                                                Submodules
                                                -ALGO_BEST_FIRST = 2[source]
                                                +ALGO_BEST_FIRST = 2[source]

                                                -ALGO_COMPLETE = 1[source]
                                                +ALGO_COMPLETE = 1[source]
                                                -ALGO_FAST = 0[source]
                                                +ALGO_FAST = 0[source]
                                                -ALGO_TIME_LIMIT = 3[source]
                                                +ALGO_TIME_LIMIT = 3[source]
                                                -add_m_list(matrix_sum, m_list)[source]
                                                +add_m_list(matrix_sum, m_list)[source]

                                                Add an m_list to the output_lists and updates the current minimum if the list is full.

                                                -best_case(matrix, m_list, indices_left)[source]
                                                +best_case(matrix, m_list, indices_left)[source]

                                                Compute a best case given a matrix and manipulation list.

                                                Parameters:
                                                @@ -4398,33 +4390,33 @@

                                                Submodules
                                                -property best_m_list[source]
                                                +property best_m_list[source]

                                                The best manipulation list found.

                                                -classmethod get_next_index(matrix, manipulation, indices_left)[source]
                                                +classmethod get_next_index(matrix, manipulation, indices_left)[source]

                                                Get an index that should have the most negative effect on the matrix sum.

                                                -minimize_matrix()[source]
                                                +minimize_matrix()[source]

                                                Get the permutations that produce the lowest Ewald sum calls recursive function to iterate through permutations.

                                                -property minimized_sum[source]
                                                +property minimized_sum[source]

                                                The minimized Ewald sum.

                                                -property output_lists[source]
                                                +property output_lists[source]

                                                Output lists.

                                                @@ -4432,7 +4424,7 @@

                                                Submodules
                                                -class EwaldSummation(structure, real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=12.0, w=0.7071067811865475, compute_forces=False)[source]
                                                +class EwaldSummation(structure, real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=12.0, w=0.7071067811865475, compute_forces=False)[source]

                                                Bases: MSONable

                                                Calculates the electrostatic energy of a periodic array of charges using the Ewald technique.

                                                @@ -4480,12 +4472,12 @@

                                                Submodules
                                                -CONV_FACT = 14.39964547842567[source]
                                                +CONV_FACT = 14.39964547842567[source]

                                                -as_dict(verbosity: int = 0) → dict[source]
                                                +as_dict(verbosity: int = 0) → dict[source]

                                                JSON-serialization dict representation of EwaldSummation.

                                                Parameters:
                                                @@ -4497,13 +4489,13 @@

                                                Submodules
                                                -compute_partial_energy(removed_indices)[source]
                                                +compute_partial_energy(removed_indices)[source]

                                                Get total Ewald energy for certain sites being removed, i.e. zeroed out.

                                                -compute_sub_structure(sub_structure, tol: float = 0.001)[source]
                                                +compute_sub_structure(sub_structure, tol: float = 0.001)[source]

                                                Get total Ewald energy for an sub structure in the same lattice. The sub_structure must be a subset of the original structure, with possible different charges.

                                                @@ -4522,19 +4514,19 @@

                                                Submodules
                                                -property eta[source]
                                                +property eta[source]

                                                Eta value used in Ewald summation.

                                                -property forces[source]
                                                +property forces[source]

                                                The forces on each site as a Nx3 matrix. Each row corresponds to a site.

                                                -classmethod from_dict(dct: dict[str, Any], fmt: str | None = None, **kwargs) → Self[source]
                                                +classmethod from_dict(dct: dict[str, Any], fmt: str | None = None, **kwargs) → Self[source]

                                                Create an EwaldSummation instance from JSON-serialized dictionary.

                                                Parameters:
                                                @@ -4554,7 +4546,7 @@

                                                Submodules
                                                -get_site_energy(site_index)[source]
                                                +get_site_energy(site_index)[source]

                                                Compute the energy for a single site in the structure.

                                                Parameters:
                                                @@ -4571,39 +4563,39 @@

                                                Submodules
                                                -property point_energy[source]
                                                +property point_energy[source]

                                                The point energy.

                                                -property point_energy_matrix[source]
                                                +property point_energy_matrix[source]

                                                The point space matrix. A diagonal matrix with the point terms for each site in the diagonal elements.

                                                -property real_space_energy[source]
                                                +property real_space_energy[source]

                                                The real space energy.

                                                -property real_space_energy_matrix[source]
                                                +property real_space_energy_matrix[source]

                                                The real space energy matrix. Each matrix element (i, j) corresponds to the interaction energy between site i and site j in real space.

                                                -property reciprocal_space_energy[source]
                                                +property reciprocal_space_energy[source]

                                                The reciprocal space energy.

                                                -property reciprocal_space_energy_matrix[source]
                                                +property reciprocal_space_energy_matrix[source]

                                                The reciprocal space energy matrix. Each matrix element (i, j) corresponds to the interaction energy between site i and site j in reciprocal space.

                                                @@ -4611,13 +4603,13 @@

                                                Submodules
                                                -property total_energy[source]
                                                +property total_energy[source]

                                                The total energy.

                                                -property total_energy_matrix[source]
                                                +property total_energy_matrix[source]

                                                The total energy matrix. Each matrix element (i, j) corresponds to the total interaction energy between site i and site j.

                                                Note that this does not include the charged-cell energy, which is only important @@ -4628,7 +4620,7 @@

                                                Submodules
                                                -compute_average_oxidation_state(site)[source]
                                                +compute_average_oxidation_state(site)[source]

                                                Calculates the average oxidation state of a site.

                                                Parameters:
                                                @@ -4646,12 +4638,12 @@

                                                Submodules
                                                -class ExcitationSpectrum(x, y)[source]
                                                +class ExcitationSpectrum(x, y)[source]

                                                Bases: Spectrum

                                                Basic excitation spectrum object.

                                                -x[source]
                                                +x[source]

                                                The sequence of energies.

                                                Type:
                                                @@ -4662,7 +4654,7 @@

                                                Submodules
                                                -y[source]
                                                +y[source]

                                                The sequence of mu(E).

                                                Type:
                                                @@ -4681,12 +4673,12 @@

                                                Submodules
                                                -XLABEL = 'Energy (eV)'[source]
                                                +XLABEL = 'Energy (eV)'[source]

                                                -YLABEL = 'Intensity'[source]
                                                +YLABEL = 'Intensity'[source]

                                                @@ -4697,7 +4689,7 @@

                                                Submodules
                                                -class Fragmenter(molecule: Molecule, edges: list | None = None, depth: int = 1, open_rings: bool = False, use_metal_edge_extender: bool = False, opt_steps: int = 10000, prev_unique_frag_dict: dict | None = None, assume_previous_thoroughness: bool = True)[source]
                                                +class Fragmenter(molecule: Molecule, edges: list | None = None, depth: int = 1, open_rings: bool = False, use_metal_edge_extender: bool = False, opt_steps: int = 10000, prev_unique_frag_dict: dict | None = None, assume_previous_thoroughness: bool = True)[source]

                                                Bases: MSONable

                                                Molecule fragmenter class.

                                                Standard constructor for molecule fragmentation.

                                                @@ -4741,7 +4733,7 @@

                                                Submodules
                                                -open_ring(mol_graph: MoleculeGraph, bond: list, opt_steps: int) → MoleculeGraph[source]
                                                +open_ring(mol_graph: MoleculeGraph, bond: list, opt_steps: int) → MoleculeGraph[source]

                                                Open a ring using OpenBabel’s local opt. Given a molecule graph and a bond, convert the molecule graph into an OpenBabel molecule, remove the given bond, perform the local opt with the number of steps determined by @@ -4755,7 +4747,7 @@

                                                Submodules
                                                -class FunctionalGroupExtractor(molecule, optimize=False)[source]
                                                +class FunctionalGroupExtractor(molecule, optimize=False)[source]

                                                Bases: object

                                                This class is used to algorithmically parse a molecule (represented by an instance of pymatgen.analysis.graphs.MoleculeGraph) and determine arbitrary @@ -4773,7 +4765,7 @@

                                                Submodules
                                                -categorize_functional_groups(groups)[source]
                                                +categorize_functional_groups(groups)[source]

                                                Determine classes of functional groups present in a set.

                                                Parameters:
                                                @@ -4789,7 +4781,7 @@

                                                Submodules
                                                -get_all_functional_groups(elements=None, func_groups=None, catch_basic=True)[source]
                                                +get_all_functional_groups(elements=None, func_groups=None, catch_basic=True)[source]

                                                Identify all functional groups (or all within a certain subset) in the molecule, combining the methods described above.

                                                @@ -4813,7 +4805,7 @@

                                                Submodules
                                                -get_basic_functional_groups(func_groups=None)[source]
                                                +get_basic_functional_groups(func_groups=None)[source]

                                                Identify functional groups that cannot be identified by the Ertl method of get_special_carbon and get_heteroatoms, such as benzene rings, methyl groups, and ethyl groups.

                                                @@ -4833,7 +4825,7 @@

                                                Submodules
                                                -get_heteroatoms(elements=None)[source]
                                                +get_heteroatoms(elements=None)[source]

                                                Identify non-H, non-C atoms in the MoleculeGraph, returning a list of their node indices.

                                                @@ -4851,7 +4843,7 @@

                                                Submodules
                                                -get_special_carbon(elements=None)[source]
                                                +get_special_carbon(elements=None)[source]

                                                Identify Carbon atoms in the MoleculeGraph that fit the characteristics defined Ertl (2017), returning a list of their node indices.

                                                @@ -4877,7 +4869,7 @@

                                                Submodules +link_marked_atoms(atoms)[source]

                                                Take a list of marked “interesting” atoms (heteroatoms, special carbons) and attempt to connect them, returning a list of disjoint groups of special atoms (and their connected hydrogens).

                                                @@ -4900,36 +4892,36 @@

                                                Submodules
                                                -class ConnectedSite(site, jimage, index, weight, dist)[source]
                                                +class ConnectedSite(site, jimage, index, weight, dist)[source]

                                                Bases: NamedTuple

                                                Create new instance of ConnectedSite(site, jimage, index, weight, dist)

                                                -dist: float[source]
                                                +dist: float[source]

                                                Alias for field number 4

                                                -index: Any[source]
                                                +index: Any[source]

                                                Alias for field number 2

                                                -jimage: Tuple3Ints[source]
                                                +jimage: Tuple3Ints[source]

                                                Alias for field number 1

                                                -site: PeriodicSite[source]
                                                +site: PeriodicSite[source]

                                                Alias for field number 0

                                                -weight: float[source]
                                                +weight: float[source]

                                                Alias for field number 3

                                                @@ -4937,7 +4929,7 @@

                                                Submodules
                                                -exception MolGraphSplitError[source]
                                                +exception MolGraphSplitError[source]

                                                Bases: Exception

                                                Raised when a molecule graph is failed to split into two disconnected subgraphs.

                                                @@ -4945,7 +4937,7 @@

                                                Submodules
                                                -class MoleculeGraph(molecule, graph_data=None)[source]
                                                +class MoleculeGraph(molecule, graph_data=None)[source]

                                                Bases: MSONable

                                                This is a class for annotating a Molecule with bond information, stored in the form of a graph. A “bond” does @@ -4974,7 +4966,7 @@

                                                Submodules
                                                -add_edge(from_index, to_index, weight=None, warn_duplicates=True, edge_properties=None)[source]
                                                +add_edge(from_index, to_index, weight=None, warn_duplicates=True, edge_properties=None)[source]

                                                Add edge to graph.

                                                Since physically a ‘bond’ (or other connection between sites) doesn’t have a direction, from_index, @@ -4999,7 +4991,7 @@

                                                Submodules
                                                -alter_edge(from_index, to_index, new_weight=None, new_edge_properties=None)[source]
                                                +alter_edge(from_index, to_index, new_weight=None, new_edge_properties=None)[source]

                                                Alters either the weight or the edge_properties of an edge in the MoleculeGraph.

                                                @@ -5022,7 +5014,7 @@

                                                Submodules
                                                -as_dict()[source]
                                                +as_dict()[source]

                                                As in pymatgen.core.Molecule except with using to_dict_of_dicts from NetworkX to store graph information.

                                                @@ -5030,7 +5022,7 @@

                                                Submodules
                                                -break_edge(from_index, to_index, allow_reverse=False)[source]
                                                +break_edge(from_index, to_index, allow_reverse=False)[source]

                                                Remove an edge from the MoleculeGraph.

                                                Parameters:
                                                @@ -5047,14 +5039,14 @@

                                                Submodules
                                                -build_unique_fragments()[source]
                                                +build_unique_fragments()[source]

                                                Find all possible fragment combinations of the MoleculeGraphs (in other words, all connected induced subgraphs).

                                                -diff(other, strict=True)[source]
                                                +diff(other, strict=True)[source]

                                                Compares two MoleculeGraphs. Returns dict with keys ‘self’, ‘other’, ‘both’ with edges that are present in only one MoleculeGraph (‘self’ and @@ -5084,7 +5076,7 @@

                                                Submodules
                                                -draw_graph_to_file(filename='graph', diff=None, hide_unconnected_nodes=False, hide_image_edges=True, edge_colors=False, node_labels=False, weight_labels=False, image_labels=False, color_scheme='VESTA', keep_dot=False, algo='fdp')[source]
                                                +draw_graph_to_file(filename='graph', diff=None, hide_unconnected_nodes=False, hide_image_edges=True, edge_colors=False, node_labels=False, weight_labels=False, image_labels=False, color_scheme='VESTA', keep_dot=False, algo='fdp')[source]

                                                Draws graph using GraphViz.

                                                The networkx graph object itself can also be drawn with networkx’s in-built graph drawing methods, but @@ -5124,19 +5116,19 @@

                                                Submodules
                                                -property edge_weight_name[source]
                                                +property edge_weight_name[source]

                                                Name of the edge weight property of graph

                                                -property edge_weight_unit[source]
                                                +property edge_weight_unit[source]

                                                Units of the edge weight property of graph

                                                -find_rings(including=None) → list[list[tuple[int, int]]][source]
                                                +find_rings(including=None) → list[list[tuple[int, int]]][source]

                                                Find ring structures in the MoleculeGraph.

                                                Parameters:
                                                @@ -5164,7 +5156,7 @@

                                                Submodules
                                                -classmethod from_dict(dct: dict) → Self[source]
                                                +classmethod from_dict(dct: dict) → Self[source]

                                                As in pymatgen.core.Molecule except restoring graphs using from_dict_of_dicts from NetworkX to restore graph information.

                                                @@ -5172,7 +5164,7 @@

                                                Submodules
                                                -classmethod from_edges(molecule: Molecule, edges: dict[tuple[int, int], None | dict]) → Self[source]
                                                +classmethod from_edges(molecule: Molecule, edges: dict[tuple[int, int], None | dict]) → Self[source]

                                                Constructor for MoleculeGraph, using pre-existing or pre-defined edges with optional edge parameters.

                                                @@ -5193,7 +5185,7 @@

                                                Submodules
                                                -classmethod from_empty_graph(molecule, name='bonds', edge_weight_name=None, edge_weight_units=None) → Self[source]
                                                +classmethod from_empty_graph(molecule, name='bonds', edge_weight_name=None, edge_weight_units=None) → Self[source]

                                                Constructor for MoleculeGraph, returns a MoleculeGraph object with an empty graph (no edges, only nodes defined that correspond to Sites in Molecule).

                                                @@ -5216,7 +5208,7 @@

                                                Submodules
                                                -classmethod from_local_env_strategy(molecule, strategy) → Self[source]
                                                +classmethod from_local_env_strategy(molecule, strategy) → Self[source]

                                                Constructor for MoleculeGraph, using a strategy from pymatgen.analysis.local_env.

                                                @@ -5235,7 +5227,7 @@

                                                Submodules
                                                -get_connected_sites(n)[source]
                                                +get_connected_sites(n)[source]

                                                Get a named tuple of neighbors of site n: periodic_site, jimage, index, weight. Index is the index of the corresponding site @@ -5253,7 +5245,7 @@

                                                Submodules
                                                -get_coordination_of_site(n) → int[source]
                                                +get_coordination_of_site(n) → int[source]

                                                Get the number of neighbors of site n. In graph terms, simply returns degree of node corresponding to site n.

                                                @@ -5272,7 +5264,7 @@

                                                Submodules
                                                -get_disconnected_fragments(return_index_map: bool = False)[source]
                                                +get_disconnected_fragments(return_index_map: bool = False)[source]

                                                Determine if the MoleculeGraph is connected. If it is not, separate the MoleculeGraph into different MoleculeGraphs, where each resulting MoleculeGraph is a disconnected subgraph of the original. Currently, this function naively assigns @@ -5298,7 +5290,7 @@

                                                Submodules
                                                -insert_node(idx, species, coords, validate_proximity=False, site_properties=None, edges=None)[source]
                                                +insert_node(idx, species, coords, validate_proximity=False, site_properties=None, edges=None)[source]

                                                A wrapper around Molecule.insert(), which also incorporates the new site into the MoleculeGraph.

                                                @@ -5324,7 +5316,7 @@

                                                Submodules
                                                -isomorphic_to(other: MoleculeGraph) → bool[source]
                                                +isomorphic_to(other: MoleculeGraph) → bool[source]

                                                Checks if the graphs of two MoleculeGraphs are isomorphic to one another. In order to prevent problems with misdirected edges, both graphs are converted into undirected nx.Graph objects.

                                                @@ -5340,13 +5332,13 @@

                                                Submodules
                                                -property name[source]
                                                +property name[source]

                                                Name of graph

                                                -remove_nodes(indices: list[int]) → None[source]
                                                +remove_nodes(indices: list[int]) → None[source]

                                                A wrapper for Molecule.remove_sites().

                                                Parameters:
                                                @@ -5357,7 +5349,7 @@

                                                Submodules
                                                -replace_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]
                                                +replace_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]

                                                Builds off of Molecule.substitute and MoleculeGraph.substitute_group to replace a functional group in self.molecule with a functional group. This method also amends self.graph to incorporate the new functional @@ -5398,14 +5390,14 @@

                                                Submodules
                                                -set_node_attributes()[source]
                                                +set_node_attributes()[source]

                                                Replicates molecule site properties (specie, coords, etc.) in the MoleculeGraph.

                                                -sort(key: Callable[[Molecule], float] | None = None, reverse: bool = False) → None[source]
                                                +sort(key: Callable[[Molecule], float] | None = None, reverse: bool = False) → None[source]

                                                Same as Molecule.sort(). Also remaps nodes in graph.

                                                Parameters:
                                                @@ -5419,7 +5411,7 @@

                                                Submodules
                                                -split_molecule_subgraphs(bonds, allow_reverse=False, alterations=None)[source]
                                                +split_molecule_subgraphs(bonds, allow_reverse=False, alterations=None)[source]

                                                Split MoleculeGraph into two or more MoleculeGraphs by breaking a set of bonds. This function uses MoleculeGraph.break_edge repeatedly to create @@ -5458,7 +5450,7 @@

                                                Submodules
                                                -substitute_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]
                                                +substitute_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]

                                                Builds off of Molecule.substitute to replace an atom in self.molecule with a functional group. This method also amends self.graph to incorporate the new functional group.

                                                @@ -5507,24 +5499,24 @@

                                                Submodules
                                                -classmethod with_edges(*args, **kwargs)[source]
                                                +classmethod with_edges(*args, **kwargs)[source]

                                                -classmethod with_empty_graph(*args, **kwargs)[source]
                                                +classmethod with_empty_graph(*args, **kwargs)[source]
                                                -classmethod with_local_env_strategy(*args, **kwargs)[source]
                                                +classmethod with_local_env_strategy(*args, **kwargs)[source]
                                                -class StructureGraph(structure: Structure, graph_data: dict | None = None)[source]
                                                +class StructureGraph(structure: Structure, graph_data: dict | None = None)[source]

                                                Bases: MSONable

                                                This is a class for annotating a Structure with bond information, stored in the form of a graph. A “bond” does not necessarily have to be a chemical bond, but can store @@ -5552,7 +5544,7 @@

                                                Submodules
                                                -add_edge(from_index: int, to_index: int, from_jimage: Tuple3Ints = (0, 0, 0), to_jimage: Tuple3Ints | None = None, weight: float | None = None, warn_duplicates: bool = True, edge_properties: dict | None = None) → None[source]
                                                +add_edge(from_index: int, to_index: int, from_jimage: Tuple3Ints = (0, 0, 0), to_jimage: Tuple3Ints | None = None, weight: float | None = None, warn_duplicates: bool = True, edge_properties: dict | None = None) → None[source]

                                                Add edge to graph.

                                                Since physically a ‘bond’ (or other connection between sites) doesn’t have a direction, from_index, @@ -5580,7 +5572,7 @@

                                                Submodules
                                                -alter_edge(from_index: int, to_index: int, to_jimage: tuple | None = None, new_weight: float | None = None, new_edge_properties: dict | None = None)[source]
                                                +alter_edge(from_index: int, to_index: int, to_jimage: tuple | None = None, new_weight: float | None = None, new_edge_properties: dict | None = None)[source]

                                                Alters either the weight or the edge_properties of an edge in the StructureGraph.

                                                @@ -5604,7 +5596,7 @@

                                                Submodules
                                                -as_dict() → dict[source]
                                                +as_dict() → dict[source]

                                                As in pymatgen.core.Structure except with using to_dict_of_dicts from NetworkX to store graph information.

                                                @@ -5612,7 +5604,7 @@

                                                Submodules
                                                -break_edge(from_index: int, to_index: int, to_jimage: tuple | None = None, allow_reverse: bool = False) → None[source]
                                                +break_edge(from_index: int, to_index: int, to_jimage: tuple | None = None, allow_reverse: bool = False) → None[source]

                                                Remove an edge from the StructureGraph. If no image is given, this method will fail.

                                                Parameters:
                                                @@ -5630,7 +5622,7 @@

                                                Submodules
                                                -diff(other: StructureGraph, strict: bool = True) → dict[source]
                                                +diff(other: StructureGraph, strict: bool = True) → dict[source]

                                                Compares two StructureGraphs. Returns dict with keys ‘self’, ‘other’, ‘both’ with edges that are present in only one StructureGraph (‘self’ and @@ -5661,7 +5653,7 @@

                                                Submodules
                                                -draw_graph_to_file(filename: str = 'graph', diff: StructureGraph = None, hide_unconnected_nodes: bool = False, hide_image_edges: bool = True, edge_colors: bool = False, node_labels: bool = False, weight_labels: bool = False, image_labels: bool = False, color_scheme: str = 'VESTA', keep_dot: bool = False, algo: str = 'fdp')[source]
                                                +draw_graph_to_file(filename: str = 'graph', diff: StructureGraph = None, hide_unconnected_nodes: bool = False, hide_image_edges: bool = True, edge_colors: bool = False, node_labels: bool = False, weight_labels: bool = False, image_labels: bool = False, color_scheme: str = 'VESTA', keep_dot: bool = False, algo: str = 'fdp')[source]

                                                Draws graph using GraphViz.

                                                The networkx graph object itself can also be drawn with networkx’s in-built graph drawing methods, but @@ -5700,26 +5692,26 @@

                                                Submodules
                                                -property edge_weight_name: str[source]
                                                +property edge_weight_name: str[source]

                                                Name of the edge weight property of graph

                                                -property edge_weight_unit[source]
                                                +property edge_weight_unit[source]

                                                Units of the edge weight property of graph

                                                -classmethod from_dict(dct: dict) → Self[source]
                                                +classmethod from_dict(dct: dict) → Self[source]

                                                As in pymatgen.core.Structure except restoring graphs using from_dict_of_dicts from NetworkX to restore graph information.

                                                -classmethod from_edges(structure: Structure, edges: dict) → Self[source]
                                                +classmethod from_edges(structure: Structure, edges: dict) → Self[source]

                                                Constructor for MoleculeGraph, using pre-existing or pre-defined edges with optional edge parameters.

                                                @@ -5741,7 +5733,7 @@

                                                Submodules
                                                -classmethod from_empty_graph(structure: Structure, name: str = 'bonds', edge_weight_name: str | None = None, edge_weight_units: str | None = None) → Self[source]
                                                +classmethod from_empty_graph(structure: Structure, name: str = 'bonds', edge_weight_name: str | None = None, edge_weight_units: str | None = None) → Self[source]

                                                Constructor for an empty StructureGraph, i.e. no edges, containing only nodes corresponding to sites in Structure.

                                                @@ -5768,7 +5760,7 @@

                                                Submodules
                                                -classmethod from_local_env_strategy(structure: Structure, strategy: NearNeighbors, weights: bool = False, edge_properties: bool = False) → Self[source]
                                                +classmethod from_local_env_strategy(structure: Structure, strategy: NearNeighbors, weights: bool = False, edge_properties: bool = False) → Self[source]

                                                Constructor for StructureGraph, using a strategy from pymatgen.analysis.local_env.

                                                @@ -5785,7 +5777,7 @@

                                                Submodules
                                                -get_connected_sites(n: int, jimage: Tuple3Ints = (0, 0, 0)) → list[ConnectedSite][source]
                                                +get_connected_sites(n: int, jimage: Tuple3Ints = (0, 0, 0)) → list[ConnectedSite][source]

                                                Get a named tuple of neighbors of site n: periodic_site, jimage, index, weight. Index is the index of the corresponding site @@ -5807,7 +5799,7 @@

                                                Submodules
                                                -get_coordination_of_site(n: int) → int[source]
                                                +get_coordination_of_site(n: int) → int[source]

                                                Get the number of neighbors of site n. In graph terms, simply returns degree of node corresponding to site n.

                                                @@ -5825,7 +5817,7 @@

                                                Submodules
                                                -get_subgraphs_as_molecules(use_weights: bool = False) → list[Molecule][source]
                                                +get_subgraphs_as_molecules(use_weights: bool = False) → list[Molecule][source]

                                                Retrieve subgraphs as molecules, useful for extracting molecules from periodic crystals.

                                                Will only return unique molecules, not any duplicates @@ -5848,7 +5840,7 @@

                                                Submodules
                                                -insert_node(idx: int, species: Species, coords: ArrayLike, coords_are_cartesian: bool = False, validate_proximity: bool = False, site_properties: dict | None = None, edges: list | dict | None = None) → None[source]
                                                +insert_node(idx: int, species: Species, coords: ArrayLike, coords_are_cartesian: bool = False, validate_proximity: bool = False, site_properties: dict | None = None, edges: list | dict | None = None) → None[source]

                                                A wrapper around Molecule.insert(), which also incorporates the new site into the MoleculeGraph.

                                                @@ -5879,13 +5871,13 @@

                                                Submodules
                                                -property name: str[source]
                                                +property name: str[source]

                                                Name of graph

                                                -remove_nodes(indices: Sequence[int | None]) → None[source]
                                                +remove_nodes(indices: Sequence[int | None]) → None[source]

                                                A wrapper for Molecule.remove_sites().

                                                Parameters:
                                                @@ -5897,14 +5889,14 @@

                                                Submodules
                                                -set_node_attributes() → None[source]
                                                +set_node_attributes() → None[source]

                                                Get each node a “specie” and a “coords” attribute, updated with the current species and coordinates.

                                                -sort(key=None, reverse: bool = False) → None[source]
                                                +sort(key=None, reverse: bool = False) → None[source]

                                                Same as Structure.sort(). Also remaps nodes in graph.

                                                Parameters:
                                                @@ -5918,7 +5910,7 @@

                                                Submodules
                                                -substitute_group(index: int, func_grp: Molecule | str, strategy: Any, bond_order: int = 1, graph_dict: dict | None = None, strategy_params: dict | None = None)[source]
                                                +substitute_group(index: int, func_grp: Molecule | str, strategy: Any, bond_order: int = 1, graph_dict: dict | None = None, strategy_params: dict | None = None)[source]

                                                Builds off of Structure.substitute to replace an atom in self.structure with a functional group. This method also amends self.graph to incorporate the new functional group.

                                                @@ -5967,7 +5959,7 @@

                                                Submodules
                                                -property types_and_weights_of_connections: dict[source]
                                                +property types_and_weights_of_connections: dict[source]

                                                Extract a dictionary summarizing the types and weights of edges in the graph.

                                                @@ -5982,7 +5974,7 @@

                                                Submodules
                                                -types_of_coordination_environments(anonymous: bool = False) → list[str][source]
                                                +types_of_coordination_environments(anonymous: bool = False) → list[str][source]

                                                Extract information on the different co-ordination environments present in the graph.

                                                @@ -5997,7 +5989,7 @@

                                                Submodules
                                                -property weight_statistics: dict[source]
                                                +property weight_statistics: dict[source]

                                                Extract a statistical summary of edge weights present in the graph.

                                                @@ -6010,17 +6002,17 @@

                                                Submodules
                                                -classmethod with_edges(*args, **kwargs)[source]
                                                +classmethod with_edges(*args, **kwargs)[source]

                                                -classmethod with_empty_graph(*args, **kwargs)[source]
                                                +classmethod with_empty_graph(*args, **kwargs)[source]
                                                -classmethod with_local_env_strategy(*args, **kwargs)[source]
                                                +classmethod with_local_env_strategy(*args, **kwargs)[source]

                                                @@ -6042,7 +6034,7 @@

                                                Submodules
                                                -class GrandPotentialInterfacialReactivity(c1: Composition, c2: Composition, grand_pd: GrandPotentialPhaseDiagram, pd_non_grand: PhaseDiagram, include_no_mixing_energy: bool = False, norm: bool = True, use_hull_energy: bool = True)[source]
                                                +class GrandPotentialInterfacialReactivity(c1: Composition, c2: Composition, grand_pd: GrandPotentialPhaseDiagram, pd_non_grand: PhaseDiagram, include_no_mixing_energy: bool = False, norm: bool = True, use_hull_energy: bool = True)[source]

                                                Bases: InterfacialReactivity

                                                Extends upon InterfacialReactivity to allow for modelling possible reactions at the interface between two solids in the presence of an open element. The @@ -6076,7 +6068,7 @@

                                                Submodules
                                                -get_no_mixing_energy()[source]
                                                +get_no_mixing_energy()[source]

                                                Generate the opposite number of energy above grand potential convex hull for both reactants.

                                                @@ -6090,7 +6082,7 @@

                                                Submodules
                                                -class InterfacialReactivity(c1: Composition, c2: Composition, pd: PhaseDiagram, norm: bool = True, use_hull_energy: bool = False, **kwargs)[source]
                                                +class InterfacialReactivity(c1: Composition, c2: Composition, pd: PhaseDiagram, norm: bool = True, use_hull_energy: bool = False, **kwargs)[source]

                                                Bases: MSONable

                                                Model an interface between two solids and its possible reactions. The two reactants are provided as Composition objects (c1 and c2), along with the @@ -6126,12 +6118,12 @@

                                                Submodules
                                                -EV_TO_KJ_PER_MOL = 96.4853[source]
                                                +EV_TO_KJ_PER_MOL = 96.4853[source]

                                                -classmethod get_chempot_correction(element: str, temp: float, pres: float)[source]
                                                +classmethod get_chempot_correction(element: str, temp: float, pres: float)[source]

                                                Get the normalized correction term Δμ for chemical potential of a gas phase consisting of element at given temperature and pressure, referenced to that in the standard state (T_std = 298.15 K, @@ -6155,7 +6147,7 @@

                                                Submodules
                                                -get_critical_original_kink_ratio()[source]
                                                +get_critical_original_kink_ratio()[source]

                                                Get a list of molar mixing ratio for each kink between ORIGINAL (instead of processed) reactant compositions. This is the same list as mixing ratio obtained from get_kinks method @@ -6170,14 +6162,14 @@

                                                Submodules
                                                -get_dataframe() → DataFrame[source]
                                                +get_dataframe() → DataFrame[source]

                                                Get a pandas DataFrame representation of the data produced by the get_kinks() method.

                                                -get_kinks() → list[tuple[int, float, float, Reaction, float]][source]
                                                +get_kinks() → list[tuple[int, float, float, Reaction, float]][source]

                                                Find all the kinks in mixing ratio where reaction products changes along the tie-line of composition self.c1 and composition self.c2.

                                                @@ -6193,7 +6185,7 @@

                                                Submodules
                                                -property labels[source]
                                                +property labels[source]

                                                A dictionary containing kink information: {index: ‘x= mixing_ratio energy= reaction_energy reaction_equation’}. e.g. {1: ‘x= 0 energy = 0 Mn -> Mn’,

                                                @@ -6205,14 +6197,14 @@

                                                Submodules
                                                -property minimum[source]
                                                +property minimum[source]

                                                The minimum reaction energy E_min and corresponding mixing ratio x_min as tuple[float, float]: (x_min, E_min).

                                                -plot(backend: Literal['plotly', 'matplotlib'] = 'plotly') → Figure | plt.Figure[source]
                                                +plot(backend: Literal['plotly', 'matplotlib'] = 'plotly') → Figure | plt.Figure[source]

                                                Plots reaction energy as a function of mixing ratio x in self.c1 - self.c2 tie line.

                                                Parameters:
                                                @@ -6227,7 +6219,7 @@

                                                Submodules
                                                -property products[source]
                                                +property products[source]

                                                List of formulas of potential products. e.g. [‘Li’,’O2’,’Mn’].

                                                @@ -6241,7 +6233,7 @@

                                                Submodules
                                                -class BrunnerNNReal(tol: float = 0.0001, cutoff=8.0)[source]
                                                +class BrunnerNNReal(tol: float = 0.0001, cutoff=8.0)[source]

                                                Bases: NearNeighbors

                                                Determine coordination number using Brunner’s algorithm which counts the atoms that are within the largest gap in differences in real space @@ -6259,7 +6251,7 @@

                                                Submodules
                                                -get_nn_info(structure: Structure, n: int)[source]
                                                +get_nn_info(structure: Structure, n: int)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                                @@ -6285,7 +6277,7 @@

                                                Submodules
                                                -property molecules_allowed: bool[source]
                                                +property molecules_allowed: bool[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -6297,7 +6289,7 @@

                                                Submodules
                                                -property structures_allowed: bool[source]
                                                +property structures_allowed: bool[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -6311,7 +6303,7 @@

                                                Submodules
                                                -class BrunnerNNReciprocal(tol: float = 0.0001, cutoff=8.0)[source]
                                                +class BrunnerNNReciprocal(tol: float = 0.0001, cutoff=8.0)[source]

                                                Bases: NearNeighbors

                                                Determine coordination number using Brunner’s algorithm which counts the atoms that are within the largest gap in differences in real space @@ -6329,7 +6321,7 @@

                                                Submodules
                                                -get_nn_info(structure: Structure, n: int)[source]
                                                +get_nn_info(structure: Structure, n: int)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                                @@ -6354,7 +6346,7 @@

                                                Submodules
                                                -property molecules_allowed: bool[source]
                                                +property molecules_allowed: bool[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -6366,7 +6358,7 @@

                                                Submodules
                                                -property structures_allowed: bool[source]
                                                +property structures_allowed: bool[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -6380,7 +6372,7 @@

                                                Submodules
                                                -class BrunnerNNRelative(tol: float = 0.0001, cutoff=8.0)[source]
                                                +class BrunnerNNRelative(tol: float = 0.0001, cutoff=8.0)[source]

                                                Bases: NearNeighbors

                                                Determine coordination number using Brunner’s algorithm which counts the atoms that are within the largest gap in differences in real space @@ -6398,7 +6390,7 @@

                                                Submodules
                                                -get_nn_info(structure: Structure, n: int)[source]
                                                +get_nn_info(structure: Structure, n: int)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                                @@ -6424,7 +6416,7 @@

                                                Submodules
                                                -property molecules_allowed: bool[source]
                                                +property molecules_allowed: bool[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -6436,7 +6428,7 @@

                                                Submodules
                                                -property structures_allowed: bool[source]
                                                +property structures_allowed: bool[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -6450,7 +6442,7 @@

                                                Submodules
                                                -class BrunnerNN_real(*args, **kwargs)[source]
                                                +class BrunnerNN_real(*args, **kwargs)[source]

                                                Bases: BrunnerNNReal

                                                Parameters:
                                                @@ -6466,7 +6458,7 @@

                                                Submodules
                                                -class BrunnerNN_reciprocal(*args, **kwargs)[source]
                                                +class BrunnerNN_reciprocal(*args, **kwargs)[source]

                                                Bases: BrunnerNNReciprocal

                                                Parameters:
                                                @@ -6482,7 +6474,7 @@

                                                Submodules
                                                -class BrunnerNN_relative(*args, **kwargs)[source]
                                                +class BrunnerNN_relative(*args, **kwargs)[source]

                                                Bases: BrunnerNNRelative

                                                Parameters:
                                                @@ -6498,7 +6490,7 @@

                                                Submodules
                                                -class CovalentBondNN(tol: float = 0.2, order=True)[source]
                                                +class CovalentBondNN(tol: float = 0.2, order=True)[source]

                                                Bases: NearNeighbors

                                                Determine near-neighbor sites and bond orders using built-in pymatgen.Molecule CovalentBond functionality.

                                                @@ -6515,7 +6507,7 @@

                                                Submodules
                                                -property extend_structure_molecules: bool[source]
                                                +property extend_structure_molecules: bool[source]

                                                Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed is False.

                                                @@ -6528,7 +6520,7 @@

                                                Submodules
                                                -get_bonded_structure(structure: Structure, decorate: bool = False) → MoleculeGraph[source]
                                                +get_bonded_structure(structure: Structure, decorate: bool = False) → MoleculeGraph[source]

                                                Obtain a MoleculeGraph object using this NearNeighbor class.

                                                Parameters:
                                                @@ -6550,7 +6542,7 @@

                                                Submodules
                                                -get_nn_info(structure: Structure, n: int)[source]
                                                +get_nn_info(structure: Structure, n: int)[source]

                                                Get all near-neighbor sites and weights (orders) of bonds for a given atom.

                                                @@ -6569,7 +6561,7 @@

                                                Submodules
                                                -get_nn_shell_info(structure: Structure, site_idx, shell)[source]
                                                +get_nn_shell_info(structure: Structure, site_idx, shell)[source]

                                                Get a certain nearest neighbor shell for a certain site.

                                                Determines all non-backtracking paths through the neighbor network computed by get_nn_info. The weight is determined by multiplying @@ -6604,7 +6596,7 @@

                                                Submodules
                                                -property molecules_allowed: bool[source]
                                                +property molecules_allowed: bool[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -6616,7 +6608,7 @@

                                                Submodules
                                                -property structures_allowed: bool[source]
                                                +property structures_allowed: bool[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -6630,7 +6622,7 @@

                                                Submodules
                                                -class Critic2NN[source]
                                                +class Critic2NN[source]

                                                Bases: NearNeighbors

                                                Performs a topological analysis using critic2 to obtain neighbor information, using a sum of atomic charge densities. If an actual charge density is available (e.g. from a @@ -6638,7 +6630,7 @@

                                                Submodules
                                                -property extend_structure_molecules: bool[source]
                                                +property extend_structure_molecules: bool[source]

                                                Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed is False.

                                                @@ -6651,7 +6643,7 @@

                                                Submodules
                                                -get_bonded_structure(structure: Structure, decorate: bool = False) → StructureGraph[source]
                                                +get_bonded_structure(structure: Structure, decorate: bool = False) → StructureGraph[source]
                                                Parameters:
                                                  @@ -6670,7 +6662,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int) → list[dict][source]
                                                  +get_nn_info(structure: Structure, n: int) → list[dict][source]

                                                  Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                                  @@ -6695,7 +6687,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -6707,7 +6699,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -6721,7 +6713,7 @@

                                                  Submodules
                                                  -class CrystalNN(weighted_cn=False, cation_anion=False, distance_cutoffs=(0.5, 1), x_diff_weight=3.0, porous_adjustment=True, search_cutoff=7, fingerprint_length=None)[source]
                                                  +class CrystalNN(weighted_cn=False, cation_anion=False, distance_cutoffs=(0.5, 1), x_diff_weight=3.0, porous_adjustment=True, search_cutoff=7, fingerprint_length=None)[source]

                                                  Bases: NearNeighbors

                                                  This is a custom near-neighbor method intended for use in all kinds of periodic structures (metals, minerals, porous structures, etc). It is based on a Voronoi algorithm and uses the @@ -6774,24 +6766,24 @@

                                                  Submodules
                                                  -class NNData(all_nninfo, cn_weights, cn_nninfo)[source]
                                                  +class NNData(all_nninfo, cn_weights, cn_nninfo)[source]

                                                  Bases: NamedTuple

                                                  Create new instance of NNData(all_nninfo, cn_weights, cn_nninfo)

                                                  -all_nninfo: list[source]
                                                  +all_nninfo: list[source]

                                                  Alias for field number 0

                                                  -cn_nninfo: dict[source]
                                                  +cn_nninfo: dict[source]

                                                  Alias for field number 2

                                                  -cn_weights: dict[source]
                                                  +cn_weights: dict[source]

                                                  Alias for field number 1

                                                  @@ -6799,7 +6791,7 @@

                                                  Submodules
                                                  -get_cn(structure: Structure, n: int, **kwargs) → float[source]
                                                  +get_cn(structure: Structure, n: int, **kwargs) → float[source]

                                                  Get coordination number, CN, of site with index n in structure.

                                                  Parameters:
                                                  @@ -6829,7 +6821,7 @@

                                                  Submodules
                                                  -get_cn_dict(structure: Structure, n: int, use_weights: bool = False, **kwargs)[source]
                                                  +get_cn_dict(structure: Structure, n: int, use_weights: bool = False, **kwargs)[source]

                                                  Get coordination number, CN, of each element bonded to site with index n in structure.

                                                  Parameters:
                                                  @@ -6853,7 +6845,7 @@

                                                  Submodules
                                                  -get_nn_data(structure: Structure, n: int, length=None)[source]
                                                  +get_nn_data(structure: Structure, n: int, length=None)[source]

                                                  The main logic of the method to compute near neighbor.

                                                  Parameters:
                                                  @@ -6879,7 +6871,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int) → list[dict][source]
                                                  +get_nn_info(structure: Structure, n: int) → list[dict][source]

                                                  Get all near-neighbor information.

                                                  Parameters:
                                                  @@ -6907,7 +6899,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -6919,7 +6911,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -6931,7 +6923,7 @@

                                                  Submodules
                                                  -static transform_to_length(nn_data, length)[source]
                                                  +static transform_to_length(nn_data, length)[source]

                                                  Given NNData, transforms data to the specified fingerprint length

                                                  Parameters:
                                                  @@ -6947,7 +6939,7 @@

                                                  Submodules
                                                  -class CutOffDictNN(cut_off_dict: dict | None = None)[source]
                                                  +class CutOffDictNN(cut_off_dict: dict | None = None)[source]

                                                  Bases: NearNeighbors

                                                  A basic NN class using a dictionary of fixed cut-off distances. Only pairs of elements listed in the cut-off dictionary are considered @@ -6974,7 +6966,7 @@

                                                  Submodules
                                                  -property extend_structure_molecules: bool[source]
                                                  +property extend_structure_molecules: bool[source]

                                                  Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed is False.

                                                  @@ -6987,7 +6979,7 @@

                                                  Submodules
                                                  -classmethod from_preset(preset) → Self[source]
                                                  +classmethod from_preset(preset) → Self[source]

                                                  Initialize a CutOffDictNN according to a preset set of cutoffs.

                                                  Parameters:
                                                  @@ -7002,7 +6994,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int) → list[dict][source]
                                                  +get_nn_info(structure: Structure, n: int) → list[dict][source]

                                                  Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                                  @@ -7027,7 +7019,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -7039,7 +7031,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -7053,7 +7045,7 @@

                                                  Submodules
                                                  -class EconNN(tol: float = 0.2, cutoff: float = 10.0, cation_anion: bool = False, use_fictive_radius: bool = False)[source]
                                                  +class EconNN(tol: float = 0.2, cutoff: float = 10.0, cation_anion: bool = False, use_fictive_radius: bool = False)[source]

                                                  Bases: NearNeighbors

                                                  Determines the average effective coordination number for each cation in a given structure using Hoppe’s algorithm.

                                                  @@ -7076,7 +7068,7 @@

                                                  Submodules
                                                  -property extend_structure_molecules: bool[source]
                                                  +property extend_structure_molecules: bool[source]

                                                  Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed is False.

                                                  @@ -7089,7 +7081,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int)[source]
                                                  +get_nn_info(structure: Structure, n: int)[source]

                                                  Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                                  @@ -7115,7 +7107,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -7127,7 +7119,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -7141,7 +7133,7 @@

                                                  Submodules
                                                  -class IsayevNN(tol: float = 0.25, targets: Element | list[Element] | None = None, cutoff: float = 13.0, allow_pathological: bool = False, extra_nn_info: bool = True, compute_adj_neighbors: bool = True)[source]
                                                  +class IsayevNN(tol: float = 0.25, targets: Element | list[Element] | None = None, cutoff: float = 13.0, allow_pathological: bool = False, extra_nn_info: bool = True, compute_adj_neighbors: bool = True)[source]

                                                  Bases: VoronoiNN

                                                  Uses the algorithm defined in 10.1038/ncomms15679.

                                                  Sites are considered neighbors if (i) they share a Voronoi facet and (ii) the @@ -7162,7 +7154,7 @@

                                                  Submodules
                                                  -get_all_nn_info(structure: Structure) → list[list[dict[str, Any]]][source]
                                                  +get_all_nn_info(structure: Structure) → list[list[dict[str, Any]]][source]
                                                  Parameters:

                                                  structure (Structure) – input structure.

                                                  @@ -7176,7 +7168,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int) → list[dict[str, Any]][source]
                                                  +get_nn_info(structure: Structure, n: int) → list[dict[str, Any]][source]

                                                  Get all near-neighbor site information.

                                                  Gets the associated image locations and weights of the site with index n in structure using Voronoi decomposition and distance cutoff.

                                                  @@ -7206,7 +7198,7 @@

                                                  Submodules
                                                  -class JmolNN(tol: float = 0.45, min_bond_distance: float = 0.4, el_radius_updates: dict[SpeciesLike, float] | None = None)[source]
                                                  +class JmolNN(tol: float = 0.45, min_bond_distance: float = 0.4, el_radius_updates: dict[SpeciesLike, float] | None = None)[source]

                                                  Bases: NearNeighbors

                                                  Determine near-neighbor sites and coordination number using an emulation of Jmol’s default autoBond() algorithm. This version of the algorithm @@ -7226,7 +7218,7 @@

                                                  Submodules
                                                  -property extend_structure_molecules: bool[source]
                                                  +property extend_structure_molecules: bool[source]

                                                  Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed is False.

                                                  @@ -7239,7 +7231,7 @@

                                                  Submodules
                                                  -get_max_bond_distance(el1_sym, el2_sym)[source]
                                                  +get_max_bond_distance(el1_sym, el2_sym)[source]

                                                  Use Jmol algorithm to determine bond length from atomic parameters

                                                  Parameters:
                                                  @@ -7259,7 +7251,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int)[source]
                                                  +get_nn_info(structure: Structure, n: int)[source]

                                                  Get all near-neighbor sites as well as the associated image locations and weights of the site with index n using the bond identification algorithm underlying Jmol.

                                                  @@ -7287,7 +7279,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -7299,7 +7291,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -7313,7 +7305,7 @@

                                                  Submodules
                                                  -class LocalStructOrderParams(types, parameters=None, cutoff=-10.0)[source]
                                                  +class LocalStructOrderParams(types, parameters=None, cutoff=-10.0)[source]

                                                  Bases: object

                                                  This class permits the calculation of various types of local structure order parameters.

                                                  @@ -7450,7 +7442,7 @@

                                                  Submodules
                                                  -compute_trigonometric_terms(thetas, phis)[source]
                                                  +compute_trigonometric_terms(thetas, phis)[source]

                                                  Compute trigonometric terms that are required to calculate bond orientational order parameters using internal variables.

                                                  @@ -7474,7 +7466,7 @@

                                                  Submodules
                                                  -get_order_parameters(structure: Structure, n: int, indices_neighs: list[int] | None = None, tol: float = 0.0, target_spec=None)[source]
                                                  +get_order_parameters(structure: Structure, n: int, indices_neighs: list[int] | None = None, tol: float = 0.0, target_spec=None)[source]

                                                  Compute all order parameters of site n.

                                                  Parameters:
                                                  @@ -7530,7 +7522,7 @@

                                                  Submodules
                                                  -get_parameters(index)[source]
                                                  +get_parameters(index)[source]

                                                  Get list of floats that represents the parameters associated with calculation of the order @@ -7553,7 +7545,7 @@

                                                  Submodules
                                                  -get_q2(thetas=None, phis=None)[source]
                                                  +get_q2(thetas=None, phis=None)[source]

                                                  Calculates the value of the bond orientational order parameter of weight l=2. If the function is called with non-empty lists of polar and azimuthal angles the corresponding trigonometric terms @@ -7581,7 +7573,7 @@

                                                  Submodules
                                                  -get_q4(thetas=None, phis=None)[source]
                                                  +get_q4(thetas=None, phis=None)[source]

                                                  Calculates the value of the bond orientational order parameter of weight l=4. If the function is called with non-empty lists of polar and azimuthal angles the corresponding trigonometric terms @@ -7609,7 +7601,7 @@

                                                  Submodules
                                                  -get_q6(thetas=None, phis=None)[source]
                                                  +get_q6(thetas=None, phis=None)[source]

                                                  Calculates the value of the bond orientational order parameter of weight l=6. If the function is called with non-empty lists of polar and azimuthal angles the corresponding trigonometric terms @@ -7637,7 +7629,7 @@

                                                  Submodules
                                                  -get_type(index)[source]
                                                  +get_type(index)[source]

                                                  Get type of order parameter at the index provided and represented by a short string.

                                                  @@ -7656,14 +7648,14 @@

                                                  Submodules
                                                  -property last_nneigh[source]
                                                  +property last_nneigh[source]

                                                  Number of neighbors encountered during the most recent order parameter calculation. A value of -1 indicates that no such calculation has yet been performed for this instance.

                                                  -property num_ops: int[source]
                                                  +property num_ops: int[source]

                                                  Number of different order parameters that are targeted to be calculated.

                                                  @@ -7671,7 +7663,7 @@

                                                  Submodules
                                                  -class MinimumDistanceNN(tol: float = 0.1, cutoff=10, get_all_sites=False)[source]
                                                  +class MinimumDistanceNN(tol: float = 0.1, cutoff=10, get_all_sites=False)[source]

                                                  Bases: NearNeighbors

                                                  Determine near-neighbor sites and coordination number using the nearest neighbor(s) at distance, d_min, plus all neighbors @@ -7691,7 +7683,7 @@

                                                  Submodules
                                                  -property extend_structure_molecules: bool[source]
                                                  +property extend_structure_molecules: bool[source]

                                                  Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed is False.

                                                  @@ -7704,7 +7696,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int) → list[dict[str, Any]][source]
                                                  +get_nn_info(structure: Structure, n: int) → list[dict[str, Any]][source]

                                                  Get all near-neighbor sites as well as the associated image locations and weights of the site with index n using the closest neighbor distance-based method.

                                                  @@ -7731,7 +7723,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -7743,7 +7735,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -7757,7 +7749,7 @@

                                                  Submodules
                                                  -class MinimumOKeeffeNN(tol: float = 0.1, cutoff=10)[source]
                                                  +class MinimumOKeeffeNN(tol: float = 0.1, cutoff=10)[source]

                                                  Bases: NearNeighbors

                                                  Determine near-neighbor sites and coordination number using the neighbor(s) at closest relative distance, d_min_OKeffee, plus some @@ -7776,7 +7768,7 @@

                                                  Submodules
                                                  -property extend_structure_molecules: bool[source]
                                                  +property extend_structure_molecules: bool[source]

                                                  Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed is False.

                                                  @@ -7789,7 +7781,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int)[source]
                                                  +get_nn_info(structure: Structure, n: int)[source]

                                                  Get all near-neighbor sites as well as the associated image locations and weights of the site with index n using the closest relative neighbor distance-based method with O’Keeffe parameters.

                                                  @@ -7817,7 +7809,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -7829,7 +7821,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -7843,7 +7835,7 @@

                                                  Submodules
                                                  -class MinimumVIRENN(tol: float = 0.1, cutoff=10)[source]
                                                  +class MinimumVIRENN(tol: float = 0.1, cutoff=10)[source]

                                                  Bases: NearNeighbors

                                                  Determine near-neighbor sites and coordination number using the neighbor(s) at closest relative distance, d_min_VIRE, plus some @@ -7862,7 +7854,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int)[source]
                                                  +get_nn_info(structure: Structure, n: int)[source]

                                                  Get all near-neighbor sites as well as the associated image locations and weights of the site with index n using the closest relative neighbor distance-based method with VIRE atomic/ionic radii.

                                                  @@ -7890,7 +7882,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -7902,7 +7894,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -7916,13 +7908,13 @@

                                                  Submodules
                                                  -class NearNeighbors[source]
                                                  +class NearNeighbors[source]

                                                  Bases: object

                                                  Base class to determine near neighbors that typically include nearest neighbors and others that are within some tolerable distance.

                                                  -property extend_structure_molecules: bool[source]
                                                  +property extend_structure_molecules: bool[source]

                                                  Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed is False.

                                                  @@ -7935,7 +7927,7 @@

                                                  Submodules
                                                  -get_all_nn_info(structure: Structure)[source]
                                                  +get_all_nn_info(structure: Structure)[source]

                                                  Get a listing of all neighbors for all sites in a structure.

                                                  Parameters:
                                                  @@ -7953,7 +7945,7 @@

                                                  Submodules
                                                  -get_bonded_structure(structure: Structure, decorate: bool = False, weights: bool = True, edge_properties: bool = False, on_disorder: Literal['take_majority_strict', 'take_majority_drop', 'take_max_species', 'error'] = 'take_majority_strict') → StructureGraph | MoleculeGraph[source]
                                                  +get_bonded_structure(structure: Structure, decorate: bool = False, weights: bool = True, edge_properties: bool = False, on_disorder: Literal['take_majority_strict', 'take_majority_drop', 'take_max_species', 'error'] = 'take_majority_strict') → StructureGraph | MoleculeGraph[source]

                                                  Obtain a StructureGraph object using this NearNeighbor class. Requires pip install networkx.

                                                  Parameters:
                                                  @@ -7982,7 +7974,7 @@

                                                  Submodules
                                                  -get_cn(structure: Structure, n: int, use_weights: bool = False, on_disorder: Literal['take_majority_strict', 'take_majority_drop', 'take_max_species', 'error'] = 'take_majority_strict') → float[source]
                                                  +get_cn(structure: Structure, n: int, use_weights: bool = False, on_disorder: Literal['take_majority_strict', 'take_majority_drop', 'take_max_species', 'error'] = 'take_majority_strict') → float[source]

                                                  Get coordination number, CN, of site with index n in structure.

                                                  Parameters:
                                                  @@ -8010,7 +8002,7 @@

                                                  Submodules
                                                  -get_cn_dict(structure: Structure, n: int, use_weights: bool = False)[source]
                                                  +get_cn_dict(structure: Structure, n: int, use_weights: bool = False)[source]

                                                  Get coordination number, CN, of each element bonded to site with index n in structure.

                                                  Parameters:
                                                  @@ -8034,7 +8026,7 @@

                                                  Submodules
                                                  -get_local_order_parameters(structure: Structure, n: int)[source]
                                                  +get_local_order_parameters(structure: Structure, n: int)[source]

                                                  Calculate those local structure order parameters for the given site whose ideal CN corresponds to the underlying motif (e.g., CN=4, then calculate the @@ -8062,7 +8054,7 @@

                                                  Submodules
                                                  -get_nn(structure: Structure, n: int)[source]
                                                  +get_nn(structure: Structure, n: int)[source]

                                                  Get near neighbors of site with index n in structure.

                                                  Parameters:
                                                  @@ -8083,7 +8075,7 @@

                                                  Submodules
                                                  -get_nn_images(structure: Structure, n: int)[source]
                                                  +get_nn_images(structure: Structure, n: int)[source]

                                                  Get image location of all near neighbors of site with index n in structure.

                                                  @@ -8109,7 +8101,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int) → list[dict][source]
                                                  +get_nn_info(structure: Structure, n: int) → list[dict][source]

                                                  Get all near-neighbor sites as well as the associated image locations and weights of the site with index n.

                                                  @@ -8139,7 +8131,7 @@

                                                  Submodules
                                                  -get_nn_shell_info(structure: Structure, site_idx, shell)[source]
                                                  +get_nn_shell_info(structure: Structure, site_idx, shell)[source]

                                                  Get a certain nearest neighbor shell for a certain site.

                                                  Determines all non-backtracking paths through the neighbor network computed by get_nn_info. The weight is determined by multiplying @@ -8174,7 +8166,7 @@

                                                  Submodules
                                                  -get_weights_of_nn_sites(structure: Structure, n: int)[source]
                                                  +get_weights_of_nn_sites(structure: Structure, n: int)[source]

                                                  Get weight associated with each near neighbor of site with index n in structure.

                                                  @@ -8195,7 +8187,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -8207,7 +8199,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -8221,7 +8213,7 @@

                                                  Submodules
                                                  -class OpenBabelNN(order=True)[source]
                                                  +class OpenBabelNN(order=True)[source]

                                                  Bases: NearNeighbors

                                                  Determine near-neighbor sites and bond orders using OpenBabel API.

                                                  NOTE: This strategy is only appropriate for molecules, and not for @@ -8236,7 +8228,7 @@

                                                  Submodules
                                                  -property extend_structure_molecules: bool[source]
                                                  +property extend_structure_molecules: bool[source]

                                                  Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed is False.

                                                  @@ -8249,7 +8241,7 @@

                                                  Submodules
                                                  -get_bonded_structure(structure: Structure, decorate: bool = False) → StructureGraph[source]
                                                  +get_bonded_structure(structure: Structure, decorate: bool = False) → StructureGraph[source]

                                                  Obtain a MoleculeGraph object using this NearNeighbor class. Requires the optional dependency networkx (pip install networkx).

                                                  @@ -8273,7 +8265,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int)[source]
                                                  +get_nn_info(structure: Structure, n: int)[source]

                                                  Get all near-neighbor sites and weights (orders) of bonds for a given atom.

                                                  @@ -8295,7 +8287,7 @@

                                                  Submodules
                                                  -get_nn_shell_info(structure: Structure, site_idx, shell)[source]
                                                  +get_nn_shell_info(structure: Structure, site_idx, shell)[source]

                                                  Get a certain nearest neighbor shell for a certain site.

                                                  Determines all non-backtracking paths through the neighbor network computed by get_nn_info. The weight is determined by multiplying @@ -8330,7 +8322,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -8342,7 +8334,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -8356,7 +8348,7 @@

                                                  Submodules
                                                  -class ValenceIonicRadiusEvaluator(structure: Structure)[source]
                                                  +class ValenceIonicRadiusEvaluator(structure: Structure)[source]

                                                  Bases: object

                                                  Computes site valences and ionic radii for a structure using bond valence analyzer.

                                                  @@ -8367,19 +8359,19 @@

                                                  Submodules
                                                  -property radii[source]
                                                  +property radii[source]

                                                  List of ionic radii of elements in the order of sites.

                                                  -property structure[source]
                                                  +property structure[source]

                                                  Oxidation state decorated structure.

                                                  -property valences[source]
                                                  +property valences[source]

                                                  List of oxidation states of elements in the order of sites.

                                                  @@ -8387,7 +8379,7 @@

                                                  Submodules
                                                  -class VoronoiNN(tol=0, targets=None, cutoff=13.0, allow_pathological=False, weight='solid_angle', extra_nn_info=True, compute_adj_neighbors=True)[source]
                                                  +class VoronoiNN(tol=0, targets=None, cutoff=13.0, allow_pathological=False, weight='solid_angle', extra_nn_info=True, compute_adj_neighbors=True)[source]

                                                  Bases: NearNeighbors

                                                  Uses a Voronoi algorithm to determine near neighbors for each site in a structure.

                                                  @@ -8410,7 +8402,7 @@

                                                  Submodules
                                                  -get_all_nn_info(structure: Structure)[source]
                                                  +get_all_nn_info(structure: Structure)[source]
                                                  Parameters:

                                                  structure (Structure) – input structure.

                                                  @@ -8423,7 +8415,7 @@

                                                  Submodules
                                                  -get_all_voronoi_polyhedra(structure: Structure)[source]
                                                  +get_all_voronoi_polyhedra(structure: Structure)[source]

                                                  Get the Voronoi polyhedra for all site in a simulation cell.

                                                  Parameters:
                                                  @@ -8453,7 +8445,7 @@

                                                  Submodules
                                                  -get_nn_info(structure: Structure, n: int)[source]
                                                  +get_nn_info(structure: Structure, n: int)[source]

                                                  Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure using Voronoi decomposition.

                                                  @@ -8480,7 +8472,7 @@

                                                  Submodules
                                                  -get_voronoi_polyhedra(structure: Structure, n: int)[source]
                                                  +get_voronoi_polyhedra(structure: Structure, n: int)[source]

                                                  Get a weighted polyhedra around a site.

                                                  See ref: A Proposed Rigorous Definition of Coordination Number, M. O’Keeffe, Acta Cryst. (1979). A35, 772-775

                                                  @@ -8516,7 +8508,7 @@

                                                  Submodules
                                                  -property molecules_allowed: bool[source]
                                                  +property molecules_allowed: bool[source]

                                                  can this NearNeighbors class be used with Molecule objects?

                                                  @@ -8528,7 +8520,7 @@

                                                  Submodules
                                                  -property structures_allowed: bool[source]
                                                  +property structures_allowed: bool[source]

                                                  can this NearNeighbors class be used with Structure objects?

                                                  @@ -8542,7 +8534,7 @@

                                                  Submodules
                                                  -get_neighbors_of_site_with_index(struct, n, approach='min_dist', delta=0.1, cutoff=10)[source]
                                                  +get_neighbors_of_site_with_index(struct, n, approach='min_dist', delta=0.1, cutoff=10)[source]

                                                  Get the neighbors of a given site using a specific neighbor-finding method.

                                                  Parameters:
                                                  @@ -8566,7 +8558,7 @@

                                                  Submodules
                                                  -get_okeeffe_distance_prediction(el1, el2)[source]
                                                  +get_okeeffe_distance_prediction(el1, el2)[source]

                                                  Get an estimate of the bond valence parameter (bond length) using the derived parameters from ‘Atoms Sizes and Bond Lengths in Molecules and Crystals’ (O’Keeffe & Brese, 1991). The estimate is based on two @@ -8589,7 +8581,7 @@

                                                  Submodules
                                                  -get_okeeffe_params(el_symbol)[source]
                                                  +get_okeeffe_params(el_symbol)[source]

                                                  Get the elemental parameters related to atom size and electronegativity which are used for estimating bond-valence parameters (bond length) of pairs of atoms on the basis of data provided in ‘Atoms Sizes and Bond Lengths in Molecules and Crystals’ @@ -8609,7 +8601,7 @@

                                                  Submodules
                                                  -gramschmidt(vin, uin)[source]
                                                  +gramschmidt(vin, uin)[source]

                                                  Get that part of the first input vector that is orthogonal to the second input vector. The output vector is not normalized.

                                                  @@ -8625,7 +8617,7 @@

                                                  Submodules
                                                  -metal_edge_extender(mol_graph, cutoff: float = 2.5, metals: list | tuple | None = ('Li', 'Mg', 'Ca', 'Zn', 'B', 'Al'), coordinators: list | tuple = ('O', 'N', 'F', 'S', 'Cl'))[source]
                                                  +metal_edge_extender(mol_graph, cutoff: float = 2.5, metals: list | tuple | None = ('Li', 'Mg', 'Ca', 'Zn', 'B', 'Al'), coordinators: list | tuple = ('O', 'N', 'F', 'S', 'Cl'))[source]

                                                  Identify and add missed coordinate bond edges for metals.

                                                  Parameters:
                                                  @@ -8661,7 +8653,7 @@

                                                  Submodules
                                                  -oxygen_edge_extender(mol_graph: MoleculeGraph) → MoleculeGraph[source]
                                                  +oxygen_edge_extender(mol_graph: MoleculeGraph) → MoleculeGraph[source]

                                                  Identify and add missed O-C or O-H bonds. This is particularly important when oxygen is forming three bonds, e.g. in H3O+ or XOH2+. See https://github.com/materialsproject/pymatgen/pull/2903 for details.

                                                  @@ -8680,7 +8672,7 @@

                                                  Submodules
                                                  -site_is_of_motif_type(struct, n, approach='min_dist', delta=0.1, cutoff=10, thresh=None)[source]
                                                  +site_is_of_motif_type(struct, n, approach='min_dist', delta=0.1, cutoff=10, thresh=None)[source]

                                                  Get the motif type of the site with index n in structure struct; currently featuring “tetrahedral”, “octahedral”, “bcc”, and “cp” (close-packed: fcc and hcp) as well as “square pyramidal” and @@ -8715,7 +8707,7 @@

                                                  Submodules
                                                  -solid_angle(center, coords)[source]
                                                  +solid_angle(center, coords)[source]

                                                  Helper method to calculate the solid angle of a set of coords from the center.

                                                  @@ -8733,7 +8725,7 @@

                                                  Submodules
                                                  -vol_tetra(vt1, vt2, vt3, vt4)[source]
                                                  +vol_tetra(vt1, vt2, vt3, vt4)[source]

                                                  Calculate the volume of a tetrahedron, given the four vertices of vt1, vt2, vt3 and vt4.

                                                  @@ -8766,14 +8758,14 @@

                                                  Submoduleshttps://github.com/charnley/rmsd.

                                                  -class AbstractMolAtomMapper[source]
                                                  +class AbstractMolAtomMapper[source]

                                                  Bases: MSONable, ABC

                                                  Abstract molecular atom order mapping class. A mapping will be able to find the uniform atom order of two molecules that can pair the geometrically equivalent atoms.

                                                  -classmethod from_dict(dct: dict) → Self[source]
                                                  +classmethod from_dict(dct: dict) → Self[source]
                                                  Parameters:

                                                  dct (dict) – Dict representation.

                                                  @@ -8786,7 +8778,7 @@

                                                  Submodules
                                                  -abstract get_molecule_hash(mol)[source]
                                                  +abstract get_molecule_hash(mol)[source]

                                                  Defines a hash for molecules. This allows molecules to be grouped efficiently for comparison.

                                                  @@ -8801,7 +8793,7 @@

                                                  Submodules
                                                  -abstract uniform_labels(mol1, mol2)[source]
                                                  +abstract uniform_labels(mol1, mol2)[source]

                                                  Pair the geometrically equivalent atoms of the molecules.

                                                  Parameters:
                                                  @@ -8831,7 +8823,7 @@

                                                  Submodules
                                                  -class BruteForceOrderMatcher(target: Molecule)[source]
                                                  +class BruteForceOrderMatcher(target: Molecule)[source]

                                                  Bases: KabschMatcher

                                                  Finding the best match between molecules by selecting molecule order with the smallest RMSD from all the possible order combinations.

                                                  @@ -8846,7 +8838,7 @@

                                                  Submodules
                                                  -fit(p: Molecule, ignore_warning=False)[source]
                                                  +fit(p: Molecule, ignore_warning=False)[source]

                                                  Order, rotate and transform p molecule according to the best match.

                                                  A ValueError will be raised when the total number of possible combinations become unfeasible (more than a million combinations).

                                                  @@ -8869,7 +8861,7 @@

                                                  Submodules
                                                  -match(mol: Molecule, ignore_warning: bool = False) → tuple[ndarray, ndarray, ndarray, float][source]
                                                  +match(mol: Molecule, ignore_warning: bool = False) → tuple[ndarray, ndarray, ndarray, float][source]

                                                  Similar as KabschMatcher.match but this method also finds the order of atoms which belongs to the best match.

                                                  A ValueError will be raised when the total number of possible combinations @@ -8895,7 +8887,7 @@

                                                  Submodules
                                                  -static permutations(atoms)[source]
                                                  +static permutations(atoms)[source]

                                                  Generate all the possible permutations of atom order. To achieve better performance all the cases where the atoms are different has been ignored.

                                                  @@ -8904,7 +8896,7 @@

                                                  Submodules
                                                  -class GeneticOrderMatcher(target: Molecule, threshold: float)[source]
                                                  +class GeneticOrderMatcher(target: Molecule, threshold: float)[source]

                                                  Bases: KabschMatcher

                                                  This method was inspired by genetic algorithms and tries to match molecules based on their already matched fragments.

                                                  @@ -8933,7 +8925,7 @@

                                                  Submodules
                                                  -fit(p: Molecule)[source]
                                                  +fit(p: Molecule)[source]

                                                  Order, rotate and transform all of the matched p molecule according to the given threshold.

                                                  @@ -8956,7 +8948,7 @@

                                                  Submodules
                                                  -match(p: Molecule)[source]
                                                  +match(p: Molecule)[source]

                                                  Similar as KabschMatcher.match but this method also finds all of the possible atomic orders according to the threshold.

                                                  @@ -8977,7 +8969,7 @@

                                                  Submodules
                                                  -permutations(p: Molecule)[source]
                                                  +permutations(p: Molecule)[source]

                                                  Generate all of possible permutations of atom order according the threshold.

                                                  Parameters:
                                                  @@ -8993,7 +8985,7 @@

                                                  Submodules
                                                  -class HungarianOrderMatcher(target: Molecule)[source]
                                                  +class HungarianOrderMatcher(target: Molecule)[source]

                                                  Bases: KabschMatcher

                                                  Pre-align the molecules based on their principal inertia axis and then re-orders the input atom list using the Hungarian method.

                                                  @@ -9009,7 +9001,7 @@

                                                  Submodules
                                                  -fit(p: Molecule)[source]
                                                  +fit(p: Molecule)[source]

                                                  Order, rotate and transform p molecule according to the best match.

                                                  Parameters:
                                                  @@ -9027,7 +9019,7 @@

                                                  Submodules
                                                  -static get_principal_axis(coords, weights)[source]
                                                  +static get_principal_axis(coords, weights)[source]

                                                  Get the molecule’s principal axis.

                                                  Parameters:
                                                  @@ -9044,7 +9036,7 @@

                                                  Submodules
                                                  -match(p: Molecule)[source]
                                                  +match(p: Molecule)[source]

                                                  Similar as KabschMatcher.match but this method also finds the order of atoms which belongs to the best match.

                                                  @@ -9065,7 +9057,7 @@

                                                  Submodules
                                                  -static permutations(p_atoms, p_centroid, p_weights, q_atoms, q_centroid, q_weights)[source]
                                                  +static permutations(p_atoms, p_centroid, p_weights, q_atoms, q_centroid, q_weights)[source]

                                                  Generate two possible permutations of atom order. This method uses the principle component of the inertia tensor to pre-align the molecules and hungarian method to determine the order. There are always two possible permutation depending on the way to pre-aligning the molecules.

                                                  @@ -9088,7 +9080,7 @@

                                                  Submodules
                                                  -static rotation_matrix_vectors(v1, v2)[source]
                                                  +static rotation_matrix_vectors(v1, v2)[source]

                                                  Get the rotation matrix that rotates v1 onto v2 using Rodrigues’ rotation formula.

                                                  See more: https://math.stackexchange.com/a/476311

                                                  @@ -9109,7 +9101,7 @@

                                                  Submodules
                                                  -class InchiMolAtomMapper(angle_tolerance=10.0)[source]
                                                  +class InchiMolAtomMapper(angle_tolerance=10.0)[source]

                                                  Bases: AbstractMolAtomMapper

                                                  Pair atoms by inchi labels.

                                                  @@ -9119,13 +9111,13 @@

                                                  Submodules
                                                  -as_dict()[source]
                                                  +as_dict()[source]

                                                  Get MSONable dict.

                                                  -classmethod from_dict(dct: dict) → Self[source]
                                                  +classmethod from_dict(dct: dict) → Self[source]
                                                  Parameters:

                                                  dct (dict) – Dict Representation.

                                                  @@ -9138,13 +9130,13 @@

                                                  Submodules
                                                  -get_molecule_hash(mol)[source]
                                                  +get_molecule_hash(mol)[source]

                                                  Return inchi as molecular hash.

                                                  -uniform_labels(mol1, mol2)[source]
                                                  +uniform_labels(mol1, mol2)[source]
                                                  Parameters:
                                                    @@ -9162,18 +9154,18 @@

                                                    Submodules
                                                    -class IsomorphismMolAtomMapper[source]
                                                    +class IsomorphismMolAtomMapper[source]

                                                    Bases: AbstractMolAtomMapper

                                                    Pair atoms by isomorphism permutations in the OpenBabel::OBAlign class.

                                                    -as_dict()[source]
                                                    +as_dict()[source]

                                                    Get MSONable dict.

                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                    Parameters:

                                                    dct (dict) – Dict representation.

                                                    @@ -9186,13 +9178,13 @@

                                                    Submodules
                                                    -get_molecule_hash(mol)[source]
                                                    +get_molecule_hash(mol)[source]

                                                    Return inchi as molecular hash.

                                                    -uniform_labels(mol1, mol2)[source]
                                                    +uniform_labels(mol1, mol2)[source]

                                                    Pair the geometrically equivalent atoms of the molecules. Calculate RMSD on all possible isomorphism mappings and return mapping with the least RMSD.

                                                    @@ -9224,7 +9216,7 @@

                                                    Submodules
                                                    -class KabschMatcher(target: Molecule)[source]
                                                    +class KabschMatcher(target: Molecule)[source]

                                                    Bases: MSONable

                                                    Molecule matcher using Kabsch algorithm.

                                                    The Kabsch algorithm capable aligning two molecules by finding the parameters @@ -9241,7 +9233,7 @@

                                                    Submodules
                                                    -fit(p: Molecule)[source]
                                                    +fit(p: Molecule)[source]

                                                    Rotate and transform p molecule according to the best match.

                                                    Parameters:
                                                    @@ -9259,7 +9251,7 @@

                                                    Submodules
                                                    -static kabsch(P: ndarray, Q: ndarray)[source]
                                                    +static kabsch(P: ndarray, Q: ndarray)[source]

                                                    The Kabsch algorithm is a method for calculating the optimal rotation matrix that minimizes the root mean squared deviation (RMSD) between two paired sets of points P and Q, centered around the their centroid.

                                                    @@ -9284,7 +9276,7 @@

                                                    Submodules
                                                    -match(p: Molecule)[source]
                                                    +match(p: Molecule)[source]

                                                    Using the Kabsch algorithm the alignment of two molecules (P, Q) happens in three steps: - translate the P and Q into their centroid @@ -9314,7 +9306,7 @@

                                                    Submodules
                                                    -class MoleculeMatcher(tolerance: float = 0.01, mapper=None)[source]
                                                    +class MoleculeMatcher(tolerance: float = 0.01, mapper=None)[source]

                                                    Bases: MSONable

                                                    Match molecules and identify whether molecules are the same.

                                                    @@ -9329,13 +9321,13 @@

                                                    Submodules
                                                    -as_dict()[source]
                                                    +as_dict()[source]

                                                    Get MSONable dict.

                                                    -fit(mol1, mol2)[source]
                                                    +fit(mol1, mol2)[source]

                                                    Fit two molecules.

                                                    Parameters:
                                                    @@ -9352,7 +9344,7 @@

                                                    Submodules
                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                    Parameters:

                                                    dct (dict) – Dict representation.

                                                    @@ -9365,7 +9357,7 @@

                                                    Submodules
                                                    -get_rmsd(mol1, mol2)[source]
                                                    +get_rmsd(mol1, mol2)[source]

                                                    Get RMSD between two molecule with arbitrary atom order.

                                                    Returns:
                                                    @@ -9377,7 +9369,7 @@

                                                    Submodules
                                                    -group_molecules(mol_list)[source]
                                                    +group_molecules(mol_list)[source]

                                                    Group molecules by structural equality.

                                                    Parameters:
                                                    @@ -9405,20 +9397,20 @@

                                                    Submodules
                                                    -class CovalentRadius[source]
                                                    +class CovalentRadius[source]

                                                    Bases: object

                                                    Covalent radius of the elements.

                                                    Beatriz C. et al. Dalton Trans. 2008, 2832-2838. https://doi.org/10.1039/b801115j

                                                    -radius: ClassVar = {'Ac': 2.15, 'Ag': 1.45, 'Al': 1.21, 'Am': 1.8, 'Ar': 1.06, 'As': 1.19, 'At': 1.5, 'Au': 1.36, 'B': 0.84, 'Ba': 2.15, 'Be': 0.96, 'Bi': 1.48, 'Br': 1.2, 'C': 0.73, 'Ca': 1.76, 'Cd': 1.44, 'Ce': 2.04, 'Cl': 1.02, 'Cm': 1.69, 'Co': 1.38, 'Cr': 1.39, 'Cs': 2.44, 'Cu': 1.32, 'Dy': 1.92, 'Er': 1.89, 'Eu': 1.98, 'F': 0.57, 'Fe': 1.42, 'Fr': 2.6, 'Ga': 1.22, 'Gd': 1.96, 'Ge': 1.2, 'H': 0.31, 'He': 0.28, 'Hf': 1.75, 'Hg': 1.32, 'Ho': 1.92, 'I': 1.39, 'In': 1.42, 'Ir': 1.41, 'K': 2.03, 'Kr': 1.16, 'La': 2.07, 'Li': 1.28, 'Lu': 1.87, 'Mg': 1.41, 'Mn': 1.5, 'Mo': 1.54, 'N': 0.71, 'Na': 1.66, 'Nb': 1.64, 'Nd': 2.01, 'Ne': 0.58, 'Ni': 1.24, 'Np': 1.9, 'O': 0.66, 'Os': 1.44, 'P': 1.07, 'Pa': 2, 'Pb': 1.46, 'Pd': 1.39, 'Pm': 1.99, 'Po': 1.4, 'Pr': 2.03, 'Pt': 1.36, 'Pu': 1.87, 'Ra': 2.21, 'Rb': 2.2, 'Re': 1.51, 'Rh': 1.42, 'Rn': 1.5, 'Ru': 1.46, 'S': 1.05, 'Sb': 1.39, 'Sc': 1.7, 'Se': 1.2, 'Si': 1.11, 'Sm': 1.98, 'Sn': 1.39, 'Sr': 1.95, 'Ta': 1.7, 'Tb': 1.94, 'Tc': 1.47, 'Te': 1.38, 'Th': 2.06, 'Ti': 1.6, 'Tl': 1.45, 'Tm': 1.9, 'U': 1.96, 'V': 1.53, 'W': 1.62, 'Xe': 1.4, 'Y': 1.9, 'Yb': 1.87, 'Zn': 1.22, 'Zr': 1.75}[source]
                                                    +radius: ClassVar = {'Ac': 2.15, 'Ag': 1.45, 'Al': 1.21, 'Am': 1.8, 'Ar': 1.06, 'As': 1.19, 'At': 1.5, 'Au': 1.36, 'B': 0.84, 'Ba': 2.15, 'Be': 0.96, 'Bi': 1.48, 'Br': 1.2, 'C': 0.73, 'Ca': 1.76, 'Cd': 1.44, 'Ce': 2.04, 'Cl': 1.02, 'Cm': 1.69, 'Co': 1.38, 'Cr': 1.39, 'Cs': 2.44, 'Cu': 1.32, 'Dy': 1.92, 'Er': 1.89, 'Eu': 1.98, 'F': 0.57, 'Fe': 1.42, 'Fr': 2.6, 'Ga': 1.22, 'Gd': 1.96, 'Ge': 1.2, 'H': 0.31, 'He': 0.28, 'Hf': 1.75, 'Hg': 1.32, 'Ho': 1.92, 'I': 1.39, 'In': 1.42, 'Ir': 1.41, 'K': 2.03, 'Kr': 1.16, 'La': 2.07, 'Li': 1.28, 'Lu': 1.87, 'Mg': 1.41, 'Mn': 1.5, 'Mo': 1.54, 'N': 0.71, 'Na': 1.66, 'Nb': 1.64, 'Nd': 2.01, 'Ne': 0.58, 'Ni': 1.24, 'Np': 1.9, 'O': 0.66, 'Os': 1.44, 'P': 1.07, 'Pa': 2, 'Pb': 1.46, 'Pd': 1.39, 'Pm': 1.99, 'Po': 1.4, 'Pr': 2.03, 'Pt': 1.36, 'Pu': 1.87, 'Ra': 2.21, 'Rb': 2.2, 'Re': 1.51, 'Rh': 1.42, 'Rn': 1.5, 'Ru': 1.46, 'S': 1.05, 'Sb': 1.39, 'Sc': 1.7, 'Se': 1.2, 'Si': 1.11, 'Sm': 1.98, 'Sn': 1.39, 'Sr': 1.95, 'Ta': 1.7, 'Tb': 1.94, 'Tc': 1.47, 'Te': 1.38, 'Th': 2.06, 'Ti': 1.6, 'Tl': 1.45, 'Tm': 1.9, 'U': 1.96, 'V': 1.53, 'W': 1.62, 'Xe': 1.4, 'Y': 1.9, 'Yb': 1.87, 'Zn': 1.22, 'Zr': 1.75}[source]

                                                    -class MoleculeStructureComparator(bond_length_cap=0.3, covalent_radius={'Ac': 2.15, 'Ag': 1.45, 'Al': 1.21, 'Am': 1.8, 'Ar': 1.06, 'As': 1.19, 'At': 1.5, 'Au': 1.36, 'B': 0.84, 'Ba': 2.15, 'Be': 0.96, 'Bi': 1.48, 'Br': 1.2, 'C': 0.73, 'Ca': 1.76, 'Cd': 1.44, 'Ce': 2.04, 'Cl': 1.02, 'Cm': 1.69, 'Co': 1.38, 'Cr': 1.39, 'Cs': 2.44, 'Cu': 1.32, 'Dy': 1.92, 'Er': 1.89, 'Eu': 1.98, 'F': 0.57, 'Fe': 1.42, 'Fr': 2.6, 'Ga': 1.22, 'Gd': 1.96, 'Ge': 1.2, 'H': 0.31, 'He': 0.28, 'Hf': 1.75, 'Hg': 1.32, 'Ho': 1.92, 'I': 1.39, 'In': 1.42, 'Ir': 1.41, 'K': 2.03, 'Kr': 1.16, 'La': 2.07, 'Li': 1.28, 'Lu': 1.87, 'Mg': 1.41, 'Mn': 1.5, 'Mo': 1.54, 'N': 0.71, 'Na': 1.66, 'Nb': 1.64, 'Nd': 2.01, 'Ne': 0.58, 'Ni': 1.24, 'Np': 1.9, 'O': 0.66, 'Os': 1.44, 'P': 1.07, 'Pa': 2, 'Pb': 1.46, 'Pd': 1.39, 'Pm': 1.99, 'Po': 1.4, 'Pr': 2.03, 'Pt': 1.36, 'Pu': 1.87, 'Ra': 2.21, 'Rb': 2.2, 'Re': 1.51, 'Rh': 1.42, 'Rn': 1.5, 'Ru': 1.46, 'S': 1.05, 'Sb': 1.39, 'Sc': 1.7, 'Se': 1.2, 'Si': 1.11, 'Sm': 1.98, 'Sn': 1.39, 'Sr': 1.95, 'Ta': 1.7, 'Tb': 1.94, 'Tc': 1.47, 'Te': 1.38, 'Th': 2.06, 'Ti': 1.6, 'Tl': 1.45, 'Tm': 1.9, 'U': 1.96, 'V': 1.53, 'W': 1.62, 'Xe': 1.4, 'Y': 1.9, 'Yb': 1.87, 'Zn': 1.22, 'Zr': 1.75}, priority_bonds=(), priority_cap=0.8, ignore_ionic_bond=True, bond_13_cap=0.05)[source]
                                                    +class MoleculeStructureComparator(bond_length_cap=0.3, covalent_radius={'Ac': 2.15, 'Ag': 1.45, 'Al': 1.21, 'Am': 1.8, 'Ar': 1.06, 'As': 1.19, 'At': 1.5, 'Au': 1.36, 'B': 0.84, 'Ba': 2.15, 'Be': 0.96, 'Bi': 1.48, 'Br': 1.2, 'C': 0.73, 'Ca': 1.76, 'Cd': 1.44, 'Ce': 2.04, 'Cl': 1.02, 'Cm': 1.69, 'Co': 1.38, 'Cr': 1.39, 'Cs': 2.44, 'Cu': 1.32, 'Dy': 1.92, 'Er': 1.89, 'Eu': 1.98, 'F': 0.57, 'Fe': 1.42, 'Fr': 2.6, 'Ga': 1.22, 'Gd': 1.96, 'Ge': 1.2, 'H': 0.31, 'He': 0.28, 'Hf': 1.75, 'Hg': 1.32, 'Ho': 1.92, 'I': 1.39, 'In': 1.42, 'Ir': 1.41, 'K': 2.03, 'Kr': 1.16, 'La': 2.07, 'Li': 1.28, 'Lu': 1.87, 'Mg': 1.41, 'Mn': 1.5, 'Mo': 1.54, 'N': 0.71, 'Na': 1.66, 'Nb': 1.64, 'Nd': 2.01, 'Ne': 0.58, 'Ni': 1.24, 'Np': 1.9, 'O': 0.66, 'Os': 1.44, 'P': 1.07, 'Pa': 2, 'Pb': 1.46, 'Pd': 1.39, 'Pm': 1.99, 'Po': 1.4, 'Pr': 2.03, 'Pt': 1.36, 'Pu': 1.87, 'Ra': 2.21, 'Rb': 2.2, 'Re': 1.51, 'Rh': 1.42, 'Rn': 1.5, 'Ru': 1.46, 'S': 1.05, 'Sb': 1.39, 'Sc': 1.7, 'Se': 1.2, 'Si': 1.11, 'Sm': 1.98, 'Sn': 1.39, 'Sr': 1.95, 'Ta': 1.7, 'Tb': 1.94, 'Tc': 1.47, 'Te': 1.38, 'Th': 2.06, 'Ti': 1.6, 'Tl': 1.45, 'Tm': 1.9, 'U': 1.96, 'V': 1.53, 'W': 1.62, 'Xe': 1.4, 'Y': 1.9, 'Yb': 1.87, 'Zn': 1.22, 'Zr': 1.75}, priority_bonds=(), priority_cap=0.8, ignore_ionic_bond=True, bond_13_cap=0.05)[source]

                                                    Bases: MSONable

                                                    Check whether the connection tables of the two molecules are the same. The atom in the two molecule must be paired accordingly.

                                                    @@ -9441,7 +9433,7 @@

                                                    Submodules
                                                    -are_equal(mol1, mol2) → bool[source]
                                                    +are_equal(mol1, mol2) → bool[source]

                                                    Compare the bond table of the two molecules.

                                                    Parameters:
                                                    @@ -9455,13 +9447,13 @@

                                                    Submodules
                                                    -as_dict()[source]
                                                    +as_dict()[source]

                                                    Get MSONable dict.

                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                    Parameters:

                                                    dct (dict) – Dict representation.

                                                    @@ -9474,7 +9466,7 @@

                                                    Submodules
                                                    -static get_13_bonds(priority_bonds)[source]
                                                    +static get_13_bonds(priority_bonds)[source]
                                                    Parameters:

                                                    () (priority_bonds)

                                                    @@ -9490,12 +9482,12 @@

                                                    Submodules
                                                    -halogen_list = ('F', 'Cl', 'Br', 'I')[source]
                                                    +halogen_list = ('F', 'Cl', 'Br', 'I')[source]

                                                    -ionic_element_list = ('Na', 'Mg', 'Al', 'Sc', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Rb', 'Sr')[source]
                                                    +ionic_element_list = ('Na', 'Mg', 'Al', 'Sc', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Rb', 'Sr')[source]

                                                    @@ -9506,7 +9498,7 @@

                                                    Submodules
                                                    -class ChemicalShielding(cs_matrix, vscale=None)[source]
                                                    +class ChemicalShielding(cs_matrix, vscale=None)[source]

                                                    Bases: SquareTensor

                                                    This class extends the SquareTensor to perform extra analysis unique to NMR Chemical shielding tensors.

                                                    @@ -9531,30 +9523,30 @@

                                                    Submodules
                                                    -class HaeberlenNotation(sigma_iso, delta_sigma_iso, zeta, eta)[source]
                                                    +class HaeberlenNotation(sigma_iso, delta_sigma_iso, zeta, eta)[source]

                                                    Bases: NamedTuple

                                                    Create new instance of HaeberlenNotation(sigma_iso, delta_sigma_iso, zeta, eta)

                                                    -delta_sigma_iso: Any[source]
                                                    +delta_sigma_iso: Any[source]

                                                    Alias for field number 1

                                                    -eta: Any[source]
                                                    +eta: Any[source]

                                                    Alias for field number 3

                                                    -sigma_iso: Any[source]
                                                    +sigma_iso: Any[source]

                                                    Alias for field number 0

                                                    -zeta: Any[source]
                                                    +zeta: Any[source]

                                                    Alias for field number 2

                                                    @@ -9562,24 +9554,24 @@

                                                    Submodules
                                                    -class MarylandNotation(sigma_iso, omega, kappa)[source]
                                                    +class MarylandNotation(sigma_iso, omega, kappa)[source]

                                                    Bases: NamedTuple

                                                    Create new instance of MarylandNotation(sigma_iso, omega, kappa)

                                                    -kappa: Any[source]
                                                    +kappa: Any[source]

                                                    Alias for field number 2

                                                    -omega: Any[source]
                                                    +omega: Any[source]

                                                    Alias for field number 1

                                                    -sigma_iso: Any[source]
                                                    +sigma_iso: Any[source]

                                                    Alias for field number 0

                                                    @@ -9587,30 +9579,30 @@

                                                    Submodules
                                                    -class MehringNotation(sigma_iso, sigma_11, sigma_22, sigma_33)[source]
                                                    +class MehringNotation(sigma_iso, sigma_11, sigma_22, sigma_33)[source]

                                                    Bases: NamedTuple

                                                    Create new instance of MehringNotation(sigma_iso, sigma_11, sigma_22, sigma_33)

                                                    -sigma_11: Any[source]
                                                    +sigma_11: Any[source]

                                                    Alias for field number 1

                                                    -sigma_22: Any[source]
                                                    +sigma_22: Any[source]

                                                    Alias for field number 2

                                                    -sigma_33: Any[source]
                                                    +sigma_33: Any[source]

                                                    Alias for field number 3

                                                    -sigma_iso: Any[source]
                                                    +sigma_iso: Any[source]

                                                    Alias for field number 0

                                                    @@ -9618,7 +9610,7 @@

                                                    Submodules
                                                    -classmethod from_maryland_notation(sigma_iso, omega, kappa) → Self[source]
                                                    +classmethod from_maryland_notation(sigma_iso, omega, kappa) → Self[source]

                                                    Initialize from Maryland notation.

                                                    Parameters:
                                                    @@ -9636,25 +9628,25 @@

                                                    Submodules
                                                    -property haeberlen_values[source]
                                                    +property haeberlen_values[source]

                                                    The Chemical shielding tensor in Haeberlen Notation.

                                                    -property maryland_values[source]
                                                    +property maryland_values[source]

                                                    The Chemical shielding tensor in Maryland Notation.

                                                    -property mehring_values[source]
                                                    +property mehring_values[source]

                                                    The Chemical shielding tensor in Mehring Notation.

                                                    -property principal_axis_system[source]
                                                    +property principal_axis_system[source]

                                                    A chemical shielding tensor aligned to the principle axis system so that only the 3 diagonal components are non-zero.

                                                    @@ -9663,7 +9655,7 @@

                                                    Submodules
                                                    -class ElectricFieldGradient(efg_matrix, vscale=None)[source]
                                                    +class ElectricFieldGradient(efg_matrix, vscale=None)[source]

                                                    Bases: SquareTensor

                                                    This class extends the SquareTensor to perform extra analysis unique to NMR Electric Field Gradient tensors in units of V/Angstrom^2.

                                                    @@ -9686,31 +9678,31 @@

                                                    Submodules
                                                    -property V_xx[source]
                                                    +property V_xx[source]

                                                    First diagonal element.

                                                    -property V_yy[source]
                                                    +property V_yy[source]

                                                    Second diagonal element.

                                                    -property V_zz[source]
                                                    +property V_zz[source]

                                                    Third diagonal element.

                                                    -property asymmetry[source]
                                                    +property asymmetry[source]

                                                    Asymmetry of the electric field tensor defined as (V_yy - V_xx)/V_zz.

                                                    -coupling_constant(specie)[source]
                                                    +coupling_constant(specie)[source]

                                                    Compute the coupling constant C_q as defined in:

                                                    Wasylishen R E, Ashbrook S E, Wimperis S. NMR of quadrupolar nuclei @@ -9739,7 +9731,7 @@

                                                    Submodules
                                                    -property principal_axis_system[source]
                                                    +property principal_axis_system[source]

                                                    An electric field gradient tensor aligned to the principle axis system so that only the 3 diagonal components are non-zero.

                                                    @@ -9752,7 +9744,7 @@

                                                    Submodules
                                                    -class CompoundPhaseDiagram(entries, terminal_compositions, normalize_terminal_compositions=True)[source]
                                                    +class CompoundPhaseDiagram(entries, terminal_compositions, normalize_terminal_compositions=True)[source]

                                                    Bases: PhaseDiagram

                                                    Generates phase diagrams from compounds as terminations instead of elements.

                                                    @@ -9776,18 +9768,18 @@

                                                    Submodules
                                                    -amount_tol = 1e-05[source]
                                                    +amount_tol = 1e-05[source]

                                                    -as_dict()[source]
                                                    +as_dict()[source]

                                                    Get MSONable dict representation of CompoundPhaseDiagram.

                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                    Parameters:

                                                    dct (dict) – dictionary representation of CompoundPhaseDiagram.

                                                    @@ -9800,7 +9792,7 @@

                                                    Submodules
                                                    -transform_entries(entries, terminal_compositions)[source]
                                                    +transform_entries(entries, terminal_compositions)[source]

                                                    Method to transform all entries to the composition coordinate in the terminal compositions. If the entry does not fall within the space defined by the terminal compositions, they are excluded. For example, @@ -9823,7 +9815,7 @@

                                                    Submodules
                                                    -class GrandPotPDEntry(entry, chempots, name=None)[source]
                                                    +class GrandPotPDEntry(entry, chempots, name=None)[source]

                                                    Bases: PDEntry

                                                    A grand potential pd entry object encompassing all relevant data for phase diagrams. Chemical potentials are given as a element-chemical potential @@ -9840,13 +9832,13 @@

                                                    Submodules
                                                    -as_dict()[source]
                                                    +as_dict()[source]

                                                    Get MSONable dict representation of GrandPotPDEntry.

                                                    -property chemical_energy[source]
                                                    +property chemical_energy[source]

                                                    The chemical energy term mu*N in the grand potential.

                                                    Returns:
                                                    @@ -9857,7 +9849,7 @@

                                                    Submodules
                                                    -property composition: Composition[source]
                                                    +property composition: Composition[source]

                                                    The composition after removing free species.

                                                    Returns:
                                                    @@ -9868,13 +9860,13 @@

                                                    Submodules
                                                    -property energy: float[source]
                                                    +property energy: float[source]

                                                    Grand potential energy.

                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                    Parameters:

                                                    dct (dict) – dictionary representation of GrandPotPDEntry.

                                                    @@ -9889,7 +9881,7 @@

                                                    Submodules
                                                    -class GrandPotentialPhaseDiagram(entries, chempots, elements=None, *, computed_data=None)[source]
                                                    +class GrandPotentialPhaseDiagram(entries, chempots, elements=None, *, computed_data=None)[source]

                                                    Bases: PhaseDiagram

                                                    A class representing a Grand potential phase diagram. Grand potential phase diagrams are essentially phase diagrams that are open to one or more @@ -9928,13 +9920,13 @@

                                                    Submodules
                                                    -as_dict()[source]
                                                    +as_dict()[source]

                                                    Get MSONable dict representation of GrandPotentialPhaseDiagram.

                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                    Parameters:

                                                    dct (dict) – dictionary representation of GrandPotentialPhaseDiagram.

                                                    @@ -9949,12 +9941,12 @@

                                                    Submodules
                                                    -class PDEntry(composition: Composition, energy: float, name: str | None = None, attribute: object = None)[source]
                                                    +class PDEntry(composition: Composition, energy: float, name: str | None = None, attribute: object = None)[source]

                                                    Bases: Entry

                                                    An object encompassing all relevant data for phase diagrams.

                                                    -composition[source]
                                                    +composition[source]

                                                    The composition associated with the PDEntry.

                                                    Type:
                                                    @@ -9965,7 +9957,7 @@

                                                    Submodules
                                                    -energy[source]
                                                    +energy[source]

                                                    The energy associated with the entry.

                                                    Type:
                                                    @@ -9976,7 +9968,7 @@

                                                    Submodules
                                                    -name[source]
                                                    +name[source]

                                                    A name for the entry. This is the string shown in the phase diagrams. By default, this is the reduced formula for the composition, but can be set to some other string for display purposes.

                                                    @@ -9989,7 +9981,7 @@

                                                    Submodules
                                                    -attribute[source]
                                                    +attribute[source]

                                                    A arbitrary attribute. Can be used to specify that the entry is a newly found compound, or to specify a particular label for the entry, etc. An attribute can be anything but must be MSONable.

                                                    @@ -10013,19 +10005,19 @@

                                                    Submodules
                                                    -as_dict()[source]
                                                    +as_dict()[source]

                                                    Get MSONable dict representation of PDEntry.

                                                    -property energy: float[source]
                                                    +property energy: float[source]

                                                    The entry’s energy.

                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                    Parameters:

                                                    dct (dict) – dictionary representation of PDEntry.

                                                    @@ -10040,7 +10032,7 @@

                                                    Submodules
                                                    -class PDPlotter(phasediagram: PhaseDiagram, show_unstable: float = 0.2, backend: Literal['plotly', 'matplotlib'] = 'plotly', ternary_style: Literal['2d', '3d'] = '2d', **plotkwargs)[source]
                                                    +class PDPlotter(phasediagram: PhaseDiagram, show_unstable: float = 0.2, backend: Literal['plotly', 'matplotlib'] = 'plotly', ternary_style: Literal['2d', '3d'] = '2d', **plotkwargs)[source]

                                                    Bases: object

                                                    A plotting class for compositional phase diagrams.

                                                    To use, initialize this class with a PhaseDiagram object containing 1-4 components @@ -10076,7 +10068,7 @@

                                                    Submodules
                                                    -get_chempot_range_map_plot(elements, referenced=True)[source]
                                                    +get_chempot_range_map_plot(elements, referenced=True)[source]

                                                    Get a plot of the chemical potential range _map. Currently works only for 3-component PDs.

                                                    Note: this functionality is now included in the ChemicalPotentialDiagram @@ -10103,7 +10095,7 @@

                                                    Submodules
                                                    -get_contour_pd_plot()[source]
                                                    +get_contour_pd_plot()[source]

                                                    Plot a contour phase diagram plot, where phase triangles are colored according to degree of instability by interpolation. Currently only works for 3-component phase diagrams.

                                                    @@ -10116,7 +10108,7 @@

                                                    Submodules
                                                    -get_plot(label_stable: bool = True, label_unstable: bool = True, ordering: Sequence[str] | None = None, energy_colormap=None, process_attributes: bool = False, ax: plt.Axes = None, label_uncertainties: bool = False, fill: bool = True, highlight_entries: Collection[PDEntry] | None = None) → go.Figure | plt.Axes[source]
                                                    +get_plot(label_stable: bool = True, label_unstable: bool = True, ordering: Sequence[str] | None = None, energy_colormap=None, process_attributes: bool = False, ax: plt.Axes = None, label_uncertainties: bool = False, fill: bool = True, highlight_entries: Collection[PDEntry] | None = None) → go.Figure | plt.Axes[source]
                                                    Parameters:
                                                      @@ -10149,7 +10141,7 @@

                                                      Submodules
                                                      -property pd_plot_data[source]
                                                      +property pd_plot_data[source]

                                                      Plotting data for phase diagram. Cached for repetitive calls.

                                                      2-comp - Full hull with energies 3/4-comp - Projection into 2D or 3D Gibbs triangles

                                                      @@ -10179,7 +10171,7 @@

                                                      Submodules
                                                      -plot_chempot_range_map(elements, referenced=True) → None[source]
                                                      +plot_chempot_range_map(elements, referenced=True) → None[source]

                                                      Plot the chemical potential range _map using matplotlib. Currently works only for 3-component PDs. This shows the plot but does not return it.

                                                      Note: this functionality is now included in the ChemicalPotentialDiagram @@ -10200,7 +10192,7 @@

                                                      Submodules
                                                      -plot_element_profile(element, comp, show_label_index=None, xlim=5)[source]
                                                      +plot_element_profile(element, comp, show_label_index=None, xlim=5)[source]

                                                      Draw the element profile plot for a composition varying different chemical potential of an element.

                                                      X value is the negative value of the chemical potential reference to @@ -10234,7 +10226,7 @@

                                                      Submodules
                                                      -show(*args, **kwargs) → None[source]
                                                      +show(*args, **kwargs) → None[source]

                                                      Draw the phase diagram with the provided arguments and display it. This shows the figure but does not return it.

                                                      @@ -10249,7 +10241,7 @@

                                                      Submodules
                                                      -write_image(stream: str | StringIO, image_format: str = 'svg', **kwargs) → None[source]
                                                      +write_image(stream: str | StringIO, image_format: str = 'svg', **kwargs) → None[source]

                                                      Directly save the plot to a file. This is a wrapper for calling plt.savefig() or fig.write_image(), depending on the backend. For more customization, it is recommended to call those methods directly.

                                                      @@ -10269,7 +10261,7 @@

                                                      Submodules
                                                      -class PatchedPhaseDiagram(entries: Sequence[PDEntry] | set[PDEntry], elements: Sequence[Element] | None = None, keep_all_spaces: bool = False, verbose: bool = False)[source]
                                                      +class PatchedPhaseDiagram(entries: Sequence[PDEntry] | set[PDEntry], elements: Sequence[Element] | None = None, keep_all_spaces: bool = False, verbose: bool = False)[source]

                                                      Bases: PhaseDiagram

                                                      Computing the Convex Hull of a large set of data in multiple dimensions is highly expensive. This class acts to breakdown large chemical spaces into @@ -10291,7 +10283,7 @@

                                                      Submodules
                                                      -all_entries[source]
                                                      +all_entries[source]

                                                      All entries provided for Phase Diagram construction. Note that this does not mean that all these entries are actually used in the phase diagram. For example, this includes the positive formation energy @@ -10305,7 +10297,7 @@

                                                      Submodules
                                                      -min_entries[source]
                                                      +min_entries[source]

                                                      List of the lowest energy entries for each composition in the data provided for Phase Diagram construction.

                                                      @@ -10317,7 +10309,7 @@

                                                      Submodules
                                                      -el_refs[source]
                                                      +el_refs[source]

                                                      List of elemental references for the phase diagrams. These are entries corresponding to the lowest energy element entries for simple compositional phase diagrams.

                                                      @@ -10330,7 +10322,7 @@

                                                      Submodules
                                                      -elements[source]
                                                      +elements[source]

                                                      List of elements in the phase diagram.

                                                      Type:
                                                      @@ -10357,7 +10349,7 @@

                                                      Submodules
                                                      -as_dict() → dict[str, Any][source]
                                                      +as_dict() → dict[str, Any][source]
                                                      Returns:

                                                      MSONable dictionary representation of PatchedPhaseDiagram.

                                                      @@ -10370,7 +10362,7 @@

                                                      Submodules
                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                      Parameters:

                                                      dct (dict) – dictionary representation of PatchedPhaseDiagram.

                                                      @@ -10383,44 +10375,44 @@

                                                      Submodules
                                                      -get_all_chempots()[source]
                                                      +get_all_chempots()[source]

                                                      Not Implemented - See PhaseDiagram.

                                                      -get_chempot_range_map()[source]
                                                      +get_chempot_range_map()[source]

                                                      Not Implemented - See PhaseDiagram.

                                                      -get_chempot_range_stability_phase()[source]
                                                      +get_chempot_range_stability_phase()[source]

                                                      Not Implemented - See PhaseDiagram.

                                                      -get_composition_chempots()[source]
                                                      +get_composition_chempots()[source]

                                                      Not Implemented - See PhaseDiagram.

                                                      -get_critical_compositions()[source]
                                                      +get_critical_compositions()[source]

                                                      Not Implemented - See PhaseDiagram.

                                                      -get_decomp_and_e_above_hull(entry: PDEntry, allow_negative: bool = False, check_stable: bool = False, on_error: Literal['raise', 'warn', 'ignore'] = 'raise') → tuple[dict[PDEntry, float], float] | tuple[None, None][source]
                                                      +get_decomp_and_e_above_hull(entry: PDEntry, allow_negative: bool = False, check_stable: bool = False, on_error: Literal['raise', 'warn', 'ignore'] = 'raise') → tuple[dict[PDEntry, float], float] | tuple[None, None][source]

                                                      Same as method on parent class PhaseDiagram except check_stable defaults to False for speed. See https://github.com/materialsproject/pymatgen/issues/2840 for details.

                                                      -get_decomposition(comp: Composition) → dict[PDEntry, float][source]
                                                      +get_decomposition(comp: Composition) → dict[PDEntry, float][source]

                                                      See PhaseDiagram.

                                                      Parameters:
                                                      @@ -10438,13 +10430,13 @@

                                                      Submodules
                                                      -get_element_profile()[source]
                                                      +get_element_profile()[source]

                                                      Not Implemented - See PhaseDiagram.

                                                      -get_equilibrium_reaction_energy(entry: Entry) → float[source]
                                                      +get_equilibrium_reaction_energy(entry: Entry) → float[source]

                                                      See PhaseDiagram.

                                                      NOTE this is only approximately the same as the what we would get from PhaseDiagram as we make use of the slsqp approach inside @@ -10462,7 +10454,7 @@

                                                      Submodules
                                                      -get_pd_for_entry(entry: Entry | Composition) → PhaseDiagram[source]
                                                      +get_pd_for_entry(entry: Entry | Composition) → PhaseDiagram[source]

                                                      Get the possible phase diagrams for an entry.

                                                      Parameters:
                                                      @@ -10482,13 +10474,13 @@

                                                      Submodules
                                                      -get_transition_chempots()[source]
                                                      +get_transition_chempots()[source]

                                                      Not Implemented - See PhaseDiagram.

                                                      -getmu_vertices_stability_phase()[source]
                                                      +getmu_vertices_stability_phase()[source]

                                                      Not Implemented - See PhaseDiagram.

                                                      @@ -10496,7 +10488,7 @@

                                                      Submodules
                                                      -class PhaseDiagram(entries: Sequence[PDEntry] | set[PDEntry], elements: Sequence[Element] = (), *, computed_data: dict[str, Any] | None = None)[source]
                                                      +class PhaseDiagram(entries: Sequence[PDEntry] | set[PDEntry], elements: Sequence[Element] = (), *, computed_data: dict[str, Any] | None = None)[source]

                                                      Bases: MSONable

                                                      Simple phase diagram class taking in elements and entries as inputs. The algorithm is based on the work in the following papers:

                                                      @@ -10527,7 +10519,7 @@

                                                      Submodules
                                                      -dim[source]
                                                      +dim[source]

                                                      The dimensionality of the phase diagram.

                                                      Type:
                                                      @@ -10538,13 +10530,13 @@

                                                      Submodules
                                                      -elements[source]
                                                      +elements[source]

                                                      Elements in the phase diagram.

                                                      -el_refs[source]
                                                      +el_refs[source]

                                                      List of elemental references for the phase diagrams. These are entries corresponding to the lowest energy element entries for simple compositional phase diagrams.

                                                      @@ -10552,7 +10544,7 @@

                                                      Submodules
                                                      -all_entries[source]
                                                      +all_entries[source]

                                                      All entries provided for Phase Diagram construction. Note that this does not mean that all these entries are actually used in the phase diagram. For example, this includes the positive formation energy @@ -10561,21 +10553,21 @@

                                                      Submodules
                                                      -qhull_entries[source]
                                                      +qhull_entries[source]

                                                      Actual entries used in convex hull. Excludes all positive formation energy entries.

                                                      -qhull_data[source]
                                                      +qhull_data[source]

                                                      Data used in the convex hull operation. This is essentially a matrix of composition data and energy per atom values created from qhull_entries.

                                                      -facets[source]
                                                      +facets[source]

                                                      Facets of the phase diagram in the form of [[1,2,3],[4,5,6]…]. For a ternary, it is the indices (references to qhull_entries and qhull_data) for the vertices of the phase triangles. Similarly @@ -10584,7 +10576,7 @@

                                                      Submodules
                                                      -simplices[source]
                                                      +simplices[source]

                                                      The simplices of the phase diagram as a list of np.ndarray, i.e., the list of stable compositional coordinates in the phase diagram.

                                                      @@ -10609,24 +10601,24 @@

                                                      Submodules
                                                      -property all_entries_hulldata[source]
                                                      +property all_entries_hulldata[source]

                                                      The ndarray used to construct the convex hull.

                                                      -as_dict()[source]
                                                      +as_dict()[source]

                                                      Get MSONable dict representation of PhaseDiagram.

                                                      -formation_energy_tol = 1e-11[source]
                                                      +formation_energy_tol = 1e-11[source]
                                                      -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                      +classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                      Parameters:

                                                      dct (dict) – dictionary representation of PhaseDiagram.

                                                      @@ -10639,7 +10631,7 @@

                                                      Submodules
                                                      -get_all_chempots(comp)[source]
                                                      +get_all_chempots(comp)[source]

                                                      Get chemical potentials at a given composition.

                                                      Parameters:
                                                      @@ -10653,7 +10645,7 @@

                                                      Submodules
                                                      -get_chempot_range_map(elements: Sequence[Element], referenced: bool = True, joggle: bool = True) → dict[Element, list[Simplex]][source]
                                                      +get_chempot_range_map(elements: Sequence[Element], referenced: bool = True, joggle: bool = True) → dict[Element, list[Simplex]][source]

                                                      Get a chemical potential range map for each stable entry.

                                                      Parameters:
                                                      @@ -10681,7 +10673,7 @@

                                                      Submodules
                                                      -get_chempot_range_stability_phase(target_comp, open_elt)[source]
                                                      +get_chempot_range_stability_phase(target_comp, open_elt)[source]

                                                      Get a set of chemical potentials corresponding to the max and min chemical potential of the open element for a given composition. It is quite common to have for instance a ternary oxide (e.g., ABO3) for @@ -10708,7 +10700,7 @@

                                                      Submodules
                                                      -get_composition_chempots(comp)[source]
                                                      +get_composition_chempots(comp)[source]

                                                      Get the chemical potentials for all elements at a given composition.

                                                      Parameters:
                                                      @@ -10722,7 +10714,7 @@

                                                      Submodules
                                                      -get_critical_compositions(comp1, comp2)[source]
                                                      +get_critical_compositions(comp1, comp2)[source]

                                                      Get the critical compositions along the tieline between two compositions. I.e. where the decomposition products change. The endpoints are also returned.

                                                      @@ -10748,7 +10740,7 @@

                                                      Submodules
                                                      -get_decomp_and_e_above_hull(entry: PDEntry, allow_negative: bool = False, check_stable: bool = True, on_error: Literal['raise', 'warn', 'ignore'] = 'raise') → tuple[dict[PDEntry, float], float] | tuple[None, None][source]
                                                      +get_decomp_and_e_above_hull(entry: PDEntry, allow_negative: bool = False, check_stable: bool = True, on_error: Literal['raise', 'warn', 'ignore'] = 'raise') → tuple[dict[PDEntry, float], float] | tuple[None, None][source]

                                                      Provides the decomposition and energy above convex hull for an entry. Due to caching, can be much faster if entries with the same composition are processed together.

                                                      @@ -10789,7 +10781,7 @@

                                                      Submodules
                                                      -get_decomp_and_hull_energy_per_atom(comp: Composition) → tuple[dict[PDEntry, float], float][source]
                                                      +get_decomp_and_hull_energy_per_atom(comp: Composition) → tuple[dict[PDEntry, float], float][source]
                                                      Parameters:

                                                      comp (Composition) – Input composition.

                                                      @@ -10802,7 +10794,7 @@

                                                      Submodules
                                                      -get_decomp_and_phase_separation_energy(entry: PDEntry, space_limit: int = 200, stable_only: bool = False, tols: Sequence[float] = (1e-08,), maxiter: int = 1000, **kwargs: Any) → tuple[dict[PDEntry, float], float] | tuple[None, None][source]
                                                      +get_decomp_and_phase_separation_energy(entry: PDEntry, space_limit: int = 200, stable_only: bool = False, tols: Sequence[float] = (1e-08,), maxiter: int = 1000, **kwargs: Any) → tuple[dict[PDEntry, float], float] | tuple[None, None][source]

                                                      Provides the combination of entries in the PhaseDiagram that gives the lowest formation enthalpy with the same composition as the given entry excluding entries with the same composition and the energy difference @@ -10858,7 +10850,7 @@

                                                      Submodules
                                                      -get_decomposition(comp: Composition) → dict[PDEntry, float][source]
                                                      +get_decomposition(comp: Composition) → dict[PDEntry, float][source]

                                                      Provides the decomposition at a particular composition.

                                                      Parameters:
                                                      @@ -10876,7 +10868,7 @@

                                                      Submodules
                                                      -get_e_above_hull(entry: PDEntry, **kwargs: Any) → float | None[source]
                                                      +get_e_above_hull(entry: PDEntry, **kwargs: Any) → float | None[source]

                                                      Provides the energy above convex hull for an entry.

                                                      Parameters:
                                                      @@ -10900,7 +10892,7 @@

                                                      Submodules
                                                      -get_element_profile(element, comp, comp_tol=1e-05)[source]
                                                      +get_element_profile(element, comp, comp_tol=1e-05)[source]

                                                      Provides the element evolution data for a composition. For example, can be used to analyze Li conversion voltages by varying mu_Li and looking at the phases formed. Also can be used to analyze O2 evolution by varying mu_O2.

                                                      @@ -10926,7 +10918,7 @@

                                                      Submodules
                                                      -get_equilibrium_reaction_energy(entry: PDEntry) → float | None[source]
                                                      +get_equilibrium_reaction_energy(entry: PDEntry) → float | None[source]

                                                      Provides the reaction energy of a stable entry from the neighboring equilibrium stable entries (also known as the inverse distance to hull).

                                                      @@ -10949,7 +10941,7 @@

                                                      Submodules
                                                      -get_form_energy(entry: PDEntry) → float[source]
                                                      +get_form_energy(entry: PDEntry) → float[source]

                                                      Get the formation energy for an entry (NOT normalized) from the elemental references.

                                                      @@ -10967,7 +10959,7 @@

                                                      Submodules
                                                      -get_form_energy_per_atom(entry: PDEntry) → float[source]
                                                      +get_form_energy_per_atom(entry: PDEntry) → float[source]

                                                      Get the formation energy per atom for an entry from the elemental references.

                                                      @@ -10982,7 +10974,7 @@

                                                      Submodules
                                                      -get_hull_energy(comp: Composition) → float[source]
                                                      +get_hull_energy(comp: Composition) → float[source]
                                                      Parameters:

                                                      comp (Composition) – Input composition.

                                                      @@ -10999,7 +10991,7 @@

                                                      Submodules
                                                      -get_hull_energy_per_atom(comp: Composition, **kwargs) → float[source]
                                                      +get_hull_energy_per_atom(comp: Composition, **kwargs) → float[source]
                                                      Parameters:

                                                      comp (Composition) – Input composition.

                                                      @@ -11012,7 +11004,7 @@

                                                      Submodules
                                                      -get_phase_separation_energy(entry, **kwargs)[source]
                                                      +get_phase_separation_energy(entry, **kwargs)[source]

                                                      Provides the energy to the convex hull for the given entry. For stable entries already in the phase diagram the algorithm provides the phase separation energy which is referred to as the decomposition enthalpy in:

                                                      @@ -11054,7 +11046,7 @@

                                                      Submodules
                                                      -get_plot(show_unstable: float = 0.2, backend: Literal['plotly', 'matplotlib'] = 'plotly', ternary_style: Literal['2d', '3d'] = '2d', label_stable: bool = True, label_unstable: bool = True, ordering: Sequence[str] | None = None, energy_colormap=None, process_attributes: bool = False, ax: plt.Axes = None, label_uncertainties: bool = False, fill: bool = True, **kwargs)[source]
                                                      +get_plot(show_unstable: float = 0.2, backend: Literal['plotly', 'matplotlib'] = 'plotly', ternary_style: Literal['2d', '3d'] = '2d', label_stable: bool = True, label_unstable: bool = True, ordering: Sequence[str] | None = None, energy_colormap=None, process_attributes: bool = False, ax: plt.Axes = None, label_uncertainties: bool = False, fill: bool = True, **kwargs)[source]

                                                      Convenient wrapper for PDPlotter. Initializes a PDPlotter object and calls get_plot() with provided combined arguments.

                                                      Plotting is only supported for phase diagrams with <=4 elements (unary, @@ -11093,7 +11085,7 @@

                                                      Submodules
                                                      -get_reference_energy(comp: Composition) → float[source]
                                                      +get_reference_energy(comp: Composition) → float[source]

                                                      Sum of elemental reference energies over all elements in a composition.

                                                      Parameters:
                                                      @@ -11110,7 +11102,7 @@

                                                      Submodules
                                                      -get_reference_energy_per_atom(comp: Composition) → float[source]
                                                      +get_reference_energy_per_atom(comp: Composition) → float[source]

                                                      Sum of elemental reference energies over all elements in a composition.

                                                      Parameters:
                                                      @@ -11127,7 +11119,7 @@

                                                      Submodules
                                                      -get_transition_chempots(element)[source]
                                                      +get_transition_chempots(element)[source]

                                                      Get the critical chemical potentials for an element in the Phase Diagram.

                                                      @@ -11143,7 +11135,7 @@

                                                      Submodules
                                                      -getmu_vertices_stability_phase(target_comp, dep_elt, tol_en=0.01)[source]
                                                      +getmu_vertices_stability_phase(target_comp, dep_elt, tol_en=0.01)[source]

                                                      Get a set of chemical potentials corresponding to the vertices of the simplex in the chemical potential phase diagram. The simplex is built using all elements in the target_composition @@ -11174,12 +11166,12 @@

                                                      Submodules
                                                      -numerical_tol = 1e-08[source]
                                                      +numerical_tol = 1e-08[source]

                                                      -pd_coords(comp: Composition) → ndarray[source]
                                                      +pd_coords(comp: Composition) → ndarray[source]

                                                      The phase diagram is generated in a reduced dimensional space (n_elements - 1). This function returns the coordinates in that space. These coordinates are compatible with the stored simplex objects.

                                                      @@ -11195,14 +11187,14 @@

                                                      Submodules
                                                      -property stable_entries: set[Entry][source]
                                                      +property stable_entries: set[Entry][source]

                                                      Returns: set[Entry]: of stable entries in the phase diagram.

                                                      -property unstable_entries: set[Entry][source]
                                                      +property unstable_entries: set[Entry][source]

                                                      Returns: set[Entry]: unstable entries in the phase diagram. Includes positive formation energy entries.

                                                      @@ -11211,14 +11203,14 @@

                                                      Submodules
                                                      -exception PhaseDiagramError[source]
                                                      +exception PhaseDiagramError[source]

                                                      Bases: Exception

                                                      An exception class for Phase Diagram generation.

                                                      -class ReactionDiagram(entry1, entry2, all_entries, tol: float = 0.0001, float_fmt='%.4f')[source]
                                                      +class ReactionDiagram(entry1, entry2, all_entries, tol: float = 0.0001, float_fmt='%.4f')[source]

                                                      Bases: object

                                                      Analyzes the possible reactions between a pair of compounds, e.g. an electrolyte and an electrode.

                                                      @@ -11246,7 +11238,7 @@

                                                      Submodules
                                                      -get_compound_pd()[source]
                                                      +get_compound_pd()[source]

                                                      Get the CompoundPhaseDiagram object, which can then be used for plotting.

                                                      @@ -11260,7 +11252,7 @@

                                                      Submodules
                                                      -class TransformedPDEntry(entry, sp_mapping, name=None)[source]
                                                      +class TransformedPDEntry(entry, sp_mapping, name=None)[source]

                                                      Bases: PDEntry

                                                      This class represents a TransformedPDEntry, which allows for a PDEntry to be transformed to a different composition coordinate space. It is used in the @@ -11276,18 +11268,18 @@

                                                      Submodules
                                                      -amount_tol = 1e-05[source]
                                                      +amount_tol = 1e-05[source]

                                                      -as_dict()[source]
                                                      +as_dict()[source]

                                                      Get MSONable dict representation of TransformedPDEntry.

                                                      -property composition: Composition[source]
                                                      +property composition: Composition[source]

                                                      The composition in the dummy species space.

                                                      Returns:
                                                      @@ -11298,7 +11290,7 @@

                                                      Submodules
                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                      Parameters:

                                                      dct (dict) – dictionary representation of TransformedPDEntry.

                                                      @@ -11313,14 +11305,14 @@

                                                      Submodules
                                                      -exception TransformedPDEntryError[source]
                                                      +exception TransformedPDEntryError[source]

                                                      Bases: Exception

                                                      An exception class for TransformedPDEntry.

                                                      -get_facets(qhull_data: ArrayLike, joggle: bool = False) → ConvexHull[source]
                                                      +get_facets(qhull_data: ArrayLike, joggle: bool = False) → ConvexHull[source]

                                                      Get the simplex facets for the Convex hull.

                                                      Parameters:
                                                      @@ -11343,7 +11335,7 @@

                                                      Submodules
                                                      -order_phase_diagram(lines, stable_entries, unstable_entries, ordering)[source]
                                                      +order_phase_diagram(lines, stable_entries, unstable_entries, ordering)[source]

                                                      Orders the entries (their coordinates) in a phase diagram plot according to the user specified ordering. Ordering should be given as [‘Up’, ‘Left’, ‘Right’], where Up, @@ -11380,7 +11372,7 @@

                                                      Submodules
                                                      -tet_coord(coord)[source]
                                                      +tet_coord(coord)[source]

                                                      Convert a 3D coordinate into a tetrahedron based coordinate system for a prettier phase diagram.

                                                      @@ -11395,7 +11387,7 @@

                                                      Submodules
                                                      -triangular_coord(coord)[source]
                                                      +triangular_coord(coord)[source]

                                                      Convert a 2D coordinate into a triangle-based coordinate system for a prettier phase diagram.

                                                      @@ -11410,7 +11402,7 @@

                                                      Submodules
                                                      -uniquelines(q)[source]
                                                      +uniquelines(q)[source]

                                                      Given all the facets, convert it into a set of unique lines. Specifically used for converting convex hull facets into line pairs of coordinates.

                                                      @@ -11433,7 +11425,7 @@

                                                      Submodules
                                                      -class PiezoTensor(input_array: ArrayLike, tol: float = 0.001)[source]
                                                      +class PiezoTensor(input_array: ArrayLike, tol: float = 0.001)[source]

                                                      Bases: Tensor

                                                      This class describes the 3x6 piezo tensor in Voigt notation.

                                                      Create an PiezoTensor object. The constructor throws an error if @@ -11449,7 +11441,7 @@

                                                      Submodules
                                                      -classmethod from_vasp_voigt(input_vasp_array: ArrayLike) → Self[source]
                                                      +classmethod from_vasp_voigt(input_vasp_array: ArrayLike) → Self[source]
                                                      Parameters:

                                                      input_vasp_array (nd.array) – Voigt form of tensor.

                                                      @@ -11468,7 +11460,7 @@

                                                      Submodules
                                                      -class BornEffectiveCharge(structure: Structure, bec, pointops, tol: float = 0.001)[source]
                                                      +class BornEffectiveCharge(structure: Structure, bec, pointops, tol: float = 0.001)[source]

                                                      Bases: object

                                                      This class describes the Nx3x3 born effective charge tensor.

                                                      Create an BornEffectiveChargeTensor object defined by a @@ -11483,7 +11475,7 @@

                                                      Submodules
                                                      -get_BEC_operations(eigtol=1e-05, opstol=0.001)[source]
                                                      +get_BEC_operations(eigtol=1e-05, opstol=0.001)[source]

                                                      Get the symmetry operations which maps the tensors belonging to equivalent sites onto each other in the form [site index 1, site index 2, [Symmops mapping from site @@ -11506,7 +11498,7 @@

                                                      Submodules
                                                      -get_rand_BEC(max_charge=1)[source]
                                                      +get_rand_BEC(max_charge=1)[source]

                                                      Generate a random born effective charge tensor which obeys a structure’s symmetry and the acoustic sum rule.

                                                      @@ -11523,7 +11515,7 @@

                                                      Submodules
                                                      -class ForceConstantMatrix(structure: Structure, fcm, pointops, sharedops, tol: float = 0.001)[source]
                                                      +class ForceConstantMatrix(structure: Structure, fcm, pointops, sharedops, tol: float = 0.001)[source]

                                                      Bases: object

                                                      This class describes the NxNx3x3 force constant matrix defined by a structure, point operations of the structure’s atomic sites, and the @@ -11537,7 +11529,7 @@

                                                      Submodules
                                                      -get_FCM_operations(eigtol=1e-05, opstol=1e-05)[source]
                                                      +get_FCM_operations(eigtol=1e-05, opstol=1e-05)[source]

                                                      Get the symmetry operations which maps the tensors belonging to equivalent sites onto each other in the form [site index 1a, site index 1b, site index 2a, site index 2b, @@ -11560,7 +11552,7 @@

                                                      Submodules
                                                      -get_asum_FCM(fcm: ndarray, numiter: int = 15)[source]
                                                      +get_asum_FCM(fcm: ndarray, numiter: int = 15)[source]

                                                      Generate a symmetrized force constant matrix that obeys the objects symmetry constraints and obeys the acoustic sum rule through an iterative procedure.

                                                      @@ -11579,7 +11571,7 @@

                                                      Submodules
                                                      -get_rand_FCM(asum=15, force=10)[source]
                                                      +get_rand_FCM(asum=15, force=10)[source]

                                                      Generate a symmetrized force constant matrix from an unsymmetrized matrix that has no unstable modes and also obeys the acoustic sum rule through an iterative procedure.

                                                      @@ -11599,7 +11591,7 @@

                                                      Submodules
                                                      -get_stable_FCM(fcm, fcmasum=10)[source]
                                                      +get_stable_FCM(fcm, fcmasum=10)[source]

                                                      Generate a symmetrized force constant matrix that obeys the objects symmetry constraints, has no unstable modes and also obeys the acoustic sum rule through an iterative procedure.

                                                      @@ -11619,7 +11611,7 @@

                                                      Submodules
                                                      -get_symmetrized_FCM(unsymmetrized_fcm, max_force=1)[source]
                                                      +get_symmetrized_FCM(unsymmetrized_fcm, max_force=1)[source]

                                                      Generate a symmetrized force constant matrix from an unsymmetrized matrix.

                                                      Parameters:
                                                      @@ -11636,7 +11628,7 @@

                                                      Submodules
                                                      -get_unstable_FCM(max_force=1)[source]
                                                      +get_unstable_FCM(max_force=1)[source]

                                                      Generate an unsymmetrized force constant matrix.

                                                      Parameters:
                                                      @@ -11652,7 +11644,7 @@

                                                      Submodules
                                                      -class InternalStrainTensor(structure: Structure, ist, pointops, tol: float = 0.001)[source]
                                                      +class InternalStrainTensor(structure: Structure, ist, pointops, tol: float = 0.001)[source]

                                                      Bases: object

                                                      This class describes the Nx3x3x3 internal tensor defined by a structure, point operations of the structure’s atomic sites.

                                                      @@ -11665,7 +11657,7 @@

                                                      Submodules
                                                      -get_IST_operations(opstol=0.001)[source]
                                                      +get_IST_operations(opstol=0.001)[source]

                                                      Get the symmetry operations which maps the tensors belonging to equivalent sites onto each other in the form [site index 1, site index 2, [Symmops mapping from site @@ -11686,7 +11678,7 @@

                                                      Submodules
                                                      -get_rand_IST(max_force=1)[source]
                                                      +get_rand_IST(max_force=1)[source]

                                                      Generate a random internal strain tensor which obeys a structure’s symmetry and the acoustic sum rule.

                                                      @@ -11703,7 +11695,7 @@

                                                      Submodules
                                                      -get_piezo(BEC, IST, FCM, rcond=0.0001)[source]
                                                      +get_piezo(BEC, IST, FCM, rcond=0.0001)[source]

                                                      Generate a random piezoelectric tensor based on a structure and corresponding symmetry.

                                                      @@ -11723,7 +11715,7 @@

                                                      Submodules
                                                      -rand_piezo(struct, pointops, sharedops, BEC, IST, FCM, anumiter=10)[source]
                                                      +rand_piezo(struct, pointops, sharedops, BEC, IST, FCM, anumiter=10)[source]

                                                      Generate a random piezoelectric tensor based on a structure and corresponding symmetry.

                                                      @@ -11752,13 +11744,13 @@

                                                      Submodules
                                                      -class IonEntry(ion: Ion, energy: float, name: str | None = None, attribute=None)[source]
                                                      +class IonEntry(ion: Ion, energy: float, name: str | None = None, attribute=None)[source]

                                                      Bases: PDEntry

                                                      Object similar to PDEntry, but contains an Ion object instead of a Composition object.

                                                      -name[source]
                                                      +name[source]

                                                      A name for the entry. This is the string shown in the phase diagrams. By default, this is the reduced formula for the composition, but can be set to some other string for display purposes.

                                                      @@ -11782,13 +11774,13 @@

                                                      Submodules
                                                      -as_dict()[source]
                                                      +as_dict()[source]

                                                      Create a dict of composition, energy, and ion name.

                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                      +classmethod from_dict(dct: dict) → Self[source]

                                                      Get an IonEntry object from a dict.

                                                      @@ -11796,7 +11788,7 @@

                                                      Submodules
                                                      -class MultiEntry(entry_list, weights=None)[source]
                                                      +class MultiEntry(entry_list, weights=None)[source]

                                                      Bases: PourbaixEntry

                                                      PourbaixEntry-like object for constructing multi-elemental Pourbaix diagrams.

                                                      Initialize a MultiEntry.

                                                      @@ -11810,13 +11802,13 @@

                                                      Submodules
                                                      -as_dict()[source]
                                                      +as_dict()[source]

                                                      Get MSONable dict.

                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                      Parameters:

                                                      dct (dict) – Dict representation.

                                                      @@ -11829,7 +11821,7 @@

                                                      Submodules
                                                      -property name[source]
                                                      +property name[source]

                                                      MultiEntry name, i. e. the name of each entry joined by ‘ + ‘.

                                                      @@ -11837,7 +11829,7 @@

                                                      Submodules
                                                      -class PourbaixDiagram(entries: list[PourbaixEntry] | list[MultiEntry], comp_dict: dict[str, float] | None = None, conc_dict: dict[str, float] | None = None, filter_solids: bool = True, nproc: int | None = None)[source]
                                                      +class PourbaixDiagram(entries: list[PourbaixEntry] | list[MultiEntry], comp_dict: dict[str, float] | None = None, conc_dict: dict[str, float] | None = None, filter_solids: bool = True, nproc: int | None = None)[source]

                                                      Bases: MSONable

                                                      Create a Pourbaix diagram from entries.

                                                      @@ -11865,19 +11857,19 @@

                                                      Submodules
                                                      -property all_entries[source]
                                                      +property all_entries[source]

                                                      All entries used to generate the Pourbaix diagram.

                                                      -as_dict()[source]
                                                      +as_dict()[source]

                                                      Get MSONable dict.

                                                      -find_stable_entry(pH, V)[source]
                                                      +find_stable_entry(pH, V)[source]

                                                      Find stable entry at a pH,V condition

                                                      Parameters:
                                                      @@ -11897,7 +11889,7 @@

                                                      Submodules
                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                      Parameters:

                                                      dct (dict) – Dict representation.

                                                      @@ -11910,7 +11902,7 @@

                                                      Submodules
                                                      -get_decomposition_energy(entry, pH, V)[source]
                                                      +get_decomposition_energy(entry, pH, V)[source]

                                                      Find decomposition to most stable entries in eV/atom, supports vectorized inputs for pH and V.

                                                      @@ -11934,7 +11926,7 @@

                                                      Submodules
                                                      -get_hull_energy(pH, V)[source]
                                                      +get_hull_energy(pH, V)[source]

                                                      Get the minimum energy of the Pourbaix “basin” that is formed from the stable Pourbaix planes. Vectorized.

                                                      @@ -11955,7 +11947,7 @@

                                                      Submodules
                                                      -static get_pourbaix_domains(pourbaix_entries, limits=None)[source]
                                                      +static get_pourbaix_domains(pourbaix_entries, limits=None)[source]

                                                      Get a set of Pourbaix stable domains (i. e. polygons) in pH-V space from a list of pourbaix_entries.

                                                      This function works by using scipy’s HalfspaceIntersection @@ -11988,7 +11980,7 @@

                                                      Submodules
                                                      -get_stable_entry(pH, V)[source]
                                                      +get_stable_entry(pH, V)[source]

                                                      Get the stable entry at a given pH, V condition.

                                                      Parameters:
                                                      @@ -12012,7 +12004,7 @@

                                                      Submodules
                                                      -static process_multientry(entry_list, prod_comp, coeff_threshold=0.0001)[source]
                                                      +static process_multientry(entry_list, prod_comp, coeff_threshold=0.0001)[source]

                                                      Static method for finding a multientry based on a list of entries and a product composition. Essentially checks to see if a valid aqueous @@ -12036,19 +12028,19 @@

                                                      Submodules
                                                      -property stable_entries[source]
                                                      +property stable_entries[source]

                                                      The stable entries in the Pourbaix diagram.

                                                      -property unprocessed_entries[source]
                                                      +property unprocessed_entries[source]

                                                      Unprocessed entries.

                                                      -property unstable_entries[source]
                                                      +property unstable_entries[source]

                                                      All unstable entries in the Pourbaix diagram.

                                                      @@ -12056,7 +12048,7 @@

                                                      Submodules
                                                      -class PourbaixEntry(entry, entry_id=None, concentration=1e-06)[source]
                                                      +class PourbaixEntry(entry, entry_id=None, concentration=1e-06)[source]

                                                      Bases: MSONable, Stringify

                                                      An object encompassing all data relevant to a solid or ion in a Pourbaix diagram. Each bulk solid/ion has an energy @@ -12078,7 +12070,7 @@

                                                      Submodules
                                                      -as_dict()[source]
                                                      +as_dict()[source]

                                                      Get dict which contains Pourbaix Entry data. Note that the pH, voltage, H2O factors are always calculated when constructing a PourbaixEntry object.

                                                      @@ -12086,32 +12078,32 @@

                                                      Submodules
                                                      -property composition[source]
                                                      +property composition[source]

                                                      Composition.

                                                      -property conc_term[source]
                                                      +property conc_term[source]

                                                      The concentration contribution to the free energy. Should only be present when there are ions in the entry.

                                                      -property elements[source]
                                                      +property elements[source]

                                                      Elements in the entry.

                                                      -property energy[source]
                                                      +property energy[source]

                                                      Total energy of the Pourbaix entry (at pH, V = 0 vs. SHE).

                                                      -energy_at_conditions(pH, V)[source]
                                                      +energy_at_conditions(pH, V)[source]

                                                      Get free energy for a given pH and V.

                                                      Parameters:
                                                      @@ -12128,19 +12120,19 @@

                                                      Submodules
                                                      -property energy_per_atom[source]
                                                      +property energy_per_atom[source]

                                                      Energy per atom of the Pourbaix entry.

                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                      +classmethod from_dict(dct: dict) → Self[source]

                                                      Invokes a PourbaixEntry from a dictionary.

                                                      -get_element_fraction(element)[source]
                                                      +get_element_fraction(element)[source]

                                                      Get the elemental fraction of a given non-OH element.

                                                      Parameters:
                                                      @@ -12155,38 +12147,38 @@

                                                      Submodules
                                                      -property nH2O[source]
                                                      +property nH2O[source]

                                                      The number of H2O.

                                                      -property nPhi[source]
                                                      +property nPhi[source]

                                                      The number of electrons.

                                                      -property name[source]
                                                      +property name[source]

                                                      The entry’s name.

                                                      -property normalization_factor[source]
                                                      +property normalization_factor[source]

                                                      Sum of number of atoms minus the number of H and O in composition.

                                                      -property normalized_energy[source]
                                                      +property normalized_energy[source]

                                                      Energy normalized by number of non H or O atoms, e.g. for Zn2O6, energy / 2 or for AgTe3(OH)3, energy / 4.

                                                      -normalized_energy_at_conditions(pH, V)[source]
                                                      +normalized_energy_at_conditions(pH, V)[source]

                                                      Energy at an electrochemical condition, compatible with numpy arrays for pH/V input.

                                                      @@ -12204,19 +12196,19 @@

                                                      Submodules
                                                      -property npH[source]
                                                      +property npH[source]

                                                      The number of H.

                                                      -property num_atoms[source]
                                                      +property num_atoms[source]

                                                      Number of atoms in current formula. Useful for normalization.

                                                      -to_pretty_string() → str[source]
                                                      +to_pretty_string() → str[source]

                                                      A pretty string representation.

                                                      @@ -12224,7 +12216,7 @@

                                                      Submodules
                                                      -class PourbaixPlotter(pourbaix_diagram)[source]
                                                      +class PourbaixPlotter(pourbaix_diagram)[source]

                                                      Bases: object

                                                      A plotter class for phase diagrams.

                                                      @@ -12234,7 +12226,7 @@

                                                      Submodules
                                                      -domain_vertices(entry)[source]
                                                      +domain_vertices(entry)[source]

                                                      Get the vertices of the Pourbaix domain.

                                                      Parameters:
                                                      @@ -12248,7 +12240,7 @@

                                                      Submodules
                                                      -get_pourbaix_plot(limits: tuple[float, float] | None = None, title: str = '', label_domains: bool = True, label_fontsize: int = 20, show_water_lines: bool = True, show_neutral_axes: bool = True, ax: plt.Axes = None) → plt.Axes[source]
                                                      +get_pourbaix_plot(limits: tuple[float, float] | None = None, title: str = '', label_domains: bool = True, label_fontsize: int = 20, show_water_lines: bool = True, show_neutral_axes: bool = True, ax: plt.Axes = None) → plt.Axes[source]

                                                      Plot Pourbaix diagram.

                                                      Parameters:
                                                      @@ -12275,7 +12267,7 @@

                                                      Submodules
                                                      -plot_entry_stability(entry: Any, pH_range: tuple[float, float] = (-2, 16), pH_resolution: int = 100, V_range: tuple[float, float] = (-3, 3), V_resolution: int = 100, e_hull_max: float = 1, cmap: str = 'RdYlBu_r', ax: plt.Axes | None = None, **kwargs: Any) → plt.Axes[source]
                                                      +plot_entry_stability(entry: Any, pH_range: tuple[float, float] = (-2, 16), pH_resolution: int = 100, V_range: tuple[float, float] = (-3, 3), V_resolution: int = 100, e_hull_max: float = 1, cmap: str = 'RdYlBu_r', ax: plt.Axes | None = None, **kwargs: Any) → plt.Axes[source]

                                                      Plots the stability of an entry in the Pourbaix diagram.

                                                      Parameters:
                                                      @@ -12302,7 +12294,7 @@

                                                      Submodules
                                                      -show(*args, **kwargs)[source]
                                                      +show(*args, **kwargs)[source]

                                                      Show the Pourbaix plot.

                                                      Parameters:
                                                      @@ -12318,7 +12310,7 @@

                                                      Submodules
                                                      -generate_entry_label(entry)[source]
                                                      +generate_entry_label(entry)[source]

                                                      Generates a label for the Pourbaix plotter.

                                                      Parameters:
                                                      @@ -12329,7 +12321,7 @@

                                                      Submodules
                                                      -ion_or_solid_comp_object(formula)[source]
                                                      +ion_or_solid_comp_object(formula)[source]

                                                      Get an Ion or Composition object given a formula.

                                                      Parameters:
                                                      @@ -12355,7 +12347,7 @@

                                                      Submoduleshttps://doi.org/10.1016/j.commatsci.2017.01.017

                                                      -class AflowPrototypeMatcher(initial_ltol=0.2, initial_stol=0.3, initial_angle_tol=5)[source]
                                                      +class AflowPrototypeMatcher(initial_ltol=0.2, initial_stol=0.3, initial_angle_tol=5)[source]

                                                      Bases: object

                                                      This class will match structures to their crystal prototypes, and will attempt to group species together to match structures derived from @@ -12380,7 +12372,7 @@

                                                      Submodules
                                                      -get_prototypes(structure: Structure) → list | None[source]
                                                      +get_prototypes(structure: Structure) → list | None[source]

                                                      Get prototype(s) structures for a given input structure. If you use this method in your work, please cite the appropriate AFLOW publication:

                                                      Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., & Curtarolo, @@ -12419,7 +12411,7 @@

                                                      Submodules
                                                      -class QuasiHarmonicDebyeApprox(energies, volumes, structure, t_min=300.0, t_step=100, t_max=300.0, eos='vinet', pressure=0.0, poisson=0.25, use_mie_gruneisen=False, anharmonic_contribution=False)[source]
                                                      +class QuasiHarmonicDebyeApprox(energies, volumes, structure, t_min=300.0, t_step=100, t_max=300.0, eos='vinet', pressure=0.0, poisson=0.25, use_mie_gruneisen=False, anharmonic_contribution=False)[source]

                                                      Bases: object

                                                      Quasi-harmonic approximation.

                                                      @@ -12450,7 +12442,7 @@

                                                      Submodules
                                                      -static debye_integral(y)[source]
                                                      +static debye_integral(y)[source]

                                                      Debye integral. Eq(5) in doi.org/10.1016/j.comphy.2003.12.001.

                                                      Parameters:
                                                      @@ -12467,7 +12459,7 @@

                                                      Submodules
                                                      -debye_temperature(volume: float) → float[source]
                                                      +debye_temperature(volume: float) → float[source]

                                                      Calculates the Debye temperature. Eq(6) in doi.org/10.1016/j.comphy.2003.12.001. Thanks to Joey.

                                                      Eq(6) above is equivalent to Eq(3) in doi.org/10.1103/PhysRevB.37.790 @@ -12492,13 +12484,13 @@

                                                      Submodules
                                                      -get_summary_dict()[source]
                                                      +get_summary_dict()[source]

                                                      Get a dict with a summary of the computed properties.

                                                      -gruneisen_parameter(temperature, volume)[source]
                                                      +gruneisen_parameter(temperature, volume)[source]
                                                      Slater-gamma formulation(the default):
                                                      gruneisen parameter = - d log(theta)/ d log(V) = - (1/6 + 0.5 d log(B)/ d log(V))

                                                      = - (1/6 + 0.5 V/B dB/dV), where dB/dV = d^2E/dV^2 + V * d^3E/dV^3.

                                                      @@ -12535,7 +12527,7 @@

                                                      Submodules
                                                      -optimize_gibbs_free_energy()[source]
                                                      +optimize_gibbs_free_energy()[source]

                                                      Evaluate the Gibbs free energy as a function of V, T and P i.e G(V, T, P), minimize G(V, T, P) w.r.t. V for each T and store the optimum values.

                                                      @@ -12547,7 +12539,7 @@

                                                      Submodules
                                                      -optimizer(temperature)[source]
                                                      +optimizer(temperature)[source]

                                                      Evaluate G(V, T, P) at the given temperature(and pressure) and minimize it w.r.t. V.

                                                      1. Compute the vibrational Helmholtz free energy, A_vib.

                                                        2. @@ -12578,7 +12570,7 @@

                                                        Submodules
                                                        -thermal_conductivity(temperature: float, volume: float) → float[source]
                                                        +thermal_conductivity(temperature: float, volume: float) → float[source]

                                                        Eq(17) in 10.1103/PhysRevB.90.174107.

                                                        Parameters:
                                                        @@ -12598,7 +12590,7 @@

                                                        Submodules
                                                        -vibrational_free_energy(temperature, volume)[source]
                                                        +vibrational_free_energy(temperature, volume)[source]

                                                        Vibrational Helmholtz free energy, A_vib(V, T). Eq(4) in doi.org/10.1016/j.comphy.2003.12.001.

                                                        @@ -12619,7 +12611,7 @@

                                                        Submodules
                                                        -vibrational_internal_energy(temperature, volume)[source]
                                                        +vibrational_internal_energy(temperature, volume)[source]

                                                        Vibrational internal energy, U_vib(V, T). Eq(4) in doi.org/10.1016/j.comphy.2003.12.001.

                                                        @@ -12642,7 +12634,7 @@

                                                        Submodules
                                                        -class QuasiharmonicDebyeApprox(*args, **kwargs)[source]
                                                        +class QuasiharmonicDebyeApprox(*args, **kwargs)[source]

                                                        Bases: QuasiHarmonicDebyeApprox

                                                        Parameters:
                                                        @@ -12680,14 +12672,14 @@

                                                        Submodules
                                                        -class QuasiRRHO(mol: Molecule, frequencies: list[float], energy: float, mult: int, sigma_r: float = 1, temp: float = 298.15, press: float = 101317, v0: float = 100)[source]
                                                        +class QuasiRRHO(mol: Molecule, frequencies: list[float], energy: float, mult: int, sigma_r: float = 1, temp: float = 298.15, press: float = 101317, v0: float = 100)[source]

                                                        Bases: object

                                                        Calculate thermochemistry using Grimme’s Quasi-RRHO approximation. All outputs are in atomic units, e.g. energy outputs are in Hartrees. Citation: Grimme, S. Chemistry - A European Journal 18, 9955-9964 (2012).

                                                        -temp[source]
                                                        +temp[source]

                                                        Temperature [K]

                                                        Type:
                                                        @@ -12698,7 +12690,7 @@

                                                        Submodules
                                                        -press[source]
                                                        +press[source]

                                                        Pressure [Pa]

                                                        Type:
                                                        @@ -12709,7 +12701,7 @@

                                                        Submodules
                                                        -v0[source]
                                                        +v0[source]

                                                        Cutoff frequency for Quasi-RRHO method [1/cm]

                                                        Type:
                                                        @@ -12720,7 +12712,7 @@

                                                        Submodules
                                                        -entropy_quasiRRHO[source]
                                                        +entropy_quasiRRHO[source]

                                                        Quasi-RRHO entropy [Ha/K]

                                                        Type:
                                                        @@ -12731,7 +12723,7 @@

                                                        Submodules
                                                        -entropy_ho[source]
                                                        +entropy_ho[source]

                                                        Total entropy calculated with a harmonic oscillator approximation for the vibrational entropy [Ha/K]

                                                        @@ -12743,7 +12735,7 @@

                                                        Submodules
                                                        -h_corrected[source]
                                                        +h_corrected[source]

                                                        Thermal correction to the enthalpy [Ha]

                                                        Type:
                                                        @@ -12754,7 +12746,7 @@

                                                        Submodules
                                                        -free_energy_quasiRRHO[source]
                                                        +free_energy_quasiRRHO[source]

                                                        Quasi-RRHO free energy [Ha]

                                                        Type:
                                                        @@ -12765,7 +12757,7 @@

                                                        Submodules
                                                        -free_energy_ho[source]
                                                        +free_energy_ho[source]

                                                        Free energy calculated without the Quasi-RRHO method, i.e. with a harmonic oscillator approximation for the vibrational entropy [Ha]

                                                        @@ -12792,7 +12784,7 @@

                                                        Submodules
                                                        -classmethod from_gaussian_output(output: GaussianOutput, **kwargs) → Self[source]
                                                        +classmethod from_gaussian_output(output: GaussianOutput, **kwargs) → Self[source]
                                                        Parameters:

                                                        output (GaussianOutput) – Pymatgen GaussianOutput object

                                                        @@ -12808,7 +12800,7 @@

                                                        Submodules
                                                        -classmethod from_qc_output(output: QCOutput, **kwargs) → Self[source]
                                                        +classmethod from_qc_output(output: QCOutput, **kwargs) → Self[source]
                                                        Parameters:

                                                        output (QCOutput) – Pymatgen QCOutput object

                                                        @@ -12826,7 +12818,7 @@

                                                        Submodules
                                                        -get_avg_mom_inertia(mol)[source]
                                                        +get_avg_mom_inertia(mol)[source]

                                                        Calculate the average moment of inertia of a molecule

                                                        Parameters:
                                                        @@ -12847,7 +12839,7 @@

                                                        Submodules
                                                        -class BalancedReaction(reactants_coeffs: Mapping[CompositionLike, int | float], products_coeffs: Mapping[CompositionLike, int | float])[source]
                                                        +class BalancedReaction(reactants_coeffs: Mapping[CompositionLike, int | float], products_coeffs: Mapping[CompositionLike, int | float])[source]

                                                        Bases: MSONable

                                                        Represent a complete chemical reaction.

                                                        Reactants and products to be specified as dict of {Composition: coeff}.

                                                        @@ -12861,18 +12853,18 @@

                                                        Submodules
                                                        -TOLERANCE = 1e-06[source]
                                                        +TOLERANCE = 1e-06[source]

                                                        -property all_comp: list[Composition][source]
                                                        +property all_comp: list[Composition][source]

                                                        List of all compositions in the reaction.

                                                        -as_dict() → dict[source]
                                                        +as_dict() → dict[source]
                                                        Returns:

                                                        A dictionary representation of BalancedReaction.

                                                        @@ -12882,13 +12874,13 @@

                                                        Submodules
                                                        -as_entry(energies) → ComputedEntry[source]
                                                        +as_entry(energies) → ComputedEntry[source]

                                                        Get a ComputedEntry representation of the reaction.

                                                        -calculate_energy(energies: dict[Composition, ufloat]) → ufloat[source]
                                                        +calculate_energy(energies: dict[Composition, ufloat]) → ufloat[source]
                                                        calculate_energy(energies: dict[Composition, float]) → float

                                                        Calculates the energy of the reaction.

                                                        @@ -12905,19 +12897,19 @@

                                                        Submodules
                                                        -property coeffs: list[float][source]
                                                        +property coeffs: list[float][source]

                                                        Final coefficients of the calculated reaction.

                                                        -property elements: list[Element | Species][source]
                                                        +property elements: list[Element | Species][source]

                                                        List of elements in the reaction.

                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                        +classmethod from_dict(dct: dict) → Self[source]
                                                        Parameters:

                                                        dct (dict) – from as_dict().

                                                        @@ -12930,7 +12922,7 @@

                                                        Submodules
                                                        -classmethod from_str(rxn_str: str) → Self[source]
                                                        +classmethod from_str(rxn_str: str) → Self[source]

                                                        Generate a balanced reaction from a string. The reaction must already be balanced.

                                                        @@ -12945,13 +12937,13 @@

                                                        Submodules
                                                        -get_coeff(comp: Composition) → float[source]
                                                        +get_coeff(comp: Composition) → float[source]

                                                        Get coefficient for a particular composition.

                                                        -get_el_amount(element: Element | Species) → float[source]
                                                        +get_el_amount(element: Element | Species) → float[source]

                                                        Get the amount of the element in the reaction.

                                                        Parameters:
                                                        @@ -12965,7 +12957,7 @@

                                                        Submodules
                                                        -normalize_to(comp: Composition, factor: float = 1) → None[source]
                                                        +normalize_to(comp: Composition, factor: float = 1) → None[source]

                                                        Normalizes the reaction to one of the compositions. By default, normalizes such that the composition given has a coefficient of 1. Another factor can be specified.

                                                        @@ -12981,7 +12973,7 @@

                                                        Submodules
                                                        -normalize_to_element(element: Species | Element, factor: float = 1) → None[source]
                                                        +normalize_to_element(element: Species | Element, factor: float = 1) → None[source]

                                                        Normalizes the reaction to one of the elements. By default, normalizes such that the amount of the element is 1. Another factor can be specified.

                                                        @@ -12997,27 +12989,27 @@

                                                        Submodules
                                                        -property normalized_repr: str[source]
                                                        +property normalized_repr: str[source]

                                                        A normalized representation of the reaction. All factors are converted to lowest common factors.

                                                        -normalized_repr_and_factor() → tuple[str, float][source]
                                                        +normalized_repr_and_factor() → tuple[str, float][source]

                                                        Normalized representation for a reaction For example, 4 Li + 2 O -> 2Li2O becomes 2 Li + O -> Li2O.

                                                        -property products: list[Composition][source]
                                                        +property products: list[Composition][source]

                                                        List of products.

                                                        -property reactants: list[Composition][source]
                                                        +property reactants: list[Composition][source]

                                                        List of reactants.

                                                        @@ -13025,7 +13017,7 @@

                                                        Submodules
                                                        -class ComputedReaction(reactant_entries: list[ComputedEntry], product_entries: list[ComputedEntry])[source]
                                                        +class ComputedReaction(reactant_entries: list[ComputedEntry], product_entries: list[ComputedEntry])[source]

                                                        Bases: Reaction

                                                        Convenience class to generate a reaction from ComputedEntry objects, with some additional attributes, such as a reaction energy based on computed @@ -13040,14 +13032,14 @@

                                                        Submodules
                                                        -property all_entries[source]
                                                        +property all_entries[source]

                                                        Equivalent of all_comp but returns entries, in the same order as the coefficients.

                                                        -as_dict() → dict[source]
                                                        +as_dict() → dict[source]
                                                        Returns:

                                                        A dictionary representation of ComputedReaction.

                                                        @@ -13057,21 +13049,21 @@

                                                        Submodules
                                                        -property calculated_reaction_energy: float[source]
                                                        +property calculated_reaction_energy: float[source]

                                                        Returns: float: The calculated reaction energy.

                                                        -property calculated_reaction_energy_uncertainty: float[source]
                                                        +property calculated_reaction_energy_uncertainty: float[source]

                                                        Calculates the uncertainty in the reaction energy based on the uncertainty in the energies of the products and reactants.

                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                        +classmethod from_dict(dct: dict) → Self[source]
                                                        Parameters:

                                                        dct (dict) – from as_dict().

                                                        @@ -13086,7 +13078,7 @@

                                                        Submodules
                                                        -class Reaction(reactants: list[Composition], products: list[Composition])[source]
                                                        +class Reaction(reactants: list[Composition], products: list[Composition])[source]

                                                        Bases: BalancedReaction

                                                        A more flexible class representing a Reaction. The reaction amounts will be automatically balanced. Reactants and products can swap sides so that @@ -13105,7 +13097,7 @@

                                                        Submodules
                                                        -as_dict() → dict[source]
                                                        +as_dict() → dict[source]
                                                        Returns:

                                                        A dictionary representation of Reaction.

                                                        @@ -13115,13 +13107,13 @@

                                                        Submodules
                                                        -copy() → Self[source]
                                                        +copy() → Self[source]

                                                        Get a copy of the Reaction object.

                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                        +classmethod from_dict(dct: dict) → Self[source]
                                                        Parameters:

                                                        dct (dict) – from as_dict().

                                                        @@ -13136,7 +13128,7 @@

                                                        Submodules
                                                        -exception ReactionError(msg: str)[source]
                                                        +exception ReactionError(msg: str)[source]

                                                        Bases: Exception

                                                        Exception class for Reactions. Allows more information in exception messages to cover situations not covered by standard exception classes.

                                                        @@ -13154,7 +13146,7 @@

                                                        Submodules
                                                        -class OxideType(structure: Structure, relative_cutoff=1.1)[source]
                                                        +class OxideType(structure: Structure, relative_cutoff=1.1)[source]

                                                        Bases: object

                                                        Separate class for determining oxide type.

                                                        @@ -13170,7 +13162,7 @@

                                                        Submodules
                                                        -parse_oxide() → tuple[str, int][source]
                                                        +parse_oxide() → tuple[str, int][source]

                                                        Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide.

                                                        Returns:
                                                        @@ -13190,7 +13182,7 @@

                                                        Submodules
                                                        -class RelaxationAnalyzer(initial_structure: Structure, final_structure: Structure)[source]
                                                        +class RelaxationAnalyzer(initial_structure: Structure, final_structure: Structure)[source]

                                                        Bases: object

                                                        This class analyzes the relaxation in a calculation.

                                                        Please note that the input and final structures should have the same @@ -13210,7 +13202,7 @@

                                                        Submodules
                                                        -get_percentage_bond_dist_changes(max_radius: float = 3.0) → dict[int, dict[int, float]][source]
                                                        +get_percentage_bond_dist_changes(max_radius: float = 3.0) → dict[int, dict[int, float]][source]

                                                        Get the percentage bond distance changes for each site up to a maximum radius for nearest neighbors.

                                                        @@ -13236,7 +13228,7 @@

                                                        Submodules
                                                        -get_percentage_lattice_parameter_changes() → dict[str, float][source]
                                                        +get_percentage_lattice_parameter_changes() → dict[str, float][source]

                                                        Get the percentage lattice parameter changes.

                                                        Returns:
                                                        @@ -13255,7 +13247,7 @@

                                                        Submodules
                                                        -get_percentage_volume_change() → float[source]
                                                        +get_percentage_volume_change() → float[source]

                                                        Get the percentage volume change.

                                                        Returns:
                                                        @@ -13271,7 +13263,7 @@

                                                        Submodules
                                                        -class VoronoiAnalyzer(cutoff=5.0, qhull_options='Qbb Qc Qz')[source]
                                                        +class VoronoiAnalyzer(cutoff=5.0, qhull_options='Qbb Qc Qz')[source]

                                                        Bases: object

                                                        Performs a statistical analysis of Voronoi polyhedra around each site. Each Voronoi polyhedron is described using Schaefli notation. @@ -13297,7 +13289,7 @@

                                                        Submodules
                                                        -analyze(structure: Structure, n=0)[source]
                                                        +analyze(structure: Structure, n=0)[source]

                                                        Performs Voronoi analysis and returns the polyhedra around atom n in Schlaefli notation.

                                                        @@ -13322,7 +13314,7 @@

                                                        Submodules
                                                        -analyze_structures(structures, step_freq=10, most_frequent_polyhedra=15)[source]
                                                        +analyze_structures(structures, step_freq=10, most_frequent_polyhedra=15)[source]

                                                        Perform Voronoi analysis on a list of Structures. Note that this might take a significant amount of time depending on the size and number of structures.

                                                        @@ -13346,7 +13338,7 @@

                                                        Submodules
                                                        -static plot_vor_analysis(voronoi_ensemble: list[tuple[str, float]]) → Axes[source]
                                                        +static plot_vor_analysis(voronoi_ensemble: list[tuple[str, float]]) → Axes[source]

                                                        Plot the Voronoi analysis.

                                                        Parameters:
                                                        @@ -13366,7 +13358,7 @@

                                                        Submodules
                                                        -class VoronoiConnectivity(structure: Structure, cutoff=10)[source]
                                                        +class VoronoiConnectivity(structure: Structure, cutoff=10)[source]

                                                        Bases: object

                                                        Computes the solid angles swept out by the shared face of the voronoi polyhedron between two sites.

                                                        @@ -13380,7 +13372,7 @@

                                                        Submodules
                                                        -property connectivity_array[source]
                                                        +property connectivity_array[source]

                                                        The connectivity array of shape [atom_i, atom_j, image_j]. atom_i is the index of the atom in the input structure. Since the second atom can be outside of the unit cell, it must be described by both an atom index and an image index. Array data is the solid @@ -13389,14 +13381,14 @@

                                                        Submodules
                                                        -get_connections()[source]
                                                        +get_connections()[source]

                                                        Get a list of site pairs that are Voronoi Neighbors, along with their real-space distances.

                                                        -get_sitej(site_index, image_index)[source]
                                                        +get_sitej(site_index, image_index)[source]

                                                        Assuming there is some value in the connectivity array at indices (1, 3, 12). site_i can be obtained directly from the input structure (structure[1]). site_j can be obtained by passing 3, 12 to this function.

                                                        @@ -13412,7 +13404,7 @@

                                                        Submodules
                                                        -property max_connectivity[source]
                                                        +property max_connectivity[source]

                                                        The 2d array [site_i, site_j] that represents the maximum connectivity of site i to any periodic image of site j.

                                                        @@ -13421,7 +13413,7 @@

                                                        Submodules
                                                        -average_coordination_number(structures, freq=10)[source]
                                                        +average_coordination_number(structures, freq=10)[source]

                                                        Calculates the ensemble averaged Voronoi coordination numbers of a list of Structures using VoronoiNN. Typically used for analyzing the output of a Molecular Dynamics run.

                                                        @@ -13440,7 +13432,7 @@

                                                        Submodules
                                                        -contains_peroxide(structure, relative_cutoff=1.1)[source]
                                                        +contains_peroxide(structure, relative_cutoff=1.1)[source]

                                                        Determines if a structure contains peroxide anions.

                                                        Parameters:
                                                        @@ -13459,7 +13451,7 @@

                                                        Submodules
                                                        -get_max_bond_lengths(structure, el_radius_updates=None)[source]
                                                        +get_max_bond_lengths(structure, el_radius_updates=None)[source]

                                                        Provides max bond length estimates for a structure based on the JMol table and algorithms.

                                                        @@ -13480,7 +13472,7 @@

                                                        Submodules
                                                        -oxide_type(structure: Structure, relative_cutoff: float = 1.1, return_nbonds: bool = False) → str | tuple[str, int][source]
                                                        +oxide_type(structure: Structure, relative_cutoff: float = 1.1, return_nbonds: bool = False) → str | tuple[str, int][source]

                                                        Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide.

                                                        Parameters:
                                                        @@ -13496,7 +13488,7 @@

                                                        Submodules
                                                        -solid_angle(center, coords)[source]
                                                        +solid_angle(center, coords)[source]

                                                        Helper method to calculate the solid angle of a set of coords from the center.

                                                        Parameters:
                                                        @@ -13516,7 +13508,7 @@

                                                        Submodules
                                                        -sulfide_type(structure)[source]
                                                        +sulfide_type(structure)[source]

                                                        Determines if a structure is a sulfide/polysulfide/sulfate.

                                                        Parameters:
                                                        @@ -13537,13 +13529,13 @@

                                                        Submodules
                                                        -class AbstractComparator[source]
                                                        +class AbstractComparator[source]

                                                        Bases: MSONable, ABC

                                                        Abstract Comparator class. A Comparator defines how sites are compared in a structure.

                                                        -abstract are_equal(sp1, sp2) → bool[source]
                                                        +abstract are_equal(sp1, sp2) → bool[source]

                                                        Defines how the species of two sites are considered equal. For example, one can consider sites to have the same species only when the species are exactly the same, i.e., Fe2+ matches Fe2+ but not @@ -13566,13 +13558,13 @@

                                                        Submodules
                                                        -as_dict()[source]
                                                        +as_dict()[source]

                                                        MSONable dict

                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                        +classmethod from_dict(dct: dict) → Self[source]
                                                        Parameters:

                                                        dct (dict) – Dict representation

                                                        @@ -13585,7 +13577,7 @@

                                                        Submodules
                                                        -abstract get_hash(composition)[source]
                                                        +abstract get_hash(composition)[source]

                                                        Defines a hash to group structures. This allows structures to be grouped efficiently for comparison. The hash must be invariant under supercell creation. (e.g. composition is not a good hash, but @@ -13608,13 +13600,13 @@

                                                        Submodules
                                                        -class ElementComparator[source]
                                                        +class ElementComparator[source]

                                                        Bases: AbstractComparator

                                                        A Comparator that matches elements. i.e. oxidation states are ignored.

                                                        -are_equal(sp1, sp2) → bool[source]
                                                        +are_equal(sp1, sp2) → bool[source]

                                                        True if element:amounts are exactly the same, i.e., oxidation state is not considered.

                                                        @@ -13635,7 +13627,7 @@

                                                        Submodules
                                                        -get_hash(composition)[source]
                                                        +get_hash(composition)[source]

                                                        Get the fractional element composition.

                                                        @@ -13643,12 +13635,12 @@

                                                        Submodules
                                                        -class FrameworkComparator[source]
                                                        +class FrameworkComparator[source]

                                                        Bases: AbstractComparator

                                                        A Comparator that matches sites, regardless of species.

                                                        -are_equal(sp1, sp2) → bool[source]
                                                        +are_equal(sp1, sp2) → bool[source]

                                                        True if there are atoms on both sites.

                                                        Parameters:
                                                        @@ -13667,7 +13659,7 @@

                                                        Submodules
                                                        -get_hash(composition)[source]
                                                        +get_hash(composition)[source]

                                                        No hash possible.

                                                        @@ -13675,13 +13667,13 @@

                                                        Submodules
                                                        -class OccupancyComparator[source]
                                                        +class OccupancyComparator[source]

                                                        Bases: AbstractComparator

                                                        A Comparator that matches occupancies on sites, irrespective of the species of those sites.

                                                        -are_equal(sp1, sp2) → bool[source]
                                                        +are_equal(sp1, sp2) → bool[source]
                                                        Parameters:
                                                          @@ -13702,7 +13694,7 @@

                                                          Submodules
                                                          -get_hash(composition)[source]
                                                          +get_hash(composition)[source]
                                                          Parameters:

                                                          composition – Composition.

                                                          @@ -13723,13 +13715,13 @@

                                                          Submodules
                                                          -class OrderDisorderElementComparator[source]
                                                          +class OrderDisorderElementComparator[source]

                                                          Bases: AbstractComparator

                                                          A Comparator that matches sites, given some overlap in the element composition.

                                                          -are_equal(sp1, sp2) → bool[source]
                                                          +are_equal(sp1, sp2) → bool[source]

                                                          True if there is some overlap in composition between the species.

                                                          Parameters:
                                                          @@ -13748,7 +13740,7 @@

                                                          Submodules
                                                          -get_hash(composition)[source]
                                                          +get_hash(composition)[source]

                                                          Get the fractional composition.

                                                          @@ -13756,12 +13748,12 @@

                                                          Submodules
                                                          -class SpeciesComparator[source]
                                                          +class SpeciesComparator[source]

                                                          Bases: AbstractComparator

                                                          A Comparator that matches species exactly. The default used in StructureMatcher.

                                                          -are_equal(sp1, sp2) → bool[source]
                                                          +are_equal(sp1, sp2) → bool[source]

                                                          True if species are exactly the same, i.e., Fe2+ == Fe2+ but not Fe3+.

                                                          Parameters:
                                                          @@ -13780,7 +13772,7 @@

                                                          Submodules
                                                          -get_hash(composition: Composition)[source]
                                                          +get_hash(composition: Composition)[source]

                                                          Get the fractional composition.

                                                          @@ -13788,14 +13780,14 @@

                                                          Submodules
                                                          -class SpinComparator[source]
                                                          +class SpinComparator[source]

                                                          Bases: AbstractComparator

                                                          A Comparator that matches magnetic structures to their inverse spins. This comparator is primarily used to filter magnetically ordered structures with opposite spins, which are equivalent.

                                                          -are_equal(sp1, sp2) → bool[source]
                                                          +are_equal(sp1, sp2) → bool[source]

                                                          True if species are exactly the same, i.e., Fe2+ == Fe2+ but not Fe3+. and the spins are reversed. i.e., spin up maps to spin down, and vice versa.

                                                          @@ -13816,7 +13808,7 @@

                                                          Submodules
                                                          -get_hash(composition)[source]
                                                          +get_hash(composition)[source]

                                                          Get the fractional composition.

                                                          @@ -13824,7 +13816,7 @@

                                                          Submodules
                                                          -class StructureMatcher(ltol: float = 0.2, stol: float = 0.3, angle_tol: float = 5, primitive_cell: bool = True, scale: bool = True, attempt_supercell: bool = False, allow_subset: bool = False, comparator: AbstractComparator | None = None, supercell_size: Literal['num_sites', 'num_atoms', 'volume'] = 'num_sites', ignored_species: Sequence[SpeciesLike] = ())[source]
                                                          +class StructureMatcher(ltol: float = 0.2, stol: float = 0.3, angle_tol: float = 5, primitive_cell: bool = True, scale: bool = True, attempt_supercell: bool = False, allow_subset: bool = False, comparator: AbstractComparator | None = None, supercell_size: Literal['num_sites', 'num_atoms', 'volume'] = 'num_sites', ignored_species: Sequence[SpeciesLike] = ())[source]

                                                          Bases: MSONable

                                                          Match structures by similarity.

                                                          Algorithm: @@ -13920,13 +13912,13 @@

                                                          Submodules
                                                          -as_dict()[source]
                                                          +as_dict()[source]

                                                          MSONable dict

                                                          -fit(struct1: Structure, struct2: Structure, symmetric: bool = False, skip_structure_reduction: bool = False) → bool[source]
                                                          +fit(struct1: Structure, struct2: Structure, symmetric: bool = False, skip_structure_reduction: bool = False) → bool[source]

                                                          Fit two structures.

                                                          Parameters:
                                                          @@ -13951,7 +13943,7 @@

                                                          Submodules
                                                          -fit_anonymous(struct1: Structure, struct2: Structure, niggli: bool = True, skip_structure_reduction: bool = False) → bool[source]
                                                          +fit_anonymous(struct1: Structure, struct2: Structure, niggli: bool = True, skip_structure_reduction: bool = False) → bool[source]

                                                          Performs an anonymous fitting, which allows distinct species in one structure to map to another. e.g. to compare if the Li2O and Na2O structures are similar.

                                                          @@ -13975,7 +13967,7 @@

                                                          Submodules
                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                          +classmethod from_dict(dct: dict) → Self[source]
                                                          Parameters:

                                                          dct (dict) – Dict representation

                                                          @@ -13988,7 +13980,7 @@

                                                          Submodules
                                                          -get_all_anonymous_mappings(struct1, struct2, niggli=True, include_dist=False)[source]
                                                          +get_all_anonymous_mappings(struct1, struct2, niggli=True, include_dist=False)[source]

                                                          Performs an anonymous fitting, which allows distinct species in one structure to map to another. Returns a dictionary of species substitutions that are within tolerance.

                                                          @@ -14009,7 +14001,7 @@

                                                          Submodules
                                                          -get_best_electronegativity_anonymous_mapping(struct1: Structure, struct2: Structure) → dict | None[source]
                                                          +get_best_electronegativity_anonymous_mapping(struct1: Structure, struct2: Structure) → dict | None[source]

                                                          Performs an anonymous fitting, which allows distinct species in one structure to map to another. e.g. to compare if the Li2O and Na2O structures are similar. If multiple substitutions are within tolerance @@ -14033,7 +14025,7 @@

                                                          Submodules
                                                          -get_mapping(superset, subset)[source]
                                                          +get_mapping(superset, subset)[source]

                                                          Calculate the mapping from superset to subset.

                                                          Parameters:
                                                          @@ -14053,7 +14045,7 @@

                                                          Submodules
                                                          -get_rms_anonymous(struct1, struct2)[source]
                                                          +get_rms_anonymous(struct1, struct2)[source]

                                                          Performs an anonymous fitting, which allows distinct species in one structure to map to another. e.g. to compare if the Li2O and Na2O structures are similar.

                                                          @@ -14081,7 +14073,7 @@

                                                          Submodules
                                                          -get_rms_dist(struct1, struct2)[source]
                                                          +get_rms_dist(struct1, struct2)[source]

                                                          Calculate RMS displacement between two structures.

                                                          Parameters:
                                                          @@ -14100,7 +14092,7 @@

                                                          Submodules
                                                          -get_s2_like_s1(struct1, struct2, include_ignored_species=True)[source]
                                                          +get_s2_like_s1(struct1, struct2, include_ignored_species=True)[source]

                                                          Performs transformations on struct2 to put it in a basis similar to struct1 (without changing any of the inter-site distances).

                                                          @@ -14123,7 +14115,7 @@

                                                          Submodules
                                                          -get_supercell_matrix(supercell, struct) → ndarray | None[source]
                                                          +get_supercell_matrix(supercell, struct) → ndarray | None[source]

                                                          Get the matrix for transforming struct to supercell. This can be used for very distorted ‘supercells’ where the primitive cell is impossible to find.

                                                          @@ -14131,7 +14123,7 @@

                                                          Submodules
                                                          -get_transformation(struct1, struct2)[source]
                                                          +get_transformation(struct1, struct2)[source]

                                                          Get the supercell transformation, fractional translation vector, and a mapping to transform struct2 to be similar to struct1.

                                                          @@ -14161,7 +14153,7 @@

                                                          Submodules
                                                          -group_structures(s_list, anonymous=False)[source]
                                                          +group_structures(s_list, anonymous=False)[source]

                                                          Given a list of structures, use fit to group them by structural equality.

                                                          @@ -14227,7 +14219,7 @@

                                                          Submodules
                                                          -class NanoscaleStability(se_analyzers, symprec=1e-05)[source]
                                                          +class NanoscaleStability(se_analyzers, symprec=1e-05)[source]

                                                          Bases: object

                                                          A class for analyzing the stability of nanoparticles of different polymorphs with respect to size. The Wulff shape will be the model for the @@ -14243,7 +14235,7 @@

                                                          Submodules
                                                          -se_analyzers[source]
                                                          +se_analyzers[source]

                                                          Each item corresponds to a different polymorph.

                                                          Type:
                                                          @@ -14254,7 +14246,7 @@

                                                          Submodules
                                                          -symprec[source]
                                                          +symprec[source]

                                                          Tolerance for symmetry finding. See WulffShape.

                                                          Type:
                                                          @@ -14266,7 +14258,7 @@

                                                          Submodules
                                                          -static bulk_gform(bulk_entry)[source]
                                                          +static bulk_gform(bulk_entry)[source]

                                                          Get the formation energy of the bulk.

                                                          Parameters:
                                                          @@ -14283,7 +14275,7 @@

                                                          Submodules
                                                          -plot_all_stability_map(max_r, increments=50, delu_dict=None, delu_default=0, ax=None, labels=None, from_sphere_area=False, e_units='keV', r_units='nanometers', normalize=False, scale_per_atom=False)[source]
                                                          +plot_all_stability_map(max_r, increments=50, delu_dict=None, delu_default=0, ax=None, labels=None, from_sphere_area=False, e_units='keV', r_units='nanometers', normalize=False, scale_per_atom=False)[source]
                                                          Get the plot of the formation energy of a particles

                                                          of different polymorphs against its effect radius.

                                                          @@ -14316,7 +14308,7 @@

                                                          Submodules
                                                          -plot_one_stability_map(analyzer, max_r, delu_dict=None, label='', increments=50, delu_default=0, ax=None, from_sphere_area=False, e_units='keV', r_units='nanometers', normalize=False, scale_per_atom=False)[source]
                                                          +plot_one_stability_map(analyzer, max_r, delu_dict=None, label='', increments=50, delu_default=0, ax=None, from_sphere_area=False, e_units='keV', r_units='nanometers', normalize=False, scale_per_atom=False)[source]
                                                          Get the plot of the formation energy of a particle against its

                                                          effect radius.

                                                          @@ -14353,7 +14345,7 @@

                                                          Submodules
                                                          -scaled_wulff(wulff_shape, r)[source]
                                                          +scaled_wulff(wulff_shape, r)[source]
                                                          Scales the Wulff shape with an effective radius r. Note that the resulting

                                                          Wulff does not necessarily have the same effective radius as the one provided. The Wulff shape is scaled by its surface energies where first @@ -14376,7 +14368,7 @@

                                                          Submodules
                                                          -solve_equilibrium_point(analyzer1, analyzer2, delu_dict=None, delu_default=0, units='nanometers')[source]
                                                          +solve_equilibrium_point(analyzer1, analyzer2, delu_dict=None, delu_default=0, units='nanometers')[source]

                                                          Get the radial size of two particles where equilibrium is reached between both particles. NOTE: the solution here is not the same as the solution visualized in the plot because solving for r requires that both the total surface area and @@ -14406,7 +14398,7 @@

                                                          Submodules
                                                          -wulff_gform_and_r(wulff_shape, bulk_entry, r, from_sphere_area=False, r_units='nanometers', e_units='keV', normalize=False, scale_per_atom=False)[source]
                                                          +wulff_gform_and_r(wulff_shape, bulk_entry, r, from_sphere_area=False, r_units='nanometers', e_units='keV', normalize=False, scale_per_atom=False)[source]

                                                          Calculates the formation energy of the particle with arbitrary radius r.

                                                          Parameters:
                                                          @@ -14434,7 +14426,7 @@

                                                          Submodules
                                                          -class SlabEntry(structure, energy, miller_index, correction=0.0, parameters=None, data=None, entry_id=None, label=None, adsorbates=None, clean_entry=None, marker=None, color=None)[source]
                                                          +class SlabEntry(structure, energy, miller_index, correction=0.0, parameters=None, data=None, entry_id=None, label=None, adsorbates=None, clean_entry=None, marker=None, color=None)[source]

                                                          Bases: ComputedStructureEntry

                                                          A ComputedStructureEntry object encompassing all data relevant to a

                                                          slab for analyzing surface thermodynamics.

                                                          @@ -14442,7 +14434,7 @@

                                                          Submodules
                                                          -miller_index[source]
                                                          +miller_index[source]

                                                          Miller index of plane parallel to surface.

                                                          Type:
                                                          @@ -14453,7 +14445,7 @@

                                                          Submodules
                                                          -label[source]
                                                          +label[source]

                                                          Brief description for this slab.

                                                          Type:
                                                          @@ -14464,7 +14456,7 @@

                                                          Submodules
                                                          -adsorbates[source]
                                                          +adsorbates[source]

                                                          List of ComputedStructureEntry for the types of adsorbates.

                                                          Type:
                                                          @@ -14475,7 +14467,7 @@

                                                          Submodules
                                                          -clean_entry[source]
                                                          +clean_entry[source]

                                                          SlabEntry for the corresponding clean slab for an adsorbed slab.

                                                          Type:
                                                          @@ -14486,7 +14478,7 @@

                                                          Submodules
                                                          -ads_entries_dict[source]
                                                          +ads_entries_dict[source]

                                                          Dictionary where the key is the reduced composition of the adsorbate entry and value is the entry itself.

                                                          @@ -14526,61 +14518,61 @@

                                                          Submodules
                                                          -property Nads_in_slab[source]
                                                          +property Nads_in_slab[source]

                                                          The TOTAL number of adsorbates in the slab on BOTH sides.

                                                          -property Nsurfs_ads_in_slab[source]
                                                          +property Nsurfs_ads_in_slab[source]

                                                          The TOTAL number of adsorbed surfaces in the slab.

                                                          -as_dict()[source]
                                                          +as_dict()[source]

                                                          Get dict which contains Slab Entry data.

                                                          -property cleaned_up_slab[source]
                                                          +property cleaned_up_slab[source]

                                                          A slab with the adsorbates removed.

                                                          -property create_slab_label[source]
                                                          +property create_slab_label[source]

                                                          A label (str) for this particular slab based on composition, coverage and Miller index.

                                                          -classmethod from_computed_structure_entry(entry, miller_index, label=None, adsorbates=None, clean_entry=None, **kwargs) → Self[source]
                                                          +classmethod from_computed_structure_entry(entry, miller_index, label=None, adsorbates=None, clean_entry=None, **kwargs) → Self[source]

                                                          Get SlabEntry from a ComputedStructureEntry.

                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                          +classmethod from_dict(dct: dict) → Self[source]

                                                          Get a SlabEntry by reading in an dictionary.

                                                          -property get_monolayer[source]
                                                          +property get_monolayer[source]

                                                          The primitive unit surface area density of the adsorbate.

                                                          -property get_unit_primitive_area[source]
                                                          +property get_unit_primitive_area[source]

                                                          The surface area of the adsorbed system per unit area of the primitive slab system.

                                                          -gibbs_binding_energy(eads=False)[source]
                                                          +gibbs_binding_energy(eads=False)[source]

                                                          Get the adsorption energy or Gibbs binding energy of an adsorbate on a surface.

                                                          Parameters:
                                                          @@ -14593,13 +14585,13 @@

                                                          Submodules
                                                          -property surface_area[source]
                                                          +property surface_area[source]

                                                          Calculate the surface area of the slab.

                                                          -surface_energy(ucell_entry, ref_entries=None)[source]
                                                          +surface_energy(ucell_entry, ref_entries=None)[source]

                                                          Calculates the surface energy of this SlabEntry.

                                                          Parameters:
                                                          @@ -14626,7 +14618,7 @@

                                                          Submodules
                                                          -class SurfaceEnergyPlotter(all_slab_entries, ucell_entry, ref_entries=None)[source]
                                                          +class SurfaceEnergyPlotter(all_slab_entries, ucell_entry, ref_entries=None)[source]

                                                          Bases: object

                                                          A class used for generating plots to analyze the thermodynamics of surfaces of a material. Produces stability maps of different slab configurations, @@ -14634,7 +14626,7 @@

                                                          Submodules
                                                          -all_slab_entries[source]
                                                          +all_slab_entries[source]

                                                          Either a list of SlabEntry objects (note for a list, the SlabEntry must have the adsorbates and clean_entry parameter plugged in) or a Nested dictionary containing a list of entries for slab calculations as @@ -14664,7 +14656,7 @@

                                                          Submodules
                                                          -color_dict[source]
                                                          +color_dict[source]

                                                          Dictionary of colors (r,g,b,a) when plotting surface energy stability. The keys are individual surface entries where clean surfaces have a solid color while the corresponding adsorbed surface will be transparent.

                                                          @@ -14677,7 +14669,7 @@

                                                          Submodules
                                                          -ucell_entry[source]
                                                          +ucell_entry[source]

                                                          ComputedStructureEntry of the bulk reference for this particular material.

                                                          @@ -14689,7 +14681,7 @@

                                                          Submodules
                                                          -ref_entries[source]
                                                          +ref_entries[source]

                                                          List of ComputedStructureEntries to be used for calculating chemical potential.

                                                          Type:
                                                          @@ -14700,7 +14692,7 @@

                                                          Submodules
                                                          -facet_color_dict[source]
                                                          +facet_color_dict[source]

                                                          Randomly generated dictionary of colors associated with each facet.

                                                          Type:
                                                          @@ -14737,7 +14729,7 @@

                                                          Submodules
                                                          -BE_vs_clean_SE(delu_dict, delu_default=0, plot_eads=False, annotate_monolayer=True, JPERM2=False)[source]
                                                          +BE_vs_clean_SE(delu_dict, delu_default=0, plot_eads=False, annotate_monolayer=True, JPERM2=False)[source]
                                                          For each facet, plot the clean surface energy against the most

                                                          stable binding energy.

                                                          @@ -14772,7 +14764,7 @@

                                                          Submodules
                                                          -area_frac_vs_chempot_plot(ref_delu: Symbol, chempot_range: list[float], delu_dict: dict[Symbol, float] | None = None, delu_default: float = 0, increments: int = 10, no_clean: bool = False, no_doped: bool = False) → Axes[source]
                                                          +area_frac_vs_chempot_plot(ref_delu: Symbol, chempot_range: list[float], delu_dict: dict[Symbol, float] | None = None, delu_default: float = 0, increments: int = 10, no_clean: bool = False, no_doped: bool = False) → Axes[source]

                                                          1D plot. Plots the change in the area contribution of each facet as a function of chemical potential.

                                                          @@ -14802,7 +14794,7 @@

                                                          Submodules
                                                          -static chempot_plot_addons(ax, xrange, ref_el, pad=2.4, rect=None, ylim=None)[source]
                                                          +static chempot_plot_addons(ax, xrange, ref_el, pad=2.4, rect=None, ylim=None)[source]

                                                          Helper function to a chempot plot look nicer.

                                                          Parameters:
                                                          @@ -14823,7 +14815,7 @@

                                                          Submodules
                                                          -chempot_vs_gamma(ref_delu, chempot_range, miller_index=(), delu_dict=None, delu_default=0, JPERM2=False, show_unstable=False, ylim=None, plt=None, no_clean=False, no_doped=False, use_entry_labels=False, no_label=False)[source]
                                                          +chempot_vs_gamma(ref_delu, chempot_range, miller_index=(), delu_dict=None, delu_default=0, JPERM2=False, show_unstable=False, ylim=None, plt=None, no_clean=False, no_doped=False, use_entry_labels=False, no_label=False)[source]
                                                          Plots the surface energy as a function of chemical potential.

                                                          Each facet will be associated with its own distinct colors. Dashed lines will represent stoichiometries different from that @@ -14868,7 +14860,7 @@

                                                          Submodules
                                                          -chempot_vs_gamma_plot_one(ax: Axes, entry: SlabEntry, ref_delu: Symbol, chempot_range: list[float], delu_dict: dict[Symbol, float] | None = None, delu_default: float = 0, label: str = '', JPERM2: bool = False) → Axes[source]
                                                          +chempot_vs_gamma_plot_one(ax: Axes, entry: SlabEntry, ref_delu: Symbol, chempot_range: list[float], delu_dict: dict[Symbol, float] | None = None, delu_default: float = 0, label: str = '', JPERM2: bool = False) → Axes[source]

                                                          Helper function to help plot the surface energy of a single SlabEntry as a function of chemical potential.

                                                          @@ -14898,7 +14890,7 @@

                                                          Submodules
                                                          -color_palette_dict(alpha=0.35)[source]
                                                          +color_palette_dict(alpha=0.35)[source]

                                                          Helper function to assign each facet a unique color using a dictionary.

                                                          Parameters:
                                                          @@ -14915,7 +14907,7 @@

                                                          Submodules
                                                          -get_stable_entry_at_u(miller_index, delu_dict=None, delu_default=0, no_doped=False, no_clean=False) → tuple[SlabEntry, float][source]
                                                          +get_stable_entry_at_u(miller_index, delu_dict=None, delu_default=0, no_doped=False, no_clean=False) → tuple[SlabEntry, float][source]
                                                          Get the entry corresponding to the most stable slab for a particular

                                                          facet at a specific chempot. We assume that surface energy is constant so all free variables must be set with delu_dict, otherwise they are @@ -14945,7 +14937,7 @@

                                                          Submodules
                                                          -get_surface_equilibrium(slab_entries, delu_dict=None)[source]
                                                          +get_surface_equilibrium(slab_entries, delu_dict=None)[source]
                                                          Takes in a list of SlabEntries and calculates the chemical potentials

                                                          at which all slabs in the list coexists simultaneously. Useful for building surface phase diagrams. Note that to solve for x equations @@ -14977,7 +14969,7 @@

                                                          Submodules
                                                          -monolayer_vs_BE(plot_eads=False)[source]
                                                          +monolayer_vs_BE(plot_eads=False)[source]
                                                          Plots the binding energy as a function of monolayers (ML), i.e.

                                                          the fractional area adsorbate density for all facets. For each facet at a specific monolayer, only plot the lowest binding energy.

                                                          @@ -14999,7 +14991,7 @@

                                                          Submodules
                                                          -set_all_variables(delu_dict, delu_default)[source]
                                                          +set_all_variables(delu_dict, delu_default)[source]
                                                          Set all chemical potential values and returns a dictionary where

                                                          the key is a sympy Symbol and the value is a float (chempot).

                                                          @@ -15022,7 +15014,7 @@

                                                          Submodules
                                                          -stable_u_range_dict(chempot_range, ref_delu, no_doped=True, no_clean=False, delu_dict=None, miller_index=(), dmu_at_0=False, return_se_dict=False)[source]
                                                          +stable_u_range_dict(chempot_range, ref_delu, no_doped=True, no_clean=False, delu_dict=None, miller_index=(), dmu_at_0=False, return_se_dict=False)[source]

                                                          Creates a dictionary where each entry is a key pointing to a chemical potential range where the surface of that entry is stable. Does so by enumerating through all possible solutions (intersect) @@ -15058,7 +15050,7 @@

                                                          Submodules
                                                          -surface_chempot_range_map(elements, miller_index, ranges, incr=50, no_doped=False, no_clean=False, delu_dict=None, ax=None, annotate=True, show_unphysical_only=False, fontsize=10) → Axes[source]
                                                          +surface_chempot_range_map(elements, miller_index, ranges, incr=50, no_doped=False, no_clean=False, delu_dict=None, ax=None, annotate=True, show_unphysical_only=False, fontsize=10) → Axes[source]
                                                          Adapted from the get_chempot_range_map() method in the PhaseDiagram

                                                          class. Plot the chemical potential range map based on surface energy stability. Currently works only for 2-component PDs. At @@ -15098,7 +15090,7 @@

                                                          Submodules
                                                          -wulff_from_chempot(delu_dict=None, delu_default=0, symprec=1e-05, no_clean=False, no_doped=False) → WulffShape[source]
                                                          +wulff_from_chempot(delu_dict=None, delu_default=0, symprec=1e-05, no_clean=False, no_doped=False) → WulffShape[source]

                                                          Method to get the Wulff shape at a specific chemical potential.

                                                          Parameters:
                                                          @@ -15125,13 +15117,13 @@

                                                          Submodules
                                                          -class WorkFunctionAnalyzer(structure: Structure, locpot_along_c, efermi, shift=0, blength=3.5)[source]
                                                          +class WorkFunctionAnalyzer(structure: Structure, locpot_along_c, efermi, shift=0, blength=3.5)[source]

                                                          Bases: object

                                                          A class used for calculating the work function from a slab model and visualizing the behavior of the local potential along the slab.

                                                          -efermi[source]
                                                          +efermi[source]

                                                          The Fermi energy.

                                                          Type:
                                                          @@ -15142,7 +15134,7 @@

                                                          Submodules
                                                          -locpot_along_c[source]
                                                          +locpot_along_c[source]

                                                          Local potential in eV along points along the c axis.

                                                          Type:
                                                          @@ -15153,7 +15145,7 @@

                                                          Submodules
                                                          -vacuum_locpot[source]
                                                          +vacuum_locpot[source]

                                                          The maximum local potential along the c direction for the slab model, i.e. the potential at the vacuum.

                                                          @@ -15165,7 +15157,7 @@

                                                          Submodules
                                                          -work_function[source]
                                                          +work_function[source]

                                                          The minimum energy needed to move an electron from the surface to infinity. Defined as the difference between the potential at the vacuum and the Fermi energy.

                                                          @@ -15177,7 +15169,7 @@

                                                          Submodules
                                                          -slab[source]
                                                          +slab[source]

                                                          The slab structure model.

                                                          Type:
                                                          @@ -15188,7 +15180,7 @@

                                                          Submodules
                                                          -along_c[source]
                                                          +along_c[source]

                                                          Points along the c direction with same increments as the locpot in the c axis.

                                                          Type:
                                                          @@ -15199,7 +15191,7 @@

                                                          Submodules
                                                          -ave_locpot[source]
                                                          +ave_locpot[source]

                                                          Mean of the minimum and maximum (vacuum) locpot along c.

                                                          Type:
                                                          @@ -15210,7 +15202,7 @@

                                                          Submodules
                                                          -sorted_sites[source]
                                                          +sorted_sites[source]

                                                          List of sites from the slab sorted along the c direction.

                                                          Type:
                                                          @@ -15221,7 +15213,7 @@

                                                          Submodules
                                                          -ave_bulk_p[source]
                                                          +ave_bulk_p[source]

                                                          The average locpot of the slab region along the c direction.

                                                          Type:
                                                          @@ -15247,7 +15239,7 @@

                                                          Submodules
                                                          -classmethod from_files(poscar_filename, locpot_filename, outcar_filename, shift=0, blength=3.5) → Self[source]
                                                          +classmethod from_files(poscar_filename, locpot_filename, outcar_filename, shift=0, blength=3.5) → Self[source]

                                                          Initialize a WorkFunctionAnalyzer from POSCAR, LOCPOT, and OUTCAR files.

                                                          Parameters:
                                                          @@ -15271,7 +15263,7 @@

                                                          Submodules
                                                          -get_labels(plt, label_fontsize=10)[source]
                                                          +get_labels(plt, label_fontsize=10)[source]

                                                          Handles the optional labelling of the plot with relevant quantities

                                                          Parameters:
                                                          @@ -15286,7 +15278,7 @@

                                                          Submodules
                                                          -get_locpot_along_slab_plot(label_energies=True, plt=None, label_fontsize=10)[source]
                                                          +get_locpot_along_slab_plot(label_energies=True, plt=None, label_fontsize=10)[source]
                                                          Get a plot of the local potential (eV) vs the

                                                          position along the c axis of the slab model (Ang).

                                                          @@ -15307,7 +15299,7 @@

                                                          Submodules
                                                          -is_converged(min_points_frac=0.015, tol: float = 0.0025)[source]
                                                          +is_converged(min_points_frac=0.015, tol: float = 0.0025)[source]
                                                          A well converged work function should have a flat electrostatic

                                                          potential within some distance (min_point) about where the peak electrostatic potential is found along the c direction of the @@ -15332,7 +15324,7 @@

                                                          Submodules
                                                          -entry_dict_from_list(all_slab_entries) → dict[source]
                                                          +entry_dict_from_list(all_slab_entries) → dict[source]

                                                          Converts a list of SlabEntry to an appropriate dictionary. It is assumed that if there is no adsorbate, then it is a clean SlabEntry and that adsorbed SlabEntry has the clean_entry parameter set.

                                                          @@ -15356,7 +15348,7 @@

                                                          Submodules
                                                          -sub_chempots(gamma_dict, chempots)[source]
                                                          +sub_chempots(gamma_dict, chempots)[source]
                                                          Uses dot product of numpy array to sub chemical potentials

                                                          into the surface grand potential. This is much faster than using the subs function in sympy.

                                                          @@ -15383,7 +15375,7 @@

                                                          Submodules
                                                          -class ThermoData(data_type, cpdname, phaseinfo, formula, value, ref='', method='', temp_range=(298, 298), uncertainty=None)[source]
                                                          +class ThermoData(data_type, cpdname, phaseinfo, formula, value, ref='', method='', temp_range=(298, 298), uncertainty=None)[source]

                                                          Bases: object

                                                          Container for experimental thermo-chemical data.

                                                          @@ -15411,13 +15403,13 @@

                                                          Submodules
                                                          -as_dict()[source]
                                                          +as_dict()[source]

                                                          Get MSONable dict.

                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                          +classmethod from_dict(dct: dict) → Self[source]
                                                          Parameters:

                                                          dct (dict) – Dict representation.

                                                          @@ -15439,7 +15431,7 @@

                                                          Submodules
                                                          -class NEBAnalysis(r, energies, forces, structures, spline_options=None)[source]
                                                          +class NEBAnalysis(r, energies, forces, structures, spline_options=None)[source]

                                                          Bases: MSONable

                                                          An NEBAnalysis class.

                                                          Initialize an NEBAnalysis from the cumulative root mean squared distances @@ -15461,7 +15453,7 @@

                                                          Submodules
                                                          -as_dict()[source]
                                                          +as_dict()[source]

                                                          Dict representation of NEBAnalysis.

                                                          Returns:
                                                          @@ -15472,7 +15464,7 @@

                                                          Submodules
                                                          -classmethod from_dir(root_dir, relaxation_dirs=None, **kwargs) → Self[source]
                                                          +classmethod from_dir(root_dir, relaxation_dirs=None, **kwargs) → Self[source]

                                                          Initialize a NEBAnalysis object from a directory of a NEB run. Note that OUTCARs must be present in all image directories. For the terminal OUTCARs from relaxation calculations, you can specify the @@ -15513,7 +15505,7 @@

                                                          Submodules
                                                          -classmethod from_outcars(outcars, structures, **kwargs) → Self[source]
                                                          +classmethod from_outcars(outcars, structures, **kwargs) → Self[source]

                                                          Initialize an NEBAnalysis from Outcar and Structure objects. Use the static constructors, e.g. from_dir instead if you prefer to have these automatically generated from a directory of NEB @@ -15535,7 +15527,7 @@

                                                          Submodules
                                                          -get_extrema(normalize_rxn_coordinate=True)[source]
                                                          +get_extrema(normalize_rxn_coordinate=True)[source]

                                                          Get the positions of the extrema along the MEP. Both local minimums and maximums are returned.

                                                          @@ -15554,7 +15546,7 @@

                                                          Submodules
                                                          -get_plot(normalize_rxn_coordinate: bool = True, label_barrier: bool = True) → Axes[source]
                                                          +get_plot(normalize_rxn_coordinate: bool = True, label_barrier: bool = True) → Axes[source]

                                                          Get an NEB plot. Uses Henkelman’s approach of spline fitting each section of the reaction path based on tangent force and energies.

                                                          @@ -15576,7 +15568,7 @@

                                                          Submodules
                                                          -setup_spline(spline_options=None)[source]
                                                          +setup_spline(spline_options=None)[source]

                                                          Setup of the options for the spline interpolation.

                                                          Parameters:
                                                          @@ -15591,7 +15583,7 @@

                                                          Submodules
                                                          -combine_neb_plots(neb_analyses, arranged_neb_analyses=False, reverse_plot=False)[source]
                                                          +combine_neb_plots(neb_analyses, arranged_neb_analyses=False, reverse_plot=False)[source]

                                                          neb_analyses: a list of NEBAnalysis objects.

                                                          arranged_neb_analyses: The code connects two end points with the smallest-energy difference. If all end points have very close energies, it’s @@ -15625,7 +15617,7 @@

                                                          Submodules
                                                          -class WulffFacet(normal, e_surf, normal_pt, dual_pt, index, m_ind_orig, miller)[source]
                                                          +class WulffFacet(normal, e_surf, normal_pt, dual_pt, index, m_ind_orig, miller)[source]

                                                          Bases: object

                                                          Helper container for each Wulff plane.

                                                          @@ -15645,7 +15637,7 @@

                                                          Submodules
                                                          -class WulffShape(lattice: Lattice, miller_list, e_surf_list, symprec=1e-05)[source]
                                                          +class WulffShape(lattice: Lattice, miller_list, e_surf_list, symprec=1e-05)[source]

                                                          Bases: object

                                                          Generate Wulff Shape from list of miller index and surface energies, with given conventional unit cell. @@ -15663,7 +15655,7 @@

                                                          Submodules
                                                          -debug[source]
                                                          +debug[source]

                                                          Whether to print debug information.

                                                          Type:
                                                          @@ -15674,7 +15666,7 @@

                                                          Submodules
                                                          -alpha[source]
                                                          +alpha[source]

                                                          Transparency of the Wulff shape.

                                                          Type:
                                                          @@ -15685,7 +15677,7 @@

                                                          Submodules
                                                          -color_set[source]
                                                          +color_set[source]

                                                          colors to use for facets.

                                                          Type:
                                                          @@ -15696,7 +15688,7 @@

                                                          Submodules
                                                          -grid_off[source]
                                                          +grid_off[source]

                                                          Whether to turn off the grid.

                                                          Type:
                                                          @@ -15707,7 +15699,7 @@

                                                          Submodules
                                                          -axis_off[source]
                                                          +axis_off[source]

                                                          Whether to turn off the axis.

                                                          Type:
                                                          @@ -15718,7 +15710,7 @@

                                                          Submodules
                                                          -show_area[source]
                                                          +show_area[source]

                                                          Whether to show the area of each facet.

                                                          Type:
                                                          @@ -15729,7 +15721,7 @@

                                                          Submodules
                                                          -off_color[source]
                                                          +off_color[source]

                                                          Color of facets not on the Wulff shape.

                                                          Type:
                                                          @@ -15740,7 +15732,7 @@

                                                          Submodules
                                                          -structure[source]
                                                          +structure[source]

                                                          Input conventional unit cell (with H) from lattice.

                                                          Type:
                                                          @@ -15751,7 +15743,7 @@

                                                          Submodules
                                                          -miller_list[source]
                                                          +miller_list[source]

                                                          input Miller indices, for hcp in the form of hkil.

                                                          Type:
                                                          @@ -15762,7 +15754,7 @@

                                                          Submodules
                                                          -hkl_list[source]
                                                          +hkl_list[source]

                                                          Modified Miller indices in the same order as input_miller.

                                                          Type:
                                                          @@ -15773,7 +15765,7 @@

                                                          Submodules
                                                          -e_surf_list[source]
                                                          +e_surf_list[source]

                                                          input surface energies in the same order as input_miller.

                                                          Type:
                                                          @@ -15784,7 +15776,7 @@

                                                          Submodules
                                                          -lattice[source]
                                                          +lattice[source]

                                                          Input lattice for the conventional unit cell.

                                                          Type:
                                                          @@ -15795,7 +15787,7 @@

                                                          Submodules
                                                          -facets[source]
                                                          +facets[source]

                                                          WulffFacet objects considering symmetry.

                                                          Type:
                                                          @@ -15806,7 +15798,7 @@

                                                          Submodules
                                                          -dual_cv_simp[source]
                                                          +dual_cv_simp[source]

                                                          Simplices from the dual convex hull (dual_pt).

                                                          Type:
                                                          @@ -15817,7 +15809,7 @@

                                                          Submodules
                                                          -wulff_pt_list[source]
                                                          +wulff_pt_list[source]

                                                          Wulff points.

                                                          Type:
                                                          @@ -15828,7 +15820,7 @@

                                                          Submodules
                                                          -wulff_cv_simp[source]
                                                          +wulff_cv_simp[source]

                                                          Simplices from the convex hull of wulff_pt_list.

                                                          Type:
                                                          @@ -15839,7 +15831,7 @@

                                                          Submodules
                                                          -on_wulff[source]
                                                          +on_wulff[source]

                                                          List for all input_miller, True if on the Wulff shape.

                                                          Type:
                                                          @@ -15850,7 +15842,7 @@

                                                          Submodules
                                                          -color_area[source]
                                                          +color_area[source]

                                                          List for all input_miller, total area on the Wulff shape, off_wulff = 0.

                                                          Type:
                                                          @@ -15861,7 +15853,7 @@

                                                          Submodules
                                                          -miller_area[source]
                                                          +miller_area[source]

                                                          Dictionary of Miller indices and their corresponding areas.

                                                          Type:
                                                          @@ -15882,21 +15874,21 @@

                                                          Submodules
                                                          -property anisotropy: float[source]
                                                          +property anisotropy: float[source]

                                                          Returns: float: Coefficient of Variation from weighted surface energy. The ideal sphere is 0.

                                                          -property area_fraction_dict: dict[tuple, float][source]
                                                          +property area_fraction_dict: dict[tuple, float][source]

                                                          Returns: dict: {hkl: area_hkl/total area on wulff}.

                                                          -property effective_radius: float[source]
                                                          +property effective_radius: float[source]

                                                          Radius of the WulffShape (in Angstroms) when the WulffShape is approximated as a sphere.

                                                          Returns:
                                                          @@ -15910,13 +15902,13 @@

                                                          Submodules
                                                          -get_line_in_facet(facet)[source]
                                                          +get_line_in_facet(facet)[source]

                                                          Get the sorted pts in a facet used to draw a line.

                                                          -get_plot(color_set='PuBu', grid_off=True, axis_off=True, show_area=False, alpha=1, off_color='red', direction=None, bar_pos=(0.75, 0.15, 0.05, 0.65), bar_on=False, units_in_JPERM2=True, legend_on=True, aspect_ratio=(8, 8), custom_colors=None)[source]
                                                          +get_plot(color_set='PuBu', grid_off=True, axis_off=True, show_area=False, alpha=1, off_color='red', direction=None, bar_pos=(0.75, 0.15, 0.05, 0.65), bar_on=False, units_in_JPERM2=True, legend_on=True, aspect_ratio=(8, 8), custom_colors=None)[source]

                                                          Get the Wulff shape plot.

                                                          Parameters:
                                                          @@ -15962,7 +15954,7 @@

                                                          Submodules
                                                          -get_plotly(color_set='PuBu', off_color='red', alpha=1, custom_colors=None, units_in_JPERM2=True)[source]
                                                          +get_plotly(color_set='PuBu', off_color='red', alpha=1, custom_colors=None, units_in_JPERM2=True)[source]

                                                          Get the Wulff shape as a plotly Figure object.

                                                          Parameters:
                                                          @@ -15997,7 +15989,7 @@

                                                          Submodules
                                                          -property miller_area_dict: dict[tuple, float][source]
                                                          +property miller_area_dict: dict[tuple, float][source]

                                                          area_hkl on wulff}.

                                                          Type:
                                                          @@ -16008,7 +16000,7 @@

                                                          Submodules
                                                          -property miller_energy_dict: dict[tuple, float][source]
                                                          +property miller_energy_dict: dict[tuple, float][source]

                                                          surface energy_hkl}.

                                                          Type:
                                                          @@ -16019,7 +16011,7 @@

                                                          Submodules
                                                          -property shape_factor: float[source]
                                                          +property shape_factor: float[source]

                                                          Determine the critical nucleus size. A large shape factor indicates great anisotropy. See Ballufi, R. W., Allen, S. M. & Carter, W. C. Kinetics

                                                          @@ -16038,7 +16030,7 @@

                                                          Submodules
                                                          -show(*args, **kwargs)[source]
                                                          +show(*args, **kwargs)[source]

                                                          Show the Wulff plot.

                                                          Parameters:
                                                          @@ -16052,27 +16044,27 @@

                                                          Submodules
                                                          -property surface_area: float[source]
                                                          +property surface_area: float[source]

                                                          Total surface area of Wulff shape.

                                                          -property tot_corner_sites[source]
                                                          +property tot_corner_sites[source]

                                                          The number of vertices in the convex hull. Useful for identifying catalytically active sites.

                                                          -property tot_edges[source]
                                                          +property tot_edges[source]

                                                          The number of edges in the convex hull. Useful for identifying catalytically active sites.

                                                          -property total_surface_energy: float[source]
                                                          +property total_surface_energy: float[source]

                                                          Total surface energy of the Wulff shape.

                                                          Returns:
                                                          @@ -16086,13 +16078,13 @@

                                                          Submodules
                                                          -property volume: float[source]
                                                          +property volume: float[source]

                                                          Volume of the Wulff shape.

                                                          -property weighted_surface_energy: float[source]
                                                          +property weighted_surface_energy: float[source]

                                                          Returns: sum(surface_energy_hkl * area_hkl)/ sum(area_hkl).

                                                          @@ -16101,7 +16093,7 @@

                                                          Submodules
                                                          -get_tri_area(pts)[source]
                                                          +get_tri_area(pts)[source]

                                                          Given a list of coords for 3 points, Compute the area of this triangle.

                                                          @@ -16113,7 +16105,7 @@

                                                          Submodules
                                                          -hkl_tuple_to_str(hkl)[source]
                                                          +hkl_tuple_to_str(hkl)[source]

                                                          Prepare for display on plots “(hkl)” for surfaces

                                                          Parameters:
                                                          @@ -16142,7 +16134,7 @@

                                                          Submodules
                                                          -class XPS(x: NDArray, y: NDArray, *args, **kwargs)[source]
                                                          +class XPS(x: NDArray, y: NDArray, *args, **kwargs)[source]

                                                          Bases: Spectrum

                                                          An X-ray photoelectron spectra.

                                                          @@ -16161,17 +16153,17 @@

                                                          Submodules
                                                          -XLABEL = 'Binding Energy (eV)'[source]
                                                          +XLABEL = 'Binding Energy (eV)'[source]

                                                          -YLABEL = 'Intensity'[source]
                                                          +YLABEL = 'Intensity'[source]
                                                          -classmethod from_dos(dos: CompleteDos) → Self[source]
                                                          +classmethod from_dos(dos: CompleteDos) → Self[source]
                                                          Parameters:
                                                          -film_transformation: list[source]
                                                          +film_transformation: list[source]
                                                          -film_vectors: list[source]
                                                          +film_vectors: list[source]
                                                          -property match_area[source]
                                                          +property match_area[source]

                                                          The area of the match between the substrate and film super lattice vectors.

                                                          -property match_transformation[source]
                                                          +property match_transformation[source]

                                                          The transformation matrix to convert the film super lattice vectors to the substrate.

                                                          -substrate_sl_vectors: list[source]
                                                          +substrate_sl_vectors: list[source]
                                                          -substrate_transformation: list[source]
                                                          +substrate_transformation: list[source]
                                                          -substrate_vectors: list[source]
                                                          +substrate_vectors: list[source]
                                                          -fast_norm(a)[source]
                                                          +fast_norm(a)[source]

                                                          Much faster variant of numpy linalg norm.

                                                          Note that if numba is installed, this cannot be provided a list of ints; please ensure input a is an np.array of floats.

                                                          @@ -487,7 +487,7 @@

                                                          Submodules
                                                          -gen_sl_transform_matrices(area_multiple)[source]
                                                          +gen_sl_transform_matrices(area_multiple)[source]

                                                          Generates the transformation matrices that convert a set of 2D vectors into a super lattice of integer area multiple as proven in Cassels:

                                                          @@ -512,13 +512,13 @@

                                                          Submodules
                                                          -get_factors(n)[source]
                                                          +get_factors(n)[source]

                                                          Generate all factors of n.

                                                          -is_same_vectors(vec_set1, vec_set2, bidirectional=False, max_length_tol=0.03, max_angle_tol=0.01) → bool[source]
                                                          +is_same_vectors(vec_set1, vec_set2, bidirectional=False, max_length_tol=0.03, max_angle_tol=0.01) → bool[source]

                                                          Determine if two sets of vectors are the same within length and angle tolerances :param vec_set1: an array of two vectors @@ -529,14 +529,14 @@

                                                          Submodules
                                                          -reduce_vectors(a, b)[source]
                                                          +reduce_vectors(a, b)[source]

                                                          Generate independent and unique basis vectors based on the methodology of Zur and McGill.

                                                          -rel_angle(vec_set1, vec_set2)[source]
                                                          +rel_angle(vec_set1, vec_set2)[source]

                                                          Calculate the relative angle between two vector sets.

                                                          Parameters:
                                                          @@ -550,19 +550,19 @@

                                                          Submodules
                                                          -rel_strain(vec1, vec2)[source]
                                                          +rel_strain(vec1, vec2)[source]

                                                          Calculate relative strain between two vectors.

                                                          -vec_angle(a, b)[source]
                                                          +vec_angle(a, b)[source]

                                                          Calculate angle between two vectors.

                                                          -vec_area(a, b)[source]
                                                          +vec_area(a, b)[source]

                                                          Area of lattice plane defined by two vectors.

                                                          diff --git a/docs/pymatgen.analysis.magnetism.html b/docs/pymatgen.analysis.magnetism.html index 6070f7ebeee..3091c5d7075 100644 --- a/docs/pymatgen.analysis.magnetism.html +++ b/docs/pymatgen.analysis.magnetism.html @@ -4,7 +4,7 @@ - pymatgen.analysis.magnetism package — pymatgen 2024.6.4 documentation + pymatgen.analysis.magnetism package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                          - 2024.6.4 + 2024.6.10
                                                          @@ -179,7 +179,7 @@

                                                          Submodules
                                                          -class CollinearMagneticStructureAnalyzer(structure: Structure, overwrite_magmom_mode: str | OverwriteMagmomMode = OverwriteMagmomMode.none, round_magmoms: bool = False, detect_valences: bool = False, make_primitive: bool = True, default_magmoms: dict | None = None, set_net_positive: bool = True, threshold: float = 0, threshold_nonmag: float = 0.1, threshold_ordering: float = 1e-08)[source]
                                                          +class CollinearMagneticStructureAnalyzer(structure: Structure, overwrite_magmom_mode: str | OverwriteMagmomMode = OverwriteMagmomMode.none, round_magmoms: bool = False, detect_valences: bool = False, make_primitive: bool = True, default_magmoms: dict | None = None, set_net_positive: bool = True, threshold: float = 0, threshold_nonmag: float = 0.1, threshold_ordering: float = 1e-08)[source]

                                                          Bases: object

                                                          A class which provides a few helpful methods to analyze collinear magnetic structures.

                                                          @@ -240,7 +240,7 @@

                                                          Submodules
                                                          -get_exchange_group_info(symprec: float = 0.01, angle_tolerance: float = 5) → tuple[str, int][source]
                                                          +get_exchange_group_info(symprec: float = 0.01, angle_tolerance: float = 5) → tuple[str, int][source]

                                                          Get the information on the symmetry of the Hamiltonian describing the exchange energy of the system, taking into account relative direction of magnetic moments but not their @@ -264,7 +264,7 @@

                                                          Submodules
                                                          -get_ferromagnetic_structure(make_primitive: bool = True) → Structure[source]
                                                          +get_ferromagnetic_structure(make_primitive: bool = True) → Structure[source]

                                                          Get a Structure with all magnetic moments positive or zero.

                                                          @@ -280,7 +280,7 @@

                                                          Submodules
                                                          -get_nonmagnetic_structure(make_primitive: bool = True) → Structure[source]
                                                          +get_nonmagnetic_structure(make_primitive: bool = True) → Structure[source]

                                                          Get a Structure without magnetic moments defined.

                                                          Parameters:
                                                          @@ -295,7 +295,7 @@

                                                          Submodules
                                                          -get_structure_with_only_magnetic_atoms(make_primitive: bool = True) → Structure[source]
                                                          +get_structure_with_only_magnetic_atoms(make_primitive: bool = True) → Structure[source]

                                                          Get a Structure with only magnetic atoms present.

                                                          Parameters:
                                                          @@ -310,26 +310,26 @@

                                                          Submodules
                                                          -get_structure_with_spin() → Structure[source]
                                                          +get_structure_with_spin() → Structure[source]

                                                          Get a Structure with species decorated with spin values instead of using magmom site properties.

                                                          -property is_magnetic: bool[source]
                                                          +property is_magnetic: bool[source]

                                                          Convenience property, returns True if any non-zero magmoms present.

                                                          -property magmoms: ndarray[source]
                                                          +property magmoms: ndarray[source]

                                                          Convenience property, returns magmoms as a numpy array.

                                                          -property magnetic_species_and_magmoms: dict[str, Any][source]
                                                          +property magnetic_species_and_magmoms: dict[str, Any][source]

                                                          A dict of magnetic species and the magnitude of their associated magmoms. Will return a list if there are multiple magmoms per species.

                                                          @@ -342,7 +342,7 @@

                                                          Submodules
                                                          -matches_ordering(other: Structure) → bool[source]
                                                          +matches_ordering(other: Structure) → bool[source]

                                                          Compares the magnetic orderings of one structure with another.

                                                          Parameters:
                                                          @@ -359,13 +359,13 @@

                                                          Submodules
                                                          -property number_of_magnetic_sites: int[source]
                                                          +property number_of_magnetic_sites: int[source]

                                                          Number of magnetic sites present in structure.

                                                          -number_of_unique_magnetic_sites(symprec: float = 0.001, angle_tolerance: float = 5) → int[source]
                                                          +number_of_unique_magnetic_sites(symprec: float = 0.001, angle_tolerance: float = 5) → int[source]
                                                          Parameters:
                                                          -property types_of_magnetic_species: tuple[Element | Species | DummySpecies, ...][source]
                                                          +property types_of_magnetic_species: tuple[Element | Species | DummySpecies, ...][source]

                                                          Equivalent to Structure.types_of_specie but only returns magnetic species.

                                                          Returns:
                                                          @@ -429,18 +429,18 @@

                                                          Submodules
                                                          -class MagneticDeformation(deformation, type)[source]
                                                          +class MagneticDeformation(deformation, type)[source]

                                                          Bases: NamedTuple

                                                          Create new instance of MagneticDeformation(deformation, type)

                                                          -deformation: float[source]
                                                          +deformation: float[source]

                                                          Alias for field number 0

                                                          -type: str[source]
                                                          +type: str[source]

                                                          Alias for field number 1

                                                          @@ -448,7 +448,7 @@

                                                          Submodules
                                                          -class MagneticStructureEnumerator(structure: Structure, default_magmoms: dict[str, float] | None = None, strategies: list[str] | tuple[str, ...] = ('ferromagnetic', 'antiferromagnetic'), automatic: bool = True, truncate_by_symmetry: bool = True, transformation_kwargs: dict | None = None)[source]
                                                          +class MagneticStructureEnumerator(structure: Structure, default_magmoms: dict[str, float] | None = None, strategies: list[str] | tuple[str, ...] = ('ferromagnetic', 'antiferromagnetic'), automatic: bool = True, truncate_by_symmetry: bool = True, transformation_kwargs: dict | None = None)[source]

                                                          Bases: object

                                                          Combines MagneticStructureAnalyzer and MagOrderingTransformation to automatically generate a set of transformations for a given structure @@ -481,83 +481,83 @@

                                                          Submodules
                                                          -available_strategies = ('ferromagnetic', 'antiferromagnetic', 'ferrimagnetic_by_motif', 'ferrimagnetic_by_species', 'antiferromagnetic_by_motif', 'nonmagnetic')[source]
                                                          +available_strategies = ('ferromagnetic', 'antiferromagnetic', 'ferrimagnetic_by_motif', 'ferrimagnetic_by_species', 'antiferromagnetic_by_motif', 'nonmagnetic')[source]

                                                          -class Ordering(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                          +class Ordering(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                          Bases: Enum

                                                          Enumeration defining possible magnetic orderings.

                                                          -AFM = 'AFM'[source]
                                                          +AFM = 'AFM'[source]
                                                          -FM = 'FM'[source]
                                                          +FM = 'FM'[source]
                                                          -FiM = 'FiM'[source]
                                                          +FiM = 'FiM'[source]
                                                          -NM = 'NM'[source]
                                                          +NM = 'NM'[source]
                                                          -Unknown = 'Unknown'[source]
                                                          +Unknown = 'Unknown'[source]
                                                          -class OverwriteMagmomMode(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                          +class OverwriteMagmomMode(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                          Bases: Enum

                                                          Enumeration defining different modes for analyzer.

                                                          -none = 'none'[source]
                                                          +none = 'none'[source]
                                                          -normalize = 'normalize'[source]
                                                          +normalize = 'normalize'[source]
                                                          -replace_all = 'replace_all'[source]
                                                          +replace_all = 'replace_all'[source]
                                                          -replace_all_if_undefined = 'replace_all_if_undefined'[source]
                                                          +replace_all_if_undefined = 'replace_all_if_undefined'[source]
                                                          -respect_sign = 'respect_sign'[source]
                                                          +respect_sign = 'respect_sign'[source]
                                                          -respect_zeros = 'respect_zeros'[source]
                                                          +respect_zeros = 'respect_zeros'[source]
                                                          -magnetic_deformation(structure_A: Structure, structure_B: Structure) → MagneticDeformation[source]
                                                          +magnetic_deformation(structure_A: Structure, structure_B: Structure) → MagneticDeformation[source]

                                                          Calculate ‘magnetic deformation proxy’, a measure of deformation (norm of finite strain) between ‘non-magnetic’ (non-spin-polarized) and @@ -585,12 +585,12 @@

                                                          Submodules
                                                          -class HeisenbergMapper(ordered_structures, energies, cutoff=0, tol: float = 0.02)[source]
                                                          +class HeisenbergMapper(ordered_structures, energies, cutoff=0, tol: float = 0.02)[source]

                                                          Bases: object

                                                          Compute exchange parameters from low energy magnetic orderings.

                                                          -strategy[source]
                                                          +strategy[source]

                                                          Class from pymatgen.analysis.local_env for constructing graphs.

                                                          Type:
                                                          @@ -601,7 +601,7 @@

                                                          Submodules
                                                          -sgraphs[source]
                                                          +sgraphs[source]

                                                          StructureGraph objects.

                                                          Type:
                                                          @@ -612,7 +612,7 @@

                                                          Submodules
                                                          -unique_site_ids[source]
                                                          +unique_site_ids[source]

                                                          Maps each site to its unique numerical identifier.

                                                          Type:
                                                          @@ -623,7 +623,7 @@

                                                          Submodules
                                                          -wyckoff_ids[source]
                                                          +wyckoff_ids[source]

                                                          Maps unique numerical identifier to wyckoff position.

                                                          Type:
                                                          @@ -634,7 +634,7 @@

                                                          Submodules
                                                          -nn_interactions[source]
                                                          +nn_interactions[source]

                                                          {i: j} pairs of NN interactions between unique sites.

                                                          Type:
                                                          @@ -645,7 +645,7 @@

                                                          Submodules
                                                          -dists[source]
                                                          +dists[source]

                                                          NN, NNN, and NNNN interaction distances

                                                          Type:
                                                          @@ -656,7 +656,7 @@

                                                          Submodules
                                                          -ex_mat[source]
                                                          +ex_mat[source]

                                                          Invertible Heisenberg Hamiltonian for each graph.

                                                          Type:
                                                          @@ -667,7 +667,7 @@

                                                          Submodules
                                                          -ex_params[source]
                                                          +ex_params[source]

                                                          Exchange parameter values (meV/atom)

                                                          Type:
                                                          @@ -700,7 +700,7 @@

                                                          Submodules
                                                          -estimate_exchange(fm_struct=None, afm_struct=None, fm_e=None, afm_e=None)[source]
                                                          +estimate_exchange(fm_struct=None, afm_struct=None, fm_e=None, afm_e=None)[source]

                                                          Estimate <J> for a structure based on low energy FM and AFM orderings.

                                                          Parameters:
                                                          @@ -722,7 +722,7 @@

                                                          Submodules
                                                          -get_exchange()[source]
                                                          +get_exchange()[source]

                                                          Take Heisenberg Hamiltonian and corresponding energy for each row and solve for the exchange parameters.

                                                          @@ -737,7 +737,7 @@

                                                          Submodules
                                                          -get_heisenberg_model()[source]
                                                          +get_heisenberg_model()[source]

                                                          Save results of mapping to a HeisenbergModel object.

                                                          Returns:
                                                          @@ -751,7 +751,7 @@

                                                          Submodules
                                                          -get_interaction_graph(filename=None)[source]
                                                          +get_interaction_graph(filename=None)[source]

                                                          Get a StructureGraph with edges and weights that correspond to exchange interactions and J_ij values, respectively.

                                                          @@ -769,7 +769,7 @@

                                                          Submodules
                                                          -get_low_energy_orderings()[source]
                                                          +get_low_energy_orderings()[source]

                                                          Find lowest energy FM and AFM orderings to compute E_AFM - E_FM.

                                                          Returns:
                                                          @@ -786,7 +786,7 @@

                                                          Submodules
                                                          -get_mft_temperature(j_avg)[source]
                                                          +get_mft_temperature(j_avg)[source]

                                                          Crude mean field estimate of critical temperature based on <J> for one sublattice, or solving the coupled equations for a multi-sublattice material.

                                                          @@ -807,7 +807,7 @@

                                                          Submodules
                                                          -class HeisenbergModel(formula=None, structures=None, energies=None, cutoff=None, tol=None, sgraphs=None, unique_site_ids=None, wyckoff_ids=None, nn_interactions=None, dists=None, ex_mat=None, ex_params=None, javg=None, igraph=None)[source]
                                                          +class HeisenbergModel(formula=None, structures=None, energies=None, cutoff=None, tol=None, sgraphs=None, unique_site_ids=None, wyckoff_ids=None, nn_interactions=None, dists=None, ex_mat=None, ex_params=None, javg=None, igraph=None)[source]

                                                          Bases: MSONable

                                                          Store a Heisenberg model fit to low-energy magnetic orderings. Intended to be generated by HeisenbergMapper.get_heisenberg_model().

                                                          @@ -837,13 +837,13 @@

                                                          Submodules
                                                          -as_dict()[source]
                                                          +as_dict()[source]

                                                          Because some dicts have tuple keys, some sanitization is required for JSON compatibility.

                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                          +classmethod from_dict(dct: dict) → Self[source]

                                                          Create a HeisenbergModel from a dict.

                                                          @@ -851,7 +851,7 @@

                                                          Submodules
                                                          -class HeisenbergScreener(structures, energies, screen=False)[source]
                                                          +class HeisenbergScreener(structures, energies, screen=False)[source]

                                                          Bases: object

                                                          Clean and screen magnetic orderings.

                                                          Pre-processes magnetic orderings and energies for HeisenbergMapper. @@ -867,7 +867,7 @@

                                                          Submodules
                                                          -screened_structures[source]
                                                          +screened_structures[source]

                                                          Sorted structures.

                                                          Type:
                                                          @@ -878,7 +878,7 @@

                                                          Submodules
                                                          -screened_energies[source]
                                                          +screened_energies[source]

                                                          Sorted energies.

                                                          Type:
                                                          @@ -895,7 +895,7 @@

                                                          Submodules
                                                          -class JahnTellerAnalyzer[source]
                                                          +class JahnTellerAnalyzer[source]

                                                          Bases: object

                                                          Will attempt to classify if structure may be Jahn-Teller active. Class currently uses datafile of hard-coded common Jahn-Teller @@ -906,7 +906,7 @@

                                                          Submodules
                                                          -get_analysis(structure: Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → dict[source]
                                                          +get_analysis(structure: Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → dict[source]

                                                          Convenience method, uses get_analysis_and_structure method.

                                                          Obtain an analysis of a given structure and if it may be Jahn-Teller active or not. This is a heuristic, and may give false positives and @@ -934,7 +934,7 @@

                                                          Submodules
                                                          -get_analysis_and_structure(structure: Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → tuple[dict, Structure][source]
                                                          +get_analysis_and_structure(structure: Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → tuple[dict, Structure][source]

                                                          Obtain an analysis of a given structure and if it may be Jahn-Teller active or not. This is a heuristic, and may give false positives and false negatives (false positives are preferred).

                                                          @@ -961,7 +961,7 @@

                                                          Submodules
                                                          -get_magnitude_of_effect_from_species(species: str | Species, spin_state: str, motif: str) → str[source]
                                                          +get_magnitude_of_effect_from_species(species: str | Species, spin_state: str, motif: str) → str[source]

                                                          Get magnitude of Jahn-Teller effect from provided species, spin state and motif.

                                                          Parameters:
                                                          @@ -982,7 +982,7 @@

                                                          Submodules
                                                          -static get_magnitude_of_effect_from_spin_config(motif: str, spin_config: dict[str, float]) → str[source]
                                                          +static get_magnitude_of_effect_from_spin_config(motif: str, spin_config: dict[str, float]) → str[source]

                                                          Roughly, the magnitude of Jahn-Teller distortion will be: * in octahedral environments, strong if e_g orbitals unevenly occupied but weak if t_2g orbitals unevenly @@ -1006,7 +1006,7 @@

                                                          Submodules
                                                          -is_jahn_teller_active(structure: Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → bool[source]
                                                          +is_jahn_teller_active(structure: Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → bool[source]

                                                          Convenience method, uses get_analysis_and_structure method. Check if a given structure and if it may be Jahn-Teller active or not. This is a heuristic, and may give false positives and @@ -1033,7 +1033,7 @@

                                                          Submodules
                                                          -static mu_so(species: str | Species, motif: Literal['oct', 'tet'], spin_state: Literal['high', 'low']) → float | None[source]
                                                          +static mu_so(species: str | Species, motif: Literal['oct', 'tet'], spin_state: Literal['high', 'low']) → float | None[source]

                                                          Calculate the spin-only magnetic moment for a given species. Only supports transition metals.

                                                          Parameters:
                                                          @@ -1058,7 +1058,7 @@

                                                          Submodules
                                                          -tag_structure(structure: Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → Structure[source]
                                                          +tag_structure(structure: Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → Structure[source]

                                                          Convenience method, uses get_analysis_and_structure method. Add a “possible_jt_active” site property on Structure.

                                                          diff --git a/docs/pymatgen.analysis.solar.html b/docs/pymatgen.analysis.solar.html index 6482797f847..735a3a187b5 100644 --- a/docs/pymatgen.analysis.solar.html +++ b/docs/pymatgen.analysis.solar.html @@ -4,7 +4,7 @@ - pymatgen.analysis.solar package — pymatgen 2024.6.4 documentation + pymatgen.analysis.solar package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                          - 2024.6.4 + 2024.6.10
                                                          @@ -49,15 +49,7 @@
                                                          @@ -92,123 +84,8 @@

                                                          Submodules

                                                          -
                                                          -

                                                          pymatgen.analysis.solar.slme module

                                                          -

                                                          Calculate spectroscopy limited maximum efficiency (SLME) given dielectric function data.

                                                          -

                                                          Forked and adjusted from : -https://github.com/usnistgov/jarvis

                                                          -
                                                          -
                                                          References: 1) https://doi.org/10.1021/acs.chemmater.9b02166 &
                                                            -

                                                          1. https://doi.org/10.1103/PhysRevLett.108.068701

                                                            2. -
                                                          -
                                                          -
                                                          -
                                                          -
                                                          -absorption_coefficient(dielectric)[source]
                                                          -

                                                          Calculate the optical absorption coefficient from an input set of -pymatgen vasprun dielectric constant data.

                                                          -
                                                          -
                                                          Parameters:
                                                          -

                                                          dielectric (list) – A list containing the dielectric response function -in the pymatgen vasprun format. -- element 0: list of energies -- element 1: real dielectric tensors, in [xx, yy, zz, xy, xz, yz] format. -- element 2: imaginary dielectric tensors, in [xx, yy, zz, xy, xz, yz] format.

                                                          -
                                                          -
                                                          Returns:
                                                          -

                                                          absorption coefficient using eV as frequency units (cm^-1).

                                                          -
                                                          -
                                                          Return type:
                                                          -

                                                          np.array

                                                          -
                                                          -
                                                          -
                                                          - -
                                                          -
                                                          -get_dir_indir_gap(run='')[source]
                                                          -

                                                          Get direct and indirect bandgaps for a vasprun.xml.

                                                          -
                                                          - -
                                                          -
                                                          -optics(path='')[source]
                                                          -

                                                          Helper function to calculate optical absorption coefficient.

                                                          -
                                                          - -
                                                          -
                                                          -parse_dielectric_data(data)[source]
                                                          -

                                                          Convert a set of 2D vasprun formatted dielectric data to -the eigenvalues of each corresponding 3x3 symmetric numpy matrices.

                                                          -
                                                          -
                                                          Parameters:
                                                          -

                                                          data (list) – length N list of dielectric data. Each entry should be -a list of [xx, yy, zz, xy , xz, yz ] dielectric tensor elements.

                                                          -
                                                          -
                                                          Returns:
                                                          -

                                                          -
                                                          a Nx3 numpy array. Each row contains the eigenvalues

                                                          for the corresponding row in data.

                                                          -
                                                          -
                                                          -

                                                          -
                                                          -
                                                          Return type:
                                                          -

                                                          np.array

                                                          -
                                                          -
                                                          -
                                                          - -
                                                          -
                                                          -slme(material_energy_for_absorbance_data, material_absorbance_data, material_direct_allowed_gap, material_indirect_gap, thickness=5e-05, temperature=293.15, absorbance_in_inverse_centimeters=False, cut_off_absorbance_below_direct_allowed_gap=True, plot_current_voltage=False)[source]
                                                          -

                                                          Calculate the SLME.

                                                          -
                                                          -
                                                          Parameters:
                                                          -
                                                            -

                                                          • material_energy_for_absorbance_data – energy grid for absorbance data

                                                            • -

                                                          • material_absorbance_data – absorption coefficient in m^-1

                                                            • -

                                                          • material_direct_allowed_gap – direct bandgap in eV

                                                            • -

                                                          • material_indirect_gap – indirect bandgap in eV

                                                            • -

                                                          • thickness – thickness of the material in m

                                                            • -

                                                          • temperature – working temperature in K

                                                            • -

                                                          • absorbance_in_inverse_centimeters – whether the absorbance data is in the unit of cm^-1

                                                            • -

                                                          • cut_off_absorbance_below_direct_allowed_gap – whether to discard all absorption below bandgap

                                                            • -

                                                          • plot_current_voltage – whether to plot the current-voltage curve

                                                            • -
                                                          -
                                                          -
                                                          Returns:
                                                          -

                                                          The calculated maximum efficiency.

                                                          -
                                                          -
                                                          -
                                                          - -
                                                          -
                                                          -to_matrix(xx, yy, zz, xy, yz, xz)[source]
                                                          -

                                                          Convert a list of matrix components to a symmetric 3x3 matrix. -Inputs should be in the order xx, yy, zz, xy, yz, xz.

                                                          -
                                                          -
                                                          Parameters:
                                                          -
                                                            -

                                                          • xx (float) – xx component of the matrix.

                                                            • -

                                                          • yy (float) – yy component of the matrix.

                                                            • -

                                                          • zz (float) – zz component of the matrix.

                                                            • -

                                                          • xy (float) – xy component of the matrix.

                                                            • -

                                                          • yz (float) – yz component of the matrix.

                                                            • -

                                                          • xz (float) – xz component of the matrix.

                                                            • -
                                                          -
                                                          -
                                                          Returns:
                                                          -

                                                          The matrix, as a 3x3 numpy array.

                                                          -
                                                          -
                                                          Return type:
                                                          -

                                                          np.array

                                                          -
                                                          -
                                                          -
                                                          - +
                                                          +

                                                          pymatgen.analysis.solar.slme module

                                                          diff --git a/docs/pymatgen.analysis.structure_prediction.html b/docs/pymatgen.analysis.structure_prediction.html index 910463b5208..1ab5134270c 100644 --- a/docs/pymatgen.analysis.structure_prediction.html +++ b/docs/pymatgen.analysis.structure_prediction.html @@ -4,7 +4,7 @@ - pymatgen.analysis.structure_prediction package — pymatgen 2024.6.4 documentation + pymatgen.analysis.structure_prediction package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                          - 2024.6.4 + 2024.6.10
                                                          @@ -128,7 +128,7 @@

                                                          Submodules
                                                          -get_dopants_from_shannon_radii(bonded_structure, num_dopants=5, match_oxi_sign=False)[source]
                                                          +get_dopants_from_shannon_radii(bonded_structure, num_dopants=5, match_oxi_sign=False)[source]

                                                          Get dopant suggestions based on Shannon radii differences.

                                                          Parameters:
                                                          @@ -165,7 +165,7 @@

                                                          Submodules
                                                          -get_dopants_from_substitution_probabilities(structure, num_dopants=5, threshold=0.001, match_oxi_sign=False) → dict[source]
                                                          +get_dopants_from_substitution_probabilities(structure, num_dopants=5, threshold=0.001, match_oxi_sign=False) → dict[source]

                                                          Get dopant suggestions based on substitution probabilities.

                                                          Parameters:
                                                          @@ -206,7 +206,7 @@

                                                          Submodules
                                                          -class SubstitutionPredictor(lambda_table=None, alpha=-5, threshold=0.001)[source]
                                                          +class SubstitutionPredictor(lambda_table=None, alpha=-5, threshold=0.001)[source]

                                                          Bases: object

                                                          Predicts likely substitutions either to or from a given composition or species list using the SubstitutionProbability.

                                                          @@ -221,7 +221,7 @@

                                                          Submodules
                                                          -composition_prediction(composition, to_this_composition=True)[source]
                                                          +composition_prediction(composition, to_this_composition=True)[source]

                                                          Get charged balanced substitutions from a starting or ending composition.

                                                          @@ -245,7 +245,7 @@

                                                          Submodules
                                                          -list_prediction(species, to_this_composition=True)[source]
                                                          +list_prediction(species, to_this_composition=True)[source]
                                                          Parameters:
                                                          -charge_balanced_tol: float = 1e-09[source]
                                                          +charge_balanced_tol: float = 1e-09[source]
                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                          +classmethod from_dict(dct: dict) → Self[source]
                                                          Parameters:

                                                          dct (dict) – Dict representation.

                                                          @@ -340,21 +340,21 @@

                                                          Submodules
                                                          -get_allowed_species()[source]
                                                          +get_allowed_species()[source]

                                                          Get the species in the domain of the probability function any other specie will not work.

                                                          -pred_from_comp(composition) → list[dict][source]
                                                          +pred_from_comp(composition) → list[dict][source]

                                                          Similar to pred_from_list except this method returns a list after checking that compositions are charge balanced.

                                                          -pred_from_list(species_list) → list[dict][source]
                                                          +pred_from_list(species_list) → list[dict][source]

                                                          There are an exceptionally large number of substitutions to look at (260^n), where n is the number of species in the list. We need a more efficient than brute force way of going @@ -384,7 +384,7 @@

                                                          Submodules
                                                          -pred_from_structures(target_species, structures, remove_duplicates=True, remove_existing=False) → list[TransformedStructure][source]
                                                          +pred_from_structures(target_species, structures, remove_duplicates=True, remove_existing=False) → list[TransformedStructure][source]

                                                          Performs a structure prediction targeting compounds containing all of the target_species, based on a list of structure (those structures can for instance come from a database like the ICSD). It will return @@ -423,7 +423,7 @@

                                                          Submodules
                                                          -class DLSVolumePredictor(cutoff=4.0, min_scaling=0.5, max_scaling=1.5)[source]
                                                          +class DLSVolumePredictor(cutoff=4.0, min_scaling=0.5, max_scaling=1.5)[source]

                                                          Bases: object

                                                          Data-mined lattice scaling (DLS) scheme that relies on data-mined bond lengths to predict the crystal volume of a given structure.

                                                          @@ -449,7 +449,7 @@

                                                          Submodules
                                                          -get_predicted_structure(structure: Structure, icsd_vol=False)[source]
                                                          +get_predicted_structure(structure: Structure, icsd_vol=False)[source]

                                                          Given a structure, returns back the structure scaled to predicted volume.

                                                          @@ -464,7 +464,7 @@

                                                          Submodules
                                                          -predict(structure: Structure, icsd_vol=False)[source]
                                                          +predict(structure: Structure, icsd_vol=False)[source]

                                                          Given a structure, returns the predicted volume.

                                                          Parameters:
                                                          @@ -483,7 +483,7 @@

                                                          Submodules
                                                          -class RLSVolumePredictor(check_isostructural=True, radii_type='ionic-atomic', use_bv=True)[source]
                                                          +class RLSVolumePredictor(check_isostructural=True, radii_type='ionic-atomic', use_bv=True)[source]

                                                          Bases: object

                                                          Reference lattice scaling (RLS) scheme that predicts the volume of a structure based on a known crystal structure.

                                                          @@ -504,7 +504,7 @@

                                                          Submodules
                                                          -get_predicted_structure(structure: Structure, ref_structure)[source]
                                                          +get_predicted_structure(structure: Structure, ref_structure)[source]

                                                          Given a structure, returns back the structure scaled to predicted volume.

                                                          @@ -523,7 +523,7 @@

                                                          Submodules
                                                          -predict(structure: Structure, ref_structure)[source]
                                                          +predict(structure: Structure, ref_structure)[source]

                                                          Given a structure, returns the predicted volume.

                                                          Parameters:
                                                          diff --git a/docs/pymatgen.analysis.topological.html b/docs/pymatgen.analysis.topological.html index a77b56c4f11..6cbbaf34c43 100644 --- a/docs/pymatgen.analysis.topological.html +++ b/docs/pymatgen.analysis.topological.html @@ -4,7 +4,7 @@ - pymatgen.analysis.topological package — pymatgen 2024.6.4 documentation + pymatgen.analysis.topological package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                          - 2024.6.4 + 2024.6.10
                                                          @@ -100,7 +100,7 @@

                                                          Submoduleshttps://www.nature.com/articles/s41524-020-0319-4.

                                                          -class SOCSpillage(wf_noso='', wf_so='')[source]
                                                          +class SOCSpillage(wf_noso='', wf_so='')[source]

                                                          Bases: object

                                                          Spin-orbit spillage criteria to predict whether a material is topologically non-trivial. The spillage criteria physically signifies number of band-inverted electrons. @@ -116,19 +116,19 @@

                                                          Submodules
                                                          -static isclose(n1, n2, rel_tol=1e-07)[source]
                                                          +static isclose(n1, n2, rel_tol=1e-07)[source]

                                                          Checking if the numbers are close enough.

                                                          -static orth(A)[source]
                                                          +static orth(A)[source]

                                                          Helper function to create orthonormal basis.

                                                          -overlap_so_spinpol()[source]
                                                          +overlap_so_spinpol()[source]

                                                          Main function to calculate SOC spillage.

                                                          diff --git a/docs/pymatgen.analysis.xas.html b/docs/pymatgen.analysis.xas.html index 16d63fcce0e..95dbdffa75b 100644 --- a/docs/pymatgen.analysis.xas.html +++ b/docs/pymatgen.analysis.xas.html @@ -4,7 +4,7 @@ - pymatgen.analysis.xas package — pymatgen 2024.6.4 documentation + pymatgen.analysis.xas package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                          - 2024.6.4 + 2024.6.10
                                                          @@ -104,7 +104,7 @@

                                                          Submodules
                                                          -class XAS(x, y, structure, absorbing_element, edge='K', spectrum_type='XANES', absorbing_index=None)[source]
                                                          +class XAS(x, y, structure, absorbing_element, edge='K', spectrum_type='XANES', absorbing_index=None)[source]

                                                          Bases: Spectrum

                                                          Basic XAS object.

                                                          @@ -124,7 +124,7 @@

                                                          Submodules
                                                          -x[source]
                                                          +x[source]

                                                          The sequence of energies.

                                                          Type:
                                                          @@ -135,7 +135,7 @@

                                                          Submodules
                                                          -y[source]
                                                          +y[source]

                                                          The sequence of mu(E).

                                                          Type:
                                                          @@ -146,7 +146,7 @@

                                                          Submodules
                                                          -absorbing_element[source]
                                                          +absorbing_element[source]

                                                          The absorbing element of the spectrum.

                                                          Type:
                                                          @@ -157,7 +157,7 @@

                                                          Submodules
                                                          -edge[source]
                                                          +edge[source]

                                                          The edge of the spectrum.

                                                          Type:
                                                          @@ -168,7 +168,7 @@

                                                          Submodules
                                                          -spectrum_type[source]
                                                          +spectrum_type[source]

                                                          The type of the spectrum (XANES or EXAFS).

                                                          Type:
                                                          @@ -179,7 +179,7 @@

                                                          Submodules
                                                          -absorbing_index[source]
                                                          +absorbing_index[source]

                                                          The absorbing index of the spectrum.

                                                          Type:
                                                          @@ -191,17 +191,17 @@

                                                          Submodules
                                                          -XLABEL = 'Energy'[source]
                                                          +XLABEL = 'Energy'[source]

                                                          -YLABEL = 'Intensity'[source]
                                                          +YLABEL = 'Intensity'[source]
                                                          -stitch(other: XAS, num_samples: int = 500, mode: Literal['XAFS', 'L23'] = 'XAFS') → XAS[source]
                                                          +stitch(other: XAS, num_samples: int = 500, mode: Literal['XAFS', 'L23'] = 'XAFS') → XAS[source]

                                                          Stitch XAS objects to get the full XAFS spectrum or L23 edge XANES spectrum depending on the mode.

                                                            @@ -245,7 +245,7 @@

                                                            Submodules
                                                            -site_weighted_spectrum(xas_list: list[XAS], num_samples: int = 500) → XAS[source]
                                                            +site_weighted_spectrum(xas_list: list[XAS], num_samples: int = 500) → XAS[source]

                                                            Obtain site-weighted XAS object based on site multiplicity for each absorbing index and its corresponding site-wise spectrum.

                                                            diff --git a/docs/pymatgen.apps.battery.html b/docs/pymatgen.apps.battery.html index 2a41a8e486e..4ede38e9854 100644 --- a/docs/pymatgen.apps.battery.html +++ b/docs/pymatgen.apps.battery.html @@ -4,7 +4,7 @@ - pymatgen.apps.battery package — pymatgen 2024.6.4 documentation + pymatgen.apps.battery package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                            - 2024.6.4 + 2024.6.10
                                                            @@ -231,7 +231,7 @@

                                                            Submodules
                                                            -class BatteryAnalyzer(struct_oxid, working_ion='Li', oxi_override=None)[source]
                                                            +class BatteryAnalyzer(struct_oxid, working_ion='Li', oxi_override=None)[source]

                                                            Bases: object

                                                            A suite of methods for starting with an oxidized structure and determining its potential as a battery.

                                                            Pass in a structure for analysis.

                                                            @@ -248,7 +248,7 @@

                                                            Submodules
                                                            -get_max_capgrav(remove=True, insert=True)[source]
                                                            +get_max_capgrav(remove=True, insert=True)[source]

                                                            Give max capacity in mAh/g for inserting and removing a charged ion Note that the weight is normalized to the most ion-packed state, thus removal of 1 Li from LiFePO4 gives the same capacity as insertion of 1 Li into FePO4.

                                                            @@ -267,7 +267,7 @@

                                                            Submodules
                                                            -get_max_capvol(remove=True, insert=True, volume=None)[source]
                                                            +get_max_capvol(remove=True, insert=True, volume=None)[source]

                                                            Give max capacity in mAh/cc for inserting and removing a charged ion into base structure.

                                                            Parameters:
                                                            @@ -285,7 +285,7 @@

                                                            Submodules
                                                            -get_removals_int_oxid()[source]
                                                            +get_removals_int_oxid()[source]

                                                            Get a set of ion removal steps, e.g. set([1 2 4]) etc. in order to produce integer oxidation states of the redox metals. If multiple redox metals are present, all combinations of reduction/oxidation are tested. @@ -303,7 +303,7 @@

                                                            Submodules
                                                            -property max_ion_insertion[source]
                                                            +property max_ion_insertion[source]

                                                            Maximum number of ion A that can be inserted while maintaining charge-balance. No consideration is given to whether there (geometrically speaking) are ion sites to actually accommodate the extra ions.

                                                            @@ -316,7 +316,7 @@

                                                            Submodules
                                                            -property max_ion_removal[source]
                                                            +property max_ion_removal[source]

                                                            Maximum number of ion A that can be removed while maintaining charge-balance.

                                                            Returns:
                                                            @@ -329,7 +329,7 @@

                                                            Submodules
                                                            -is_redox_active_intercalation(element) → bool[source]
                                                            +is_redox_active_intercalation(element) → bool[source]

                                                            True if element is redox active and interesting for intercalation materials.

                                                            Parameters:
                                                            @@ -348,7 +348,7 @@

                                                            Submodules
                                                            -class AbstractElectrode(voltage_pairs: tuple[AbstractVoltagePair, ...], working_ion_entry: ComputedEntry, framework_formula: str)[source]
                                                            +class AbstractElectrode(voltage_pairs: tuple[AbstractVoltagePair, ...], working_ion_entry: ComputedEntry, framework_formula: str)[source]

                                                            Bases: Sequence, MSONable

                                                            An Abstract Base Class representing an Electrode. It is essentially a sequence of VoltagePairs. Generally, subclasses only need to implement @@ -381,7 +381,7 @@

                                                            Submodules
                                                            -voltage_pairs[source]
                                                            +voltage_pairs[source]

                                                            Objects that represent each voltage step

                                                            Type:
                                                            @@ -392,13 +392,13 @@

                                                            Submodules
                                                            -working_ion[source]
                                                            +working_ion[source]

                                                            Representation of the working ion that only contains element type

                                                            -working_ion_entry[source]
                                                            +working_ion_entry[source]

                                                            Representation of the working_ion that contains the energy

                                                            Type:
                                                            @@ -409,7 +409,7 @@

                                                            Submodules
                                                            -framework_formula[source]
                                                            +framework_formula[source]

                                                            The compositions of one formula unit of the host material

                                                            Type:
                                                            @@ -420,18 +420,18 @@

                                                            Submodules
                                                            -property framework[source]
                                                            +property framework[source]

                                                            The composition object representing the framework.

                                                            -framework_formula: str[source]
                                                            +framework_formula: str[source]
                                                            -get_average_voltage(min_voltage=None, max_voltage=None)[source]
                                                            +get_average_voltage(min_voltage=None, max_voltage=None)[source]

                                                            Average voltage for path satisfying between a min and max voltage.

                                                            Parameters:
                                                            @@ -451,7 +451,7 @@

                                                            Submodules
                                                            -get_capacity_grav(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]
                                                            +get_capacity_grav(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]

                                                            Get the gravimetric capacity of the electrode.

                                                            Parameters:
                                                            @@ -475,7 +475,7 @@

                                                            Submodules
                                                            -get_capacity_vol(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]
                                                            +get_capacity_vol(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]

                                                            Get the volumetric capacity of the electrode.

                                                            Parameters:
                                                            @@ -499,7 +499,7 @@

                                                            Submodules
                                                            -get_energy_density(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]
                                                            +get_energy_density(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]
                                                            Parameters:
                                                              @@ -522,7 +522,7 @@

                                                              Submodules
                                                              -get_specific_energy(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]
                                                              +get_specific_energy(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]

                                                              Get the specific energy of the battery in mAh/g.

                                                              Parameters:
                                                              @@ -546,7 +546,7 @@

                                                              Submodules
                                                              -get_sub_electrodes(adjacent_only=True)[source]
                                                              +get_sub_electrodes(adjacent_only=True)[source]

                                                              If this electrode contains multiple voltage steps, then it is possible to use only a subset of the voltage steps to define other electrodes. Must be implemented for each electrode object.

                                                              @@ -564,7 +564,7 @@

                                                              Submodules
                                                              -get_summary_dict(print_subelectrodes=True) → dict[source]
                                                              +get_summary_dict(print_subelectrodes=True) → dict[source]

                                                              Generate a summary dict.

                                                              Parameters:
                                                              @@ -579,74 +579,74 @@

                                                              Submodules
                                                              -property max_delta_volume[source]
                                                              +property max_delta_volume[source]

                                                              Maximum volume change along insertion.

                                                              -property max_voltage[source]
                                                              +property max_voltage[source]

                                                              Highest voltage along insertion.

                                                              -property max_voltage_step[source]
                                                              +property max_voltage_step[source]

                                                              Maximum absolute difference in adjacent voltage steps.

                                                              -property min_voltage[source]
                                                              +property min_voltage[source]

                                                              Lowest voltage along insertion.

                                                              -property normalization_mass[source]
                                                              +property normalization_mass[source]

                                                              The mass used for normalization. This is the mass of the discharged electrode of the last voltage pair.

                                                              -property normalization_volume[source]
                                                              +property normalization_volume[source]

                                                              The mass used for normalization. This is the vol of the discharged electrode of the last voltage pair.

                                                              -property num_steps[source]
                                                              +property num_steps[source]

                                                              The number of distinct voltage steps in from fully charge to discharge based on the stable intermediate states.

                                                              -voltage_pairs: tuple[AbstractVoltagePair, ...][source]
                                                              +voltage_pairs: tuple[AbstractVoltagePair, ...][source]
                                                              -property working_ion[source]
                                                              +property working_ion[source]

                                                              Working ion as pymatgen Element object.

                                                              -working_ion_entry: ComputedEntry[source]
                                                              +working_ion_entry: ComputedEntry[source]
                                                              -property x_charge: float[source]
                                                              +property x_charge: float[source]

                                                              The number of working ions per formula unit of host in the charged state.

                                                              -property x_discharge: float[source]
                                                              +property x_discharge: float[source]

                                                              The number of working ions per formula unit of host in the discharged state.

                                                              @@ -654,12 +654,12 @@

                                                              Submodules
                                                              -class AbstractVoltagePair(voltage: float, mAh: float, mass_charge: float, mass_discharge: float, vol_charge: float, vol_discharge: float, frac_charge: float, frac_discharge: float, working_ion_entry: ComputedEntry, framework_formula: str)[source]
                                                              +class AbstractVoltagePair(voltage: float, mAh: float, mass_charge: float, mass_discharge: float, vol_charge: float, vol_discharge: float, frac_charge: float, frac_discharge: float, working_ion_entry: ComputedEntry, framework_formula: str)[source]

                                                              Bases: MSONable

                                                              An Abstract Base Class for a Voltage Pair.

                                                              -voltage[source]
                                                              +voltage[source]

                                                              Voltage of voltage pair.

                                                              Type:
                                                              @@ -670,7 +670,7 @@

                                                              Submodules
                                                              -mAh[source]
                                                              +mAh[source]

                                                              Energy in mAh.

                                                              Type:
                                                              @@ -681,7 +681,7 @@

                                                              Submodules
                                                              -mass_charge[source]
                                                              +mass_charge[source]

                                                              Mass of charged pair.

                                                              Type:
                                                              @@ -692,7 +692,7 @@

                                                              Submodules
                                                              -mass_discharge[source]
                                                              +mass_discharge[source]

                                                              Mass of discharged pair.

                                                              Type:
                                                              @@ -703,7 +703,7 @@

                                                              Submodules
                                                              -vol_charge[source]
                                                              +vol_charge[source]

                                                              Vol of charged pair.

                                                              Type:
                                                              @@ -714,7 +714,7 @@

                                                              Submodules
                                                              -vol_discharge[source]
                                                              +vol_discharge[source]

                                                              Vol of discharged pair.

                                                              Type:
                                                              @@ -725,7 +725,7 @@

                                                              Submodules
                                                              -frac_charge[source]
                                                              +frac_charge[source]

                                                              Frac of working ion in charged pair.

                                                              Type:
                                                              @@ -736,7 +736,7 @@

                                                              Submodules
                                                              -frac_discharge[source]
                                                              +frac_discharge[source]

                                                              Frac of working ion in discharged pair.

                                                              Type:
                                                              @@ -747,7 +747,7 @@

                                                              Submodules
                                                              -working_ion_entry[source]
                                                              +working_ion_entry[source]

                                                              Working ion as an entry.

                                                              Type:
                                                              @@ -758,7 +758,7 @@

                                                              Submodules
                                                              -framework_formula[source]
                                                              +framework_formula[source]

                                                              The compositions of one formula unit of the host material

                                                              Type:
                                                              @@ -769,75 +769,75 @@

                                                              Submodules
                                                              -frac_charge: float[source]
                                                              +frac_charge: float[source]

                                                              -frac_discharge: float[source]
                                                              +frac_discharge: float[source]
                                                              -property framework: Composition[source]
                                                              +property framework: Composition[source]

                                                              The composition object representing the framework.

                                                              -framework_formula: str[source]
                                                              +framework_formula: str[source]
                                                              -mAh: float[source]
                                                              +mAh: float[source]
                                                              -mass_charge: float[source]
                                                              +mass_charge: float[source]
                                                              -mass_discharge: float[source]
                                                              +mass_discharge: float[source]
                                                              -vol_charge: float[source]
                                                              +vol_charge: float[source]
                                                              -vol_discharge: float[source]
                                                              +vol_discharge: float[source]
                                                              -voltage: float[source]
                                                              +voltage: float[source]
                                                              -property working_ion: Element[source]
                                                              +property working_ion: Element[source]

                                                              Working ion as pymatgen Element object.

                                                              -working_ion_entry: ComputedEntry[source]
                                                              +working_ion_entry: ComputedEntry[source]
                                                              -property x_charge: float[source]
                                                              +property x_charge: float[source]

                                                              The number of working ions per formula unit of host in the charged state.

                                                              -property x_discharge: float[source]
                                                              +property x_discharge: float[source]

                                                              The number of working ions per formula unit of host in the discharged state.

                                                              @@ -849,7 +849,7 @@

                                                              Submodules
                                                              -class ConversionElectrode(voltage_pairs: tuple[AbstractVoltagePair, ...], working_ion_entry: ComputedEntry, framework_formula: str, initial_comp_formula: str)[source]
                                                              +class ConversionElectrode(voltage_pairs: tuple[AbstractVoltagePair, ...], working_ion_entry: ComputedEntry, framework_formula: str, initial_comp_formula: str)[source]

                                                              Bases: AbstractElectrode

                                                              A ConversionElectrode, since it is dataclass this object can be constructed for the attributes. @@ -870,7 +870,7 @@

                                                              Submodules
                                                              -classmethod from_composition_and_entries(comp, entries_in_chemsys, working_ion_symbol='Li', allow_unstable=False) → Self | None[source]
                                                              +classmethod from_composition_and_entries(comp, entries_in_chemsys, working_ion_symbol='Li', allow_unstable=False) → Self | None[source]

                                                              Convenience constructor to make a ConversionElectrode from a composition and all entries in a chemical system.

                                                              @@ -891,7 +891,7 @@

                                                              Submodules
                                                              -classmethod from_composition_and_pd(comp, pd: PhaseDiagram, working_ion_symbol: str = 'Li', allow_unstable: bool = False) → Self | None[source]
                                                              +classmethod from_composition_and_pd(comp, pd: PhaseDiagram, working_ion_symbol: str = 'Li', allow_unstable: bool = False) → Self | None[source]

                                                              Convenience constructor to make a ConversionElectrode from a composition and a phase diagram.

                                                              @@ -909,7 +909,7 @@

                                                              Submodules
                                                              -get_sub_electrodes(adjacent_only=True)[source]
                                                              +get_sub_electrodes(adjacent_only=True)[source]

                                                              If this electrode contains multiple voltage steps, then it is possible to use only a subset of the voltage steps to define other electrodes. For example, an LiTiO2 electrode might contain three subelectrodes: @@ -930,7 +930,7 @@

                                                              Submodules
                                                              -get_summary_dict(print_subelectrodes=True) → dict[source]
                                                              +get_summary_dict(print_subelectrodes=True) → dict[source]

                                                              Generate a summary dict. Populates the summary dict with the basic information from the parent method then populates more information. Since the parent method calls self.get_summary_dict(print_subelectrodes=True) for the subelectrodes. @@ -948,18 +948,18 @@

                                                              Submodules
                                                              -property initial_comp: Composition[source]
                                                              +property initial_comp: Composition[source]

                                                              The pymatgen Composition representation of the initial composition.

                                                              -initial_comp_formula: str[source]
                                                              +initial_comp_formula: str[source]
                                                              -is_super_electrode(conversion_electrode) → bool[source]
                                                              +is_super_electrode(conversion_electrode) → bool[source]

                                                              Check if a particular conversion electrode is a sub electrode of the current electrode. Starting from a more lithiated state may result in a subelectrode that is essentially on the same path. For example, a @@ -972,13 +972,13 @@

                                                              Submodules
                                                              -class ConversionVoltagePair(voltage: float, mAh: float, mass_charge: float, mass_discharge: float, vol_charge: float, vol_discharge: float, frac_charge: float, frac_discharge: float, working_ion_entry: ComputedEntry, framework_formula: str, rxn: BalancedReaction, entries_charge: Iterable[ComputedEntry], entries_discharge: Iterable[ComputedEntry])[source]
                                                              +class ConversionVoltagePair(voltage: float, mAh: float, mass_charge: float, mass_discharge: float, vol_charge: float, vol_discharge: float, frac_charge: float, frac_discharge: float, working_ion_entry: ComputedEntry, framework_formula: str, rxn: BalancedReaction, entries_charge: Iterable[ComputedEntry], entries_discharge: Iterable[ComputedEntry])[source]

                                                              Bases: AbstractVoltagePair

                                                              A VoltagePair representing a Conversion Reaction with a defined voltage. Typically not initialized directly but rather used by ConversionElectrode.

                                                              -rxn[source]
                                                              +rxn[source]

                                                              BalancedReaction for the step

                                                              Type:
                                                              @@ -989,7 +989,7 @@

                                                              Submodules
                                                              -voltage[source]
                                                              +voltage[source]

                                                              Voltage for the step

                                                              Type:
                                                              @@ -1000,7 +1000,7 @@

                                                              Submodules
                                                              -mAh[source]
                                                              +mAh[source]

                                                              Capacity of the step

                                                              Type:
                                                              @@ -1011,7 +1011,7 @@

                                                              Submodules
                                                              -vol_charge[source]
                                                              +vol_charge[source]

                                                              Volume of charged state

                                                              Type:
                                                              @@ -1022,7 +1022,7 @@

                                                              Submodules
                                                              -vol_discharge[source]
                                                              +vol_discharge[source]

                                                              Volume of discharged state

                                                              Type:
                                                              @@ -1033,7 +1033,7 @@

                                                              Submodules
                                                              -mass_charge[source]
                                                              +mass_charge[source]

                                                              Mass of charged state

                                                              Type:
                                                              @@ -1044,7 +1044,7 @@

                                                              Submodules
                                                              -mass_discharge[source]
                                                              +mass_discharge[source]

                                                              Mass of discharged state

                                                              Type:
                                                              @@ -1055,7 +1055,7 @@

                                                              Submodules
                                                              -frac_charge[source]
                                                              +frac_charge[source]

                                                              Fraction of working ion in the charged state

                                                              Type:
                                                              @@ -1066,7 +1066,7 @@

                                                              Submodules
                                                              -frac_discharge[source]
                                                              +frac_discharge[source]

                                                              Fraction of working ion in the discharged state

                                                              Type:
                                                              @@ -1077,7 +1077,7 @@

                                                              Submodules
                                                              -entries_charge[source]
                                                              +entries_charge[source]

                                                              Entries representing decompositions products in the charged state. Enumerates the decompositions products at the tieline, so the number of entries will be one fewer than the dimensions of the phase @@ -1091,7 +1091,7 @@

                                                              Submodules
                                                              -entries_discharge[source]
                                                              +entries_discharge[source]

                                                              Entries representing decompositions products in the discharged state. Enumerates the decompositions products at the tieline, so the number of entries will be one fewer than the dimensions of the phase @@ -1105,7 +1105,7 @@

                                                              Submodules
                                                              -working_ion_entry[source]
                                                              +working_ion_entry[source]

                                                              Entry of the working ion.

                                                              Type:
                                                              @@ -1116,17 +1116,17 @@

                                                              Submodules
                                                              -entries_charge: Iterable[ComputedEntry][source]
                                                              +entries_charge: Iterable[ComputedEntry][source]

                                                              -entries_discharge: Iterable[ComputedEntry][source]
                                                              +entries_discharge: Iterable[ComputedEntry][source]
                                                              -classmethod from_steps(step1, step2, normalization_els, framework_formula) → Self[source]
                                                              +classmethod from_steps(step1, step2, normalization_els, framework_formula) → Self[source]

                                                              Create a ConversionVoltagePair from two steps in the element profile from a PD analysis.

                                                              @@ -1144,7 +1144,7 @@

                                                              Submodules
                                                              -rxn: BalancedReaction[source]
                                                              +rxn: BalancedReaction[source]

                                                              @@ -1156,20 +1156,20 @@

                                                              Submodules
                                                              -class InsertionElectrode(voltage_pairs: tuple[AbstractVoltagePair, ...], working_ion_entry: ComputedEntry, framework_formula: str, stable_entries: Iterable[ComputedEntry], unstable_entries: Iterable[ComputedEntry])[source]
                                                              +class InsertionElectrode(voltage_pairs: tuple[AbstractVoltagePair, ...], working_ion_entry: ComputedEntry, framework_formula: str, stable_entries: Iterable[ComputedEntry], unstable_entries: Iterable[ComputedEntry])[source]

                                                              Bases: AbstractElectrode

                                                              A set of topotactically related compounds, with different amounts of a single element, e.g. TiO2 and LiTiO2, that can be used to define an insertion battery electrode.

                                                              -as_dict_legacy()[source]
                                                              +as_dict_legacy()[source]

                                                              Get MSONable dict.

                                                              -classmethod from_dict_legacy(dct) → Self[source]
                                                              +classmethod from_dict_legacy(dct) → Self[source]
                                                              Parameters:

                                                              dct (dict) – Dict representation.

                                                              @@ -1182,7 +1182,7 @@

                                                              Submodules
                                                              -classmethod from_entries(entries: Iterable[ComputedEntry | ComputedStructureEntry], working_ion_entry: ComputedEntry | ComputedStructureEntry | PDEntry, strip_structures: bool = False) → Self[source]
                                                              +classmethod from_entries(entries: Iterable[ComputedEntry | ComputedStructureEntry], working_ion_entry: ComputedEntry | ComputedStructureEntry | PDEntry, strip_structures: bool = False) → Self[source]

                                                              Create a new InsertionElectrode.

                                                              Parameters:
                                                              @@ -1206,19 +1206,19 @@

                                                              Submodules
                                                              -property fully_charged_entry[source]
                                                              +property fully_charged_entry[source]

                                                              The most charged entry along the topotactic path.

                                                              -property fully_discharged_entry[source]
                                                              +property fully_discharged_entry[source]

                                                              The most discharged entry along the topotactic path.

                                                              -get_all_entries(charge_to_discharge=True)[source]
                                                              +get_all_entries(charge_to_discharge=True)[source]

                                                              Return all entries input for the electrode.

                                                              Parameters:
                                                              @@ -1234,7 +1234,7 @@

                                                              Submodules
                                                              -get_max_instability(min_voltage=None, max_voltage=None)[source]
                                                              +get_max_instability(min_voltage=None, max_voltage=None)[source]

                                                              The maximum instability along a path for a specific voltage range.

                                                              Parameters:
                                                              @@ -1252,7 +1252,7 @@

                                                              Submodules
                                                              -get_max_muO2(min_voltage=None, max_voltage=None)[source]
                                                              +get_max_muO2(min_voltage=None, max_voltage=None)[source]

                                                              Maximum critical oxygen chemical potential along path.

                                                              Parameters:
                                                              @@ -1271,7 +1271,7 @@

                                                              Submodules
                                                              -get_min_instability(min_voltage=None, max_voltage=None)[source]
                                                              +get_min_instability(min_voltage=None, max_voltage=None)[source]

                                                              The minimum instability along a path for a specific voltage range.

                                                              Parameters:
                                                              @@ -1289,7 +1289,7 @@

                                                              Submodules
                                                              -get_min_muO2(min_voltage=None, max_voltage=None)[source]
                                                              +get_min_muO2(min_voltage=None, max_voltage=None)[source]

                                                              Minimum critical oxygen chemical potential along path.

                                                              Parameters:
                                                              @@ -1309,7 +1309,7 @@

                                                              Submodules
                                                              -get_stable_entries(charge_to_discharge=True)[source]
                                                              +get_stable_entries(charge_to_discharge=True)[source]

                                                              Get the stable entries.

                                                              Parameters:
                                                              @@ -1325,7 +1325,7 @@

                                                              Submodules
                                                              -get_sub_electrodes(adjacent_only=True, include_myself=True)[source]
                                                              +get_sub_electrodes(adjacent_only=True, include_myself=True)[source]

                                                              If this electrode contains multiple voltage steps, then it is possible to use only a subset of the voltage steps to define other electrodes. For example, an LiTiO2 electrode might contain three subelectrodes: @@ -1350,7 +1350,7 @@

                                                              Submodules
                                                              -get_summary_dict(print_subelectrodes=True) → dict[source]
                                                              +get_summary_dict(print_subelectrodes=True) → dict[source]

                                                              Generate a summary dict. Populates the summary dict with the basic information from the parent method then populates more information. Since the parent method calls self.get_summary_dict(print_subelectrodes=True) for the subelectrodes. @@ -1368,7 +1368,7 @@

                                                              Submodules
                                                              -get_unstable_entries(charge_to_discharge=True)[source]
                                                              +get_unstable_entries(charge_to_discharge=True)[source]

                                                              Get the unstable entries for the electrode.

                                                              Parameters:
                                                              @@ -1384,34 +1384,34 @@

                                                              Submodules
                                                              -stable_entries: Iterable[ComputedEntry][source]
                                                              +stable_entries: Iterable[ComputedEntry][source]

                                                              -unstable_entries: Iterable[ComputedEntry][source]
                                                              +unstable_entries: Iterable[ComputedEntry][source]

                                                              -class InsertionVoltagePair(voltage: float, mAh: float, mass_charge: float, mass_discharge: float, vol_charge: float, vol_discharge: float, frac_charge: float, frac_discharge: float, working_ion_entry: ComputedEntry, framework_formula: str, entry_charge: ComputedEntry, entry_discharge: ComputedEntry)[source]
                                                              +class InsertionVoltagePair(voltage: float, mAh: float, mass_charge: float, mass_discharge: float, vol_charge: float, vol_discharge: float, frac_charge: float, frac_discharge: float, working_ion_entry: ComputedEntry, framework_formula: str, entry_charge: ComputedEntry, entry_discharge: ComputedEntry)[source]

                                                              Bases: AbstractVoltagePair

                                                              A voltage pair for an insertion battery, e.g. LiFePO4 -> FePO4.

                                                              -entry_charge: ComputedEntry[source]
                                                              +entry_charge: ComputedEntry[source]
                                                              -entry_discharge: ComputedEntry[source]
                                                              +entry_discharge: ComputedEntry[source]
                                                              -classmethod from_entries(entry1, entry2, working_ion_entry) → Self[source]
                                                              +classmethod from_entries(entry1, entry2, working_ion_entry) → Self[source]
                                                              Parameters:
                                                                @@ -1432,7 +1432,7 @@

                                                                Submodules
                                                                -class VoltageProfilePlotter(xaxis: str = 'capacity', hide_negative: bool = False)[source]
                                                                +class VoltageProfilePlotter(xaxis: str = 'capacity', hide_negative: bool = False)[source]

                                                                Bases: object

                                                                A plotter to make voltage profile plots for batteries.

                                                                @@ -1449,7 +1449,7 @@

                                                                Submodules
                                                                -add_electrode(electrode: AbstractElectrode, label: str | None = None) → None[source]
                                                                +add_electrode(electrode: AbstractElectrode, label: str | None = None) → None[source]

                                                                Add an electrode to the plot.

                                                                Parameters:
                                                                @@ -1465,7 +1465,7 @@

                                                                Submodules
                                                                -get_plot(width: float = 8, height: float = 8, term_zero: bool = True, ax: Axes = None) → Axes[source]
                                                                +get_plot(width: float = 8, height: float = 8, term_zero: bool = True, ax: Axes = None) → Axes[source]

                                                                Get a plot object.

                                                                Parameters:
                                                                @@ -1487,7 +1487,7 @@

                                                                Submodules
                                                                -get_plot_data(electrode: AbstractElectrode, term_zero: bool = True) → tuple[list, list][source]
                                                                +get_plot_data(electrode: AbstractElectrode, term_zero: bool = True) → tuple[list, list][source]
                                                                Parameters:
                                                                  @@ -1503,7 +1503,7 @@

                                                                  Submodules
                                                                  -get_plotly_figure(width: float = 800, height: float = 600, font_dict: dict | None = None, term_zero: bool = True, **kwargs) → Figure[source]
                                                                  +get_plotly_figure(width: float = 800, height: float = 600, font_dict: dict | None = None, term_zero: bool = True, **kwargs) → Figure[source]

                                                                  Return plotly Figure object.

                                                                  Parameters:
                                                                  @@ -1520,7 +1520,7 @@

                                                                  Submodules
                                                                  -save(filename: str, width: float = 8, height: float = 6) → None[source]
                                                                  +save(filename: str, width: float = 8, height: float = 6) → None[source]

                                                                  Save the plot to an image file.

                                                                  Parameters:
                                                                  @@ -1535,7 +1535,7 @@

                                                                  Submodules
                                                                  -show(width: float = 8, height: float = 6) → None[source]
                                                                  +show(width: float = 8, height: float = 6) → None[source]

                                                                  Show the voltage profile plot.

                                                                  Parameters:
                                                                  diff --git a/docs/pymatgen.apps.borg.html b/docs/pymatgen.apps.borg.html index 65dd67bbf43..279894cf233 100644 --- a/docs/pymatgen.apps.borg.html +++ b/docs/pymatgen.apps.borg.html @@ -4,7 +4,7 @@ - pymatgen.apps.borg package — pymatgen 2024.6.4 documentation + pymatgen.apps.borg package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                  - 2024.6.4 + 2024.6.10
                                                                  @@ -129,7 +129,7 @@

                                                                  Submodules
                                                                  -class AbstractDrone[source]
                                                                  +class AbstractDrone[source]

                                                                  Bases: MSONable, ABC

                                                                  Abstract drone class that defines the various methods that must be implemented by drones. Because of the quirky nature of Python”s @@ -139,7 +139,7 @@

                                                                  Submodules
                                                                  -abstract assimilate(path)[source]
                                                                  +abstract assimilate(path)[source]

                                                                  Assimilate data in a directory path into a pymatgen object. Because of the quirky nature of Python’s multiprocessing, the object must support pymatgen’s as_dict() for parallel processing.

                                                                  @@ -155,7 +155,7 @@

                                                                  Submodules
                                                                  -abstract get_valid_paths(path)[source]
                                                                  +abstract get_valid_paths(path)[source]

                                                                  Check if path contains valid data for assimilation, and then returns the valid paths. The paths returned can be a list of directory or file paths, depending on what kind of data you are assimilating. For @@ -178,7 +178,7 @@

                                                                  Submodules
                                                                  -class GaussianToComputedEntryDrone(inc_structure=False, parameters=None, data=None, file_extensions=('.log',))[source]
                                                                  +class GaussianToComputedEntryDrone(inc_structure=False, parameters=None, data=None, file_extensions=('.log',))[source]

                                                                  Bases: AbstractDrone

                                                                  GaussianToEntryDrone assimilates directories containing Gaussian output to ComputedEntry/ComputedStructureEntry objects. By default, it is assumed @@ -210,13 +210,13 @@

                                                                  Submodules
                                                                  -as_dict()[source]
                                                                  +as_dict()[source]

                                                                  Get MSONable dict.

                                                                  -assimilate(path)[source]
                                                                  +assimilate(path)[source]

                                                                  Assimilate data in a directory path into a ComputedEntry object.

                                                                  Parameters:
                                                                  @@ -230,7 +230,7 @@

                                                                  Submodules
                                                                  -classmethod from_dict(dct: dict) → Self[source]
                                                                  +classmethod from_dict(dct: dict) → Self[source]
                                                                  Parameters:

                                                                  dct (dict) – Dict Representation.

                                                                  @@ -243,7 +243,7 @@

                                                                  Submodules
                                                                  -get_valid_paths(path)[source]
                                                                  +get_valid_paths(path)[source]

                                                                  Check if path contains files with define extensions.

                                                                  Parameters:
                                                                  @@ -260,7 +260,7 @@

                                                                  Submodules
                                                                  -class SimpleVaspToComputedEntryDrone(inc_structure=False)[source]
                                                                  +class SimpleVaspToComputedEntryDrone(inc_structure=False)[source]

                                                                  Bases: VaspToComputedEntryDrone

                                                                  A simpler VaspToComputedEntryDrone. Instead of parsing vasprun.xml, it parses only the INCAR, POTCAR, OSZICAR and KPOINTS files, which are much @@ -274,13 +274,13 @@

                                                                  Submodules
                                                                  -as_dict()[source]
                                                                  +as_dict()[source]

                                                                  Get MSONable dict.

                                                                  -assimilate(path)[source]
                                                                  +assimilate(path)[source]

                                                                  Assimilate data in a directory path into a ComputedEntry object.

                                                                  Parameters:
                                                                  @@ -294,7 +294,7 @@

                                                                  Submodules
                                                                  -classmethod from_dict(dct: dict) → Self[source]
                                                                  +classmethod from_dict(dct: dict) → Self[source]
                                                                  Parameters:

                                                                  dct (dict) – Dict Representation.

                                                                  @@ -309,7 +309,7 @@

                                                                  Submodules
                                                                  -class VaspToComputedEntryDrone(inc_structure=False, parameters=None, data=None)[source]
                                                                  +class VaspToComputedEntryDrone(inc_structure=False, parameters=None, data=None)[source]

                                                                  Bases: AbstractDrone

                                                                  VaspToEntryDrone assimilates directories containing VASP output to ComputedEntry/ComputedStructureEntry objects.

                                                                  @@ -338,13 +338,13 @@

                                                                  Submodules
                                                                  -as_dict()[source]
                                                                  +as_dict()[source]

                                                                  Get MSONable dict.

                                                                  -assimilate(path)[source]
                                                                  +assimilate(path)[source]

                                                                  Assimilate data in a directory path into a ComputedEntry object.

                                                                  Parameters:
                                                                  @@ -358,7 +358,7 @@

                                                                  Submodules
                                                                  -classmethod from_dict(dct: dict) → Self[source]
                                                                  +classmethod from_dict(dct: dict) → Self[source]
                                                                  Parameters:

                                                                  dct (dict) – Dict Representation.

                                                                  @@ -371,7 +371,7 @@

                                                                  Submodules
                                                                  -get_valid_paths(path)[source]
                                                                  +get_valid_paths(path)[source]

                                                                  Check if paths contains vasprun.xml or (POSCAR+OSZICAR).

                                                                  Parameters:
                                                                  @@ -393,7 +393,7 @@

                                                                  Submodules
                                                                  -class BorgQueen(drone, rootpath=None, number_of_drones=1)[source]
                                                                  +class BorgQueen(drone, rootpath=None, number_of_drones=1)[source]

                                                                  Bases: object

                                                                  The Borg Queen controls the drones to assimilate data in an entire directory tree. Uses multiprocessing to speed up things considerably. It @@ -418,25 +418,25 @@

                                                                  Submodules
                                                                  -get_data()[source]
                                                                  +get_data()[source]

                                                                  Get an list of assimilated objects.

                                                                  -load_data(filename)[source]
                                                                  +load_data(filename)[source]

                                                                  Load assimilated data from a file.

                                                                  -parallel_assimilate(rootpath)[source]
                                                                  +parallel_assimilate(rootpath)[source]

                                                                  Assimilate the entire subdirectory structure in rootpath.

                                                                  -save_data(filename: str | Path) → None[source]
                                                                  +save_data(filename: str | Path) → None[source]

                                                                  Save the assimilated data to a file.

                                                                  Parameters:
                                                                  @@ -449,7 +449,7 @@

                                                                  Submodules
                                                                  -serial_assimilate(root: str | Path) → None[source]
                                                                  +serial_assimilate(root: str | Path) → None[source]

                                                                  Assimilate the entire subdirectory structure in rootpath serially.

                                                                  @@ -457,7 +457,7 @@

                                                                  Submodules
                                                                  -order_assimilation(args)[source]
                                                                  +order_assimilation(args)[source]

                                                                  Internal helper method for BorgQueen to process assimilation.

                                                                  diff --git a/docs/pymatgen.apps.html b/docs/pymatgen.apps.html index 0cebdee29d2..b154bd3e8b3 100644 --- a/docs/pymatgen.apps.html +++ b/docs/pymatgen.apps.html @@ -4,7 +4,7 @@ - pymatgen.apps package — pymatgen 2024.6.4 documentation + pymatgen.apps package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                  - 2024.6.4 + 2024.6.10
                                                                  diff --git a/docs/pymatgen.cli.html b/docs/pymatgen.cli.html index 4b1744fe395..7afb68eb973 100644 --- a/docs/pymatgen.cli.html +++ b/docs/pymatgen.cli.html @@ -4,7 +4,7 @@ - pymatgen.cli package — pymatgen 2024.6.4 documentation + pymatgen.cli package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                  - 2024.6.4 + 2024.6.10
                                                                  @@ -145,7 +145,7 @@

                                                                  Submodules
                                                                  -main()[source]
                                                                  +main()[source]

                                                                  Main function.

                                                                  @@ -156,7 +156,7 @@

                                                                  Submodules
                                                                  -main()[source]
                                                                  +main()[source]

                                                                  Main function.

                                                                  @@ -166,7 +166,7 @@

                                                                  Submodules
                                                                  -main() → int[source]
                                                                  +main() → int[source]

                                                                  Main function for get_environment CLI.

                                                                  @@ -176,7 +176,7 @@

                                                                  Submodules
                                                                  -diff_incar(args)[source]
                                                                  +diff_incar(args)[source]

                                                                  Handle diff commands.

                                                                  Parameters:
                                                                  @@ -187,13 +187,13 @@

                                                                  Submodules
                                                                  -main()[source]
                                                                  +main()[source]

                                                                  Handle main.

                                                                  -parse_view(args)[source]
                                                                  +parse_view(args)[source]

                                                                  Handle view commands.

                                                                  Parameters:
                                                                  @@ -208,7 +208,7 @@

                                                                  Submodules
                                                                  -analyze(args)[source]
                                                                  +analyze(args)[source]

                                                                  Master function controlling which analysis to call.

                                                                  Parameters:
                                                                  @@ -219,7 +219,7 @@

                                                                  Submodules
                                                                  -get_energies(rootdir, reanalyze, verbose, quick, sort, fmt)[source]
                                                                  +get_energies(rootdir, reanalyze, verbose, quick, sort, fmt)[source]

                                                                  Get energies of all vaspruns in directory (nested).

                                                                  Parameters:
                                                                  @@ -238,7 +238,7 @@

                                                                  Submodules
                                                                  -get_magnetizations(dir: str, ion_list: list[int])[source]
                                                                  +get_magnetizations(dir: str, ion_list: list[int])[source]

                                                                  Get magnetization info from OUTCARs.

                                                                  Parameters:
                                                                  @@ -262,13 +262,13 @@

                                                                  Submodules
                                                                  -add_config_var(tokens: list[str], backup_suffix: str) → None[source]
                                                                  +add_config_var(tokens: list[str], backup_suffix: str) → None[source]

                                                                  Add/update keys in .pmgrc.yaml config file.

                                                                  -build_bader(fortran_command='gfortran')[source]
                                                                  +build_bader(fortran_command='gfortran')[source]

                                                                  Build bader package.

                                                                  Parameters:
                                                                  @@ -279,7 +279,7 @@

                                                                  Submodules
                                                                  -build_enum(fortran_command: str = 'gfortran') → bool[source]
                                                                  +build_enum(fortran_command: str = 'gfortran') → bool[source]

                                                                  Build enum.

                                                                  Parameters:
                                                                  @@ -290,25 +290,25 @@

                                                                  Submodules
                                                                  -configure_pmg(args: Namespace)[source]
                                                                  +configure_pmg(args: Namespace)[source]

                                                                  Handle configure command.

                                                                  -install_software(install: Literal['enumlib', 'bader'])[source]
                                                                  +install_software(install: Literal['enumlib', 'bader'])[source]

                                                                  Install all optional external software.

                                                                  -setup_cp2k_data(cp2k_data_dirs: list[str]) → None[source]
                                                                  +setup_cp2k_data(cp2k_data_dirs: list[str]) → None[source]

                                                                  Setup CP2K basis and potential data directory.

                                                                  -setup_potcars(potcar_dirs: list[str])[source]
                                                                  +setup_potcars(potcar_dirs: list[str])[source]

                                                                  Setup POTCAR directories.

                                                                  @@ -318,7 +318,7 @@

                                                                  Submodules
                                                                  -get_chgint_plot(args, ax: Axes = None) → Axes[source]
                                                                  +get_chgint_plot(args, ax: Axes = None) → Axes[source]

                                                                  Plot integrated charge.

                                                                  Parameters:
                                                                  @@ -338,7 +338,7 @@

                                                                  Submodules
                                                                  -get_dos_plot(args)[source]
                                                                  +get_dos_plot(args)[source]

                                                                  Plot DOS.

                                                                  Parameters:
                                                                  @@ -349,7 +349,7 @@

                                                                  Submodules
                                                                  -get_xrd_plot(args)[source]
                                                                  +get_xrd_plot(args)[source]

                                                                  Plot XRD.

                                                                  Parameters:
                                                                  @@ -360,7 +360,7 @@

                                                                  Submodules
                                                                  -plot(args)[source]
                                                                  +plot(args)[source]

                                                                  Master control method calling other plot methods based on args.

                                                                  Parameters:
                                                                  @@ -375,7 +375,7 @@

                                                                  Submodules
                                                                  -gen_potcar(dirname, filename)[source]
                                                                  +gen_potcar(dirname, filename)[source]

                                                                  Generate POTCAR from POTCAR.spec in directories.

                                                                  Parameters:
                                                                  @@ -389,7 +389,7 @@

                                                                  Submodules
                                                                  -generate_potcar(args)[source]
                                                                  +generate_potcar(args)[source]

                                                                  Generate POTCAR.

                                                                  Parameters:
                                                                  @@ -400,7 +400,7 @@

                                                                  Submodules
                                                                  -proc_dir(dirname, proc_file_function)[source]
                                                                  +proc_dir(dirname, proc_file_function)[source]

                                                                  Process a directory.

                                                                  Parameters:
                                                                  @@ -418,7 +418,7 @@

                                                                  Submodules
                                                                  -analyze_localenv(args)[source]
                                                                  +analyze_localenv(args)[source]

                                                                  Analyze local env of structures in files.

                                                                  Parameters:
                                                                  @@ -429,7 +429,7 @@

                                                                  Submodules
                                                                  -analyze_structures(args)[source]
                                                                  +analyze_structures(args)[source]

                                                                  Master function to handle which operation to perform.

                                                                  Parameters:
                                                                  @@ -440,7 +440,7 @@

                                                                  Submodules
                                                                  -analyze_symmetry(args)[source]
                                                                  +analyze_symmetry(args)[source]

                                                                  Analyze symmetry of structures in files.

                                                                  Parameters:
                                                                  @@ -451,7 +451,7 @@

                                                                  Submodules
                                                                  -compare_structures(args)[source]
                                                                  +compare_structures(args)[source]

                                                                  Compare structures in files for similarity using structure matcher.

                                                                  Parameters:
                                                                  @@ -462,7 +462,7 @@

                                                                  Submodules
                                                                  -convert_fmt(args)[source]
                                                                  +convert_fmt(args)[source]

                                                                  Convert files from one format to another.

                                                                  Parameters:
                                                                  diff --git a/docs/pymatgen.command_line.html b/docs/pymatgen.command_line.html index 58209a8b42d..c9b5d4d613e 100644 --- a/docs/pymatgen.command_line.html +++ b/docs/pymatgen.command_line.html @@ -4,7 +4,7 @@ - pymatgen.command_line package — pymatgen 2024.6.4 documentation + pymatgen.command_line package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                  - 2024.6.4 + 2024.6.10
                                                                  @@ -219,12 +219,12 @@

                                                                  Submodules
                                                                  -class BaderAnalysis(chgcar_filename: str = '', potcar_filename: str = '', chgref_filename: str = '', cube_filename: str = '', bader_path: str | None = None, parse_atomic_densities: bool = False)[source]
                                                                  +class BaderAnalysis(chgcar_filename: str = '', potcar_filename: str = '', chgref_filename: str = '', cube_filename: str = '', bader_path: str | None = None, parse_atomic_densities: bool = False)[source]

                                                                  Bases: object

                                                                  Perform Bader charge analysis for Cube files or VASP outputs.

                                                                  -data[source]
                                                                  +data[source]

                                                                  Atomic data parsed from bader analysis. Each dictionary in the list has the keys: “atomic_vol”, “min_dist”, “charge”, “x”, “y”, “z”.

                                                                  @@ -237,7 +237,7 @@

                                                                  Submodules
                                                                  -vacuum_volume[source]
                                                                  +vacuum_volume[source]

                                                                  Vacuum volume of the Bader analysis.

                                                                  Type:
                                                                  @@ -248,7 +248,7 @@

                                                                  Submodules
                                                                  -vacuum_charge[source]
                                                                  +vacuum_charge[source]

                                                                  Vacuum charge of the Bader analysis.

                                                                  Type:
                                                                  @@ -259,7 +259,7 @@

                                                                  Submodules
                                                                  -nelectrons[source]
                                                                  +nelectrons[source]

                                                                  Number of electrons of the Bader analysis.

                                                                  Type:
                                                                  @@ -270,7 +270,7 @@

                                                                  Submodules
                                                                  -chgcar[source]
                                                                  +chgcar[source]

                                                                  Chgcar object associated with input CHGCAR file.

                                                                  Type:
                                                                  @@ -281,7 +281,7 @@

                                                                  Submodules
                                                                  -atomic_densities[source]
                                                                  +atomic_densities[source]

                                                                  List of charge densities for each atom centered on the atom. Each dictionary has the keys: “data”, “shift”, “dim”, where “data” is the charge density array, @@ -311,7 +311,7 @@

                                                                  Submodules
                                                                  -classmethod from_path(path: str, suffix: str = '') → Self[source]
                                                                  +classmethod from_path(path: str, suffix: str = '') → Self[source]

                                                                  Convenient constructor that takes in the path name of VASP run to perform Bader analysis.

                                                                  @@ -329,7 +329,7 @@

                                                                  Submodules
                                                                  -get_charge(atom_index: int) → float[source]
                                                                  +get_charge(atom_index: int) → float[source]

                                                                  Convenience method to get the charge on a particular atom. This is the “raw” charge generated by the Bader program, not a partial atomic charge. If the cube file is a spin-density file, then this will return the spin density per atom with @@ -349,7 +349,7 @@

                                                                  Submodules
                                                                  -get_charge_decorated_structure() → Structure[source]
                                                                  +get_charge_decorated_structure() → Structure[source]

                                                                  Get a charge decorated structure.

                                                                  Note, this assumes that the Bader analysis was correctly performed on a file with electron densities

                                                                  @@ -357,7 +357,7 @@

                                                                  Submodules
                                                                  -get_charge_transfer(atom_index: int, nelect: int | None = None) → float[source]
                                                                  +get_charge_transfer(atom_index: int, nelect: int | None = None) → float[source]

                                                                  Get the charge transferred for a particular atom. A positive value means that the site has gained electron density (i.e. exhibits anionic character) whereas a negative value means the site has lost electron density (i.e. exhibits @@ -381,7 +381,7 @@

                                                                  Submodules
                                                                  -get_decorated_structure(property_name: str, average: bool = False) → Structure[source]
                                                                  +get_decorated_structure(property_name: str, average: bool = False) → Structure[source]

                                                                  Get a property-decorated structure from the Bader analysis.

                                                                  This is distinct from getting charge decorated structure, which assumes the “standard” Bader analysis of electron densities followed by converting @@ -412,7 +412,7 @@

                                                                  Submodules
                                                                  -get_oxidation_state_decorated_structure(nelects: list[int] | None = None) → Structure[source]
                                                                  +get_oxidation_state_decorated_structure(nelects: list[int] | None = None) → Structure[source]

                                                                  Get an oxidation state decorated structure based on bader analysis results. Each site is assigned a charge based on the computed partial atomic charge from bader.

                                                                  Note, this assumes that the Bader analysis was correctly performed on a file @@ -432,7 +432,7 @@

                                                                  Submodules
                                                                  -get_partial_charge(atom_index: int, nelect: int | None = None) → float[source]
                                                                  +get_partial_charge(atom_index: int, nelect: int | None = None) → float[source]

                                                                  Convenience method to get the partial charge on a particular atom. This is simply the negative value of the charge transferred. A positive value indicates that the atom has cationic character, whereas a negative value indicates the @@ -454,7 +454,7 @@

                                                                  Submodules
                                                                  -property summary: dict[str, Any][source]
                                                                  +property summary: dict[str, Any][source]

                                                                  Dict summary of key analysis, e.g. atomic volume, charge, etc.

                                                                  @@ -462,7 +462,7 @@

                                                                  Submodules
                                                                  -bader_analysis_from_objects(chgcar: Chgcar, potcar: Potcar | None = None, aeccar0: Chgcar | None = None, aeccar2: Chgcar | None = None) → dict[str, Any][source]
                                                                  +bader_analysis_from_objects(chgcar: Chgcar, potcar: Potcar | None = None, aeccar0: Chgcar | None = None, aeccar2: Chgcar | None = None) → dict[str, Any][source]

                                                                  Convenience method to run Bader analysis from a set of pymatgen Chgcar and Potcar objects.

                                                                  This method will:

                                                                  @@ -487,7 +487,7 @@

                                                                  Submodules
                                                                  -bader_analysis_from_path(path: str, suffix: str = '') → dict[str, Any][source]
                                                                  +bader_analysis_from_path(path: str, suffix: str = '') → dict[str, Any][source]

                                                                  Convenience method to run Bader analysis on a folder containing typical VASP output files.

                                                                  This method will:

                                                                  @@ -548,7 +548,7 @@

                                                                  Submodules
                                                                  -class ChargemolAnalysis(path: str | Path | None = None, atomic_densities_path: str | Path | None = None, run_chargemol: bool = True)[source]
                                                                  +class ChargemolAnalysis(path: str | Path | None = None, atomic_densities_path: str | Path | None = None, run_chargemol: bool = True)[source]

                                                                  Bases: object

                                                                  Chargemol analysis for DDEC3, DDEC6, and/or CM5 population analyses, including the calculation of partial atomic charges, atomic spin moments, @@ -570,7 +570,7 @@

                                                                  Submodules
                                                                  -get_bond_order(index_from, index_to)[source]
                                                                  +get_bond_order(index_from, index_to)[source]

                                                                  Convenience method to get the bond order between two atoms.

                                                                  Parameters:
                                                                  @@ -590,7 +590,7 @@

                                                                  Submodules
                                                                  -get_charge(atom_index, nelect=None, charge_type: Literal['ddec', 'cm5'] = 'ddec')[source]
                                                                  +get_charge(atom_index, nelect=None, charge_type: Literal['ddec', 'cm5'] = 'ddec')[source]

                                                                  Convenience method to get the charge on a particular atom using the same sign convention as the BaderAnalysis. Note that this is not the partial atomic charge. This value is nelect (e.g. ZVAL from the POTCAR) + the @@ -619,7 +619,7 @@

                                                                  Submodules
                                                                  -get_charge_transfer(atom_index, charge_type='ddec')[source]
                                                                  +get_charge_transfer(atom_index, charge_type='ddec')[source]

                                                                  Get the charge transferred for a particular atom. A positive value means that the site has gained electron density (i.e. exhibits anionic character) whereas a negative value means the site has lost electron density (i.e. exhibits @@ -643,7 +643,7 @@

                                                                  Submodules
                                                                  -get_partial_charge(atom_index, charge_type: Literal['ddec', 'cm5'] = 'ddec')[source]
                                                                  +get_partial_charge(atom_index, charge_type: Literal['ddec', 'cm5'] = 'ddec')[source]

                                                                  Convenience method to get the partial atomic charge on a particular atom. This is the value printed in the Chargemol analysis.

                                                                  @@ -658,7 +658,7 @@

                                                                  Submodules
                                                                  -get_property_decorated_structure()[source]
                                                                  +get_property_decorated_structure()[source]

                                                                  Takes CHGCAR’s structure object and updates it with properties from the Chargemol analysis.

                                                                  @@ -670,7 +670,7 @@

                                                                  Submodules
                                                                  -property summary[source]
                                                                  +property summary[source]

                                                                  A dictionary summary of the Chargemol analysis {

                                                                  @@ -734,7 +734,7 @@

                                                                  Submoduleshttps://doi.org/10.1016/j.cpc.2008.07.018)

                                                                  -class Critic2Analysis(structure: Structure, stdout: str | None = None, stderr: str | None = None, cpreport: dict | None = None, yt: dict | None = None, zpsp: dict | None = None)[source]
                                                                  +class Critic2Analysis(structure: Structure, stdout: str | None = None, stderr: str | None = None, cpreport: dict | None = None, yt: dict | None = None, zpsp: dict | None = None)[source]

                                                                  Bases: MSONable

                                                                  Process the standard output from critic2 into pymatgen-compatible objects.

                                                                  This class is used to store results from the Critic2Caller.

                                                                  @@ -782,7 +782,7 @@

                                                                  Submodules
                                                                  -get_critical_point_for_site(n: int)[source]
                                                                  +get_critical_point_for_site(n: int)[source]
                                                                  Parameters:

                                                                  n (int) – Site index.

                                                                  @@ -795,7 +795,7 @@

                                                                  Submodules
                                                                  -get_volume_and_charge_for_site(idx)[source]
                                                                  +get_volume_and_charge_for_site(idx)[source]
                                                                  Parameters:

                                                                  idx – Site index.

                                                                  @@ -811,7 +811,7 @@

                                                                  Submodules
                                                                  -structure_graph(include_critical_points=('bond', 'ring', 'cage'))[source]
                                                                  +structure_graph(include_critical_points=('bond', 'ring', 'cage'))[source]

                                                                  A StructureGraph object describing bonding information in the crystal.

                                                                  Parameters:
                                                                  @@ -828,7 +828,7 @@

                                                                  Submodules
                                                                  -class Critic2Caller(input_script: str)[source]
                                                                  +class Critic2Caller(input_script: str)[source]

                                                                  Bases: object

                                                                  Call critic2 and store standard output for further processing.

                                                                  Run Critic2 on a given input script.

                                                                  @@ -839,7 +839,7 @@

                                                                  Submodules
                                                                  -classmethod from_chgcar(structure, chgcar=None, chgcar_ref=None, user_input_settings=None, write_cml=False, write_json=True, zpsp=None) → Self[source]
                                                                  +classmethod from_chgcar(structure, chgcar=None, chgcar_ref=None, user_input_settings=None, write_cml=False, write_json=True, zpsp=None) → Self[source]

                                                                  Run Critic2 in automatic mode on a supplied structure, charge density (chgcar) and reference charge density (chgcar_ref).

                                                                  The reason for a separate reference field is that in @@ -901,7 +901,7 @@

                                                                  Submodules
                                                                  -classmethod from_path(path, suffix='', zpsp=None) → Self[source]
                                                                  +classmethod from_path(path, suffix='', zpsp=None) → Self[source]

                                                                  Convenience method to run critic2 analysis on a folder with typical VASP output files.

                                                                  This method will:

                                                                  1. Look for files CHGCAR, AECAR0, AECAR2, POTCAR or their gzipped @@ -926,7 +926,7 @@

                                                                  Submodules
                                                                  -class CriticalPoint(index, type, frac_coords, point_group, multiplicity, field, field_gradient, coords=None, field_hessian=None)[source]
                                                                  +class CriticalPoint(index, type, frac_coords, point_group, multiplicity, field, field_gradient, coords=None, field_hessian=None)[source]

                                                                  Bases: MSONable

                                                                  Access information about a critical point and the field values at that point.

                                                                  Characterize a critical point from a topological @@ -950,7 +950,7 @@

                                                                  Submodules
                                                                  -property ellipticity[source]
                                                                  +property ellipticity[source]

                                                                  Most meaningful for bond critical points, can be physically interpreted as e.g. degree of pi-bonding in organic molecules. Consult literature for more info.

                                                                  @@ -965,13 +965,13 @@

                                                                  Submodules
                                                                  -property laplacian: float[source]
                                                                  +property laplacian: float[source]

                                                                  The Laplacian of the field at the critical point.

                                                                  -property type: CriticalPointType[source]
                                                                  +property type: CriticalPointType[source]

                                                                  Instance of CriticalPointType.

                                                                  @@ -979,39 +979,39 @@

                                                                  Submodules
                                                                  -class CriticalPointType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                  +class CriticalPointType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                  Bases: Enum

                                                                  Enum type for the different varieties of critical point.

                                                                  -bond = 'bond'[source]
                                                                  +bond = 'bond'[source]
                                                                  -cage = 'cage'[source]
                                                                  +cage = 'cage'[source]
                                                                  -nnattr = 'nnattr'[source]
                                                                  +nnattr = 'nnattr'[source]
                                                                  -nucleus = 'nucleus'[source]
                                                                  +nucleus = 'nucleus'[source]
                                                                  -ring = 'ring'[source]
                                                                  +ring = 'ring'[source]

                                                                  -get_filepath(filename, warning, path, suffix)[source]
                                                                  +get_filepath(filename, warning, path, suffix)[source]
                                                                  Parameters:
                                                                  -EnumlibAdaptor(structure, min_cell_size=1, max_cell_size=1, symm_prec=0.1, enum_precision_parameter=0.001, refine_structure=False, check_ordered_symmetry=True, timeout=None)[source]
                                                                  +EnumlibAdaptor(structure, min_cell_size=1, max_cell_size=1, symm_prec=0.1, enum_precision_parameter=0.001, refine_structure=False, check_ordered_symmetry=True, timeout=None)[source]

                                                                  An adaptor for enumlib.

                                                                  -structures[source]
                                                                  +structures[source]

                                                                  all enumerated structures.

                                                                  Type:
                                                                  @@ -1076,7 +1076,7 @@

                                                                  Submodules
                                                                  -class BuckinghamPotential(bush_lewis_flag)[source]
                                                                  +class BuckinghamPotential(bush_lewis_flag)[source]

                                                                  Bases: object

                                                                  Generate the Buckingham Potential Table from the bush.lib and lewis.lib.

                                                                  Ref: @@ -1093,7 +1093,7 @@

                                                                  Submodules
                                                                  -class GulpCaller(cmd='gulp')[source]
                                                                  +class GulpCaller(cmd='gulp')[source]

                                                                  Bases: object

                                                                  Run gulp from command line.

                                                                  Initialize with the executable if not in the standard path.

                                                                  @@ -1104,7 +1104,7 @@

                                                                  Submodules
                                                                  -run(gin)[source]
                                                                  +run(gin)[source]

                                                                  Run GULP using the gin as input.

                                                                  Parameters:
                                                                  @@ -1123,7 +1123,7 @@

                                                                  Submodules
                                                                  -exception GulpConvergenceError(msg='')[source]
                                                                  +exception GulpConvergenceError(msg='')[source]

                                                                  Bases: Exception

                                                                  Exception class for GULP. Raised when proper convergence is not reached in Mott-Littleton @@ -1137,7 +1137,7 @@

                                                                  Submodules
                                                                  -exception GulpError(msg)[source]
                                                                  +exception GulpError(msg)[source]

                                                                  Bases: Exception

                                                                  Exception class for GULP. Raised when the GULP gives an error.

                                                                  @@ -1150,12 +1150,12 @@

                                                                  Submodules
                                                                  -class GulpIO[source]
                                                                  +class GulpIO[source]

                                                                  Bases: object

                                                                  To generate GULP input and process output.

                                                                  -buckingham_input(structure: Structure, keywords, library=None, uc=True, valence_dict=None)[source]
                                                                  +buckingham_input(structure: Structure, keywords, library=None, uc=True, valence_dict=None)[source]

                                                                  Get a GULP input for an oxide structure and buckingham potential from library.

                                                                  @@ -1173,7 +1173,7 @@

                                                                  Submodules
                                                                  -static buckingham_potential(structure, val_dict=None)[source]
                                                                  +static buckingham_potential(structure, val_dict=None)[source]

                                                                  Generate species, buckingham, and spring options for an oxide structure using the parameters in default libraries.

                                                                  @@ -1198,7 +1198,7 @@

                                                                  Submodules
                                                                  -static get_energy(gout: str)[source]
                                                                  +static get_energy(gout: str)[source]
                                                                  Parameters:

                                                                  gout (str) – GULP output string.

                                                                  @@ -1211,7 +1211,7 @@

                                                                  Submodules
                                                                  -static get_relaxed_structure(gout: str)[source]
                                                                  +static get_relaxed_structure(gout: str)[source]
                                                                  Parameters:

                                                                  gout (str) – GULP output string.

                                                                  @@ -1227,7 +1227,7 @@

                                                                  Submodules
                                                                  -static keyword_line(*args)[source]
                                                                  +static keyword_line(*args)[source]

                                                                  Check if the input args are proper gulp keywords and generates the 1st line of gulp input. Full keywords are expected.

                                                                  @@ -1239,7 +1239,7 @@

                                                                  Submodules
                                                                  -static library_line(file_name)[source]
                                                                  +static library_line(file_name)[source]

                                                                  Specify GULP library file to read species and potential parameters. If using library don’t specify species and potential in the input file and vice versa. Make sure the elements of @@ -1256,7 +1256,7 @@

                                                                  Submodules
                                                                  -static specie_potential_lines(structure, potential, **kwargs)[source]
                                                                  +static specie_potential_lines(structure, potential, **kwargs)[source]

                                                                  Generate GULP input species and potential string for pymatgen structure.

                                                                  Parameters:
                                                                  @@ -1286,7 +1286,7 @@

                                                                  Submodules
                                                                  -static structure_lines(structure: Structure, cell_flg: bool = True, frac_flg: bool = True, anion_shell_flg: bool = True, cation_shell_flg: bool = False, symm_flg: bool = True)[source]
                                                                  +static structure_lines(structure: Structure, cell_flg: bool = True, frac_flg: bool = True, anion_shell_flg: bool = True, cation_shell_flg: bool = False, symm_flg: bool = True)[source]

                                                                  Generate GULP input string corresponding to pymatgen structure.

                                                                  Parameters:
                                                                  @@ -1319,7 +1319,7 @@

                                                                  Submodules
                                                                  -tersoff_input(structure: Structure, periodic=False, uc=True, *keywords)[source]
                                                                  +tersoff_input(structure: Structure, periodic=False, uc=True, *keywords)[source]

                                                                  Get a GULP input with Tersoff potential for an oxide structure.

                                                                  Parameters:
                                                                  @@ -1337,7 +1337,7 @@

                                                                  Submodules
                                                                  -static tersoff_potential(structure)[source]
                                                                  +static tersoff_potential(structure)[source]

                                                                  Generate the species, Tersoff potential lines for an oxide structure.

                                                                  Parameters:
                                                                  @@ -1350,7 +1350,7 @@

                                                                  Submodules
                                                                  -class TersoffPotential[source]
                                                                  +class TersoffPotential[source]

                                                                  Bases: object

                                                                  Generate Tersoff Potential Table from “OxideTersoffPotentialentials” file.

                                                                  Init TersoffPotential.

                                                                  @@ -1358,7 +1358,7 @@

                                                                  Submodules
                                                                  -get_energy_buckingham(structure, gulp_cmd='gulp', keywords=('optimise', 'conp', 'qok'), valence_dict=None)[source]
                                                                  +get_energy_buckingham(structure, gulp_cmd='gulp', keywords=('optimise', 'conp', 'qok'), valence_dict=None)[source]

                                                                  Compute the energy of a structure using Buckingham potential.

                                                                  Parameters:
                                                                  @@ -1375,7 +1375,7 @@

                                                                  Submodules
                                                                  -get_energy_relax_structure_buckingham(structure, gulp_cmd='gulp', keywords=('optimise', 'conp'), valence_dict=None)[source]
                                                                  +get_energy_relax_structure_buckingham(structure, gulp_cmd='gulp', keywords=('optimise', 'conp'), valence_dict=None)[source]

                                                                  Relax a structure and compute the energy using Buckingham potential.

                                                                  Parameters:
                                                                  @@ -1392,7 +1392,7 @@

                                                                  Submodules
                                                                  -get_energy_tersoff(structure, gulp_cmd='gulp')[source]
                                                                  +get_energy_tersoff(structure, gulp_cmd='gulp')[source]

                                                                  Compute the energy of a structure using Tersoff potential.

                                                                  Parameters:
                                                                  @@ -1411,37 +1411,37 @@

                                                                  Submoduleshttps://www.brown.edu/Departments/Engineering/Labs/avdw/atat/.

                                                                  -class Sqs(bestsqs: Structure | IStructure, objective_function: float | str, allsqs: list, clusters: list | str, directory: str)[source]
                                                                  +class Sqs(bestsqs: Structure | IStructure, objective_function: float | str, allsqs: list, clusters: list | str, directory: str)[source]

                                                                  Bases: NamedTuple

                                                                  Return type for run_mcsqs.

                                                                  Create new instance of Sqs(bestsqs, objective_function, allsqs, clusters, directory)

                                                                  -allsqs: list[source]
                                                                  +allsqs: list[source]

                                                                  Alias for field number 2

                                                                  -bestsqs: Structure | IStructure[source]
                                                                  +bestsqs: Structure | IStructure[source]

                                                                  Alias for field number 0

                                                                  -clusters: list | str[source]
                                                                  +clusters: list | str[source]

                                                                  Alias for field number 3

                                                                  -directory: str[source]
                                                                  +directory: str[source]

                                                                  Alias for field number 4

                                                                  -objective_function: float | str[source]
                                                                  +objective_function: float | str[source]

                                                                  Alias for field number 1

                                                                  @@ -1449,7 +1449,7 @@

                                                                  Submodules
                                                                  -run_mcsqs(structure: Structure, clusters: dict[int, float], scaling: int | list[int] = 1, search_time: float = 60, directory: str | None = None, instances: int | None = None, temperature: float = 1, wr: float = 1, wn: float = 1, wd: float = 0.5, tol: float = 0.001) → Sqs[source]
                                                                  +run_mcsqs(structure: Structure, clusters: dict[int, float], scaling: int | list[int] = 1, search_time: float = 60, directory: str | None = None, instances: int | None = None, temperature: float = 1, wr: float = 1, wn: float = 1, wd: float = 0.5, tol: float = 0.001) → Sqs[source]

                                                                  Helper function for calling mcsqs with different arguments :param structure: Disordered pymatgen Structure object :type structure: Structure @@ -1511,7 +1511,7 @@

                                                                  Submodules
                                                                  -class VampireCaller(ordered_structures=None, energies=None, mc_box_size=4.0, equil_timesteps=2000, mc_timesteps=4000, save_inputs=False, hm=None, avg=True, user_input_settings=None)[source]
                                                                  +class VampireCaller(ordered_structures=None, energies=None, mc_box_size=4.0, equil_timesteps=2000, mc_timesteps=4000, save_inputs=False, hm=None, avg=True, user_input_settings=None)[source]

                                                                  Bases: object

                                                                  Run Vampire on a material with magnetic ordering and exchange parameter information to compute the critical temperature with classical Monte Carlo.

                                                                  @@ -1538,7 +1538,7 @@

                                                                  Submodules
                                                                  -sgraph[source]
                                                                  +sgraph[source]

                                                                  Ground state graph.

                                                                  Type:
                                                                  @@ -1549,7 +1549,7 @@

                                                                  Submodules
                                                                  -unique_site_ids[source]
                                                                  +unique_site_ids[source]

                                                                  Maps each site to its unique identifier

                                                                  Type:
                                                                  @@ -1560,7 +1560,7 @@

                                                                  Submodules
                                                                  -nn_interactions[source]
                                                                  +nn_interactions[source]

                                                                  {i: j} pairs of NN interactions between unique sites.

                                                                  @@ -1572,7 +1572,7 @@

                                                                  Submodules
                                                                  -ex_params[source]
                                                                  +ex_params[source]

                                                                  Exchange parameter values (meV/atom)

                                                                  Type:
                                                                  @@ -1583,7 +1583,7 @@

                                                                  Submodules
                                                                  -mft_t[source]
                                                                  +mft_t[source]

                                                                  Mean field theory estimate of critical T

                                                                  Type:
                                                                  @@ -1594,7 +1594,7 @@

                                                                  Submodules
                                                                  -mat_name[source]
                                                                  +mat_name[source]

                                                                  Formula unit label for input files

                                                                  Type:
                                                                  @@ -1605,7 +1605,7 @@

                                                                  Submodules
                                                                  -mat_id_dict[source]
                                                                  +mat_id_dict[source]

                                                                  Maps sites to material id # for vampire indexing.

                                                                  @@ -1617,7 +1617,7 @@

                                                                  Submodules
                                                                  -static parse_stdout(vamp_stdout, n_mats: int) → tuple[source]
                                                                  +static parse_stdout(vamp_stdout, n_mats: int) → tuple[source]

                                                                  Parse stdout from Vampire.

                                                                  Parameters:
                                                                  @@ -1640,7 +1640,7 @@

                                                                  Submodules
                                                                  -class VampireOutput(parsed_out=None, nmats=None, critical_temp=None)[source]
                                                                  +class VampireOutput(parsed_out=None, nmats=None, critical_temp=None)[source]

                                                                  Bases: MSONable

                                                                  This class processes results from a Vampire Monte Carlo simulation and returns the critical temperature.

                                                                  diff --git a/docs/pymatgen.core.html b/docs/pymatgen.core.html index c19c8aa0820..1b40a0b7d11 100644 --- a/docs/pymatgen.core.html +++ b/docs/pymatgen.core.html @@ -4,7 +4,7 @@ - pymatgen.core package — pymatgen 2024.6.4 documentation + pymatgen.core package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                  - 2024.6.4 + 2024.6.10
                                                                  @@ -1457,7 +1457,7 @@

                                                                  Submodules
                                                                  -class CovalentBond(site1: Site, site2: Site)[source]
                                                                  +class CovalentBond(site1: Site, site2: Site)[source]

                                                                  Bases: object

                                                                  A covalent bond between two sites.

                                                                  Initialize a covalent bond between two sites.

                                                                  @@ -1471,7 +1471,7 @@

                                                                  Submodules
                                                                  -get_bond_order(tol: float = 0.2, default_bl: float | None = None) → float[source]
                                                                  +get_bond_order(tol: float = 0.2, default_bl: float | None = None) → float[source]

                                                                  The bond order according the distance between the two sites.

                                                                  Parameters:
                                                                  @@ -1498,7 +1498,7 @@

                                                                  Submodules
                                                                  -static is_bonded(site1: Site, site2: Site, tol: float = 0.2, bond_order: float | None = None, default_bl: float | None = None) → bool[source]
                                                                  +static is_bonded(site1: Site, site2: Site, tol: float = 0.2, bond_order: float | None = None, default_bl: float | None = None) → bool[source]

                                                                  Check if two sites are bonded, up to a certain limit.

                                                                  Parameters:
                                                                  @@ -1526,7 +1526,7 @@

                                                                  Submodules
                                                                  -property length: float[source]
                                                                  +property length: float[source]

                                                                  Length of the bond.

                                                                  @@ -1534,7 +1534,7 @@

                                                                  Submodules
                                                                  -get_bond_length(sp1: SpeciesLike, sp2: SpeciesLike, bond_order: float = 1) → float[source]
                                                                  +get_bond_length(sp1: SpeciesLike, sp2: SpeciesLike, bond_order: float = 1) → float[source]

                                                                  Get the bond length between two species.

                                                                  Parameters:
                                                                  @@ -1562,7 +1562,7 @@

                                                                  Submodules
                                                                  -get_bond_order(sp1: SpeciesLike, sp2: SpeciesLike, dist: float, tol: float = 0.2, default_bl: float | None = None) → float[source]
                                                                  +get_bond_order(sp1: SpeciesLike, sp2: SpeciesLike, dist: float, tol: float = 0.2, default_bl: float | None = None) → float[source]

                                                                  Calculate the bond order given the distance of 2 species.

                                                                  Parameters:
                                                                  @@ -1591,7 +1591,7 @@

                                                                  Submodules
                                                                  -obtain_all_bond_lengths(sp1: SpeciesLike, sp2: SpeciesLike, default_bl: float | None = None) → dict[float, float][source]
                                                                  +obtain_all_bond_lengths(sp1: SpeciesLike, sp2: SpeciesLike, default_bl: float | None = None) → dict[float, float][source]

                                                                  Obtain bond lengths for all bond orders from bond length database.

                                                                  Parameters:
                                                                  @@ -1616,7 +1616,7 @@

                                                                  Submodules
                                                                  -class ChemicalPotential(*args, **kwargs)[source]
                                                                  +class ChemicalPotential(*args, **kwargs)[source]

                                                                  Bases: dict, MSONable

                                                                  Represent set of chemical potentials. Can be: multiplied/divided by a Number multiplied by a Composition (returns an energy) added/subtracted with other ChemicalPotentials.

                                                                  @@ -1630,7 +1630,7 @@

                                                                  Submodules
                                                                  -get_energy(composition: Composition, strict: bool = True) → float[source]
                                                                  +get_energy(composition: Composition, strict: bool = True) → float[source]

                                                                  Calculate the energy of a composition.

                                                                  Parameters:
                                                                  @@ -1646,7 +1646,7 @@

                                                                  Submodules
                                                                  -class Composition(*args, strict: bool = False, **kwargs)[source]
                                                                  +class Composition(*args, strict: bool = False, **kwargs)[source]

                                                                  Bases: Hashable, Mapping, MSONable, Stringify

                                                                  Represents a Composition, which is essentially a {element:amount} mapping type. Composition is written to be immutable and hashable, @@ -1711,7 +1711,7 @@

                                                                  Submodules
                                                                  -add_charges_from_oxi_state_guesses(oxi_states_override: dict | None = None, target_charge: float = 0, all_oxi_states: bool = False, max_sites: int | None = None) → Self[source]
                                                                  +add_charges_from_oxi_state_guesses(oxi_states_override: dict | None = None, target_charge: float = 0, all_oxi_states: bool = False, max_sites: int | None = None) → Self[source]

                                                                  Assign oxidation states based on guessed oxidation states.

                                                                  See oxi_state_guesses for an explanation of how oxidation states are guessed. This operation uses the set of oxidation states for each site @@ -1748,7 +1748,7 @@

                                                                  Submodules
                                                                  -almost_equals(other: Composition, rtol: float = 0.1, atol: float = 1e-08) → bool[source]
                                                                  +almost_equals(other: Composition, rtol: float = 0.1, atol: float = 1e-08) → bool[source]

                                                                  Get true if compositions are equal within a tolerance.

                                                                  Parameters:
                                                                  @@ -1763,19 +1763,19 @@

                                                                  Submodules
                                                                  -property alphabetical_formula: str[source]
                                                                  +property alphabetical_formula: str[source]

                                                                  A formula string, with elements sorted by alphabetically e.g. Fe4 Li4 O16 P4.

                                                                  -amount_tolerance = 1e-08[source]
                                                                  +amount_tolerance = 1e-08[source]
                                                                  -property anonymized_formula: str[source]
                                                                  +property anonymized_formula: str[source]

                                                                  An anonymized formula. Unique species are arranged in ordering of increasing amounts and assigned ascending alphabets. Useful for prototyping formulas. For example, all stoichiometric perovskites have @@ -1784,7 +1784,7 @@

                                                                  Submodules
                                                                  -as_dict() → dict[str, float][source]
                                                                  +as_dict() → dict[str, float][source]

                                                                  Subtly different from get_el_amt_dict in that they keys here are str(Element) instead of Element.symbol.

                                                                  @@ -1803,13 +1803,13 @@

                                                                  Submodules
                                                                  -property average_electroneg: float[source]
                                                                  +property average_electroneg: float[source]

                                                                  Average electronegativity of the composition.

                                                                  -property charge: float | None[source]
                                                                  +property charge: float | None[source]

                                                                  Total charge based on oxidation states. If any oxidation states are None or they’re all 0, returns None. Use add_charges_from_oxi_state_guesses to assign oxidation states to elements based on charge balancing.

                                                                  @@ -1817,7 +1817,7 @@

                                                                  Submodules
                                                                  -property charge_balanced: bool | None[source]
                                                                  +property charge_balanced: bool | None[source]

                                                                  True if composition is charge balanced, False otherwise. If any oxidation states are None, returns None. Use add_charges_from_oxi_state_guesses to assign oxidation states to elements.

                                                                  @@ -1825,12 +1825,12 @@

                                                                  Submodules
                                                                  -charge_balanced_tolerance = 1e-08[source]
                                                                  +charge_balanced_tolerance = 1e-08[source]

                                                                  -property chemical_system: str[source]
                                                                  +property chemical_system: str[source]

                                                                  The chemical system of a Composition, for example “O-Si” for SiO2. Chemical system is a string of a list of elements sorted alphabetically and joined by dashes, by convention for use @@ -1839,13 +1839,13 @@

                                                                  Submodules
                                                                  -property chemical_system_set: set[str][source]
                                                                  +property chemical_system_set: set[str][source]

                                                                  The set of elements in the Composition. E.g. {“O”, “Si”} for SiO2.

                                                                  -contains_element_type(category: str) → bool[source]
                                                                  +contains_element_type(category: str) → bool[source]

                                                                  Check if Composition contains any elements matching a given category.

                                                                  Parameters:
                                                                  @@ -1865,32 +1865,32 @@

                                                                  Submodules
                                                                  -copy() → Self[source]
                                                                  +copy() → Self[source]

                                                                  A copy of the composition.

                                                                  -property element_composition: Self[source]
                                                                  +property element_composition: Self[source]

                                                                  The composition replacing any species by the corresponding element.

                                                                  -property elements: list[Element | Species | DummySpecies][source]
                                                                  +property elements: list[Element | Species | DummySpecies][source]

                                                                  List of elements in Composition.

                                                                  -property formula: str[source]
                                                                  +property formula: str[source]

                                                                  A formula string, with elements sorted by electronegativity, e.g. Li4 Fe4 P4 O16.

                                                                  -property fractional_composition: Self[source]
                                                                  +property fractional_composition: Self[source]

                                                                  The normalized composition in which the amounts of each species sum to 1. E.g. “Fe2 O3”.fractional_composition = “Fe0.4 O0.6”.

                                                                  @@ -1898,7 +1898,7 @@

                                                                  Submodules
                                                                  -classmethod from_dict(dct: dict) → Self[source]
                                                                  +classmethod from_dict(dct: dict) → Self[source]

                                                                  Create a composition from a dict generated by as_dict(). Strictly not necessary given that the standard constructor already takes in such an input, but this method preserves the standard pymatgen API of having @@ -1913,7 +1913,7 @@

                                                                  Submodules
                                                                  -classmethod from_weight_dict(weight_dict: dict[SpeciesLike, float]) → Self[source]
                                                                  +classmethod from_weight_dict(weight_dict: dict[SpeciesLike, float]) → Self[source]

                                                                  Create a Composition based on a dict of atomic fractions calculated from a dict of weight fractions. Allows for quick creation of the class from weight-based notations commonly used in the industry, such as @@ -1930,7 +1930,7 @@

                                                                  Submodules
                                                                  -get_atomic_fraction(el: SpeciesLike) → float[source]
                                                                  +get_atomic_fraction(el: SpeciesLike) → float[source]

                                                                  Calculate atomic fraction of an Element or Species.

                                                                  Parameters:
                                                                  @@ -1944,7 +1944,7 @@

                                                                  Submodules
                                                                  -get_el_amt_dict() → dict[str, float][source]
                                                                  +get_el_amt_dict() → dict[str, float][source]
                                                                  Returns:

                                                                  @@ -1961,7 +1961,7 @@

                                                                  Submodules
                                                                  -get_integer_formula_and_factor(max_denominator: int = 10000, iupac_ordering: bool = False) → tuple[str, float][source]
                                                                  +get_integer_formula_and_factor(max_denominator: int = 10000, iupac_ordering: bool = False) → tuple[str, float][source]

                                                                  Calculate an integer formula and factor.

                                                                  Parameters:
                                                                  @@ -1987,7 +1987,7 @@

                                                                  Submodules
                                                                  -get_reduced_composition_and_factor() → tuple[Self, float][source]
                                                                  +get_reduced_composition_and_factor() → tuple[Self, float][source]

                                                                  Calculate a reduced composition and factor.

                                                                  Returns:
                                                                  @@ -1999,7 +1999,7 @@

                                                                  Submodules
                                                                  -get_reduced_formula_and_factor(iupac_ordering: bool = False) → tuple[str, float][source]
                                                                  +get_reduced_formula_and_factor(iupac_ordering: bool = False) → tuple[str, float][source]

                                                                  Calculate a reduced formula and factor.

                                                                  Parameters:
                                                                  @@ -2021,7 +2021,7 @@

                                                                  Submodules
                                                                  -get_wt_fraction(el: SpeciesLike) → float[source]
                                                                  +get_wt_fraction(el: SpeciesLike) → float[source]

                                                                  Calculate weight fraction of an Element or Species.

                                                                  Parameters:
                                                                  @@ -2038,7 +2038,7 @@

                                                                  Submodules
                                                                  -property hill_formula: str[source]
                                                                  +property hill_formula: str[source]

                                                                  The Hill system (or Hill notation) is a system of writing empirical chemical formulas, molecular chemical formulas and components of a condensed formula such that the number of carbon atoms in a molecule is indicated first, the number of @@ -2050,13 +2050,13 @@

                                                                  Submodules
                                                                  -property is_element: bool[source]
                                                                  +property is_element: bool[source]

                                                                  True if composition is an element.

                                                                  -property iupac_formula: str[source]
                                                                  +property iupac_formula: str[source]

                                                                  A formula string, with elements sorted by the IUPAC electronegativity ordering defined in Table VI of “Nomenclature of Inorganic Chemistry (IUPAC Recommendations 2005)”. This ordering @@ -2068,19 +2068,19 @@

                                                                  Submodules
                                                                  -property num_atoms: float[source]
                                                                  +property num_atoms: float[source]

                                                                  Total number of atoms in Composition. For negative amounts, sum of absolute values.

                                                                  -oxi_prob = None[source]
                                                                  +oxi_prob = None[source]
                                                                  -oxi_state_guesses(oxi_states_override: dict | None = None, target_charge: float = 0, all_oxi_states: bool = False, max_sites: int | None = None) → tuple[dict[str, float]][source]
                                                                  +oxi_state_guesses(oxi_states_override: dict | None = None, target_charge: float = 0, all_oxi_states: bool = False, max_sites: int | None = None) → tuple[dict[str, float]][source]

                                                                  Check if the composition is charge-balanced and returns back all charge-balanced oxidation state combinations. Composition must have integer values. Note that more num_atoms in the composition gives @@ -2125,7 +2125,7 @@

                                                                  Submodules
                                                                  -static ranked_compositions_from_indeterminate_formula(fuzzy_formula: str, lock_if_strict: bool = True) → list[Composition][source]
                                                                  +static ranked_compositions_from_indeterminate_formula(fuzzy_formula: str, lock_if_strict: bool = True) → list[Composition][source]

                                                                  Takes in a formula where capitalization might not be correctly entered, and suggests a ranked list of potential Composition matches. Author: Anubhav Jain.

                                                                  @@ -2148,21 +2148,21 @@

                                                                  Submodules
                                                                  -property reduced_composition: Self[source]
                                                                  +property reduced_composition: Self[source]

                                                                  The reduced composition, i.e. amounts normalized by greatest common denominator. E.g. “Fe4 P4 O16”.reduced_composition = “Fe P O4”.

                                                                  -property reduced_formula: str[source]
                                                                  +property reduced_formula: str[source]

                                                                  A pretty normalized formula, i.e., LiFePO4 instead of Li4Fe4P4O16.

                                                                  -remove_charges() → Self[source]
                                                                  +remove_charges() → Self[source]

                                                                  Get a new Composition with charges from each Species removed.

                                                                  Returns:
                                                                  @@ -2174,7 +2174,7 @@

                                                                  Submodules
                                                                  -replace(elem_map: dict[str, str | dict[str, float]]) → Self[source]
                                                                  +replace(elem_map: dict[str, str | dict[str, float]]) → Self[source]

                                                                  Replace elements in a composition. Returns a new Composition, leaving the old one unchanged.

                                                                  Parameters:
                                                                  @@ -2193,12 +2193,12 @@

                                                                  Submodules
                                                                  -special_formulas: ClassVar[dict[str, str]] = {'Cl': 'Cl2', 'CsO': 'Cs2O2', 'F': 'F2', 'H': 'H2', 'HO': 'H2O2', 'KO': 'K2O2', 'LiO': 'Li2O2', 'N': 'N2', 'NaO': 'Na2O2', 'O': 'O2', 'RbO': 'Rb2O2'}[source]
                                                                  +special_formulas: ClassVar[dict[str, str]] = {'Cl': 'Cl2', 'CsO': 'Cs2O2', 'F': 'F2', 'H': 'H2', 'HO': 'H2O2', 'KO': 'K2O2', 'LiO': 'Li2O2', 'N': 'N2', 'NaO': 'Na2O2', 'O': 'O2', 'RbO': 'Rb2O2'}[source]

                                                                  -property to_data_dict: dict[str, Any][source]
                                                                  +property to_data_dict: dict[str, Any][source]

                                                                  Returns: A dict with many keys and values relating to Composition/Formula, including reduced_cell_composition, unit_cell_composition, @@ -2207,7 +2207,7 @@

                                                                  Submodules
                                                                  -to_pretty_string() → str[source]
                                                                  +to_pretty_string() → str[source]
                                                                  Returns:

                                                                  Same output as __str__() but without spaces.

                                                                  @@ -2220,34 +2220,34 @@

                                                                  Submodules
                                                                  -property to_reduced_dict: dict[str, float][source]
                                                                  +property to_reduced_dict: dict[str, float][source]

                                                                  Returns: dict[str, float]: element symbols mapped to reduced amount e.g. {“Fe”: 2.0, “O”:3.0}.

                                                                  -property to_weight_dict: dict[str, float][source]
                                                                  +property to_weight_dict: dict[str, float][source]

                                                                  Returns: dict[str, float] with weight fraction of each component {“Ti”: 0.90, “V”: 0.06, “Al”: 0.04}.

                                                                  -property total_electrons: float[source]
                                                                  +property total_electrons: float[source]

                                                                  Total number of electrons in composition.

                                                                  -property valid: bool[source]
                                                                  +property valid: bool[source]

                                                                  True if Composition contains valid elements or species and False if the Composition contains any dummy species.

                                                                  -property weight: float[source]
                                                                  +property weight: float[source]

                                                                  Total molecular weight of Composition.

                                                                  @@ -2255,14 +2255,14 @@

                                                                  Submodules
                                                                  -exception CompositionError[source]
                                                                  +exception CompositionError[source]

                                                                  Bases: Exception

                                                                  Exception class for composition errors.

                                                                  -reduce_formula(sym_amt: dict[str, float] | dict[str, int], iupac_ordering: bool = False) → tuple[str, float][source]
                                                                  +reduce_formula(sym_amt: dict[str, float] | dict[str, int], iupac_ordering: bool = False) → tuple[str, float][source]

                                                                  Helper function to reduce a sym_amt dict to a reduced formula and factor.

                                                                  Parameters:
                                                                  @@ -2294,7 +2294,7 @@

                                                                  Submodules
                                                                  -class GrainBoundary(lattice: np.ndarray | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], rotation_axis: Tuple3Ints | Tuple4Ints, rotation_angle: float, gb_plane: Tuple3Ints, join_plane: Tuple3Ints, init_cell: Structure, vacuum_thickness: float, ab_shift: tuple[float, float], site_properties: dict[str, Any], oriented_unit_cell: Structure, validate_proximity: bool = False, coords_are_cartesian: bool = False, properties: dict | None = None)[source]
                                                                  +class GrainBoundary(lattice: np.ndarray | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], rotation_axis: Tuple3Ints | Tuple4Ints, rotation_angle: float, gb_plane: Tuple3Ints, join_plane: Tuple3Ints, init_cell: Structure, vacuum_thickness: float, ab_shift: tuple[float, float], site_properties: dict[str, Any], oriented_unit_cell: Structure, validate_proximity: bool = False, coords_are_cartesian: bool = False, properties: dict | None = None)[source]

                                                                  Bases: Structure

                                                                  Representation of grain boundary (GB). Implements additional attributes pertaining to GBs, but the init method does not actually implement any @@ -2353,7 +2353,7 @@

                                                                  Submodules
                                                                  -as_dict() → dict[source]
                                                                  +as_dict() → dict[source]
                                                                  Returns:

                                                                  Dictionary representation of GrainBoundary object.

                                                                  @@ -2363,25 +2363,25 @@

                                                                  Submodules
                                                                  -property bottom_grain: Structure[source]
                                                                  +property bottom_grain: Structure[source]

                                                                  The bottom grain (Structure) of the GB.

                                                                  -property coincidents: list[Site][source]
                                                                  +property coincidents: list[Site][source]

                                                                  A list of coincident sites.

                                                                  -copy() → Self[source]
                                                                  +copy() → Self[source]

                                                                  Make a copy of the GrainBoundary.

                                                                  -classmethod from_dict(dct: dict) → Self[source]
                                                                  +classmethod from_dict(dct: dict) → Self[source]

                                                                  Generate GrainBoundary from a dict created by as_dict().

                                                                  Parameters:
                                                                  @@ -2395,7 +2395,7 @@

                                                                  Submodules
                                                                  -get_sorted_structure(key: Callable | None = None, reverse: bool = False) → Self[source]
                                                                  +get_sorted_structure(key: Callable | None = None, reverse: bool = False) → Self[source]

                                                                  Get a sorted copy of the Structure. The parameters have the same meaning as in list.sort. By default, sites are sorted by the electronegativity of the species. Note that Slab has to override this @@ -2415,13 +2415,13 @@

                                                                  Submodules
                                                                  -property sigma: int[source]
                                                                  +property sigma: int[source]

                                                                  The sigma value of the GB. If using ‘quick_gen’ to generate GB, this value is not valid.

                                                                  -property sigma_from_site_prop: int[source]
                                                                  +property sigma_from_site_prop: int[source]

                                                                  The sigma value of the GB from site properties. If the GB structure merge some atoms due to the atoms too close with each other, this property will not work.

                                                                  @@ -2429,7 +2429,7 @@

                                                                  Submodules
                                                                  -property top_grain: Structure[source]
                                                                  +property top_grain: Structure[source]

                                                                  The top grain (Structure) of the GB.

                                                                  @@ -2437,7 +2437,7 @@

                                                                  Submodules
                                                                  -class GrainBoundaryGenerator(initial_structure: Structure, symprec: float = 0.1, angle_tolerance: float = 1.0)[source]
                                                                  +class GrainBoundaryGenerator(initial_structure: Structure, symprec: float = 0.1, angle_tolerance: float = 1.0)[source]

                                                                  Bases: object

                                                                  Generate grain boundaries (GBs) from bulk conventional cell (FCC, BCC can from the primitive cell), and works for Cubic, Tetragonal, Orthorhombic, @@ -2474,7 +2474,7 @@

                                                                  Submodules
                                                                  -static enum_possible_plane_cubic(plane_cutoff: int, r_axis: tuple[int, int, int], r_angle: float) → dict[Literal['Twist', 'Symmetric tilt', 'Normal tilt', 'Mixed'], list[list]][source]
                                                                  +static enum_possible_plane_cubic(plane_cutoff: int, r_axis: tuple[int, int, int], r_angle: float) → dict[Literal['Twist', 'Symmetric tilt', 'Normal tilt', 'Mixed'], list[list]][source]

                                                                  Find all possible plane combinations for GBs given a rotation axis and angle for cubic system, and classify them to different categories, including “Twist”, “Symmetric tilt”, “Normal tilt”, “Mixed” GBs.

                                                                  @@ -2501,7 +2501,7 @@

                                                                  Submodules
                                                                  -static enum_sigma_cubic(cutoff: int, r_axis: tuple[int, int, int]) → dict[int, list[float]][source]
                                                                  +static enum_sigma_cubic(cutoff: int, r_axis: tuple[int, int, int]) → dict[int, list[float]][source]

                                                                  Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in cubic system. The algorithm for this code is from reference, Acta Cryst, A40,108(1984).

                                                                  @@ -2534,7 +2534,7 @@

                                                                  Submodules
                                                                  -static enum_sigma_hex(cutoff: int, r_axis: tuple[int, int, int] | tuple[int, int, int, int], c2_a2_ratio: tuple[int, int]) → dict[int, list[float]][source]
                                                                  +static enum_sigma_hex(cutoff: int, r_axis: tuple[int, int, int] | tuple[int, int, int, int], c2_a2_ratio: tuple[int, int]) → dict[int, list[float]][source]

                                                                  Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in hexagonal system. The algorithm for this code is from reference, Acta Cryst, A38,550(1982).

                                                                  @@ -2569,7 +2569,7 @@

                                                                  Submodules
                                                                  -static enum_sigma_ort(cutoff: int, r_axis: Tuple3Ints, c2_b2_a2_ratio: Tuple3Floats) → dict[int, list[float]][source]
                                                                  +static enum_sigma_ort(cutoff: int, r_axis: Tuple3Ints, c2_b2_a2_ratio: Tuple3Floats) → dict[int, list[float]][source]

                                                                  Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in orthorhombic system.

                                                                  Reference: Scipta Metallurgica 27, 291(1992).

                                                                  @@ -2605,7 +2605,7 @@

                                                                  Submodules
                                                                  -static enum_sigma_rho(cutoff: int, r_axis: tuple[int, int, int] | tuple[int, int, int, int], ratio_alpha: tuple[int, int]) → dict[int, list[float]][source]
                                                                  +static enum_sigma_rho(cutoff: int, r_axis: tuple[int, int, int] | tuple[int, int, int, int], ratio_alpha: tuple[int, int]) → dict[int, list[float]][source]

                                                                  Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in rhombohedral system. The algorithm for this code is from reference, Acta Cryst, A45,505(1989).

                                                                  @@ -2639,7 +2639,7 @@

                                                                  Submodules
                                                                  -static enum_sigma_tet(cutoff: int, r_axis: tuple[int, int, int], c2_a2_ratio: tuple[int, int]) → dict[int, list[float]][source]
                                                                  +static enum_sigma_tet(cutoff: int, r_axis: tuple[int, int, int], c2_a2_ratio: tuple[int, int]) → dict[int, list[float]][source]

                                                                  Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in tetragonal system. The algorithm for this code is from reference, Acta Cryst, B46,117(1990).

                                                                  @@ -2674,7 +2674,7 @@

                                                                  Submodules
                                                                  -gb_from_parameters(rotation_axis: tuple[int, int, int], rotation_angle: float, expand_times: int = 4, vacuum_thickness: float = 0.0, ab_shift: tuple[float, float] = (0, 0), normal: bool = False, ratio: list[int] | None = None, plane: tuple[int, int, int] | None = None, max_search: int = 20, tol_coi: float = 1e-08, rm_ratio: float = 0.7, quick_gen: bool = False) → GrainBoundary[source]
                                                                  +gb_from_parameters(rotation_axis: tuple[int, int, int], rotation_angle: float, expand_times: int = 4, vacuum_thickness: float = 0.0, ab_shift: tuple[float, float] = (0, 0), normal: bool = False, ratio: list[int] | None = None, plane: tuple[int, int, int] | None = None, max_search: int = 20, tol_coi: float = 1e-08, rm_ratio: float = 0.7, quick_gen: bool = False) → GrainBoundary[source]
                                                                  Parameters:
                                                                    @@ -2737,7 +2737,7 @@

                                                                    Submodules
                                                                    -get_ratio(max_denominator: int = 5, index_none: int | None = None) → list[int] | None[source]
                                                                    +get_ratio(max_denominator: int = 5, index_none: int | None = None) → list[int] | None[source]

                                                                    Find the axial ratio needed for GB generator input.

                                                                    Parameters:
                                                                    @@ -2756,7 +2756,7 @@

                                                                    Submodules
                                                                    -static get_rotation_angle_from_sigma(sigma: int, r_axis: tuple[int, int, int] | tuple[int, int, int, int], lat_type: str = 'c', ratio: tuple[int, int] | tuple[int, int, int] | None = None) → list[float][source]
                                                                    +static get_rotation_angle_from_sigma(sigma: int, r_axis: tuple[int, int, int] | tuple[int, int, int, int], lat_type: str = 'c', ratio: tuple[int, int] | tuple[int, int, int] | None = None) → list[float][source]

                                                                    Find all possible rotation angles for the given sigma value.

                                                                    Parameters:
                                                                    @@ -2794,7 +2794,7 @@

                                                                    Submodules
                                                                    -static get_trans_mat(r_axis: Tuple3Ints | Tuple4Ints, angle: float, normal: bool = False, trans_cry: NDArray | None = None, lat_type: str = 'c', ratio: list[int] | None = None, surface: Tuple3Ints | Tuple4Ints | None = None, max_search: int = 20, quick_gen: bool = False)[source]
                                                                    +static get_trans_mat(r_axis: Tuple3Ints | Tuple4Ints, angle: float, normal: bool = False, trans_cry: NDArray | None = None, lat_type: str = 'c', ratio: list[int] | None = None, surface: Tuple3Ints | Tuple4Ints | None = None, max_search: int = 20, quick_gen: bool = False)[source]

                                                                    Find the two transformation matrix for each grain from given rotation axis, GB plane, rotation angle and corresponding ratio (see explanation for ratio below). @@ -2851,7 +2851,7 @@

                                                                    Submodules
                                                                    -static reduce_mat(mat: NDArray, mag: int, r_matrix: NDArray) → NDArray[source]
                                                                    +static reduce_mat(mat: NDArray, mag: int, r_matrix: NDArray) → NDArray[source]

                                                                    Reduce integer array mat’s determinant mag times by linear combination of its row vectors, so that the new array after rotation (r_matrix) is still an integer array.

                                                                    @@ -2871,7 +2871,7 @@

                                                                    Submodules
                                                                    -static slab_from_csl(csl: NDArray, surface: Tuple3Ints, normal: bool, trans_cry: NDArray, max_search: int = 20, quick_gen: bool = False) → Matrix3D[source]
                                                                    +static slab_from_csl(csl: NDArray, surface: Tuple3Ints, normal: bool, trans_cry: NDArray, max_search: int = 20, quick_gen: bool = False) → Matrix3D[source]

                                                                    By linear operation of csl lattice vectors to get the best corresponding slab lattice. That is the area of a,b vectors (within the surface plane) is the smallest, the c vector first, has shortest length perpendicular @@ -2902,7 +2902,7 @@

                                                                    Submodules
                                                                    -static vec_to_surface(vec: Vector3D) → MillerIndex[source]
                                                                    +static vec_to_surface(vec: Vector3D) → MillerIndex[source]

                                                                    Transform a float vector to a surface miller index with integers.

                                                                    Parameters:
                                                                    @@ -2918,7 +2918,7 @@

                                                                    Submodules
                                                                    -class Interface(lattice: Lattice | NDArray, species: list[Any], coords: NDArray, site_properties: dict[str, Any], validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, in_plane_offset: tuple[float, float] = (0, 0), gap: float = 0, vacuum_over_film: float = 0, interface_properties: dict | None = None)[source]
                                                                    +class Interface(lattice: Lattice | NDArray, species: list[Any], coords: NDArray, site_properties: dict[str, Any], validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, in_plane_offset: tuple[float, float] = (0, 0), gap: float = 0, vacuum_over_film: float = 0, interface_properties: dict | None = None)[source]

                                                                    Bases: Structure

                                                                    Store data for defining an interface between two Structures.

                                                                    Make an Interface, a Structure with additional information @@ -2965,49 +2965,49 @@

                                                                    Submodules
                                                                    -as_dict() → dict[source]
                                                                    +as_dict() → dict[source]

                                                                    MSONable dict.

                                                                    -copy() → Self[source]
                                                                    +copy() → Self[source]

                                                                    Make a copy of the Interface.

                                                                    -property film: Structure[source]
                                                                    +property film: Structure[source]

                                                                    A Structure for just the film.

                                                                    -property film_indices: list[int][source]
                                                                    +property film_indices: list[int][source]

                                                                    Site indices of the film sites.

                                                                    -property film_layers: int[source]
                                                                    +property film_layers: int[source]

                                                                    Number of layers of the minimum element in the film composition.

                                                                    -property film_sites: list[Site][source]
                                                                    +property film_sites: list[Site][source]

                                                                    The film sites of the interface.

                                                                    -property film_termination: str[source]
                                                                    +property film_termination: str[source]

                                                                    Label for the film termination chemistry.

                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                                    Parameters:

                                                                    dct – dict.

                                                                    @@ -3020,7 +3020,7 @@

                                                                    Submodules
                                                                    -classmethod from_slabs(substrate_slab: Slab, film_slab: Slab, in_plane_offset: tuple[float, float] = (0, 0), gap: float = 1.6, vacuum_over_film: float = 0, interface_properties: dict | None = None, center_slab: bool = True) → Self[source]
                                                                    +classmethod from_slabs(substrate_slab: Slab, film_slab: Slab, in_plane_offset: tuple[float, float] = (0, 0), gap: float = 1.6, vacuum_over_film: float = 0, interface_properties: dict | None = None, center_slab: bool = True) → Self[source]

                                                                    Make an Interface by merging a substrate and film slabs The film a- and b-vectors will be forced to be the substrate slab’s a- and b-vectors.

                                                                    @@ -3047,13 +3047,13 @@

                                                                    Submodules
                                                                    -property gap: float[source]
                                                                    +property gap: float[source]

                                                                    The gap in Cartesian units between the film and the substrate.

                                                                    -get_shifts_based_on_adsorbate_sites(tolerance: float = 0.1) → list[tuple[float, float]][source]
                                                                    +get_shifts_based_on_adsorbate_sites(tolerance: float = 0.1) → list[tuple[float, float]][source]

                                                                    Compute possible in-plane shifts based on an adsorbate site algorithm.

                                                                    Parameters:
                                                                    @@ -3065,7 +3065,7 @@

                                                                    Submodules
                                                                    -get_sorted_structure(key: Callable | None = None, reverse: bool = False) → Structure[source]
                                                                    +get_sorted_structure(key: Callable | None = None, reverse: bool = False) → Structure[source]

                                                                    Get a sorted structure for the Interface. The parameters have the same meaning as in list.sort. By default, sites are sorted by the electronegativity of the species.

                                                                    @@ -3084,43 +3084,43 @@

                                                                    Submodules
                                                                    -property in_plane_offset: ndarray[source]
                                                                    +property in_plane_offset: ndarray[source]

                                                                    The shift between the film and substrate in fractional coordinates.

                                                                    -property substrate: Structure[source]
                                                                    +property substrate: Structure[source]

                                                                    A Structure for just the substrate.

                                                                    -property substrate_indices: list[int][source]
                                                                    +property substrate_indices: list[int][source]

                                                                    Site indices for the substrate atoms.

                                                                    -property substrate_layers: int[source]
                                                                    +property substrate_layers: int[source]

                                                                    Number of layers of the minimum element in the substrate composition.

                                                                    -property substrate_sites: list[Site][source]
                                                                    +property substrate_sites: list[Site][source]

                                                                    The site objects in the substrate.

                                                                    -property substrate_termination: str[source]
                                                                    +property substrate_termination: str[source]

                                                                    Label for the substrate termination chemistry.

                                                                    -property vacuum_over_film: float[source]
                                                                    +property vacuum_over_film: float[source]

                                                                    The vacuum space over the film in Cartesian units.

                                                                    @@ -3128,13 +3128,13 @@

                                                                    Submodules
                                                                    -count_layers(struct: Structure, el: Element | None = None) → int[source]
                                                                    +count_layers(struct: Structure, el: Element | None = None) → int[source]

                                                                    Count the number of layers along the c-axis.

                                                                    -fix_pbc(structure: Structure, matrix: NDArray = None) → Structure[source]
                                                                    +fix_pbc(structure: Structure, matrix: NDArray = None) → Structure[source]

                                                                    Wrap all frac_coords of the input structure within [0, 1].

                                                                    Parameters:
                                                                    @@ -3152,13 +3152,13 @@

                                                                    Submodules
                                                                    -label_termination(slab: Structure) → str[source]
                                                                    +label_termination(slab: Structure) → str[source]

                                                                    Label the slab surface termination.

                                                                    -symm_group_cubic(mat: NDArray) → list[source]
                                                                    +symm_group_cubic(mat: NDArray) → list[source]

                                                                    Obtain cubic symmetric equivalents of the list of vectors.

                                                                    Parameters:
                                                                    @@ -3176,7 +3176,7 @@

                                                                    Submodules
                                                                    -class Ion(composition: Composition, charge: float = 0.0, **kwargs)[source]
                                                                    +class Ion(composition: Composition, charge: float = 0.0, **kwargs)[source]

                                                                    Bases: Composition, MSONable, Stringify

                                                                    Just a Composition object with an additional variable to store charge.

                                                                    The net charge can either be represented as Mn++, Mn+2, Mn[2+], Mn[++], or @@ -3185,21 +3185,21 @@

                                                                    Submodules
                                                                    -property alphabetical_formula: str[source]
                                                                    +property alphabetical_formula: str[source]

                                                                    A formula string, with elements sorted by alphabetically and appended charge.

                                                                    -property anonymized_formula: str[source]
                                                                    +property anonymized_formula: str[source]

                                                                    An anonymized formula. Appends charge to the end of anonymized composition.

                                                                    -as_dict() → dict[str, float][source]
                                                                    +as_dict() → dict[str, float][source]
                                                                    Returns:

                                                                    dict with composition, as well as charge.

                                                                    @@ -3209,19 +3209,19 @@

                                                                    Submodules
                                                                    -property charge: float[source]
                                                                    +property charge: float[source]

                                                                    Charge of the ion.

                                                                    -property composition: Composition[source]
                                                                    +property composition: Composition[source]

                                                                    Composition of ion.

                                                                    -property formula: str[source]
                                                                    +property formula: str[source]

                                                                    A formula string with appended charge. The charge is written with the sign preceding the magnitude, e.g. ‘Ca1 +2’. Uncharged species have “(aq)” appended, e.g. “O2 (aq)”.

                                                                    @@ -3229,7 +3229,7 @@

                                                                    Submodules
                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]

                                                                    Generate an ion object from a dict created by as_dict().

                                                                    Parameters:
                                                                    @@ -3240,7 +3240,7 @@

                                                                    Submodules
                                                                    -classmethod from_formula(formula: str) → Self[source]
                                                                    +classmethod from_formula(formula: str) → Self[source]

                                                                    Create Ion from formula. The net charge can either be represented as Mn++, Mn+2, Mn[2+], Mn[++], or Mn[+2]. Note the order of the sign and magnitude in each representation.

                                                                    @@ -3257,7 +3257,7 @@

                                                                    Submodules
                                                                    -get_reduced_formula_and_factor(iupac_ordering: bool = False, hydrates: bool = False) → tuple[str, float][source]
                                                                    +get_reduced_formula_and_factor(iupac_ordering: bool = False, hydrates: bool = False) → tuple[str, float][source]

                                                                    Calculate a reduced formula and factor.

                                                                    Similar to Composition.get_reduced_formula_and_factor except that O-H formulas receive special handling to differentiate between hydrogen peroxide and OH-. @@ -3298,7 +3298,7 @@

                                                                    Submodules
                                                                    -oxi_state_guesses(oxi_states_override: dict | None = None, all_oxi_states: bool = False, max_sites: int | None = None) → list[dict[str, float]][source]
                                                                    +oxi_state_guesses(oxi_states_override: dict | None = None, all_oxi_states: bool = False, max_sites: int | None = None) → list[dict[str, float]][source]

                                                                    Check if the composition is charge-balanced and returns all charge-balanced oxidation state combinations. Composition must have integer values. Note that more num_atoms in the composition gives @@ -3338,7 +3338,7 @@

                                                                    Submodules
                                                                    -property reduced_formula: str[source]
                                                                    +property reduced_formula: str[source]

                                                                    A reduced formula string with appended charge. The charge is placed in brackets with the sign preceding the magnitude, e.g. ‘Ca[+2]’. Uncharged species have “(aq)” appended, e.g. “O2(aq)”.

                                                                    @@ -3346,13 +3346,13 @@

                                                                    Submodules
                                                                    -to_pretty_string() → str[source]
                                                                    +to_pretty_string() → str[source]

                                                                    Pretty string with proper superscripts.

                                                                    -property to_reduced_dict: dict[source]
                                                                    +property to_reduced_dict: dict[source]

                                                                    Returns: dict with element symbol and reduced amount e.g.

                                                                    @@ -3369,7 +3369,7 @@

                                                                    Submodules
                                                                    -class Lattice(matrix: ArrayLike, pbc: PbcLike = (True, True, True))[source]
                                                                    +class Lattice(matrix: ArrayLike, pbc: PbcLike = (True, True, True))[source]

                                                                    Bases: MSONable

                                                                    Essentially a matrix with conversion matrices. In general, it is assumed that lengths are in Angstrom and angles are in @@ -3397,25 +3397,25 @@

                                                                    Submodules
                                                                    -property a: float[source]
                                                                    +property a: float[source]

                                                                    a lattice parameter.

                                                                    -property abc: Vector3D[source]
                                                                    +property abc: Vector3D[source]

                                                                    Lengths of the lattice vectors, i.e. (a, b, c).

                                                                    -property alpha: float[source]
                                                                    +property alpha: float[source]

                                                                    Angle alpha of lattice in degrees.

                                                                    -property angles: Vector3D[source]
                                                                    +property angles: Vector3D[source]

                                                                    Lattice angles.

                                                                    Returns:
                                                                    @@ -3426,7 +3426,7 @@

                                                                    Submodules
                                                                    -as_dict(verbosity: int = 0) → dict[source]
                                                                    +as_dict(verbosity: int = 0) → dict[source]

                                                                    MSONable dict representation of the Lattice.

                                                                    Parameters:
                                                                    @@ -3438,31 +3438,31 @@

                                                                    Submodules
                                                                    -property b: float[source]
                                                                    +property b: float[source]

                                                                    b lattice parameter.

                                                                    -property beta: float[source]
                                                                    +property beta: float[source]

                                                                    Angle beta of lattice in degrees.

                                                                    -property c: float[source]
                                                                    +property c: float[source]

                                                                    c lattice parameter.

                                                                    -copy() → Self[source]
                                                                    +copy() → Self[source]

                                                                    Make a copy of this lattice.

                                                                    -classmethod cubic(a: float, pbc: PbcLike = (True, True, True)) → Self[source]
                                                                    +classmethod cubic(a: float, pbc: PbcLike = (True, True, True)) → Self[source]

                                                                    Convenience constructor for a cubic lattice.

                                                                    Parameters:
                                                                    @@ -3480,7 +3480,7 @@

                                                                    Submodules
                                                                    -d_hkl(miller_index: MillerIndex) → float[source]
                                                                    +d_hkl(miller_index: MillerIndex) → float[source]

                                                                    Get the distance between the hkl plane and the origin.

                                                                    Parameters:
                                                                    @@ -3497,7 +3497,7 @@

                                                                    Submodules
                                                                    -dot(coords_a: ArrayLike, coords_b: ArrayLike, frac_coords: bool = False) → np.ndarray[source]
                                                                    +dot(coords_a: ArrayLike, coords_b: ArrayLike, frac_coords: bool = False) → np.ndarray[source]

                                                                    Compute the scalar product of vector(s).

                                                                    Parameters:
                                                                    @@ -3516,7 +3516,7 @@

                                                                    Submodules
                                                                    -find_all_mappings(other_lattice: Self, ltol: float = 1e-05, atol: float = 1, skip_rotation_matrix: bool = False) → Iterator[tuple[Lattice, np.ndarray | None, np.ndarray]][source]
                                                                    +find_all_mappings(other_lattice: Self, ltol: float = 1e-05, atol: float = 1, skip_rotation_matrix: bool = False) → Iterator[tuple[Lattice, np.ndarray | None, np.ndarray]][source]

                                                                    Find all mappings between current lattice and another lattice.

                                                                    Parameters:
                                                                    @@ -3548,7 +3548,7 @@

                                                                    Submodules
                                                                    -find_mapping(other_lattice: Self, ltol: float = 1e-05, atol: float = 1, skip_rotation_matrix: bool = False) → tuple[Lattice, np.ndarray | None, np.ndarray] | None[source]
                                                                    +find_mapping(other_lattice: Self, ltol: float = 1e-05, atol: float = 1, skip_rotation_matrix: bool = False) → tuple[Lattice, np.ndarray | None, np.ndarray] | None[source]

                                                                    Find a mapping between current lattice and another lattice. There are an infinite number of choices of basis vectors for two entirely equivalent lattices. This method returns a mapping that maps @@ -3588,7 +3588,7 @@

                                                                    Submodules
                                                                    -classmethod from_dict(dct: dict, fmt: str | None = None, **kwargs) → Self[source]
                                                                    +classmethod from_dict(dct: dict, fmt: str | None = None, **kwargs) → Self[source]

                                                                    Create a Lattice from a dictionary.

                                                                    If fmt is None, the dict should contain the a, b, c, alpha, beta, and gamma parameters.

                                                                    @@ -3601,7 +3601,7 @@

                                                                    Submodules
                                                                    -classmethod from_parameters(a: float, b: float, c: float, alpha: float, beta: float, gamma: float, *, vesta: bool = False, pbc: PbcLike = (True, True, True)) → Self[source]
                                                                    +classmethod from_parameters(a: float, b: float, c: float, alpha: float, beta: float, gamma: float, *, vesta: bool = False, pbc: PbcLike = (True, True, True)) → Self[source]

                                                                    Create a Lattice using unit cell lengths (in Angstrom) and angles (in degrees).

                                                                    Parameters:
                                                                    @@ -3625,13 +3625,13 @@

                                                                    Submodules
                                                                    -property gamma: float[source]
                                                                    +property gamma: float[source]

                                                                    Angle gamma of lattice in degrees.

                                                                    -get_all_distances(frac_coords1: ArrayLike, frac_coords2: ArrayLike) → np.ndarray[source]
                                                                    +get_all_distances(frac_coords1: ArrayLike, frac_coords2: ArrayLike) → np.ndarray[source]

                                                                    Get the distances between two lists of coordinates taking into account periodic boundary conditions and the lattice. Note that this computes an MxN array of distances (i.e. the distance between each @@ -3655,7 +3655,7 @@

                                                                    Submodules
                                                                    -get_brillouin_zone() → list[list[ndarray]][source]
                                                                    +get_brillouin_zone() → list[list[ndarray]][source]

                                                                    Get the Wigner-Seitz cell for the reciprocal lattice, aka the Brillouin Zone.

                                                                    @@ -3670,7 +3670,7 @@

                                                                    Submodules
                                                                    -get_cartesian_coords(fractional_coords: ArrayLike) → np.ndarray[source]
                                                                    +get_cartesian_coords(fractional_coords: ArrayLike) → np.ndarray[source]

                                                                    Get the Cartesian coordinates given fractional coordinates.

                                                                    Parameters:
                                                                    @@ -3684,7 +3684,7 @@

                                                                    Submodules
                                                                    -get_distance_and_image(frac_coords1: ArrayLike, frac_coords2: ArrayLike, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]
                                                                    +get_distance_and_image(frac_coords1: ArrayLike, frac_coords2: ArrayLike, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]

                                                                    Get distance between two frac_coords assuming periodic boundary conditions. If the index jimage is not specified it selects the j image nearest to the i atom and returns the distance and jimage @@ -3720,14 +3720,14 @@

                                                                    Submodules
                                                                    -get_frac_coords_from_lll(lll_frac_coords: ArrayLike) → np.ndarray[source]
                                                                    +get_frac_coords_from_lll(lll_frac_coords: ArrayLike) → np.ndarray[source]

                                                                    Given fractional coordinates in the lll basis, returns corresponding fractional coordinates in the lattice basis.

                                                                    -get_fractional_coords(cart_coords: ArrayLike) → np.ndarray[source]
                                                                    +get_fractional_coords(cart_coords: ArrayLike) → np.ndarray[source]

                                                                    Get the fractional coordinates given Cartesian coordinates.

                                                                    Parameters:
                                                                    @@ -3741,14 +3741,14 @@

                                                                    Submodules
                                                                    -get_lll_frac_coords(frac_coords: ArrayLike) → np.ndarray[source]
                                                                    +get_lll_frac_coords(frac_coords: ArrayLike) → np.ndarray[source]

                                                                    Given fractional coordinates in the lattice basis, returns corresponding fractional coordinates in the lll basis.

                                                                    -get_lll_reduced_lattice(delta: float = 0.75) → Self[source]
                                                                    +get_lll_reduced_lattice(delta: float = 0.75) → Self[source]

                                                                    Lenstra-Lenstra-Lovasz lattice basis reduction.

                                                                    Parameters:
                                                                    @@ -3765,7 +3765,7 @@

                                                                    Submodules
                                                                    -get_miller_index_from_coords(coords: ArrayLike, coords_are_cartesian: bool = True, round_dp: int = 4, verbose: bool = True) → MillerIndex[source]
                                                                    +get_miller_index_from_coords(coords: ArrayLike, coords_are_cartesian: bool = True, round_dp: int = 4, verbose: bool = True) → MillerIndex[source]

                                                                    Get the Miller index of a plane from a list of site coordinates.

                                                                    A minimum of 3 sets of coordinates are required. If more than 3 sets of coordinates are given, the best plane that minimises the distance to all @@ -3796,7 +3796,7 @@

                                                                    Submodules
                                                                    -get_niggli_reduced_lattice(tol: float = 1e-05) → Self[source]
                                                                    +get_niggli_reduced_lattice(tol: float = 1e-05) → Self[source]

                                                                    Get the Niggli reduced lattice using the numerically stable algo proposed by R. W. Grosse-Kunstleve, N. K. Sauter, & P. D. Adams, Acta Crystallographica Section A Foundations of Crystallography, 2003, @@ -3817,7 +3817,7 @@

                                                                    Submodules
                                                                    -get_points_in_sphere(frac_points: ArrayLike, center: ArrayLike, r: float, zip_results: bool = True) → list[tuple[np.ndarray, float, int, np.ndarray]] | tuple[np.ndarray, ...] | list[source]
                                                                    +get_points_in_sphere(frac_points: ArrayLike, center: ArrayLike, r: float, zip_results: bool = True) → list[tuple[np.ndarray, float, int, np.ndarray]] | tuple[np.ndarray, ...] | list[source]

                                                                    Find all points within a sphere from the point taking into account periodic boundary conditions. This includes sites in other periodic images.

                                                                    Algorithm:

                                                                    @@ -3858,12 +3858,12 @@

                                                                    Submodules
                                                                    -get_points_in_sphere_old(**kwargs)[source]
                                                                    +get_points_in_sphere_old(**kwargs)[source]

                                                                    -get_points_in_sphere_py(frac_points: ArrayLike, center: ArrayLike, r: float, zip_results: bool = True) → list[tuple[np.ndarray, float, int, np.ndarray]] | list[np.ndarray][source]
                                                                    +get_points_in_sphere_py(frac_points: ArrayLike, center: ArrayLike, r: float, zip_results: bool = True) → list[tuple[np.ndarray, float, int, np.ndarray]] | list[np.ndarray][source]

                                                                    Find all points within a sphere from the point taking into account periodic boundary conditions. This includes sites in other periodic images.

                                                                    @@ -3905,7 +3905,7 @@

                                                                    Submodules
                                                                    -get_recp_symmetry_operation(symprec: float = 0.01) → list[SymmOp][source]
                                                                    +get_recp_symmetry_operation(symprec: float = 0.01) → list[SymmOp][source]

                                                                    Find the symmetric operations of the reciprocal lattice, to be used for hkl transformations.

                                                                    @@ -3917,7 +3917,7 @@

                                                                    Submodules
                                                                    -get_vector_along_lattice_directions(cart_coords: ArrayLike) → np.ndarray[source]
                                                                    +get_vector_along_lattice_directions(cart_coords: ArrayLike) → np.ndarray[source]

                                                                    Get the coordinates along lattice directions given Cartesian coordinates.

                                                                    Note, this is different than a projection of the Cartesian vector along the lattice parameters. It is simply the fractional coordinates multiplied by the @@ -3937,7 +3937,7 @@

                                                                    Submodules
                                                                    -get_wigner_seitz_cell() → list[list[ndarray]][source]
                                                                    +get_wigner_seitz_cell() → list[list[ndarray]][source]

                                                                    Get the Wigner-Seitz cell for the given lattice.

                                                                    Returns:
                                                                    @@ -3951,7 +3951,7 @@

                                                                    Submodules
                                                                    -classmethod hexagonal(a: float, c: float, pbc: PbcLike = (True, True, True)) → Self[source]
                                                                    +classmethod hexagonal(a: float, c: float, pbc: PbcLike = (True, True, True)) → Self[source]

                                                                    Convenience constructor for a hexagonal lattice.

                                                                    Parameters:
                                                                    @@ -3970,19 +3970,19 @@

                                                                    Submodules
                                                                    -property inv_matrix: ndarray[source]
                                                                    +property inv_matrix: ndarray[source]

                                                                    Inverse of lattice matrix.

                                                                    -property is_3d_periodic: bool[source]
                                                                    +property is_3d_periodic: bool[source]

                                                                    True if the Lattice is periodic in all directions.

                                                                    -is_hexagonal(hex_angle_tol: float = 5, hex_length_tol: float = 0.01) → bool[source]
                                                                    +is_hexagonal(hex_angle_tol: float = 5, hex_length_tol: float = 0.01) → bool[source]
                                                                    Parameters:
                                                                    -property lengths: Vector3D[source]
                                                                    +property lengths: Vector3D[source]

                                                                    Lattice lengths.

                                                                    Returns:
                                                                    @@ -4015,37 +4015,37 @@

                                                                    Submodules
                                                                    -property lll_inverse: ndarray[source]
                                                                    +property lll_inverse: ndarray[source]

                                                                    Inverse of self.lll_mapping.

                                                                    -property lll_mapping: ndarray[source]
                                                                    +property lll_mapping: ndarray[source]

                                                                    The mapping between the LLL reduced lattice and the original lattice.

                                                                    -property lll_matrix: ndarray[source]
                                                                    +property lll_matrix: ndarray[source]

                                                                    The matrix for LLL reduction.

                                                                    -property matrix: ndarray[source]
                                                                    +property matrix: ndarray[source]

                                                                    Copy of matrix representing the Lattice.

                                                                    -property metric_tensor: ndarray[source]
                                                                    +property metric_tensor: ndarray[source]

                                                                    The metric tensor of the lattice.

                                                                    -classmethod monoclinic(a: float, b: float, c: float, beta: float, pbc: PbcLike = (True, True, True)) → Self[source]
                                                                    +classmethod monoclinic(a: float, b: float, c: float, beta: float, pbc: PbcLike = (True, True, True)) → Self[source]

                                                                    Convenience constructor for a monoclinic lattice.

                                                                    Parameters:
                                                                    @@ -4071,7 +4071,7 @@

                                                                    Submodules
                                                                    -norm(coords: ArrayLike, frac_coords: bool = True) → np.ndarray[source]
                                                                    +norm(coords: ArrayLike, frac_coords: bool = True) → np.ndarray[source]

                                                                    Compute the norm of vector(s).

                                                                    Parameters:
                                                                    @@ -4089,7 +4089,7 @@

                                                                    Submodules
                                                                    -classmethod orthorhombic(a: float, b: float, c: float, pbc: PbcLike = (True, True, True)) → Self[source]
                                                                    +classmethod orthorhombic(a: float, b: float, c: float, pbc: PbcLike = (True, True, True)) → Self[source]

                                                                    Convenience constructor for an orthorhombic lattice.

                                                                    Parameters:
                                                                    @@ -4109,25 +4109,25 @@

                                                                    Submodules
                                                                    -property parameters: tuple[float, float, float, float, float, float][source]
                                                                    +property parameters: tuple[float, float, float, float, float, float][source]

                                                                    6-tuple of floats (a, b, c, alpha, beta, gamma).

                                                                    -property params_dict: dict[str, float][source]
                                                                    +property params_dict: dict[str, float][source]

                                                                    Dictionary of lattice parameters.

                                                                    -property pbc: PbcLike[source]
                                                                    +property pbc: PbcLike[source]

                                                                    Tuple defining the periodicity of the Lattice.

                                                                    -property reciprocal_lattice: Self[source]
                                                                    +property reciprocal_lattice: Self[source]

                                                                    The reciprocal lattice. Note that this is the standard reciprocal lattice used for solid state physics with a factor of 2 * pi. If you are looking for the crystallographic reciprocal lattice, @@ -4137,13 +4137,13 @@

                                                                    Submodules
                                                                    -property reciprocal_lattice_crystallographic: Self[source]
                                                                    +property reciprocal_lattice_crystallographic: Self[source]

                                                                    The crystallographic reciprocal lattice, i.e. no factor of 2 * pi.

                                                                    -classmethod rhombohedral(a: float, alpha: float, pbc: PbcLike = (True, True, True)) → Self[source]
                                                                    +classmethod rhombohedral(a: float, alpha: float, pbc: PbcLike = (True, True, True)) → Self[source]

                                                                    Convenience constructor for a rhombohedral lattice.

                                                                    Parameters:
                                                                    @@ -4162,7 +4162,7 @@

                                                                    Submodules
                                                                    -scale(new_volume: float) → Self[source]
                                                                    +scale(new_volume: float) → Self[source]

                                                                    Return a new Lattice with volume new_volume by performing a scaling of the lattice vectors so that length proportions and angles are preserved.

                                                                    @@ -4178,19 +4178,19 @@

                                                                    Submodules
                                                                    -selling_dist(other: Self) → float[source]
                                                                    +selling_dist(other: Self) → float[source]

                                                                    Get the minimum Selling distance between two lattices.

                                                                    -property selling_vector: ndarray[source]
                                                                    +property selling_vector: ndarray[source]

                                                                    The (1,6) array of Selling Scalars.

                                                                    -classmethod tetragonal(a: float, c: float, pbc: PbcLike = (True, True, True)) → Self[source]
                                                                    +classmethod tetragonal(a: float, c: float, pbc: PbcLike = (True, True, True)) → Self[source]

                                                                    Convenience constructor for a tetragonal lattice.

                                                                    Parameters:
                                                                    @@ -4209,7 +4209,7 @@

                                                                    Submodules
                                                                    -property volume: float[source]
                                                                    +property volume: float[source]

                                                                    Volume of the unit cell in Angstrom^3.

                                                                    @@ -4217,7 +4217,7 @@

                                                                    Submodules
                                                                    -find_neighbors(label: ndarray, nx: int, ny: int, nz: int) → list[ndarray][source]
                                                                    +find_neighbors(label: ndarray, nx: int, ny: int, nz: int) → list[ndarray][source]

                                                                    Given a cube index, find the neighbor cube indices.

                                                                    Parameters:
                                                                    @@ -4236,7 +4236,7 @@

                                                                    Submodules
                                                                    -get_integer_index(miller_index: MillerIndex, round_dp: int = 4, verbose: bool = True) → MillerIndex[source]
                                                                    +get_integer_index(miller_index: MillerIndex, round_dp: int = 4, verbose: bool = True) → MillerIndex[source]

                                                                    Attempt to convert a vector of floats to whole numbers.

                                                                    Parameters:
                                                                    @@ -4258,7 +4258,7 @@

                                                                    Submodules
                                                                    -get_points_in_spheres(all_coords: np.ndarray, center_coords: np.ndarray, r: float, pbc: bool | list[bool] | PbcLike = True, numerical_tol: float = 1e-08, lattice: Lattice | None = None, return_fcoords: bool = False) → list[list[tuple[np.ndarray, float, int, np.ndarray]]][source]
                                                                    +get_points_in_spheres(all_coords: np.ndarray, center_coords: np.ndarray, r: float, pbc: bool | list[bool] | PbcLike = True, numerical_tol: float = 1e-08, lattice: Lattice | None = None, return_fcoords: bool = False) → list[list[tuple[np.ndarray, float, int, np.ndarray]]][source]

                                                                    For each point in center_coords, get all the neighboring points in all_coords that are within the cutoff radius r.

                                                                    @@ -4289,7 +4289,7 @@

                                                                    Submodules
                                                                    -class LibxcFunc(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                    +class LibxcFunc(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                    Bases: Enum

                                                                    Enumerator with the identifiers. This object is used by Xcfunc declared in xcfunc.py to create an internal representation of the XC functional. @@ -4302,1824 +4302,1824 @@

                                                                    Submodules
                                                                    -GGA_C_AM05 = 135[source]
                                                                    +GGA_C_AM05 = 135[source]

                                                                    -GGA_C_APBE = 186[source]
                                                                    +GGA_C_APBE = 186[source]
                                                                    -GGA_C_BGCP = 39[source]
                                                                    +GGA_C_BGCP = 39[source]
                                                                    -GGA_C_FT97 = 88[source]
                                                                    +GGA_C_FT97 = 88[source]
                                                                    -GGA_C_GAM = 33[source]
                                                                    +GGA_C_GAM = 33[source]
                                                                    -GGA_C_HCTH_A = 97[source]
                                                                    +GGA_C_HCTH_A = 97[source]
                                                                    -GGA_C_LM = 137[source]
                                                                    +GGA_C_LM = 137[source]
                                                                    -GGA_C_LYP = 131[source]
                                                                    +GGA_C_LYP = 131[source]
                                                                    -GGA_C_N12 = 80[source]
                                                                    +GGA_C_N12 = 80[source]
                                                                    -GGA_C_N12_SX = 79[source]
                                                                    +GGA_C_N12_SX = 79[source]
                                                                    -GGA_C_OPTC = 200[source]
                                                                    +GGA_C_OPTC = 200[source]
                                                                    -GGA_C_OP_B88 = 87[source]
                                                                    +GGA_C_OP_B88 = 87[source]
                                                                    -GGA_C_OP_G96 = 85[source]
                                                                    +GGA_C_OP_G96 = 85[source]
                                                                    -GGA_C_OP_PBE = 86[source]
                                                                    +GGA_C_OP_PBE = 86[source]
                                                                    -GGA_C_OP_PW91 = 262[source]
                                                                    +GGA_C_OP_PW91 = 262[source]
                                                                    -GGA_C_OP_XALPHA = 84[source]
                                                                    +GGA_C_OP_XALPHA = 84[source]
                                                                    -GGA_C_P86 = 132[source]
                                                                    +GGA_C_P86 = 132[source]
                                                                    -GGA_C_PBE = 130[source]
                                                                    +GGA_C_PBE = 130[source]
                                                                    -GGA_C_PBEFE = 258[source]
                                                                    +GGA_C_PBEFE = 258[source]
                                                                    -GGA_C_PBEINT = 62[source]
                                                                    +GGA_C_PBEINT = 62[source]
                                                                    -GGA_C_PBELOC = 246[source]
                                                                    +GGA_C_PBELOC = 246[source]
                                                                    -GGA_C_PBE_JRGX = 138[source]
                                                                    +GGA_C_PBE_JRGX = 138[source]
                                                                    -GGA_C_PBE_SOL = 133[source]
                                                                    +GGA_C_PBE_SOL = 133[source]
                                                                    -GGA_C_PW91 = 134[source]
                                                                    +GGA_C_PW91 = 134[source]
                                                                    -GGA_C_Q2D = 47[source]
                                                                    +GGA_C_Q2D = 47[source]
                                                                    -GGA_C_REGTPSS = 83[source]
                                                                    +GGA_C_REGTPSS = 83[source]
                                                                    -GGA_C_REVTCA = 99[source]
                                                                    +GGA_C_REVTCA = 99[source]
                                                                    -GGA_C_RGE2 = 143[source]
                                                                    +GGA_C_RGE2 = 143[source]
                                                                    -GGA_C_SOGGA11 = 152[source]
                                                                    +GGA_C_SOGGA11 = 152[source]
                                                                    -GGA_C_SOGGA11_X = 159[source]
                                                                    +GGA_C_SOGGA11_X = 159[source]
                                                                    -GGA_C_SPBE = 89[source]
                                                                    +GGA_C_SPBE = 89[source]
                                                                    -GGA_C_TCA = 100[source]
                                                                    +GGA_C_TCA = 100[source]
                                                                    -GGA_C_WI = 148[source]
                                                                    +GGA_C_WI = 148[source]
                                                                    -GGA_C_WI0 = 153[source]
                                                                    +GGA_C_WI0 = 153[source]
                                                                    -GGA_C_WL = 147[source]
                                                                    +GGA_C_WL = 147[source]
                                                                    -GGA_C_XPBE = 136[source]
                                                                    +GGA_C_XPBE = 136[source]
                                                                    -GGA_C_ZPBEINT = 61[source]
                                                                    +GGA_C_ZPBEINT = 61[source]
                                                                    -GGA_C_ZPBESOL = 63[source]
                                                                    +GGA_C_ZPBESOL = 63[source]
                                                                    -GGA_K_ABSP1 = 506[source]
                                                                    +GGA_K_ABSP1 = 506[source]
                                                                    -GGA_K_ABSP2 = 507[source]
                                                                    +GGA_K_ABSP2 = 507[source]
                                                                    -GGA_K_APBE = 185[source]
                                                                    +GGA_K_APBE = 185[source]
                                                                    -GGA_K_APBEINT = 54[source]
                                                                    +GGA_K_APBEINT = 54[source]
                                                                    -GGA_K_BALTIN = 504[source]
                                                                    +GGA_K_BALTIN = 504[source]
                                                                    -GGA_K_DK = 516[source]
                                                                    +GGA_K_DK = 516[source]
                                                                    -GGA_K_ERNZERHOF = 520[source]
                                                                    +GGA_K_ERNZERHOF = 520[source]
                                                                    -GGA_K_FR_B88 = 514[source]
                                                                    +GGA_K_FR_B88 = 514[source]
                                                                    -GGA_K_FR_PW86 = 515[source]
                                                                    +GGA_K_FR_PW86 = 515[source]
                                                                    -GGA_K_GE2 = 501[source]
                                                                    +GGA_K_GE2 = 501[source]
                                                                    -GGA_K_GOLDEN = 502[source]
                                                                    +GGA_K_GOLDEN = 502[source]
                                                                    -GGA_K_GP85 = 510[source]
                                                                    +GGA_K_GP85 = 510[source]
                                                                    -GGA_K_GR = 508[source]
                                                                    +GGA_K_GR = 508[source]
                                                                    -GGA_K_LC94 = 521[source]
                                                                    +GGA_K_LC94 = 521[source]
                                                                    -GGA_K_LIEB = 505[source]
                                                                    +GGA_K_LIEB = 505[source]
                                                                    -GGA_K_LLP = 522[source]
                                                                    +GGA_K_LLP = 522[source]
                                                                    -GGA_K_LUDENA = 509[source]
                                                                    +GGA_K_LUDENA = 509[source]
                                                                    -GGA_K_MEYER = 57[source]
                                                                    +GGA_K_MEYER = 57[source]
                                                                    -GGA_K_OL1 = 512[source]
                                                                    +GGA_K_OL1 = 512[source]
                                                                    -GGA_K_OL2 = 513[source]
                                                                    +GGA_K_OL2 = 513[source]
                                                                    -GGA_K_PEARSON = 511[source]
                                                                    +GGA_K_PEARSON = 511[source]
                                                                    -GGA_K_PERDEW = 517[source]
                                                                    +GGA_K_PERDEW = 517[source]
                                                                    -GGA_K_REVAPBE = 55[source]
                                                                    +GGA_K_REVAPBE = 55[source]
                                                                    -GGA_K_REVAPBEINT = 53[source]
                                                                    +GGA_K_REVAPBEINT = 53[source]
                                                                    -GGA_K_TFVW = 52[source]
                                                                    +GGA_K_TFVW = 52[source]
                                                                    -GGA_K_THAKKAR = 523[source]
                                                                    +GGA_K_THAKKAR = 523[source]
                                                                    -GGA_K_TW1 = 187[source]
                                                                    +GGA_K_TW1 = 187[source]
                                                                    -GGA_K_TW2 = 188[source]
                                                                    +GGA_K_TW2 = 188[source]
                                                                    -GGA_K_TW3 = 189[source]
                                                                    +GGA_K_TW3 = 189[source]
                                                                    -GGA_K_TW4 = 190[source]
                                                                    +GGA_K_TW4 = 190[source]
                                                                    -GGA_K_VJKS = 519[source]
                                                                    +GGA_K_VJKS = 519[source]
                                                                    -GGA_K_VSK = 518[source]
                                                                    +GGA_K_VSK = 518[source]
                                                                    -GGA_K_VW = 500[source]
                                                                    +GGA_K_VW = 500[source]
                                                                    -GGA_K_YT65 = 503[source]
                                                                    +GGA_K_YT65 = 503[source]
                                                                    -GGA_XC_B97_D = 170[source]
                                                                    +GGA_XC_B97_D = 170[source]
                                                                    -GGA_XC_B97_GGA1 = 96[source]
                                                                    +GGA_XC_B97_GGA1 = 96[source]
                                                                    -GGA_XC_EDF1 = 165[source]
                                                                    +GGA_XC_EDF1 = 165[source]
                                                                    -GGA_XC_HCTH_120 = 162[source]
                                                                    +GGA_XC_HCTH_120 = 162[source]
                                                                    -GGA_XC_HCTH_147 = 163[source]
                                                                    +GGA_XC_HCTH_147 = 163[source]
                                                                    -GGA_XC_HCTH_407 = 164[source]
                                                                    +GGA_XC_HCTH_407 = 164[source]
                                                                    -GGA_XC_HCTH_407P = 93[source]
                                                                    +GGA_XC_HCTH_407P = 93[source]
                                                                    -GGA_XC_HCTH_93 = 161[source]
                                                                    +GGA_XC_HCTH_93 = 161[source]
                                                                    -GGA_XC_HCTH_P14 = 95[source]
                                                                    +GGA_XC_HCTH_P14 = 95[source]
                                                                    -GGA_XC_HCTH_P76 = 94[source]
                                                                    +GGA_XC_HCTH_P76 = 94[source]
                                                                    -GGA_XC_KT2 = 146[source]
                                                                    +GGA_XC_KT2 = 146[source]
                                                                    -GGA_XC_MOHLYP = 194[source]
                                                                    +GGA_XC_MOHLYP = 194[source]
                                                                    -GGA_XC_MOHLYP2 = 195[source]
                                                                    +GGA_XC_MOHLYP2 = 195[source]
                                                                    -GGA_XC_MPWLYP1W = 174[source]
                                                                    +GGA_XC_MPWLYP1W = 174[source]
                                                                    -GGA_XC_OBLYP_D = 67[source]
                                                                    +GGA_XC_OBLYP_D = 67[source]
                                                                    -GGA_XC_OPBE_D = 65[source]
                                                                    +GGA_XC_OPBE_D = 65[source]
                                                                    -GGA_XC_OPWLYP_D = 66[source]
                                                                    +GGA_XC_OPWLYP_D = 66[source]
                                                                    -GGA_XC_PBE1W = 173[source]
                                                                    +GGA_XC_PBE1W = 173[source]
                                                                    -GGA_XC_PBELYP1W = 175[source]
                                                                    +GGA_XC_PBELYP1W = 175[source]
                                                                    -GGA_XC_TH1 = 154[source]
                                                                    +GGA_XC_TH1 = 154[source]
                                                                    -GGA_XC_TH2 = 155[source]
                                                                    +GGA_XC_TH2 = 155[source]
                                                                    -GGA_XC_TH3 = 156[source]
                                                                    +GGA_XC_TH3 = 156[source]
                                                                    -GGA_XC_TH4 = 157[source]
                                                                    +GGA_XC_TH4 = 157[source]
                                                                    -GGA_XC_TH_FC = 197[source]
                                                                    +GGA_XC_TH_FC = 197[source]
                                                                    -GGA_XC_TH_FCFO = 198[source]
                                                                    +GGA_XC_TH_FCFO = 198[source]
                                                                    -GGA_XC_TH_FCO = 199[source]
                                                                    +GGA_XC_TH_FCO = 199[source]
                                                                    -GGA_XC_TH_FL = 196[source]
                                                                    +GGA_XC_TH_FL = 196[source]
                                                                    -GGA_XC_VV10 = 255[source]
                                                                    +GGA_XC_VV10 = 255[source]
                                                                    -GGA_XC_XLYP = 166[source]
                                                                    +GGA_XC_XLYP = 166[source]
                                                                    -GGA_X_2D_B86 = 128[source]
                                                                    +GGA_X_2D_B86 = 128[source]
                                                                    -GGA_X_2D_B86_MGC = 124[source]
                                                                    +GGA_X_2D_B86_MGC = 124[source]
                                                                    -GGA_X_2D_B88 = 127[source]
                                                                    +GGA_X_2D_B88 = 127[source]
                                                                    -GGA_X_2D_PBE = 129[source]
                                                                    +GGA_X_2D_PBE = 129[source]
                                                                    -GGA_X_AIRY = 192[source]
                                                                    +GGA_X_AIRY = 192[source]
                                                                    -GGA_X_AK13 = 56[source]
                                                                    +GGA_X_AK13 = 56[source]
                                                                    -GGA_X_AM05 = 120[source]
                                                                    +GGA_X_AM05 = 120[source]
                                                                    -GGA_X_APBE = 184[source]
                                                                    +GGA_X_APBE = 184[source]
                                                                    -GGA_X_B86 = 103[source]
                                                                    +GGA_X_B86 = 103[source]
                                                                    -GGA_X_B86_MGC = 105[source]
                                                                    +GGA_X_B86_MGC = 105[source]
                                                                    -GGA_X_B86_R = 41[source]
                                                                    +GGA_X_B86_R = 41[source]
                                                                    -GGA_X_B88 = 106[source]
                                                                    +GGA_X_B88 = 106[source]
                                                                    -GGA_X_BAYESIAN = 125[source]
                                                                    +GGA_X_BAYESIAN = 125[source]
                                                                    -GGA_X_BGCP = 38[source]
                                                                    +GGA_X_BGCP = 38[source]
                                                                    -GGA_X_BPCCAC = 98[source]
                                                                    +GGA_X_BPCCAC = 98[source]
                                                                    -GGA_X_C09X = 158[source]
                                                                    +GGA_X_C09X = 158[source]
                                                                    -GGA_X_CAP = 270[source]
                                                                    +GGA_X_CAP = 270[source]
                                                                    -GGA_X_DK87_R1 = 111[source]
                                                                    +GGA_X_DK87_R1 = 111[source]
                                                                    -GGA_X_DK87_R2 = 112[source]
                                                                    +GGA_X_DK87_R2 = 112[source]
                                                                    -GGA_X_EV93 = 35[source]
                                                                    +GGA_X_EV93 = 35[source]
                                                                    -GGA_X_FT97_A = 114[source]
                                                                    +GGA_X_FT97_A = 114[source]
                                                                    -GGA_X_FT97_B = 115[source]
                                                                    +GGA_X_FT97_B = 115[source]
                                                                    -GGA_X_G96 = 107[source]
                                                                    +GGA_X_G96 = 107[source]
                                                                    -GGA_X_GAM = 32[source]
                                                                    +GGA_X_GAM = 32[source]
                                                                    -GGA_X_HCTH_A = 34[source]
                                                                    +GGA_X_HCTH_A = 34[source]
                                                                    -GGA_X_HERMAN = 104[source]
                                                                    +GGA_X_HERMAN = 104[source]
                                                                    -GGA_X_HJS_B88 = 527[source]
                                                                    +GGA_X_HJS_B88 = 527[source]
                                                                    -GGA_X_HJS_B88_V2 = 46[source]
                                                                    +GGA_X_HJS_B88_V2 = 46[source]
                                                                    -GGA_X_HJS_B97X = 528[source]
                                                                    +GGA_X_HJS_B97X = 528[source]
                                                                    -GGA_X_HJS_PBE = 525[source]
                                                                    +GGA_X_HJS_PBE = 525[source]
                                                                    -GGA_X_HJS_PBE_SOL = 526[source]
                                                                    +GGA_X_HJS_PBE_SOL = 526[source]
                                                                    -GGA_X_HTBS = 191[source]
                                                                    +GGA_X_HTBS = 191[source]
                                                                    -GGA_X_ITYH = 529[source]
                                                                    +GGA_X_ITYH = 529[source]
                                                                    -GGA_X_KT1 = 145[source]
                                                                    +GGA_X_KT1 = 145[source]
                                                                    -GGA_X_LAG = 193[source]
                                                                    +GGA_X_LAG = 193[source]
                                                                    -GGA_X_LAMBDA_CH_N = 44[source]
                                                                    +GGA_X_LAMBDA_CH_N = 44[source]
                                                                    -GGA_X_LAMBDA_LO_N = 45[source]
                                                                    +GGA_X_LAMBDA_LO_N = 45[source]
                                                                    -GGA_X_LAMBDA_OC2_N = 40[source]
                                                                    +GGA_X_LAMBDA_OC2_N = 40[source]
                                                                    -GGA_X_LB = 160[source]
                                                                    +GGA_X_LB = 160[source]
                                                                    -GGA_X_LBM = 182[source]
                                                                    +GGA_X_LBM = 182[source]
                                                                    -GGA_X_LG93 = 113[source]
                                                                    +GGA_X_LG93 = 113[source]
                                                                    -GGA_X_LV_RPW86 = 58[source]
                                                                    +GGA_X_LV_RPW86 = 58[source]
                                                                    -GGA_X_MB88 = 149[source]
                                                                    +GGA_X_MB88 = 149[source]
                                                                    -GGA_X_MPBE = 122[source]
                                                                    +GGA_X_MPBE = 122[source]
                                                                    -GGA_X_MPW91 = 119[source]
                                                                    +GGA_X_MPW91 = 119[source]
                                                                    -GGA_X_N12 = 82[source]
                                                                    +GGA_X_N12 = 82[source]
                                                                    -GGA_X_OL2 = 183[source]
                                                                    +GGA_X_OL2 = 183[source]
                                                                    -GGA_X_OPTB88_VDW = 139[source]
                                                                    +GGA_X_OPTB88_VDW = 139[source]
                                                                    -GGA_X_OPTPBE_VDW = 141[source]
                                                                    +GGA_X_OPTPBE_VDW = 141[source]
                                                                    -GGA_X_OPTX = 110[source]
                                                                    +GGA_X_OPTX = 110[source]
                                                                    -GGA_X_PBE = 101[source]
                                                                    +GGA_X_PBE = 101[source]
                                                                    -GGA_X_PBEA = 121[source]
                                                                    +GGA_X_PBEA = 121[source]
                                                                    -GGA_X_PBEFE = 265[source]
                                                                    +GGA_X_PBEFE = 265[source]
                                                                    -GGA_X_PBEINT = 60[source]
                                                                    +GGA_X_PBEINT = 60[source]
                                                                    -GGA_X_PBEK1_VDW = 140[source]
                                                                    +GGA_X_PBEK1_VDW = 140[source]
                                                                    -GGA_X_PBE_JSJR = 126[source]
                                                                    +GGA_X_PBE_JSJR = 126[source]
                                                                    -GGA_X_PBE_MOL = 49[source]
                                                                    +GGA_X_PBE_MOL = 49[source]
                                                                    -GGA_X_PBE_R = 102[source]
                                                                    +GGA_X_PBE_R = 102[source]
                                                                    -GGA_X_PBE_SOL = 116[source]
                                                                    +GGA_X_PBE_SOL = 116[source]
                                                                    -GGA_X_PBE_TCA = 59[source]
                                                                    +GGA_X_PBE_TCA = 59[source]
                                                                    -GGA_X_PW86 = 108[source]
                                                                    +GGA_X_PW86 = 108[source]
                                                                    -GGA_X_PW91 = 109[source]
                                                                    +GGA_X_PW91 = 109[source]
                                                                    -GGA_X_Q2D = 48[source]
                                                                    +GGA_X_Q2D = 48[source]
                                                                    -GGA_X_RGE2 = 142[source]
                                                                    +GGA_X_RGE2 = 142[source]
                                                                    -GGA_X_RPBE = 117[source]
                                                                    +GGA_X_RPBE = 117[source]
                                                                    -GGA_X_RPW86 = 144[source]
                                                                    +GGA_X_RPW86 = 144[source]
                                                                    -GGA_X_SFAT = 530[source]
                                                                    +GGA_X_SFAT = 530[source]
                                                                    -GGA_X_SOGGA = 150[source]
                                                                    +GGA_X_SOGGA = 150[source]
                                                                    -GGA_X_SOGGA11 = 151[source]
                                                                    +GGA_X_SOGGA11 = 151[source]
                                                                    -GGA_X_SSB = 91[source]
                                                                    +GGA_X_SSB = 91[source]
                                                                    -GGA_X_SSB_D = 92[source]
                                                                    +GGA_X_SSB_D = 92[source]
                                                                    -GGA_X_SSB_SW = 90[source]
                                                                    +GGA_X_SSB_SW = 90[source]
                                                                    -GGA_X_VMT84_GE = 68[source]
                                                                    +GGA_X_VMT84_GE = 68[source]
                                                                    -GGA_X_VMT84_PBE = 69[source]
                                                                    +GGA_X_VMT84_PBE = 69[source]
                                                                    -GGA_X_VMT_GE = 70[source]
                                                                    +GGA_X_VMT_GE = 70[source]
                                                                    -GGA_X_VMT_PBE = 71[source]
                                                                    +GGA_X_VMT_PBE = 71[source]
                                                                    -GGA_X_WC = 118[source]
                                                                    +GGA_X_WC = 118[source]
                                                                    -GGA_X_WPBEH = 524[source]
                                                                    +GGA_X_WPBEH = 524[source]
                                                                    -GGA_X_XPBE = 123[source]
                                                                    +GGA_X_XPBE = 123[source]
                                                                    -HYB_GGA_XC_B1LYP = 416[source]
                                                                    +HYB_GGA_XC_B1LYP = 416[source]
                                                                    -HYB_GGA_XC_B1PW91 = 417[source]
                                                                    +HYB_GGA_XC_B1PW91 = 417[source]
                                                                    -HYB_GGA_XC_B1WC = 412[source]
                                                                    +HYB_GGA_XC_B1WC = 412[source]
                                                                    -HYB_GGA_XC_B3LYP = 402[source]
                                                                    +HYB_GGA_XC_B3LYP = 402[source]
                                                                    -HYB_GGA_XC_B3LYP5 = 475[source]
                                                                    +HYB_GGA_XC_B3LYP5 = 475[source]
                                                                    -HYB_GGA_XC_B3LYPs = 459[source]
                                                                    +HYB_GGA_XC_B3LYPs = 459[source]
                                                                    -HYB_GGA_XC_B3P86 = 403[source]
                                                                    +HYB_GGA_XC_B3P86 = 403[source]
                                                                    -HYB_GGA_XC_B3PW91 = 401[source]
                                                                    +HYB_GGA_XC_B3PW91 = 401[source]
                                                                    -HYB_GGA_XC_B97 = 407[source]
                                                                    +HYB_GGA_XC_B97 = 407[source]
                                                                    -HYB_GGA_XC_B97_1 = 408[source]
                                                                    +HYB_GGA_XC_B97_1 = 408[source]
                                                                    -HYB_GGA_XC_B97_1p = 266[source]
                                                                    +HYB_GGA_XC_B97_1p = 266[source]
                                                                    -HYB_GGA_XC_B97_2 = 410[source]
                                                                    +HYB_GGA_XC_B97_2 = 410[source]
                                                                    -HYB_GGA_XC_B97_3 = 414[source]
                                                                    +HYB_GGA_XC_B97_3 = 414[source]
                                                                    -HYB_GGA_XC_B97_K = 413[source]
                                                                    +HYB_GGA_XC_B97_K = 413[source]
                                                                    -HYB_GGA_XC_BHANDH = 435[source]
                                                                    +HYB_GGA_XC_BHANDH = 435[source]
                                                                    -HYB_GGA_XC_BHANDHLYP = 436[source]
                                                                    +HYB_GGA_XC_BHANDHLYP = 436[source]
                                                                    -HYB_GGA_XC_CAMY_B3LYP = 470[source]
                                                                    +HYB_GGA_XC_CAMY_B3LYP = 470[source]
                                                                    -HYB_GGA_XC_CAMY_BLYP = 455[source]
                                                                    +HYB_GGA_XC_CAMY_BLYP = 455[source]
                                                                    -HYB_GGA_XC_CAM_B3LYP = 433[source]
                                                                    +HYB_GGA_XC_CAM_B3LYP = 433[source]
                                                                    -HYB_GGA_XC_CAP0 = 477[source]
                                                                    +HYB_GGA_XC_CAP0 = 477[source]
                                                                    -HYB_GGA_XC_EDF2 = 476[source]
                                                                    +HYB_GGA_XC_EDF2 = 476[source]
                                                                    -HYB_GGA_XC_HJS_B88 = 431[source]
                                                                    +HYB_GGA_XC_HJS_B88 = 431[source]
                                                                    -HYB_GGA_XC_HJS_B97X = 432[source]
                                                                    +HYB_GGA_XC_HJS_B97X = 432[source]
                                                                    -HYB_GGA_XC_HJS_PBE = 429[source]
                                                                    +HYB_GGA_XC_HJS_PBE = 429[source]
                                                                    -HYB_GGA_XC_HJS_PBE_SOL = 430[source]
                                                                    +HYB_GGA_XC_HJS_PBE_SOL = 430[source]
                                                                    -HYB_GGA_XC_HPBEINT = 472[source]
                                                                    +HYB_GGA_XC_HPBEINT = 472[source]
                                                                    -HYB_GGA_XC_HSE03 = 427[source]
                                                                    +HYB_GGA_XC_HSE03 = 427[source]
                                                                    -HYB_GGA_XC_HSE06 = 428[source]
                                                                    +HYB_GGA_XC_HSE06 = 428[source]
                                                                    -HYB_GGA_XC_LCY_BLYP = 468[source]
                                                                    +HYB_GGA_XC_LCY_BLYP = 468[source]
                                                                    -HYB_GGA_XC_LCY_PBE = 467[source]
                                                                    +HYB_GGA_XC_LCY_PBE = 467[source]
                                                                    -HYB_GGA_XC_LC_VV10 = 469[source]
                                                                    +HYB_GGA_XC_LC_VV10 = 469[source]
                                                                    -HYB_GGA_XC_LRC_WPBE = 473[source]
                                                                    +HYB_GGA_XC_LRC_WPBE = 473[source]
                                                                    -HYB_GGA_XC_LRC_WPBEH = 465[source]
                                                                    +HYB_GGA_XC_LRC_WPBEH = 465[source]
                                                                    -HYB_GGA_XC_MB3LYP_RC04 = 437[source]
                                                                    +HYB_GGA_XC_MB3LYP_RC04 = 437[source]
                                                                    -HYB_GGA_XC_MPW3LYP = 419[source]
                                                                    +HYB_GGA_XC_MPW3LYP = 419[source]
                                                                    -HYB_GGA_XC_MPW3PW = 415[source]
                                                                    +HYB_GGA_XC_MPW3PW = 415[source]
                                                                    -HYB_GGA_XC_MPWLYP1M = 453[source]
                                                                    +HYB_GGA_XC_MPWLYP1M = 453[source]
                                                                    -HYB_GGA_XC_O3LYP = 404[source]
                                                                    +HYB_GGA_XC_O3LYP = 404[source]
                                                                    -HYB_GGA_XC_PBE0_13 = 456[source]
                                                                    +HYB_GGA_XC_PBE0_13 = 456[source]
                                                                    -HYB_GGA_XC_PBEH = 406[source]
                                                                    +HYB_GGA_XC_PBEH = 406[source]
                                                                    -HYB_GGA_XC_REVB3LYP = 454[source]
                                                                    +HYB_GGA_XC_REVB3LYP = 454[source]
                                                                    -HYB_GGA_XC_SB98_1a = 420[source]
                                                                    +HYB_GGA_XC_SB98_1a = 420[source]
                                                                    -HYB_GGA_XC_SB98_1b = 421[source]
                                                                    +HYB_GGA_XC_SB98_1b = 421[source]
                                                                    -HYB_GGA_XC_SB98_1c = 422[source]
                                                                    +HYB_GGA_XC_SB98_1c = 422[source]
                                                                    -HYB_GGA_XC_SB98_2a = 423[source]
                                                                    +HYB_GGA_XC_SB98_2a = 423[source]
                                                                    -HYB_GGA_XC_SB98_2b = 424[source]
                                                                    +HYB_GGA_XC_SB98_2b = 424[source]
                                                                    -HYB_GGA_XC_SB98_2c = 425[source]
                                                                    +HYB_GGA_XC_SB98_2c = 425[source]
                                                                    -HYB_GGA_XC_TUNED_CAM_B3LYP = 434[source]
                                                                    +HYB_GGA_XC_TUNED_CAM_B3LYP = 434[source]
                                                                    -HYB_GGA_XC_WB97 = 463[source]
                                                                    +HYB_GGA_XC_WB97 = 463[source]
                                                                    -HYB_GGA_XC_WB97X = 464[source]
                                                                    +HYB_GGA_XC_WB97X = 464[source]
                                                                    -HYB_GGA_XC_WB97X_D = 471[source]
                                                                    +HYB_GGA_XC_WB97X_D = 471[source]
                                                                    -HYB_GGA_XC_WB97X_V = 466[source]
                                                                    +HYB_GGA_XC_WB97X_V = 466[source]
                                                                    -HYB_GGA_XC_X3LYP = 411[source]
                                                                    +HYB_GGA_XC_X3LYP = 411[source]
                                                                    -HYB_GGA_XC_mPW1K = 405[source]
                                                                    +HYB_GGA_XC_mPW1K = 405[source]
                                                                    -HYB_GGA_XC_mPW1PW = 418[source]
                                                                    +HYB_GGA_XC_mPW1PW = 418[source]
                                                                    -HYB_GGA_X_N12_SX = 81[source]
                                                                    +HYB_GGA_X_N12_SX = 81[source]
                                                                    -HYB_GGA_X_SOGGA11_X = 426[source]
                                                                    +HYB_GGA_X_SOGGA11_X = 426[source]
                                                                    -HYB_MGGA_XC_B86B95 = 441[source]
                                                                    +HYB_MGGA_XC_B86B95 = 441[source]
                                                                    -HYB_MGGA_XC_B88B95 = 440[source]
                                                                    +HYB_MGGA_XC_B88B95 = 440[source]
                                                                    -HYB_MGGA_XC_BB1K = 443[source]
                                                                    +HYB_MGGA_XC_BB1K = 443[source]
                                                                    -HYB_MGGA_XC_M05 = 438[source]
                                                                    +HYB_MGGA_XC_M05 = 438[source]
                                                                    -HYB_MGGA_XC_M05_2X = 439[source]
                                                                    +HYB_MGGA_XC_M05_2X = 439[source]
                                                                    -HYB_MGGA_XC_M06 = 449[source]
                                                                    +HYB_MGGA_XC_M06 = 449[source]
                                                                    -HYB_MGGA_XC_M06_2X = 450[source]
                                                                    +HYB_MGGA_XC_M06_2X = 450[source]
                                                                    -HYB_MGGA_XC_M06_HF = 444[source]
                                                                    +HYB_MGGA_XC_M06_HF = 444[source]
                                                                    -HYB_MGGA_XC_M08_HX = 460[source]
                                                                    +HYB_MGGA_XC_M08_HX = 460[source]
                                                                    -HYB_MGGA_XC_M08_SO = 461[source]
                                                                    +HYB_MGGA_XC_M08_SO = 461[source]
                                                                    -HYB_MGGA_XC_M11 = 462[source]
                                                                    +HYB_MGGA_XC_M11 = 462[source]
                                                                    -HYB_MGGA_XC_MPW1B95 = 445[source]
                                                                    +HYB_MGGA_XC_MPW1B95 = 445[source]
                                                                    -HYB_MGGA_XC_MPWB1K = 446[source]
                                                                    +HYB_MGGA_XC_MPWB1K = 446[source]
                                                                    -HYB_MGGA_XC_PW6B95 = 451[source]
                                                                    +HYB_MGGA_XC_PW6B95 = 451[source]
                                                                    -HYB_MGGA_XC_PW86B95 = 442[source]
                                                                    +HYB_MGGA_XC_PW86B95 = 442[source]
                                                                    -HYB_MGGA_XC_PWB6K = 452[source]
                                                                    +HYB_MGGA_XC_PWB6K = 452[source]
                                                                    -HYB_MGGA_XC_REVTPSSH = 458[source]
                                                                    +HYB_MGGA_XC_REVTPSSH = 458[source]
                                                                    -HYB_MGGA_XC_TPSSH = 457[source]
                                                                    +HYB_MGGA_XC_TPSSH = 457[source]
                                                                    -HYB_MGGA_XC_WB97M_V = 531[source]
                                                                    +HYB_MGGA_XC_WB97M_V = 531[source]
                                                                    -HYB_MGGA_XC_X1B95 = 447[source]
                                                                    +HYB_MGGA_XC_X1B95 = 447[source]
                                                                    -HYB_MGGA_XC_XB1K = 448[source]
                                                                    +HYB_MGGA_XC_XB1K = 448[source]
                                                                    -HYB_MGGA_X_DLDF = 36[source]
                                                                    +HYB_MGGA_X_DLDF = 36[source]
                                                                    -HYB_MGGA_X_MN12_SX = 248[source]
                                                                    +HYB_MGGA_X_MN12_SX = 248[source]
                                                                    -HYB_MGGA_X_MN15 = 268[source]
                                                                    +HYB_MGGA_X_MN15 = 268[source]
                                                                    -HYB_MGGA_X_MS2H = 224[source]
                                                                    +HYB_MGGA_X_MS2H = 224[source]
                                                                    -HYB_MGGA_X_MVSH = 474[source]
                                                                    +HYB_MGGA_X_MVSH = 474[source]
                                                                    -HYB_MGGA_X_SCAN0 = 264[source]
                                                                    +HYB_MGGA_X_SCAN0 = 264[source]
                                                                    -LDA_C_1D_CSC = 18[source]
                                                                    +LDA_C_1D_CSC = 18[source]
                                                                    -LDA_C_1D_LOOS = 26[source]
                                                                    +LDA_C_1D_LOOS = 26[source]
                                                                    -LDA_C_2D_AMGB = 15[source]
                                                                    +LDA_C_2D_AMGB = 15[source]
                                                                    -LDA_C_2D_PRM = 16[source]
                                                                    +LDA_C_2D_PRM = 16[source]
                                                                    -LDA_C_GL = 5[source]
                                                                    +LDA_C_GL = 5[source]
                                                                    -LDA_C_GOMBAS = 24[source]
                                                                    +LDA_C_GOMBAS = 24[source]
                                                                    -LDA_C_HL = 4[source]
                                                                    +LDA_C_HL = 4[source]
                                                                    -LDA_C_ML1 = 22[source]
                                                                    +LDA_C_ML1 = 22[source]
                                                                    -LDA_C_ML2 = 23[source]
                                                                    +LDA_C_ML2 = 23[source]
                                                                    -LDA_C_OB_PW = 14[source]
                                                                    +LDA_C_OB_PW = 14[source]
                                                                    -LDA_C_OB_PZ = 11[source]
                                                                    +LDA_C_OB_PZ = 11[source]
                                                                    -LDA_C_PW = 12[source]
                                                                    +LDA_C_PW = 12[source]
                                                                    -LDA_C_PW_MOD = 13[source]
                                                                    +LDA_C_PW_MOD = 13[source]
                                                                    -LDA_C_PW_RPA = 25[source]
                                                                    +LDA_C_PW_RPA = 25[source]
                                                                    -LDA_C_PZ = 9[source]
                                                                    +LDA_C_PZ = 9[source]
                                                                    -LDA_C_PZ_MOD = 10[source]
                                                                    +LDA_C_PZ_MOD = 10[source]
                                                                    -LDA_C_RC04 = 27[source]
                                                                    +LDA_C_RC04 = 27[source]
                                                                    -LDA_C_RPA = 3[source]
                                                                    +LDA_C_RPA = 3[source]
                                                                    -LDA_C_VWN = 7[source]
                                                                    +LDA_C_VWN = 7[source]
                                                                    -LDA_C_VWN_1 = 28[source]
                                                                    +LDA_C_VWN_1 = 28[source]
                                                                    -LDA_C_VWN_2 = 29[source]
                                                                    +LDA_C_VWN_2 = 29[source]
                                                                    -LDA_C_VWN_3 = 30[source]
                                                                    +LDA_C_VWN_3 = 30[source]
                                                                    -LDA_C_VWN_4 = 31[source]
                                                                    +LDA_C_VWN_4 = 31[source]
                                                                    -LDA_C_VWN_RPA = 8[source]
                                                                    +LDA_C_VWN_RPA = 8[source]
                                                                    -LDA_C_WIGNER = 2[source]
                                                                    +LDA_C_WIGNER = 2[source]
                                                                    -LDA_C_XALPHA = 6[source]
                                                                    +LDA_C_XALPHA = 6[source]
                                                                    -LDA_C_vBH = 17[source]
                                                                    +LDA_C_vBH = 17[source]
                                                                    -LDA_K_LP = 51[source]
                                                                    +LDA_K_LP = 51[source]
                                                                    -LDA_K_TF = 50[source]
                                                                    +LDA_K_TF = 50[source]
                                                                    -LDA_X = 1[source]
                                                                    +LDA_X = 1[source]
                                                                    -LDA_XC_KSDT = 259[source]
                                                                    +LDA_XC_KSDT = 259[source]
                                                                    -LDA_XC_TETER93 = 20[source]
                                                                    +LDA_XC_TETER93 = 20[source]
                                                                    -LDA_XC_ZLP = 43[source]
                                                                    +LDA_XC_ZLP = 43[source]
                                                                    -LDA_X_1D = 21[source]
                                                                    +LDA_X_1D = 21[source]
                                                                    -LDA_X_2D = 19[source]
                                                                    +LDA_X_2D = 19[source]
                                                                    -MGGA_C_BC95 = 240[source]
                                                                    +MGGA_C_BC95 = 240[source]
                                                                    -MGGA_C_CC06 = 229[source]
                                                                    +MGGA_C_CC06 = 229[source]
                                                                    -MGGA_C_CS = 72[source]
                                                                    +MGGA_C_CS = 72[source]
                                                                    -MGGA_C_DLDF = 37[source]
                                                                    +MGGA_C_DLDF = 37[source]
                                                                    -MGGA_C_M05 = 237[source]
                                                                    +MGGA_C_M05 = 237[source]
                                                                    -MGGA_C_M05_2X = 238[source]
                                                                    +MGGA_C_M05_2X = 238[source]
                                                                    -MGGA_C_M06 = 235[source]
                                                                    +MGGA_C_M06 = 235[source]
                                                                    -MGGA_C_M06_2X = 236[source]
                                                                    +MGGA_C_M06_2X = 236[source]
                                                                    -MGGA_C_M06_HF = 234[source]
                                                                    +MGGA_C_M06_HF = 234[source]
                                                                    -MGGA_C_M06_L = 233[source]
                                                                    +MGGA_C_M06_L = 233[source]
                                                                    -MGGA_C_M08_HX = 78[source]
                                                                    +MGGA_C_M08_HX = 78[source]
                                                                    -MGGA_C_M08_SO = 77[source]
                                                                    +MGGA_C_M08_SO = 77[source]
                                                                    -MGGA_C_M11 = 76[source]
                                                                    +MGGA_C_M11 = 76[source]
                                                                    -MGGA_C_M11_L = 75[source]
                                                                    +MGGA_C_M11_L = 75[source]
                                                                    -MGGA_C_MN12_L = 74[source]
                                                                    +MGGA_C_MN12_L = 74[source]
                                                                    -MGGA_C_MN12_SX = 73[source]
                                                                    +MGGA_C_MN12_SX = 73[source]
                                                                    -MGGA_C_MN15 = 269[source]
                                                                    +MGGA_C_MN15 = 269[source]
                                                                    -MGGA_C_MN15_L = 261[source]
                                                                    +MGGA_C_MN15_L = 261[source]
                                                                    -MGGA_C_PKZB = 239[source]
                                                                    +MGGA_C_PKZB = 239[source]
                                                                    -MGGA_C_REVTPSS = 241[source]
                                                                    +MGGA_C_REVTPSS = 241[source]
                                                                    -MGGA_C_SCAN = 267[source]
                                                                    +MGGA_C_SCAN = 267[source]
                                                                    -MGGA_C_TPSS = 231[source]
                                                                    +MGGA_C_TPSS = 231[source]
                                                                    -MGGA_C_TPSSLOC = 247[source]
                                                                    +MGGA_C_TPSSLOC = 247[source]
                                                                    -MGGA_C_VSXC = 232[source]
                                                                    +MGGA_C_VSXC = 232[source]
                                                                    -MGGA_XC_B97M_V = 254[source]
                                                                    +MGGA_XC_B97M_V = 254[source]
                                                                    -MGGA_XC_OTPSS_D = 64[source]
                                                                    +MGGA_XC_OTPSS_D = 64[source]
                                                                    -MGGA_XC_TPSSLYP1W = 242[source]
                                                                    +MGGA_XC_TPSSLYP1W = 242[source]
                                                                    -MGGA_XC_ZLP = 42[source]
                                                                    +MGGA_XC_ZLP = 42[source]
                                                                    -MGGA_X_2D_PRHG07 = 210[source]
                                                                    +MGGA_X_2D_PRHG07 = 210[source]
                                                                    -MGGA_X_2D_PRHG07_PRP10 = 211[source]
                                                                    +MGGA_X_2D_PRHG07_PRP10 = 211[source]
                                                                    -MGGA_X_BJ06 = 207[source]
                                                                    +MGGA_X_BJ06 = 207[source]
                                                                    -MGGA_X_BLOC = 244[source]
                                                                    +MGGA_X_BLOC = 244[source]
                                                                    -MGGA_X_BR89 = 206[source]
                                                                    +MGGA_X_BR89 = 206[source]
                                                                    -MGGA_X_GVT4 = 204[source]
                                                                    +MGGA_X_GVT4 = 204[source]
                                                                    -MGGA_X_LTA = 201[source]
                                                                    +MGGA_X_LTA = 201[source]
                                                                    -MGGA_X_M05 = 214[source]
                                                                    +MGGA_X_M05 = 214[source]
                                                                    -MGGA_X_M05_2X = 215[source]
                                                                    +MGGA_X_M05_2X = 215[source]
                                                                    -MGGA_X_M06 = 217[source]
                                                                    +MGGA_X_M06 = 217[source]
                                                                    -MGGA_X_M06_2X = 218[source]
                                                                    +MGGA_X_M06_2X = 218[source]
                                                                    -MGGA_X_M06_HF = 216[source]
                                                                    +MGGA_X_M06_HF = 216[source]
                                                                    -MGGA_X_M06_L = 203[source]
                                                                    +MGGA_X_M06_L = 203[source]
                                                                    -MGGA_X_M08_HX = 219[source]
                                                                    +MGGA_X_M08_HX = 219[source]
                                                                    -MGGA_X_M08_SO = 220[source]
                                                                    +MGGA_X_M08_SO = 220[source]
                                                                    -MGGA_X_M11 = 225[source]
                                                                    +MGGA_X_M11 = 225[source]
                                                                    -MGGA_X_M11_L = 226[source]
                                                                    +MGGA_X_M11_L = 226[source]
                                                                    -MGGA_X_MBEEF = 249[source]
                                                                    +MGGA_X_MBEEF = 249[source]
                                                                    -MGGA_X_MBEEFVDW = 250[source]
                                                                    +MGGA_X_MBEEFVDW = 250[source]
                                                                    -MGGA_X_MK00 = 230[source]
                                                                    +MGGA_X_MK00 = 230[source]
                                                                    -MGGA_X_MK00B = 243[source]
                                                                    +MGGA_X_MK00B = 243[source]
                                                                    -MGGA_X_MN12_L = 227[source]
                                                                    +MGGA_X_MN12_L = 227[source]
                                                                    -MGGA_X_MN15_L = 260[source]
                                                                    +MGGA_X_MN15_L = 260[source]
                                                                    -MGGA_X_MODTPSS = 245[source]
                                                                    +MGGA_X_MODTPSS = 245[source]
                                                                    -MGGA_X_MS0 = 221[source]
                                                                    +MGGA_X_MS0 = 221[source]
                                                                    -MGGA_X_MS1 = 222[source]
                                                                    +MGGA_X_MS1 = 222[source]
                                                                    -MGGA_X_MS2 = 223[source]
                                                                    +MGGA_X_MS2 = 223[source]
                                                                    -MGGA_X_MVS = 257[source]
                                                                    +MGGA_X_MVS = 257[source]
                                                                    -MGGA_X_PKZB = 213[source]
                                                                    +MGGA_X_PKZB = 213[source]
                                                                    -MGGA_X_REVTPSS = 212[source]
                                                                    +MGGA_X_REVTPSS = 212[source]
                                                                    -MGGA_X_RPP09 = 209[source]
                                                                    +MGGA_X_RPP09 = 209[source]
                                                                    -MGGA_X_SCAN = 263[source]
                                                                    +MGGA_X_SCAN = 263[source]
                                                                    -MGGA_X_TAU_HCTH = 205[source]
                                                                    +MGGA_X_TAU_HCTH = 205[source]
                                                                    -MGGA_X_TB09 = 208[source]
                                                                    +MGGA_X_TB09 = 208[source]
                                                                    -MGGA_X_TPSS = 202[source]
                                                                    +MGGA_X_TPSS = 202[source]
                                                                    -static all_families()[source]
                                                                    +static all_families()[source]

                                                                    List of strings with the libxc families. Note that XC_FAMILY if removed from the string e.g. XC_FAMILY_LDA becomes LDA.

                                                                    -static all_kinds()[source]
                                                                    +static all_kinds()[source]

                                                                    List of strings with the libxc kinds. Also in this case, the string is obtained by remove the XC_ prefix. XC_CORRELATION –> CORRELATION.

                                                                    @@ -6127,80 +6127,80 @@

                                                                    Submodules
                                                                    -as_dict() → dict[source]
                                                                    +as_dict() → dict[source]

                                                                    Serialize to MSONable dict representation, e.g. to write to disk as JSON.

                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]

                                                                    Deserialize from MSONable dict representation.

                                                                    -property info_dict[source]
                                                                    +property info_dict[source]

                                                                    Dictionary with metadata. see libxc_docs.json.

                                                                    -property is_c_kind: bool[source]
                                                                    +property is_c_kind: bool[source]

                                                                    True if this is a correlation-only functional.

                                                                    -property is_gga_family: bool[source]
                                                                    +property is_gga_family: bool[source]

                                                                    True if this functional belongs to the GGA family.

                                                                    -property is_hyb_gga_family: bool[source]
                                                                    +property is_hyb_gga_family: bool[source]

                                                                    True if this functional belongs to the hybrid + GGA family.

                                                                    -property is_hyb_mgga_family: bool[source]
                                                                    +property is_hyb_mgga_family: bool[source]

                                                                    True if this functional belongs to the hybrid + meta-GGA family.

                                                                    -property is_k_kind: bool[source]
                                                                    +property is_k_kind: bool[source]

                                                                    True if this is a kinetic functional.

                                                                    -property is_lda_family: bool[source]
                                                                    +property is_lda_family: bool[source]

                                                                    True if this functional belongs to the LDA family.

                                                                    -property is_mgga_family: bool[source]
                                                                    +property is_mgga_family: bool[source]

                                                                    True if this functional belongs to the meta-GGA family.

                                                                    -property is_x_kind: bool[source]
                                                                    +property is_x_kind: bool[source]

                                                                    True if this is an exchange-only functional.

                                                                    -property is_xc_kind: bool[source]
                                                                    +property is_xc_kind: bool[source]

                                                                    True if this is a exchange+correlation functional.

                                                                    -to_json() → str[source]
                                                                    +to_json() → str[source]

                                                                    Get a JSON string representation of the LibxcFunc.

                                                                    @@ -6213,7 +6213,7 @@

                                                                    Submodules
                                                                    -class MolecularOrbitals(formula: str)[source]
                                                                    +class MolecularOrbitals(formula: str)[source]

                                                                    Bases: object

                                                                    Represents the character of bands in a solid. The input is a chemical formula, since no structural characteristics are taken into account.

                                                                    @@ -6234,31 +6234,31 @@

                                                                    Submodules
                                                                    -composition[source]
                                                                    +composition[source]

                                                                    the composition as a dictionary. Ex: {‘Sr’: 1, ‘Ti’: 1, ‘O’, 3}

                                                                    -elements[source]
                                                                    +elements[source]

                                                                    the dictionary keys for the composition

                                                                    -elec_neg[source]
                                                                    +elec_neg[source]

                                                                    the maximum pairwise electronegativity difference

                                                                    -aos[source]
                                                                    +aos[source]

                                                                    the constituent atomic orbitals for each element as a dictionary

                                                                    -band_edges[source]
                                                                    +band_edges[source]

                                                                    dictionary containing the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and whether the material is predicted to be a metal

                                                                    @@ -6266,7 +6266,7 @@

                                                                    Submodules
                                                                    -aos_as_list() → list[tuple[str, str, float]][source]
                                                                    +aos_as_list() → list[tuple[str, str, float]][source]

                                                                    The orbitals energies in eV are represented as [[‘O’, ‘1s’, -18.758245], [‘O’, ‘2s’, -0.871362], [‘O’, ‘2p’, -0.338381]] Data is obtained from @@ -6280,7 +6280,7 @@

                                                                    Submodules
                                                                    -max_electronegativity() → float[source]
                                                                    +max_electronegativity() → float[source]
                                                                    Returns:

                                                                    The maximum pairwise electronegativity difference.

                                                                    @@ -6290,7 +6290,7 @@

                                                                    Submodules
                                                                    -obtain_band_edges() → dict[str, Any][source]
                                                                    +obtain_band_edges() → dict[str, Any][source]

                                                                    Fill up the atomic orbitals with available electrons.

                                                                    Returns:
                                                                    @@ -6307,7 +6307,7 @@

                                                                    Submodules
                                                                    -class MagSymmOp(affine_transformation_matrix: ArrayLike, time_reversal: Literal[-1, 1], tol: float = 0.01)[source]
                                                                    +class MagSymmOp(affine_transformation_matrix: ArrayLike, time_reversal: Literal[-1, 1], tol: float = 0.01)[source]

                                                                    Bases: SymmOp

                                                                    Thin wrapper around SymmOp to extend it to support magnetic symmetry by including a time reversal operator. Magnetic symmetry is similar to conventional crystal symmetry, except @@ -6329,20 +6329,20 @@

                                                                    Submodules
                                                                    -as_dict() → dict[str, Any][source]
                                                                    +as_dict() → dict[str, Any][source]

                                                                    MSONable dict.

                                                                    -as_xyzt_str() → str[source]
                                                                    +as_xyzt_str() → str[source]

                                                                    Get a string of the form ‘x, y, z, +1’, ‘-x, -y, z, -1’, ‘-y+1/2, x+1/2, z+1/2, +1’, etc. Only works for integer rotation matrices.

                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                                    Parameters:

                                                                    dct – dict.

                                                                    @@ -6355,7 +6355,7 @@

                                                                    Submodules
                                                                    -static from_rotation_and_translation_and_time_reversal(rotation_matrix: ArrayLike = ((1, 0, 0), (0, 1, 0), (0, 0, 1)), translation_vec: ArrayLike = (0, 0, 0), time_reversal: Literal[-1, 1] = 1, tol: float = 0.1) → MagSymmOp[source]
                                                                    +static from_rotation_and_translation_and_time_reversal(rotation_matrix: ArrayLike = ((1, 0, 0), (0, 1, 0), (0, 0, 1)), translation_vec: ArrayLike = (0, 0, 0), time_reversal: Literal[-1, 1] = 1, tol: float = 0.1) → MagSymmOp[source]

                                                                    Create a symmetry operation from a rotation matrix, translation vector and time reversal operator.

                                                                    @@ -6375,7 +6375,7 @@

                                                                    Submodules
                                                                    -classmethod from_symmop(symmop: SymmOp, time_reversal: Literal[-1, 1]) → Self[source]
                                                                    +classmethod from_symmop(symmop: SymmOp, time_reversal: Literal[-1, 1]) → Self[source]

                                                                    Initialize a MagSymmOp from a SymmOp and time reversal operator.

                                                                    Parameters:
                                                                    @@ -6392,7 +6392,7 @@

                                                                    Submodules
                                                                    -classmethod from_xyzt_str(xyzt_str: str) → Self[source]
                                                                    +classmethod from_xyzt_str(xyzt_str: str) → Self[source]
                                                                    Parameters:

                                                                    xyzt_str (str) – of the form ‘x, y, z, +1’, ‘-x, -y, z, -1’, @@ -6406,7 +6406,7 @@

                                                                    Submodules
                                                                    -operate_magmom(magmom: Magmom) → Magmom[source]
                                                                    +operate_magmom(magmom: Magmom) → Magmom[source]

                                                                    Apply time reversal operator on the magnetic moment. Note that magnetic moments transform as axial vectors, not polar vectors.

                                                                    See ‘Symmetry and magnetic structures’, Rodríguez-Carvajal and @@ -6428,14 +6428,14 @@

                                                                    Submodules
                                                                    -class SymmOp(affine_transformation_matrix: ArrayLike, tol: float = 0.01)[source]
                                                                    +class SymmOp(affine_transformation_matrix: ArrayLike, tol: float = 0.01)[source]

                                                                    Bases: MSONable

                                                                    A symmetry operation in Cartesian space. Consists of a rotation plus a translation. Implementation is as an affine transformation matrix of rank 4 for efficiency. Read: http://wikipedia.org/wiki/Affine_transformation.

                                                                    -affine_matrix[source]
                                                                    +affine_matrix[source]

                                                                    A 4x4 array representing the symmetry operation.

                                                                    Type:
                                                                    @@ -6462,7 +6462,7 @@

                                                                    Submodules
                                                                    -apply_rotation_only(vector: ArrayLike) → np.ndarray[source]
                                                                    +apply_rotation_only(vector: ArrayLike) → np.ndarray[source]

                                                                    Vectors should only be operated by the rotation matrix and not the translation vector.

                                                                    @@ -6474,7 +6474,7 @@

                                                                    Submodules +are_symmetrically_related(point_a: ArrayLike, point_b: ArrayLike, tol: float = 0.001) → bool[source]

                                                                    Check if two points are symmetrically related.

                                                                    Parameters:
                                                                    @@ -6495,7 +6495,7 @@

                                                                    Submodules +are_symmetrically_related_vectors(from_a: ArrayLike, to_a: ArrayLike, r_a: ArrayLike, from_b: ArrayLike, to_b: ArrayLike, r_b: ArrayLike, tol: float = 0.001) → tuple[bool, bool][source]

                                                                    Check if two vectors, or rather two vectors that connect two points each are symmetrically related. r_a and r_b give the change of unit cells. Two vectors are also considered symmetrically equivalent if starting @@ -6528,20 +6528,20 @@

                                                                    Submodules
                                                                    -as_dict() → dict[str, Any][source]
                                                                    +as_dict() → dict[str, Any][source]

                                                                    MSONable dict.

                                                                    -as_xyz_str() → str[source]
                                                                    +as_xyz_str() → str[source]

                                                                    Get a string of the form ‘x, y, z’, ‘-x, -y, z’, ‘-y+1/2, x+1/2, z+1/2’, etc. Only works for integer rotation matrices.

                                                                    -static from_axis_angle_and_translation(axis: ArrayLike, angle: float, angle_in_radians: bool = False, translation_vec: ArrayLike = (0, 0, 0)) → SymmOp[source]
                                                                    +static from_axis_angle_and_translation(axis: ArrayLike, angle: float, angle_in_radians: bool = False, translation_vec: ArrayLike = (0, 0, 0)) → SymmOp[source]

                                                                    Generate a SymmOp for a rotation about a given axis plus translation.

                                                                    Parameters:
                                                                    @@ -6562,7 +6562,7 @@

                                                                    Submodules
                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                                    Parameters:

                                                                    dct – dict.

                                                                    @@ -6575,7 +6575,7 @@

                                                                    Submodules
                                                                    -static from_origin_axis_angle(origin: ArrayLike, axis: ArrayLike, angle: float, angle_in_radians: bool = False) → SymmOp[source]
                                                                    +static from_origin_axis_angle(origin: ArrayLike, axis: ArrayLike, angle: float, angle_in_radians: bool = False) → SymmOp[source]

                                                                    Generate a SymmOp for a rotation about a given axis through an origin.

                                                                    @@ -6597,7 +6597,7 @@

                                                                    Submodules
                                                                    -classmethod from_rotation_and_translation(rotation_matrix: ArrayLike = ((1, 0, 0), (0, 1, 0), (0, 0, 1)), translation_vec: ArrayLike = (0, 0, 0), tol: float = 0.1) → Self[source]
                                                                    +classmethod from_rotation_and_translation(rotation_matrix: ArrayLike = ((1, 0, 0), (0, 1, 0), (0, 0, 1)), translation_vec: ArrayLike = (0, 0, 0), tol: float = 0.1) → Self[source]

                                                                    Create a symmetry operation from a rotation matrix and a translation vector.

                                                                    @@ -6616,7 +6616,7 @@

                                                                    Submodules
                                                                    -classmethod from_xyz_str(xyz_str: str) → Self[source]
                                                                    +classmethod from_xyz_str(xyz_str: str) → Self[source]
                                                                    Parameters:

                                                                    xyz_str – string of the form ‘x, y, z’, ‘-x, -y, z’, ‘-2y+1/2, 3x+1/2, z-y+1/2’, etc.

                                                                    @@ -6629,13 +6629,13 @@

                                                                    Submodules
                                                                    -property inverse: Self[source]
                                                                    +property inverse: Self[source]

                                                                    Inverse of transformation.

                                                                    -static inversion(origin: ArrayLike = (0, 0, 0)) → SymmOp[source]
                                                                    +static inversion(origin: ArrayLike = (0, 0, 0)) → SymmOp[source]

                                                                    Inversion symmetry operation about axis.

                                                                    Parameters:
                                                                    @@ -6650,7 +6650,7 @@

                                                                    Submodules
                                                                    -operate(point: ArrayLike) → np.ndarray[source]
                                                                    +operate(point: ArrayLike) → np.ndarray[source]

                                                                    Apply the operation on a point.

                                                                    Parameters:
                                                                    @@ -6664,7 +6664,7 @@

                                                                    Submodules
                                                                    -operate_multi(points: ArrayLike) → np.ndarray[source]
                                                                    +operate_multi(points: ArrayLike) → np.ndarray[source]

                                                                    Apply the operation on a list of points.

                                                                    Parameters:
                                                                    @@ -6678,7 +6678,7 @@

                                                                    Submodules
                                                                    -static reflection(normal: ArrayLike, origin: ArrayLike = (0, 0, 0)) → SymmOp[source]
                                                                    +static reflection(normal: ArrayLike, origin: ArrayLike = (0, 0, 0)) → SymmOp[source]

                                                                    Get reflection symmetry operation.

                                                                    Parameters:
                                                                    @@ -6697,13 +6697,13 @@

                                                                    Submodules
                                                                    -property rotation_matrix: ndarray[source]
                                                                    +property rotation_matrix: ndarray[source]

                                                                    A 3x3 numpy.array representing the rotation matrix.

                                                                    -static rotoreflection(axis: ArrayLike, angle: float, origin: ArrayLike = (0, 0, 0)) → SymmOp[source]
                                                                    +static rotoreflection(axis: ArrayLike, angle: float, origin: ArrayLike = (0, 0, 0)) → SymmOp[source]

                                                                    Get a roto-reflection symmetry operation.

                                                                    Parameters:
                                                                    @@ -6722,7 +6722,7 @@

                                                                    Submodules
                                                                    -transform_tensor(tensor: ndarray) → ndarray[source]
                                                                    +transform_tensor(tensor: ndarray) → ndarray[source]

                                                                    Apply rotation portion to a tensor. Note that tensor has to be in full form, not the Voigt form.

                                                                    @@ -6737,7 +6737,7 @@

                                                                    Submodules
                                                                    -property translation_vector: ndarray[source]
                                                                    +property translation_vector: ndarray[source]

                                                                    A rank 1 numpy.array of dim 3 representing the translation vector.

                                                                    @@ -6749,7 +6749,7 @@

                                                                    Submodules
                                                                    -class DummySpecie(symbol: str = 'X', oxidation_state: float | None = 0, spin: float | None = None)[source]
                                                                    +class DummySpecie(symbol: str = 'X', oxidation_state: float | None = 0, spin: float | None = None)[source]

                                                                    Bases: DummySpecies

                                                                    This maps the historical grammatically inaccurate DummySpecie to DummySpecies to maintain backwards compatibility.

                                                                    @@ -6772,14 +6772,14 @@

                                                                    Submodules
                                                                    -class DummySpecies(symbol: str = 'X', oxidation_state: float | None = 0, spin: float | None = None)[source]
                                                                    +class DummySpecies(symbol: str = 'X', oxidation_state: float | None = 0, spin: float | None = None)[source]

                                                                    Bases: Species

                                                                    A special specie for representing non-traditional elements or species. For example, representation of vacancies (charged or otherwise), or special sites, etc.

                                                                    -oxi_state[source]
                                                                    +oxi_state[source]

                                                                    Oxidation state associated with Species.

                                                                    Type:
                                                                    @@ -6790,7 +6790,7 @@

                                                                    Submodules
                                                                    -Z[source]
                                                                    +Z[source]

                                                                    DummySpecies is always assigned an atomic number equal to the hash number of the symbol. Obviously, it makes no sense whatsoever to use the atomic number of a Dummy specie for anything scientific. The purpose @@ -6805,7 +6805,7 @@

                                                                    Submodules
                                                                    -A[source]
                                                                    +A[source]

                                                                    Just as for Z, to get a DummySpecies to behave like an Element, it needs atomic mass number A (arbitrarily set to twice Z).

                                                                    @@ -6817,7 +6817,7 @@

                                                                    Submodules
                                                                    -X[source]
                                                                    +X[source]

                                                                    DummySpecies is always assigned a Pauling electronegativity of 0.

                                                                    Type:
                                                                    @@ -6843,7 +6843,7 @@

                                                                    Submodules
                                                                    -property A: int | None[source]
                                                                    +property A: int | None[source]

                                                                    Atomic mass number of a DummySpecies.

                                                                    To behave like an ElementBase object (from which Species inherits), DummySpecies needs an atomic mass number. Consistent with the @@ -6852,14 +6852,14 @@

                                                                    Submodules
                                                                    -property X: float[source]
                                                                    +property X: float[source]

                                                                    DummySpecies is always assigned a Pauling electronegativity of 0. The effect of this is that DummySpecies are always sorted in front of actual Species.

                                                                    -property Z: int[source]
                                                                    +property Z: int[source]

                                                                    Proton number of DummySpecies.

                                                                    DummySpecies is always assigned an atomic number equal to the hash of the symbol. This is necessary for the DummySpecies object to behave like @@ -6868,13 +6868,13 @@

                                                                    Submodules
                                                                    -as_dict() → dict[str, Any][source]
                                                                    +as_dict() → dict[str, Any][source]

                                                                    MSONable dict representation.

                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                                    Parameters:

                                                                    dct (dict) – Dict representation.

                                                                    @@ -6887,7 +6887,7 @@

                                                                    Submodules
                                                                    -classmethod from_str(species_string: str) → Self[source]
                                                                    +classmethod from_str(species_string: str) → Self[source]

                                                                    Get a Dummy from a string representation.

                                                                    Parameters:
                                                                    @@ -6905,13 +6905,13 @@

                                                                    Submodules
                                                                    -property oxi_state: float | None[source]
                                                                    +property oxi_state: float | None[source]

                                                                    Oxidation state associated with DummySpecies.

                                                                    -property symbol: str[source]
                                                                    +property symbol: str[source]

                                                                    Symbol for DummySpecies.

                                                                    @@ -6919,7 +6919,7 @@

                                                                    Submodules
                                                                    -class Element(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                    +class Element(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                    Bases: ElementBase

                                                                    Enum representing an element in the periodic table.

                                                                    Basic immutable element object with all relevant properties.

                                                                    @@ -6934,7 +6934,7 @@

                                                                    Submodules
                                                                    -Z[source]
                                                                    +Z[source]

                                                                    Atomic number.

                                                                    Type:
                                                                    @@ -6945,7 +6945,7 @@

                                                                    Submodules
                                                                    -symbol[source]
                                                                    +symbol[source]

                                                                    Element symbol.

                                                                    Type:
                                                                    @@ -6956,7 +6956,7 @@

                                                                    Submodules
                                                                    -long_name[source]
                                                                    +long_name[source]

                                                                    Long name for element. e.g. “Hydrogen”.

                                                                    Type:
                                                                    @@ -6967,7 +6967,7 @@

                                                                    Submodules
                                                                    -A[source]
                                                                    +A[source]

                                                                    Atomic mass number (number of protons plus neutrons).

                                                                    Type:
                                                                    @@ -6978,7 +6978,7 @@

                                                                    Submodules
                                                                    -atomic_radius_calculated[source]
                                                                    +atomic_radius_calculated[source]

                                                                    Calculated atomic radius for the element. This is the empirical value. Data is obtained from http://wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page).

                                                                    @@ -6990,7 +6990,7 @@

                                                                    Submodules
                                                                    -van_der_waals_radius[source]
                                                                    +van_der_waals_radius[source]

                                                                    Van der Waals radius for the element. This is the empirical value determined from critical reviews of X-ray diffraction, gas kinetic collision cross-section, and other experimental data by Bondi and later workers. The uncertainty in these values is on the order of 0.1 Å. @@ -7005,7 +7005,7 @@

                                                                    Submodules
                                                                    -mendeleev_no[source]
                                                                    +mendeleev_no[source]

                                                                    Mendeleev number from definition given by Pettifor, D. G. (1984). A chemical scale for crystal-structure maps. Solid State Communications, 51 (1), 31-34.

                                                                    @@ -7017,7 +7017,7 @@

                                                                    Submodules
                                                                    -electrical_resistivity[source]
                                                                    +electrical_resistivity[source]

                                                                    Electrical resistivity.

                                                                    Type:
                                                                    @@ -7028,7 +7028,7 @@

                                                                    Submodules
                                                                    -velocity_of_sound[source]
                                                                    +velocity_of_sound[source]

                                                                    Velocity of sound.

                                                                    Type:
                                                                    @@ -7039,7 +7039,7 @@

                                                                    Submodules
                                                                    -reflectivity[source]
                                                                    +reflectivity[source]

                                                                    Reflectivity.

                                                                    Type:
                                                                    @@ -7050,7 +7050,7 @@

                                                                    Submodules
                                                                    -refractive_index[source]
                                                                    +refractive_index[source]

                                                                    Refractive index.

                                                                    Type:
                                                                    @@ -7061,7 +7061,7 @@

                                                                    Submodules
                                                                    -poissons_ratio[source]
                                                                    +poissons_ratio[source]

                                                                    Poisson’s ratio.

                                                                    Type:
                                                                    @@ -7072,7 +7072,7 @@

                                                                    Submodules
                                                                    -molar_volume[source]
                                                                    +molar_volume[source]

                                                                    Molar volume.

                                                                    Type:
                                                                    @@ -7083,7 +7083,7 @@

                                                                    Submodules
                                                                    -electronic_structure[source]
                                                                    +electronic_structure[source]

                                                                    Electronic structure. e.g. The electronic structure for Fe is represented as [Ar].3d6.4s2.

                                                                    @@ -7095,7 +7095,7 @@

                                                                    Submodules
                                                                    -atomic_orbitals[source]
                                                                    +atomic_orbitals[source]

                                                                    Atomic Orbitals. Energy of the atomic orbitals as a dict. e.g. The orbitals energies in Hartree are represented as {‘1s’: -1.0, ‘2s’: -0.1}. Data is obtained from https://www.nist.gov/pml/data/atomic-reference-data-electronic-structure-calculations. @@ -7109,7 +7109,7 @@

                                                                    Submodules
                                                                    -atomic_orbitals_eV[source]
                                                                    +atomic_orbitals_eV[source]

                                                                    Atomic Orbitals. Same as atomic_orbitals but energies are in eV.

                                                                    Type:
                                                                    @@ -7120,7 +7120,7 @@

                                                                    Submodules
                                                                    -thermal_conductivity[source]
                                                                    +thermal_conductivity[source]

                                                                    Thermal conductivity.

                                                                    Type:
                                                                    @@ -7131,7 +7131,7 @@

                                                                    Submodules
                                                                    -boiling_point[source]
                                                                    +boiling_point[source]

                                                                    Boiling point.

                                                                    Type:
                                                                    @@ -7142,7 +7142,7 @@

                                                                    Submodules
                                                                    -melting_point[source]
                                                                    +melting_point[source]

                                                                    Melting point.

                                                                    Type:
                                                                    @@ -7153,7 +7153,7 @@

                                                                    Submodules
                                                                    -critical_temperature[source]
                                                                    +critical_temperature[source]

                                                                    Critical temperature.

                                                                    Type:
                                                                    @@ -7164,7 +7164,7 @@

                                                                    Submodules
                                                                    -superconduction_temperature[source]
                                                                    +superconduction_temperature[source]

                                                                    Superconduction temperature.

                                                                    Type:
                                                                    @@ -7175,7 +7175,7 @@

                                                                    Submodules
                                                                    -liquid_range[source]
                                                                    +liquid_range[source]

                                                                    Liquid range.

                                                                    Type:
                                                                    @@ -7186,7 +7186,7 @@

                                                                    Submodules
                                                                    -bulk_modulus[source]
                                                                    +bulk_modulus[source]

                                                                    Bulk modulus.

                                                                    Type:
                                                                    @@ -7197,7 +7197,7 @@

                                                                    Submodules
                                                                    -youngs_modulus[source]
                                                                    +youngs_modulus[source]

                                                                    Young’s modulus.

                                                                    Type:
                                                                    @@ -7208,7 +7208,7 @@

                                                                    Submodules
                                                                    -brinell_hardness[source]
                                                                    +brinell_hardness[source]

                                                                    Brinell hardness.

                                                                    Type:
                                                                    @@ -7219,7 +7219,7 @@

                                                                    Submodules
                                                                    -rigidity_modulus[source]
                                                                    +rigidity_modulus[source]

                                                                    Rigidity modulus.

                                                                    Type:
                                                                    @@ -7230,7 +7230,7 @@

                                                                    Submodules
                                                                    -mineral_hardness[source]
                                                                    +mineral_hardness[source]

                                                                    Mineral hardness.

                                                                    Type:
                                                                    @@ -7241,7 +7241,7 @@

                                                                    Submodules
                                                                    -vickers_hardness[source]
                                                                    +vickers_hardness[source]

                                                                    Vicker’s hardness.

                                                                    Type:
                                                                    @@ -7252,7 +7252,7 @@

                                                                    Submodules
                                                                    -density_of_solid[source]
                                                                    +density_of_solid[source]

                                                                    Density of solid phase.

                                                                    Type:
                                                                    @@ -7263,7 +7263,7 @@

                                                                    Submodules
                                                                    -coefficient_of_linear_thermal_expansion[source]
                                                                    +coefficient_of_linear_thermal_expansion[source]

                                                                    Coefficient of linear thermal expansion.

                                                                    Type:
                                                                    @@ -7274,7 +7274,7 @@

                                                                    Submodules
                                                                    -ground_level[source]
                                                                    +ground_level[source]

                                                                    Ground level for element.

                                                                    Type:
                                                                    @@ -7285,7 +7285,7 @@

                                                                    Submodules
                                                                    -ionization_energies[source]
                                                                    +ionization_energies[source]

                                                                    List of ionization energies. First value is the first ionization energy, second is the second ionization energy, etc. Note that this is zero-based indexing! So Element.ionization_energies[0] refer to the 1st ionization energy. Values are from the NIST Atomic @@ -7299,609 +7299,609 @@

                                                                    Submodules
                                                                    -Ac = 'Ac'[source]
                                                                    +Ac = 'Ac'[source]

                                                                    -Ag = 'Ag'[source]
                                                                    +Ag = 'Ag'[source]
                                                                    -Al = 'Al'[source]
                                                                    +Al = 'Al'[source]
                                                                    -Am = 'Am'[source]
                                                                    +Am = 'Am'[source]
                                                                    -Ar = 'Ar'[source]
                                                                    +Ar = 'Ar'[source]
                                                                    -As = 'As'[source]
                                                                    +As = 'As'[source]
                                                                    -At = 'At'[source]
                                                                    +At = 'At'[source]
                                                                    -Au = 'Au'[source]
                                                                    +Au = 'Au'[source]
                                                                    -B = 'B'[source]
                                                                    +B = 'B'[source]
                                                                    -Ba = 'Ba'[source]
                                                                    +Ba = 'Ba'[source]
                                                                    -Be = 'Be'[source]
                                                                    +Be = 'Be'[source]
                                                                    -Bh = 'Bh'[source]
                                                                    +Bh = 'Bh'[source]
                                                                    -Bi = 'Bi'[source]
                                                                    +Bi = 'Bi'[source]
                                                                    -Bk = 'Bk'[source]
                                                                    +Bk = 'Bk'[source]
                                                                    -Br = 'Br'[source]
                                                                    +Br = 'Br'[source]
                                                                    -C = 'C'[source]
                                                                    +C = 'C'[source]
                                                                    -Ca = 'Ca'[source]
                                                                    +Ca = 'Ca'[source]
                                                                    -Cd = 'Cd'[source]
                                                                    +Cd = 'Cd'[source]
                                                                    -Ce = 'Ce'[source]
                                                                    +Ce = 'Ce'[source]
                                                                    -Cf = 'Cf'[source]
                                                                    +Cf = 'Cf'[source]
                                                                    -Cl = 'Cl'[source]
                                                                    +Cl = 'Cl'[source]
                                                                    -Cm = 'Cm'[source]
                                                                    +Cm = 'Cm'[source]
                                                                    -Cn = 'Cn'[source]
                                                                    +Cn = 'Cn'[source]
                                                                    -Co = 'Co'[source]
                                                                    +Co = 'Co'[source]
                                                                    -Cr = 'Cr'[source]
                                                                    +Cr = 'Cr'[source]
                                                                    -Cs = 'Cs'[source]
                                                                    +Cs = 'Cs'[source]
                                                                    -Cu = 'Cu'[source]
                                                                    +Cu = 'Cu'[source]
                                                                    -D = 'D'[source]
                                                                    +D = 'D'[source]
                                                                    -Db = 'Db'[source]
                                                                    +Db = 'Db'[source]
                                                                    -Ds = 'Ds'[source]
                                                                    +Ds = 'Ds'[source]
                                                                    -Dy = 'Dy'[source]
                                                                    +Dy = 'Dy'[source]
                                                                    -Er = 'Er'[source]
                                                                    +Er = 'Er'[source]
                                                                    -Es = 'Es'[source]
                                                                    +Es = 'Es'[source]
                                                                    -Eu = 'Eu'[source]
                                                                    +Eu = 'Eu'[source]
                                                                    -F = 'F'[source]
                                                                    +F = 'F'[source]
                                                                    -Fe = 'Fe'[source]
                                                                    +Fe = 'Fe'[source]
                                                                    -Fl = 'Fl'[source]
                                                                    +Fl = 'Fl'[source]
                                                                    -Fm = 'Fm'[source]
                                                                    +Fm = 'Fm'[source]
                                                                    -Fr = 'Fr'[source]
                                                                    +Fr = 'Fr'[source]
                                                                    -Ga = 'Ga'[source]
                                                                    +Ga = 'Ga'[source]
                                                                    -Gd = 'Gd'[source]
                                                                    +Gd = 'Gd'[source]
                                                                    -Ge = 'Ge'[source]
                                                                    +Ge = 'Ge'[source]
                                                                    -H = 'H'[source]
                                                                    +H = 'H'[source]
                                                                    -He = 'He'[source]
                                                                    +He = 'He'[source]
                                                                    -Hf = 'Hf'[source]
                                                                    +Hf = 'Hf'[source]
                                                                    -Hg = 'Hg'[source]
                                                                    +Hg = 'Hg'[source]
                                                                    -Ho = 'Ho'[source]
                                                                    +Ho = 'Ho'[source]
                                                                    -Hs = 'Hs'[source]
                                                                    +Hs = 'Hs'[source]
                                                                    -I = 'I'[source]
                                                                    +I = 'I'[source]
                                                                    -In = 'In'[source]
                                                                    +In = 'In'[source]
                                                                    -Ir = 'Ir'[source]
                                                                    +Ir = 'Ir'[source]
                                                                    -K = 'K'[source]
                                                                    +K = 'K'[source]
                                                                    -Kr = 'Kr'[source]
                                                                    +Kr = 'Kr'[source]
                                                                    -La = 'La'[source]
                                                                    +La = 'La'[source]
                                                                    -Li = 'Li'[source]
                                                                    +Li = 'Li'[source]
                                                                    -Lr = 'Lr'[source]
                                                                    +Lr = 'Lr'[source]
                                                                    -Lu = 'Lu'[source]
                                                                    +Lu = 'Lu'[source]
                                                                    -Lv = 'Lv'[source]
                                                                    +Lv = 'Lv'[source]
                                                                    -Mc = 'Mc'[source]
                                                                    +Mc = 'Mc'[source]
                                                                    -Md = 'Md'[source]
                                                                    +Md = 'Md'[source]
                                                                    -Mg = 'Mg'[source]
                                                                    +Mg = 'Mg'[source]
                                                                    -Mn = 'Mn'[source]
                                                                    +Mn = 'Mn'[source]
                                                                    -Mo = 'Mo'[source]
                                                                    +Mo = 'Mo'[source]
                                                                    -Mt = 'Mt'[source]
                                                                    +Mt = 'Mt'[source]
                                                                    -N = 'N'[source]
                                                                    +N = 'N'[source]
                                                                    -Na = 'Na'[source]
                                                                    +Na = 'Na'[source]
                                                                    -Nb = 'Nb'[source]
                                                                    +Nb = 'Nb'[source]
                                                                    -Nd = 'Nd'[source]
                                                                    +Nd = 'Nd'[source]
                                                                    -Ne = 'Ne'[source]
                                                                    +Ne = 'Ne'[source]
                                                                    -Nh = 'Nh'[source]
                                                                    +Nh = 'Nh'[source]
                                                                    -Ni = 'Ni'[source]
                                                                    +Ni = 'Ni'[source]
                                                                    -No = 'No'[source]
                                                                    +No = 'No'[source]
                                                                    -Np = 'Np'[source]
                                                                    +Np = 'Np'[source]
                                                                    -O = 'O'[source]
                                                                    +O = 'O'[source]
                                                                    -Og = 'Og'[source]
                                                                    +Og = 'Og'[source]
                                                                    -Os = 'Os'[source]
                                                                    +Os = 'Os'[source]
                                                                    -P = 'P'[source]
                                                                    +P = 'P'[source]
                                                                    -Pa = 'Pa'[source]
                                                                    +Pa = 'Pa'[source]
                                                                    -Pb = 'Pb'[source]
                                                                    +Pb = 'Pb'[source]
                                                                    -Pd = 'Pd'[source]
                                                                    +Pd = 'Pd'[source]
                                                                    -Pm = 'Pm'[source]
                                                                    +Pm = 'Pm'[source]
                                                                    -Po = 'Po'[source]
                                                                    +Po = 'Po'[source]
                                                                    -Pr = 'Pr'[source]
                                                                    +Pr = 'Pr'[source]
                                                                    -Pt = 'Pt'[source]
                                                                    +Pt = 'Pt'[source]
                                                                    -Pu = 'Pu'[source]
                                                                    +Pu = 'Pu'[source]
                                                                    -Ra = 'Ra'[source]
                                                                    +Ra = 'Ra'[source]
                                                                    -Rb = 'Rb'[source]
                                                                    +Rb = 'Rb'[source]
                                                                    -Re = 'Re'[source]
                                                                    +Re = 'Re'[source]
                                                                    -Rf = 'Rf'[source]
                                                                    +Rf = 'Rf'[source]
                                                                    -Rg = 'Rg'[source]
                                                                    +Rg = 'Rg'[source]
                                                                    -Rh = 'Rh'[source]
                                                                    +Rh = 'Rh'[source]
                                                                    -Rn = 'Rn'[source]
                                                                    +Rn = 'Rn'[source]
                                                                    -Ru = 'Ru'[source]
                                                                    +Ru = 'Ru'[source]
                                                                    -S = 'S'[source]
                                                                    +S = 'S'[source]
                                                                    -Sb = 'Sb'[source]
                                                                    +Sb = 'Sb'[source]
                                                                    -Sc = 'Sc'[source]
                                                                    +Sc = 'Sc'[source]
                                                                    -Se = 'Se'[source]
                                                                    +Se = 'Se'[source]
                                                                    -Sg = 'Sg'[source]
                                                                    +Sg = 'Sg'[source]
                                                                    -Si = 'Si'[source]
                                                                    +Si = 'Si'[source]
                                                                    -Sm = 'Sm'[source]
                                                                    +Sm = 'Sm'[source]
                                                                    -Sn = 'Sn'[source]
                                                                    +Sn = 'Sn'[source]
                                                                    -Sr = 'Sr'[source]
                                                                    +Sr = 'Sr'[source]
                                                                    -T = 'T'[source]
                                                                    +T = 'T'[source]
                                                                    -Ta = 'Ta'[source]
                                                                    +Ta = 'Ta'[source]
                                                                    -Tb = 'Tb'[source]
                                                                    +Tb = 'Tb'[source]
                                                                    -Tc = 'Tc'[source]
                                                                    +Tc = 'Tc'[source]
                                                                    -Te = 'Te'[source]
                                                                    +Te = 'Te'[source]
                                                                    -Th = 'Th'[source]
                                                                    +Th = 'Th'[source]
                                                                    -Ti = 'Ti'[source]
                                                                    +Ti = 'Ti'[source]
                                                                    -Tl = 'Tl'[source]
                                                                    +Tl = 'Tl'[source]
                                                                    -Tm = 'Tm'[source]
                                                                    +Tm = 'Tm'[source]
                                                                    -Ts = 'Ts'[source]
                                                                    +Ts = 'Ts'[source]
                                                                    -U = 'U'[source]
                                                                    +U = 'U'[source]
                                                                    -V = 'V'[source]
                                                                    +V = 'V'[source]
                                                                    -W = 'W'[source]
                                                                    +W = 'W'[source]
                                                                    -Xe = 'Xe'[source]
                                                                    +Xe = 'Xe'[source]
                                                                    -Y = 'Y'[source]
                                                                    +Y = 'Y'[source]
                                                                    -Yb = 'Yb'[source]
                                                                    +Yb = 'Yb'[source]
                                                                    -Zn = 'Zn'[source]
                                                                    +Zn = 'Zn'[source]
                                                                    -Zr = 'Zr'[source]
                                                                    +Zr = 'Zr'[source]

                                                                    -class ElementBase(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                    +class ElementBase(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                    Bases: Enum

                                                                    Element class defined without any enum values so it can be subclassed.

                                                                    This class is needed to get nested (as|from)_dict to work properly. All emmet classes that had @@ -7920,7 +7920,7 @@

                                                                    Submodules
                                                                    -Z[source]
                                                                    +Z[source]

                                                                    Atomic number.

                                                                    Type:
                                                                    @@ -7931,7 +7931,7 @@

                                                                    Submodules
                                                                    -symbol[source]
                                                                    +symbol[source]

                                                                    Element symbol.

                                                                    Type:
                                                                    @@ -7942,7 +7942,7 @@

                                                                    Submodules
                                                                    -long_name[source]
                                                                    +long_name[source]

                                                                    Long name for element. e.g. “Hydrogen”.

                                                                    Type:
                                                                    @@ -7953,7 +7953,7 @@

                                                                    Submodules
                                                                    -A[source]
                                                                    +A[source]

                                                                    Atomic mass number (number of protons plus neutrons).

                                                                    Type:
                                                                    @@ -7964,7 +7964,7 @@

                                                                    Submodules
                                                                    -atomic_radius_calculated[source]
                                                                    +atomic_radius_calculated[source]

                                                                    Calculated atomic radius for the element. This is the empirical value. Data is obtained from http://wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page).

                                                                    @@ -7976,7 +7976,7 @@

                                                                    Submodules
                                                                    -van_der_waals_radius[source]
                                                                    +van_der_waals_radius[source]

                                                                    Van der Waals radius for the element. This is the empirical value determined from critical reviews of X-ray diffraction, gas kinetic collision cross-section, and other experimental data by Bondi and later workers. The uncertainty in these values is on the order of 0.1 Å. @@ -7991,7 +7991,7 @@

                                                                    Submodules
                                                                    -mendeleev_no[source]
                                                                    +mendeleev_no[source]

                                                                    Mendeleev number from definition given by Pettifor, D. G. (1984). A chemical scale for crystal-structure maps. Solid State Communications, 51 (1), 31-34.

                                                                    @@ -8003,7 +8003,7 @@

                                                                    Submodules
                                                                    -electrical_resistivity[source]
                                                                    +electrical_resistivity[source]

                                                                    Electrical resistivity.

                                                                    Type:
                                                                    @@ -8014,7 +8014,7 @@

                                                                    Submodules
                                                                    -velocity_of_sound[source]
                                                                    +velocity_of_sound[source]

                                                                    Velocity of sound.

                                                                    Type:
                                                                    @@ -8025,7 +8025,7 @@

                                                                    Submodules
                                                                    -reflectivity[source]
                                                                    +reflectivity[source]

                                                                    Reflectivity.

                                                                    Type:
                                                                    @@ -8036,7 +8036,7 @@

                                                                    Submodules
                                                                    -refractive_index[source]
                                                                    +refractive_index[source]

                                                                    Refractive index.

                                                                    Type:
                                                                    @@ -8047,7 +8047,7 @@

                                                                    Submodules
                                                                    -poissons_ratio[source]
                                                                    +poissons_ratio[source]

                                                                    Poisson’s ratio.

                                                                    Type:
                                                                    @@ -8058,7 +8058,7 @@

                                                                    Submodules
                                                                    -molar_volume[source]
                                                                    +molar_volume[source]

                                                                    Molar volume.

                                                                    Type:
                                                                    @@ -8069,7 +8069,7 @@

                                                                    Submodules
                                                                    -electronic_structure[source]
                                                                    +electronic_structure[source]

                                                                    Electronic structure. e.g. The electronic structure for Fe is represented as [Ar].3d6.4s2.

                                                                    @@ -8081,7 +8081,7 @@

                                                                    Submodules
                                                                    -atomic_orbitals[source]
                                                                    +atomic_orbitals[source]

                                                                    Atomic Orbitals. Energy of the atomic orbitals as a dict. e.g. The orbitals energies in Hartree are represented as {‘1s’: -1.0, ‘2s’: -0.1}. Data is obtained from https://www.nist.gov/pml/data/atomic-reference-data-electronic-structure-calculations. @@ -8095,7 +8095,7 @@

                                                                    Submodules
                                                                    -atomic_orbitals_eV[source]
                                                                    +atomic_orbitals_eV[source]

                                                                    Atomic Orbitals. Same as atomic_orbitals but energies are in eV.

                                                                    Type:
                                                                    @@ -8106,7 +8106,7 @@

                                                                    Submodules
                                                                    -thermal_conductivity[source]
                                                                    +thermal_conductivity[source]

                                                                    Thermal conductivity.

                                                                    Type:
                                                                    @@ -8117,7 +8117,7 @@

                                                                    Submodules
                                                                    -boiling_point[source]
                                                                    +boiling_point[source]

                                                                    Boiling point.

                                                                    Type:
                                                                    @@ -8128,7 +8128,7 @@

                                                                    Submodules
                                                                    -melting_point[source]
                                                                    +melting_point[source]

                                                                    Melting point.

                                                                    Type:
                                                                    @@ -8139,7 +8139,7 @@

                                                                    Submodules
                                                                    -critical_temperature[source]
                                                                    +critical_temperature[source]

                                                                    Critical temperature.

                                                                    Type:
                                                                    @@ -8150,7 +8150,7 @@

                                                                    Submodules
                                                                    -superconduction_temperature[source]
                                                                    +superconduction_temperature[source]

                                                                    Superconduction temperature.

                                                                    Type:
                                                                    @@ -8161,7 +8161,7 @@

                                                                    Submodules
                                                                    -liquid_range[source]
                                                                    +liquid_range[source]

                                                                    Liquid range.

                                                                    Type:
                                                                    @@ -8172,7 +8172,7 @@

                                                                    Submodules
                                                                    -bulk_modulus[source]
                                                                    +bulk_modulus[source]

                                                                    Bulk modulus.

                                                                    Type:
                                                                    @@ -8183,7 +8183,7 @@

                                                                    Submodules
                                                                    -youngs_modulus[source]
                                                                    +youngs_modulus[source]

                                                                    Young’s modulus.

                                                                    Type:
                                                                    @@ -8194,7 +8194,7 @@

                                                                    Submodules
                                                                    -brinell_hardness[source]
                                                                    +brinell_hardness[source]

                                                                    Brinell hardness.

                                                                    Type:
                                                                    @@ -8205,7 +8205,7 @@

                                                                    Submodules
                                                                    -rigidity_modulus[source]
                                                                    +rigidity_modulus[source]

                                                                    Rigidity modulus.

                                                                    Type:
                                                                    @@ -8216,7 +8216,7 @@

                                                                    Submodules
                                                                    -mineral_hardness[source]
                                                                    +mineral_hardness[source]

                                                                    Mineral hardness.

                                                                    Type:
                                                                    @@ -8227,7 +8227,7 @@

                                                                    Submodules
                                                                    -vickers_hardness[source]
                                                                    +vickers_hardness[source]

                                                                    Vicker’s hardness.

                                                                    Type:
                                                                    @@ -8238,7 +8238,7 @@

                                                                    Submodules
                                                                    -density_of_solid[source]
                                                                    +density_of_solid[source]

                                                                    Density of solid phase.

                                                                    Type:
                                                                    @@ -8249,7 +8249,7 @@

                                                                    Submodules
                                                                    -coefficient_of_linear_thermal_expansion[source]
                                                                    +coefficient_of_linear_thermal_expansion[source]

                                                                    Coefficient of linear thermal expansion.

                                                                    Type:
                                                                    @@ -8260,7 +8260,7 @@

                                                                    Submodules
                                                                    -ground_level[source]
                                                                    +ground_level[source]

                                                                    Ground level for element.

                                                                    Type:
                                                                    @@ -8271,7 +8271,7 @@

                                                                    Submodules
                                                                    -ionization_energies[source]
                                                                    +ionization_energies[source]

                                                                    List of ionization energies. First value is the first ionization energy, second is the second ionization energy, etc. Note that this is zero-based indexing! So Element.ionization_energies[0] refer to the 1st ionization energy. Values are from the NIST Atomic @@ -8285,34 +8285,34 @@

                                                                    Submodules
                                                                    -property X: float[source]
                                                                    +property X: float[source]

                                                                    Pauling electronegativity of element. Note that if an element does not have an Pauling electronegativity, a NaN float is returned.

                                                                    -as_dict() → dict[Literal['element', '@module', '@class'], str][source]
                                                                    +as_dict() → dict[Literal['element', '@module', '@class'], str][source]

                                                                    Serialize to MSONable dict representation e.g. to write to disk as JSON.

                                                                    -property atomic_mass: FloatWithUnit[source]
                                                                    +property atomic_mass: FloatWithUnit[source]

                                                                    Returns: float: The atomic mass of the element in amu.

                                                                    -property atomic_mass_number: FloatWithUnit | None[source]
                                                                    +property atomic_mass_number: FloatWithUnit | None[source]

                                                                    Returns: float: The atomic mass of the element in amu.

                                                                    -property atomic_orbitals_eV: dict[str, float][source]
                                                                    +property atomic_orbitals_eV: dict[str, float][source]

                                                                    The LDA energies in eV for neutral atoms, by orbital.

                                                                    This property contains the same info as self.atomic_orbitals, but uses eV for units, per matsci issue https://matsci.org/t/unit-of-atomic-orbitals-energy/54325 @@ -8322,7 +8322,7 @@

                                                                    Submodules
                                                                    -property atomic_radius: FloatWithUnit | None[source]
                                                                    +property atomic_radius: FloatWithUnit | None[source]

                                                                    Returns: float | None: The atomic radius of the element in Ångstroms. Can be None for some elements like noble gases.

                                                                    @@ -8330,7 +8330,7 @@

                                                                    Submodules
                                                                    -property average_anionic_radius: FloatWithUnit[source]
                                                                    +property average_anionic_radius: FloatWithUnit[source]

                                                                    Average anionic radius for element (with units). The average is taken over all negative oxidation states of the element for which data is present.

                                                                    @@ -8338,7 +8338,7 @@

                                                                    Submodules
                                                                    -property average_cationic_radius: FloatWithUnit[source]
                                                                    +property average_cationic_radius: FloatWithUnit[source]

                                                                    Average cationic radius for element (with units). The average is taken over all positive oxidation states of the element for which data is present.

                                                                    @@ -8346,45 +8346,45 @@

                                                                    Submodules
                                                                    -property average_ionic_radius: FloatWithUnit[source]
                                                                    +property average_ionic_radius: FloatWithUnit[source]

                                                                    Average ionic radius for element (with units). The average is taken over all oxidation states of the element for which data is present.

                                                                    -property block: str[source]
                                                                    +property block: str[source]

                                                                    The block character “s, p, d, f”.

                                                                    -property common_oxidation_states: tuple[int, ...][source]
                                                                    +property common_oxidation_states: tuple[int, ...][source]

                                                                    Tuple of common oxidation states.

                                                                    -property data: dict[str, Any][source]
                                                                    +property data: dict[str, Any][source]

                                                                    Dict of data for element.

                                                                    -property electron_affinity: float[source]
                                                                    +property electron_affinity: float[source]

                                                                    The amount of energy released when an electron is attached to a neutral atom.

                                                                    -property electronic_structure: str[source]
                                                                    +property electronic_structure: str[source]

                                                                    Electronic structure as string, with only valence electrons. e.g. The electronic structure for Fe is represented as ‘[Ar].3d6.4s2’.

                                                                    -static from_Z(Z: int, A: int | None = None) → Element[source]
                                                                    +static from_Z(Z: int, A: int | None = None) → Element[source]

                                                                    Get an element from an atomic number.

                                                                    Parameters:
                                                                    @@ -8401,13 +8401,13 @@

                                                                    Submodules
                                                                    -static from_dict(dct: dict) → Element[source]
                                                                    +static from_dict(dct: dict) → Element[source]

                                                                    Deserialize from MSONable dict representation.

                                                                    -static from_name(name: str) → Element[source]
                                                                    +static from_name(name: str) → Element[source]

                                                                    Get an element from its long name.

                                                                    Parameters:
                                                                    @@ -8421,7 +8421,7 @@

                                                                    Submodules
                                                                    -static from_row_and_group(row: int, group: int) → Element[source]
                                                                    +static from_row_and_group(row: int, group: int) → Element[source]

                                                                    Get an element from a row and group number.

                                                                    Important Note: For lanthanoids and actinoids, the row number must be 8 and 9, respectively, and the group number must be @@ -8448,7 +8448,7 @@

                                                                    Submodules
                                                                    -property full_electronic_structure: list[tuple[int, str, int]][source]
                                                                    +property full_electronic_structure: list[tuple[int, str, int]][source]

                                                                    Full electronic structure as tuple. e.g. The electronic structure for Fe is represented as: [(1, “s”, 2), (2, “s”, 2), (2, “p”, 6), (3, “s”, 2), (3, “p”, 6), @@ -8457,131 +8457,131 @@

                                                                    Submodules
                                                                    -property ground_state_term_symbol: str[source]
                                                                    +property ground_state_term_symbol: str[source]

                                                                    Ground state term symbol. Selected based on Hund’s Rule.

                                                                    -property group: int[source]
                                                                    +property group: int[source]

                                                                    The periodic table group of the element. Note: For lanthanoids and actinoids, the group is always 3.

                                                                    -property icsd_oxidation_states: tuple[int, ...][source]
                                                                    +property icsd_oxidation_states: tuple[int, ...][source]

                                                                    Tuple of all oxidation states with at least 10 instances in ICSD database AND at least 1% of entries for that element.

                                                                    -property ionic_radii: dict[int, FloatWithUnit][source]
                                                                    +property ionic_radii: dict[int, FloatWithUnit][source]

                                                                    All ionic radii of the element as a dict of {oxidation state: ionic radii}. Radii are given in angstrom.

                                                                    -property ionization_energy: float | None[source]
                                                                    +property ionization_energy: float | None[source]

                                                                    First ionization energy of element.

                                                                    -property is_actinoid: bool[source]
                                                                    +property is_actinoid: bool[source]

                                                                    True if element is a actinoid.

                                                                    -property is_alkali: bool[source]
                                                                    +property is_alkali: bool[source]

                                                                    True if element is an alkali metal.

                                                                    -property is_alkaline: bool[source]
                                                                    +property is_alkaline: bool[source]

                                                                    True if element is an alkaline earth metal (group II).

                                                                    -property is_chalcogen: bool[source]
                                                                    +property is_chalcogen: bool[source]

                                                                    True if element is a chalcogen.

                                                                    -property is_halogen: bool[source]
                                                                    +property is_halogen: bool[source]

                                                                    True if element is a halogen.

                                                                    -property is_lanthanoid: bool[source]
                                                                    +property is_lanthanoid: bool[source]

                                                                    True if element is a lanthanoid.

                                                                    -property is_metal: bool[source]
                                                                    +property is_metal: bool[source]

                                                                    True if is a metal.

                                                                    -property is_metalloid: bool[source]
                                                                    +property is_metalloid: bool[source]

                                                                    True if element is a metalloid.

                                                                    -property is_noble_gas: bool[source]
                                                                    +property is_noble_gas: bool[source]

                                                                    True if element is noble gas.

                                                                    -property is_post_transition_metal: bool[source]
                                                                    +property is_post_transition_metal: bool[source]

                                                                    True if element is a post-transition or poor metal.

                                                                    -property is_quadrupolar: bool[source]
                                                                    +property is_quadrupolar: bool[source]

                                                                    Check if this element can be quadrupolar.

                                                                    -property is_radioactive: bool[source]
                                                                    +property is_radioactive: bool[source]

                                                                    True if element is radioactive.

                                                                    -property is_rare_earth: bool[source]
                                                                    +property is_rare_earth: bool[source]

                                                                    True if element is a rare earth element, including Lanthanides (La) series, Actinides (Ac) series, Scandium (Sc) and Yttrium (Y).

                                                                    -property is_rare_earth_metal[source]
                                                                    +property is_rare_earth_metal[source]
                                                                    -property is_transition_metal: bool[source]
                                                                    +property is_transition_metal: bool[source]

                                                                    True if element is a transition metal.

                                                                    -static is_valid_symbol(symbol: str) → bool[source]
                                                                    +static is_valid_symbol(symbol: str) → bool[source]

                                                                    Check if symbol (e.g., “H”) is a valid element symbol.

                                                                    Parameters:
                                                                    @@ -8598,7 +8598,7 @@

                                                                    Submodules
                                                                    -property iupac_ordering: int[source]
                                                                    +property iupac_ordering: int[source]

                                                                    Ordering according to Table VI of “Nomenclature of Inorganic Chemistry (IUPAC Recommendations 2005)”. This ordering effectively follows the groups and rows of the periodic table, except the Lanthanides, Actinides @@ -8607,38 +8607,38 @@

                                                                    Submodules
                                                                    -property max_oxidation_state: float[source]
                                                                    +property max_oxidation_state: float[source]

                                                                    Maximum oxidation state for element.

                                                                    -property min_oxidation_state: float[source]
                                                                    +property min_oxidation_state: float[source]

                                                                    Minimum oxidation state for element.

                                                                    -property nmr_quadrupole_moment: dict[str, FloatWithUnit][source]
                                                                    +property nmr_quadrupole_moment: dict[str, FloatWithUnit][source]

                                                                    A dictionary the nuclear electric quadrupole moment in units of e*millibarns for various isotopes.

                                                                    -property number: int[source]
                                                                    +property number: int[source]

                                                                    Alternative attribute for atomic number Z.

                                                                    -property oxidation_states: tuple[int, ...][source]
                                                                    +property oxidation_states: tuple[int, ...][source]

                                                                    Tuple of all known oxidation states.

                                                                    -static print_periodic_table(filter_function: Callable | None = None) → None[source]
                                                                    +static print_periodic_table(filter_function: Callable | None = None) → None[source]

                                                                    A pretty ASCII printer for the periodic table, based on some filter_function.

                                                                    @@ -8653,7 +8653,7 @@

                                                                    Submodules
                                                                    -property row: int[source]
                                                                    +property row: int[source]

                                                                    The periodic table row of the element. Note: For lanthanoids and actinoids, the row is always 6 or 7, respectively.

                                                                    @@ -8661,14 +8661,14 @@

                                                                    Submodules
                                                                    -property term_symbols: list[list[str]][source]
                                                                    +property term_symbols: list[list[str]][source]

                                                                    All possible Russell-Saunders term symbol of the Element. eg. L = 1, n_e = 2 (s2) returns [[‘1D2’], [‘3P0’, ‘3P1’, ‘3P2’], [‘1S0’]].

                                                                    -property valence: tuple[int | np.nan, int][source]
                                                                    +property valence: tuple[int | np.nan, int][source]

                                                                    Valence subshell angular moment (L) and number of valence e- (v_e), obtained from full electron config.

                                                                    @@ -8677,104 +8677,104 @@

                                                                    Submodules
                                                                    -class ElementType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                    +class ElementType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                    Bases: Enum

                                                                    Enum for element types.

                                                                    -actinoid = 'actinoid'[source]
                                                                    +actinoid = 'actinoid'[source]
                                                                    -alkali = 'alkali'[source]
                                                                    +alkali = 'alkali'[source]
                                                                    -alkaline = 'alkaline'[source]
                                                                    +alkaline = 'alkaline'[source]
                                                                    -chalcogen = 'chalcogen'[source]
                                                                    +chalcogen = 'chalcogen'[source]
                                                                    -d_block = 'd-block'[source]
                                                                    +d_block = 'd-block'[source]
                                                                    -f_block = 'f-block'[source]
                                                                    +f_block = 'f-block'[source]
                                                                    -halogen = 'halogen'[source]
                                                                    +halogen = 'halogen'[source]
                                                                    -lanthanoid = 'lanthanoid'[source]
                                                                    +lanthanoid = 'lanthanoid'[source]
                                                                    -metal = 'metal'[source]
                                                                    +metal = 'metal'[source]
                                                                    -metalloid = 'metalloid'[source]
                                                                    +metalloid = 'metalloid'[source]
                                                                    -noble_gas = 'noble_gas'[source]
                                                                    +noble_gas = 'noble_gas'[source]
                                                                    -p_block = 'p-block'[source]
                                                                    +p_block = 'p-block'[source]
                                                                    -post_transition_metal = 'post_transition_metal'[source]
                                                                    +post_transition_metal = 'post_transition_metal'[source]
                                                                    -quadrupolar = 'quadrupolar'[source]
                                                                    +quadrupolar = 'quadrupolar'[source]
                                                                    -radioactive = 'radioactive'[source]
                                                                    +radioactive = 'radioactive'[source]
                                                                    -rare_earth_metal = 'rare_earth_metal'[source]
                                                                    +rare_earth_metal = 'rare_earth_metal'[source]
                                                                    -s_block = 's-block'[source]
                                                                    +s_block = 's-block'[source]
                                                                    -transition_metal = 'transition_metal'[source]
                                                                    +transition_metal = 'transition_metal'[source]

                                                                    -class Specie(symbol: SpeciesLike, oxidation_state: float | None = None, spin: float | None = None)[source]
                                                                    +class Specie(symbol: SpeciesLike, oxidation_state: float | None = None, spin: float | None = None)[source]

                                                                    Bases: Species

                                                                    This maps the historical grammatically inaccurate Specie to Species to maintain backwards compatibility.

                                                                    @@ -8796,7 +8796,7 @@

                                                                    Submodules
                                                                    -class Species(symbol: SpeciesLike, oxidation_state: float | None = None, spin: float | None = None)[source]
                                                                    +class Species(symbol: SpeciesLike, oxidation_state: float | None = None, spin: float | None = None)[source]

                                                                    Bases: MSONable, Stringify

                                                                    An extension of Element with optional oxidation state and spin. Properties associated with Species should be “idealized” values, not calculated values. For example, @@ -8819,30 +8819,30 @@

                                                                    Submodules
                                                                    -STRING_MODE = 'SUPERSCRIPT'[source]
                                                                    +STRING_MODE = 'SUPERSCRIPT'[source]

                                                                    -as_dict() → dict[source]
                                                                    +as_dict() → dict[source]

                                                                    JSON-able dictionary representation.

                                                                    -property electronic_structure: list[tuple[int, str, int]][source]
                                                                    +property electronic_structure: list[tuple[int, str, int]][source]

                                                                    Electronic structure as tuple. Not implemented for Species as of now.

                                                                    -property element: Element[source]
                                                                    +property element: Element[source]

                                                                    Underlying element object.

                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]
                                                                    Parameters:

                                                                    dct (dict) – Dict representation.

                                                                    @@ -8855,7 +8855,7 @@

                                                                    Submodules
                                                                    -classmethod from_str(species_string: str) → Self[source]
                                                                    +classmethod from_str(species_string: str) → Self[source]

                                                                    Get a Species from a string representation.

                                                                    Parameters:
                                                                    @@ -8873,13 +8873,13 @@

                                                                    Submodules
                                                                    -property full_electronic_structure: list[tuple[int, str, int]][source]
                                                                    +property full_electronic_structure: list[tuple[int, str, int]][source]

                                                                    Full electronic structure as tuple. Not implemented for Species as of now.

                                                                    -get_crystal_field_spin(coordination: Literal['oct', 'tet'] = 'oct', spin_config: Literal['low', 'high'] = 'high') → float[source]
                                                                    +get_crystal_field_spin(coordination: Literal['oct', 'tet'] = 'oct', spin_config: Literal['low', 'high'] = 'high') → float[source]

                                                                    Calculate the crystal field spin based on coordination and spin configuration. Only works for transition metal species.

                                                                    @@ -8906,7 +8906,7 @@

                                                                    Submodules
                                                                    -get_nmr_quadrupole_moment(isotope: str | None = None) → float[source]
                                                                    +get_nmr_quadrupole_moment(isotope: str | None = None) → float[source]

                                                                    Get the nuclear electric quadrupole moment in units of e * millibarns.

                                                                    Parameters:
                                                                    @@ -8918,7 +8918,7 @@

                                                                    Submodules
                                                                    -get_shannon_radius(cn: str, spin: Literal['', 'Low Spin', 'High Spin'] = '', radius_type: Literal['ionic', 'crystal'] = 'ionic') → float[source]
                                                                    +get_shannon_radius(cn: str, spin: Literal['', 'Low Spin', 'High Spin'] = '', radius_type: Literal['ionic', 'crystal'] = 'ionic') → float[source]

                                                                    Get the local environment specific ionic radius for species.

                                                                    Parameters:
                                                                    @@ -8941,31 +8941,31 @@

                                                                    Submodules
                                                                    -property ionic_radius: float | None[source]
                                                                    +property ionic_radius: float | None[source]

                                                                    Ionic radius of specie. Returns None if data is not present.

                                                                    -property oxi_state: float | None[source]
                                                                    +property oxi_state: float | None[source]

                                                                    Oxidation state of Species.

                                                                    -property spin: float | None[source]
                                                                    +property spin: float | None[source]

                                                                    Spin of Species.

                                                                    -to_pretty_string() → str[source]
                                                                    +to_pretty_string() → str[source]

                                                                    String without properties.

                                                                    -property valence: tuple[int | np.nan, int][source]
                                                                    +property valence: tuple[int | np.nan, int][source]

                                                                    Valence subshell angular moment (L) and number of valence e- (v_e), obtained from full electron config. Not implemented for Species as of now.

                                                                    @@ -8974,7 +8974,7 @@

                                                                    Submodules
                                                                    -get_el_sp(obj: int | SpeciesLike) → Element | Species | DummySpecies[source]
                                                                    +get_el_sp(obj: int | SpeciesLike) → Element | Species | DummySpecies[source]

                                                                    Utility method to get an Element, Species or DummySpecies from any input.

                                                                    If obj is in itself an element or a specie, it is returned automatically. If obj is an int or a string representing an integer, the Element with the @@ -9010,7 +9010,7 @@

                                                                    Submodules
                                                                    -class PeriodicSite(species: SpeciesLike | CompositionLike, coords: ArrayLike, lattice: Lattice, to_unit_cell: bool = False, coords_are_cartesian: bool = False, properties: dict | None = None, label: str | None = None, skip_checks: bool = False)[source]
                                                                    +class PeriodicSite(species: SpeciesLike | CompositionLike, coords: ArrayLike, lattice: Lattice, to_unit_cell: bool = False, coords_are_cartesian: bool = False, properties: dict | None = None, label: str | None = None, skip_checks: bool = False)[source]

                                                                    Bases: Site, MSONable

                                                                    Extension of generic Site object to periodic systems. PeriodicSite includes a lattice system.

                                                                    @@ -9050,13 +9050,13 @@

                                                                    Submodules
                                                                    -property a: float[source]
                                                                    +property a: float[source]

                                                                    Fractional a coordinate.

                                                                    -as_dict(verbosity: int = 0) → dict[source]
                                                                    +as_dict(verbosity: int = 0) → dict[source]

                                                                    JSON-serializable dict representation of PeriodicSite.

                                                                    Parameters:
                                                                    @@ -9068,25 +9068,25 @@

                                                                    Submodules
                                                                    -property b: float[source]
                                                                    +property b: float[source]

                                                                    Fractional b coordinate.

                                                                    -property c: float[source]
                                                                    +property c: float[source]

                                                                    Fractional c coordinate.

                                                                    -property coords: ndarray[source]
                                                                    +property coords: ndarray[source]

                                                                    Cartesian coordinates.

                                                                    -distance(other: Self, jimage: ArrayLike | None = None) → float[source]
                                                                    +distance(other: Self, jimage: ArrayLike | None = None) → float[source]

                                                                    Get distance between two sites assuming periodic boundary conditions.

                                                                    Parameters:
                                                                    @@ -9109,7 +9109,7 @@

                                                                    Submodules
                                                                    -distance_and_image(other: Self, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]
                                                                    +distance_and_image(other: Self, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]

                                                                    Get distance and instance between two sites assuming periodic boundary conditions. If the index jimage of two sites atom j is not specified it selects the j image nearest to the i atom and returns the distance and @@ -9141,7 +9141,7 @@

                                                                    Submodules
                                                                    -distance_and_image_from_frac_coords(fcoords: ArrayLike, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]
                                                                    +distance_and_image_from_frac_coords(fcoords: ArrayLike, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]

                                                                    Get distance between site and a fractional coordinate assuming periodic boundary conditions. If the index jimage of two sites atom j is not specified it selects the j image nearest to the i atom and @@ -9174,13 +9174,13 @@

                                                                    Submodules
                                                                    -property frac_coords: ndarray[source]
                                                                    +property frac_coords: ndarray[source]

                                                                    Fractional coordinates.

                                                                    -classmethod from_dict(dct: dict, lattice: Lattice | None = None) → Self[source]
                                                                    +classmethod from_dict(dct: dict, lattice: Lattice | None = None) → Self[source]

                                                                    Create PeriodicSite from dict representation.

                                                                    Parameters:
                                                                    @@ -9199,7 +9199,7 @@

                                                                    Submodules
                                                                    -is_periodic_image(other: Self, tolerance: float = 1e-08, check_lattice: bool = True) → bool[source]
                                                                    +is_periodic_image(other: Self, tolerance: float = 1e-08, check_lattice: bool = True) → bool[source]

                                                                    Check if sites are periodic images of each other.

                                                                    Parameters:
                                                                    @@ -9221,31 +9221,31 @@

                                                                    Submodules
                                                                    -property lattice: Lattice[source]
                                                                    +property lattice: Lattice[source]

                                                                    Lattice associated with PeriodicSite.

                                                                    -to_unit_cell(in_place: bool = False) → Self | None[source]
                                                                    +to_unit_cell(in_place: bool = False) → Self | None[source]

                                                                    Move frac coords to within the unit cell.

                                                                    -property x: float[source]
                                                                    +property x: float[source]

                                                                    Cartesian x coordinate.

                                                                    -property y: float[source]
                                                                    +property y: float[source]

                                                                    Cartesian y coordinate.

                                                                    -property z: float[source]
                                                                    +property z: float[source]

                                                                    Cartesian z coordinate.

                                                                    @@ -9253,7 +9253,7 @@

                                                                    Submodules
                                                                    -class Site(species: SpeciesLike | CompositionLike, coords: ArrayLike, properties: dict | None = None, label: str | None = None, skip_checks: bool = False)[source]
                                                                    +class Site(species: SpeciesLike | CompositionLike, coords: ArrayLike, properties: dict | None = None, label: str | None = None, skip_checks: bool = False)[source]

                                                                    Bases: Hashable, MSONable

                                                                    A generalized non-periodic site. This is essentially a composition at a point in space, with some optional properties associated with it. A @@ -9289,13 +9289,13 @@

                                                                    Submodules
                                                                    -as_dict() → dict[source]
                                                                    +as_dict() → dict[source]

                                                                    JSON-serializable dict representation for Site.

                                                                    -distance(other: Site) → float[source]
                                                                    +distance(other: Site) → float[source]

                                                                    Get distance between two sites.

                                                                    Parameters:
                                                                    @@ -9312,7 +9312,7 @@

                                                                    Submodules
                                                                    -distance_from_point(pt: Vector3D) → float[source]
                                                                    +distance_from_point(pt: Vector3D) → float[source]

                                                                    Get distance between the site and a point in space.

                                                                    Parameters:
                                                                    @@ -9329,31 +9329,31 @@

                                                                    Submodules
                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]

                                                                    Create Site from dict representation.

                                                                    -property is_ordered: bool[source]
                                                                    +property is_ordered: bool[source]

                                                                    True if site is an ordered site, i.e., with a single species with occupancy 1.

                                                                    -property label: str[source]
                                                                    +property label: str[source]

                                                                    Site label.

                                                                    -position_atol = 1e-05[source]
                                                                    +position_atol = 1e-05[source]
                                                                    -property specie: Element | Species | DummySpecies[source]
                                                                    +property specie: Element | Species | DummySpecies[source]

                                                                    The Species/Element at the site. Only works for ordered sites. Otherwise an AttributeError is raised. Use this property sparingly. Robust design should make use of the property species instead. Note that the @@ -9368,31 +9368,31 @@

                                                                    Submodules
                                                                    -property species: Composition[source]
                                                                    +property species: Composition[source]

                                                                    The species on the site as a composition, e.g. Fe0.5Mn0.5.

                                                                    -property species_string: str[source]
                                                                    +property species_string: str[source]

                                                                    String representation of species on the site.

                                                                    -property x: float[source]
                                                                    +property x: float[source]

                                                                    Cartesian x coordinate.

                                                                    -property y: float[source]
                                                                    +property y: float[source]

                                                                    Cartesian y coordinate.

                                                                    -property z: float[source]
                                                                    +property z: float[source]

                                                                    Cartesian z coordinate.

                                                                    @@ -9405,7 +9405,7 @@

                                                                    Submodules
                                                                    -class Spectrum(x: NDArray, y: NDArray, *args, **kwargs)[source]
                                                                    +class Spectrum(x: NDArray, y: NDArray, *args, **kwargs)[source]

                                                                    Bases: MSONable

                                                                    Base class for any type of XAS, essentially just x, y values. Examples include XRD patterns, XANES, EXAFS, NMR, DOS, etc.

                                                                    @@ -9430,17 +9430,17 @@

                                                                    Submodules
                                                                    -XLABEL = 'x'[source]
                                                                    +XLABEL = 'x'[source]

                                                                    -YLABEL = 'y'[source]
                                                                    +YLABEL = 'y'[source]
                                                                    -copy() → Self[source]
                                                                    +copy() → Self[source]
                                                                    Returns:

                                                                    Copy of Spectrum object.

                                                                    @@ -9450,7 +9450,7 @@

                                                                    Submodules
                                                                    -get_interpolated_value(x: float) → float | list[float][source]
                                                                    +get_interpolated_value(x: float) → float | list[float][source]

                                                                    Get an interpolated y value for a particular x value.

                                                                    Parameters:
                                                                    @@ -9464,7 +9464,7 @@

                                                                    Submodules
                                                                    -normalize(mode: Literal['max', 'sum'] = 'max', value: float = 1.0) → None[source]
                                                                    +normalize(mode: Literal['max', 'sum'] = 'max', value: float = 1.0) → None[source]

                                                                    Normalize the spectrum with respect to the sum of intensity.

                                                                    Parameters:
                                                                    @@ -9480,7 +9480,7 @@

                                                                    Submodules
                                                                    -smear(sigma: float = 0.0, func: Literal['gaussian', 'lorentzian'] | Callable = 'gaussian') → None[source]
                                                                    +smear(sigma: float = 0.0, func: Literal['gaussian', 'lorentzian'] | Callable = 'gaussian') → None[source]

                                                                    Apply Gaussian/Lorentzian smearing to spectrum y value.

                                                                    Parameters:
                                                                    @@ -9497,7 +9497,7 @@

                                                                    Submodules
                                                                    -lorentzian(x: NDArray, x_0: float = 0, sigma: float = 1.0) → NDArray[source]
                                                                    +lorentzian(x: NDArray, x_0: float = 0, sigma: float = 1.0) → NDArray[source]

                                                                    The Lorentzian smearing function.

                                                                    Parameters:
                                                                    @@ -9521,7 +9521,7 @@

                                                                    Submodules
                                                                    -class IMolecule(species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float = 0.0, spin_multiplicity: int | None = None, validate_proximity: bool = False, site_properties: dict | None = None, labels: Sequence[str | None] | None = None, charge_spin_check: bool = True, properties: dict | None = None)[source]
                                                                    +class IMolecule(species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float = 0.0, spin_multiplicity: int | None = None, validate_proximity: bool = False, site_properties: dict | None = None, labels: Sequence[str | None] | None = None, charge_spin_check: bool = True, properties: dict | None = None)[source]

                                                                    Bases: SiteCollection, MSONable

                                                                    Basic immutable Molecule object without periodicity. Essentially a sequence of sites. IMolecule is made to be immutable so that they can @@ -9563,13 +9563,13 @@

                                                                    Submodules
                                                                    -as_dict() → dict[source]
                                                                    +as_dict() → dict[source]

                                                                    JSON-serializable dict representation of Molecule.

                                                                    -break_bond(ind1: int, ind2: int, tol: float = 0.2) → tuple[Self, Self][source]
                                                                    +break_bond(ind1: int, ind2: int, tol: float = 0.2) → tuple[Self, Self][source]

                                                                    Get two molecules based on breaking the bond between atoms at index ind1 and ind2.

                                                                    @@ -9593,19 +9593,19 @@

                                                                    Submodules
                                                                    -property center_of_mass: NDArray[source]
                                                                    +property center_of_mass: NDArray[source]

                                                                    Center of mass of molecule.

                                                                    -property charge: float[source]
                                                                    +property charge: float[source]

                                                                    Charge of molecule.

                                                                    -copy() → Self[source]
                                                                    +copy() → Self[source]

                                                                    Convenience method to get a copy of the molecule.

                                                                    Returns:
                                                                    @@ -9616,7 +9616,7 @@

                                                                    Submodules
                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]

                                                                    Reconstitute a Molecule object from a dict representation created using as_dict().

                                                                    Parameters:
                                                                    @@ -9630,7 +9630,7 @@

                                                                    Submodules
                                                                    -classmethod from_file(filename: PathLike) → Self | None[source]
                                                                    +classmethod from_file(filename: PathLike) → Self | None[source]

                                                                    Read a molecule from a file. Supported formats include xyz, gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and pymatgen’s JSON-serialized molecules. Using openbabel, @@ -9648,7 +9648,7 @@

                                                                    Submodules
                                                                    -classmethod from_sites(sites: Sequence[Site], charge: float = 0, spin_multiplicity: int | None = None, validate_proximity: bool = False, charge_spin_check: bool = True, properties: dict | None = None) → Self[source]
                                                                    +classmethod from_sites(sites: Sequence[Site], charge: float = 0, spin_multiplicity: int | None = None, validate_proximity: bool = False, charge_spin_check: bool = True, properties: dict | None = None) → Self[source]

                                                                    Convenience constructor to make a Molecule from a list of sites.

                                                                    Parameters:
                                                                    @@ -9677,7 +9677,7 @@

                                                                    Submodules
                                                                    -classmethod from_str(input_string: str, fmt: Literal['xyz', 'gjf', 'g03', 'g09', 'com', 'inp', 'json', 'yaml']) → Self | Molecule[source]
                                                                    +classmethod from_str(input_string: str, fmt: Literal['xyz', 'gjf', 'g03', 'g09', 'com', 'inp', 'json', 'yaml']) → Self | Molecule[source]

                                                                    Reads the molecule from a string.

                                                                    Parameters:
                                                                    @@ -9698,7 +9698,7 @@

                                                                    Submodules
                                                                    -get_boxed_structure(a: float, b: float, c: float, images: ArrayLike = (1, 1, 1), random_rotation: bool = False, min_dist: float = 1.0, cls=None, offset: ArrayLike | None = None, no_cross: bool = False, reorder: bool = True) → IStructure | Structure[source]
                                                                    +get_boxed_structure(a: float, b: float, c: float, images: ArrayLike = (1, 1, 1), random_rotation: bool = False, min_dist: float = 1.0, cls=None, offset: ArrayLike | None = None, no_cross: bool = False, reorder: bool = True) → IStructure | Structure[source]

                                                                    Create a Structure from a Molecule by putting the Molecule in the center of a orthorhombic box. Useful for creating Structure for calculating molecules using periodic codes.

                                                                    @@ -9735,7 +9735,7 @@

                                                                    Submodules
                                                                    -get_centered_molecule() → Self[source]
                                                                    +get_centered_molecule() → Self[source]

                                                                    Get a Molecule centered at the center of mass.

                                                                    Returns:
                                                                    @@ -9746,7 +9746,7 @@

                                                                    Submodules
                                                                    -get_covalent_bonds(tol: float = 0.2) → list[CovalentBond][source]
                                                                    +get_covalent_bonds(tol: float = 0.2) → list[CovalentBond][source]

                                                                    Determine the covalent bonds in a molecule.

                                                                    Parameters:
                                                                    @@ -9761,7 +9761,7 @@

                                                                    Submodules
                                                                    -get_distance(i: int, j: int) → float[source]
                                                                    +get_distance(i: int, j: int) → float[source]

                                                                    Get distance between site i and j.

                                                                    Parameters:
                                                                    @@ -9778,7 +9778,7 @@

                                                                    Submodules
                                                                    -get_neighbors(site: Site, r: float) → list[Neighbor][source]
                                                                    +get_neighbors(site: Site, r: float) → list[Neighbor][source]

                                                                    Get all neighbors to a site within a sphere of radius r. Excludes the site itself.

                                                                    @@ -9796,7 +9796,7 @@

                                                                    Submodules
                                                                    -get_neighbors_in_shell(origin: ArrayLike, r: float, dr: float) → list[Neighbor][source]
                                                                    +get_neighbors_in_shell(origin: ArrayLike, r: float, dr: float) → list[Neighbor][source]

                                                                    Get all sites in a shell centered on origin (coords) between radii r-dr and r+dr.

                                                                    @@ -9815,7 +9815,7 @@

                                                                    Submodules
                                                                    -get_sites_in_sphere(pt: ArrayLike, r: float) → list[Neighbor][source]
                                                                    +get_sites_in_sphere(pt: ArrayLike, r: float) → list[Neighbor][source]

                                                                    Find all sites within a sphere from a point.

                                                                    Parameters:
                                                                    @@ -9832,25 +9832,25 @@

                                                                    Submodules
                                                                    -get_zmatrix() → str[source]
                                                                    +get_zmatrix() → str[source]

                                                                    Get a z-matrix representation of the molecule.

                                                                    -property nelectrons: float[source]
                                                                    +property nelectrons: float[source]

                                                                    Number of electrons in the molecule.

                                                                    -property spin_multiplicity: float[source]
                                                                    +property spin_multiplicity: float[source]

                                                                    Spin multiplicity of molecule.

                                                                    -to(filename: str = '', fmt: str = '') → str | None[source]
                                                                    +to(filename: str = '', fmt: str = '') → str | None[source]

                                                                    Outputs the molecule to a file or string.

                                                                    Parameters:
                                                                    @@ -9882,7 +9882,7 @@

                                                                    Submodules
                                                                    -class IStructure(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float | None = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict | None = None, labels: Sequence[str | None] | None = None, properties: dict | None = None)[source]
                                                                    +class IStructure(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float | None = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict | None = None, labels: Sequence[str | None] | None = None, properties: dict | None = None)[source]

                                                                    Bases: SiteCollection, MSONable

                                                                    Basic immutable Structure object with periodicity. Essentially a sequence of PeriodicSites having a common lattice. IStructure is made to be @@ -9938,13 +9938,13 @@

                                                                    Submodules
                                                                    -CellType[source]
                                                                    +CellType[source]

                                                                    alias of Literal[‘primitive’, ‘conventional’]

                                                                    -as_dataframe() → pd.DataFrame[source]
                                                                    +as_dataframe() → pd.DataFrame[source]

                                                                    Create a Pandas DataFrame of the sites. Structure-level attributes are stored in DataFrame.attrs.

                                                                    Example

                                                                    @@ -9955,7 +9955,7 @@

                                                                    Submodules
                                                                    -as_dict(verbosity: int = 1, fmt: Literal['abivars'] | None = None, **kwargs) → dict[str, Any][source]
                                                                    +as_dict(verbosity: int = 1, fmt: Literal['abivars'] | None = None, **kwargs) → dict[str, Any][source]

                                                                    Dict representation of Structure.

                                                                    Parameters:
                                                                    @@ -9982,13 +9982,13 @@

                                                                    Submodules
                                                                    -property charge: float[source]
                                                                    +property charge: float[source]

                                                                    Overall charge of the structure.

                                                                    -copy(site_properties: dict[str, Any] | None = None, sanitize: bool = False, properties: dict[str, Any] | None = None) → Self[source]
                                                                    +copy(site_properties: dict[str, Any] | None = None, sanitize: bool = False, properties: dict[str, Any] | None = None) → Self[source]

                                                                    Convenience method to get a copy of the structure, with options to add site properties.

                                                                    @@ -10017,26 +10017,26 @@

                                                                    Submodules
                                                                    -property density: float[source]
                                                                    +property density: float[source]

                                                                    The density in units of g/cm^3.

                                                                    -property distance_matrix: ndarray[source]
                                                                    +property distance_matrix: ndarray[source]

                                                                    The distance matrix between all sites in the structure. For periodic structures, this should return the nearest image distance.

                                                                    -property frac_coords[source]
                                                                    +property frac_coords[source]

                                                                    Fractional coordinates as a Nx3 numpy array.

                                                                    -classmethod from_dict(dct: dict[str, Any], fmt: Literal['abivars'] | None = None) → Self[source]
                                                                    +classmethod from_dict(dct: dict[str, Any], fmt: Literal['abivars'] | None = None) → Self[source]

                                                                    Reconstitute a Structure from a dict representation of Structure created using as_dict().

                                                                    @@ -10054,7 +10054,7 @@

                                                                    Submodules
                                                                    -classmethod from_file(filename: PathLike, primitive: bool = False, sort: bool = False, merge_tol: float = 0.0, **kwargs) → Structure | Self[source]
                                                                    +classmethod from_file(filename: PathLike, primitive: bool = False, sort: bool = False, merge_tol: float = 0.0, **kwargs) → Structure | Self[source]

                                                                    Read a structure from a file. For example, anything ending in a “cif” is assumed to be a Crystallographic Information Format file. Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT, @@ -10079,7 +10079,7 @@

                                                                    Submodules
                                                                    -classmethod from_magnetic_spacegroup(msg: str | MagneticSpaceGroup, lattice: list | np.ndarray | Lattice, species: Sequence[str | Element | Species | DummySpecies | Composition], coords: Sequence[Sequence[float]], site_properties: dict[str, Sequence], coords_are_cartesian: bool = False, tol: float = 1e-05, labels: Sequence[str | None] | None = None) → Self[source]
                                                                    +classmethod from_magnetic_spacegroup(msg: str | MagneticSpaceGroup, lattice: list | np.ndarray | Lattice, species: Sequence[str | Element | Species | DummySpecies | Composition], coords: Sequence[Sequence[float]], site_properties: dict[str, Sequence], coords_are_cartesian: bool = False, tol: float = 1e-05, labels: Sequence[str | None] | None = None) → Self[source]

                                                                    Generate a structure using a magnetic spacegroup. Note that only symmetrically distinct species, coords and magmoms should be provided.] All equivalent sites are generated from the spacegroup operations.

                                                                    @@ -10138,7 +10138,7 @@

                                                                    Submodules
                                                                    -classmethod from_sites(sites: list[PeriodicSite], charge: float | None = None, validate_proximity: bool = False, to_unit_cell: bool = False, properties: dict | None = None) → Self[source]
                                                                    +classmethod from_sites(sites: list[PeriodicSite], charge: float | None = None, validate_proximity: bool = False, to_unit_cell: bool = False, properties: dict | None = None) → Self[source]

                                                                    Convenience constructor to make a IStructure from a list of sites.

                                                                    Parameters:
                                                                    @@ -10169,7 +10169,7 @@

                                                                    Submodules
                                                                    -classmethod from_spacegroup(sg: str | int, lattice: list | np.ndarray | Lattice, species: Sequence[str | Element | Species | DummySpecies | Composition], coords: Sequence[Sequence[float]], site_properties: dict[str, Sequence] | None = None, coords_are_cartesian: bool = False, tol: float = 1e-05, labels: Sequence[str | None] | None = None) → Self[source]
                                                                    +classmethod from_spacegroup(sg: str | int, lattice: list | np.ndarray | Lattice, species: Sequence[str | Element | Species | DummySpecies | Composition], coords: Sequence[Sequence[float]], site_properties: dict[str, Sequence] | None = None, coords_are_cartesian: bool = False, tol: float = 1e-05, labels: Sequence[str | None] | None = None) → Self[source]

                                                                    Generate a structure using a spacegroup. Note that only symmetrically distinct species and coords should be provided. All equivalent sites are generated from the spacegroup operations.

                                                                    @@ -10220,7 +10220,7 @@

                                                                    Submodules
                                                                    -classmethod from_str(input_string: str, fmt: FileFormats, primitive: bool = False, sort: bool = False, merge_tol: float = 0.0, **kwargs) → Structure | Self[source]
                                                                    +classmethod from_str(input_string: str, fmt: FileFormats, primitive: bool = False, sort: bool = False, merge_tol: float = 0.0, **kwargs) → Structure | Self[source]

                                                                    Read a structure from a string.

                                                                    Parameters:
                                                                    @@ -10246,7 +10246,7 @@

                                                                    Submodules
                                                                    -get_all_neighbors(r: float, include_index: bool = False, include_image: bool = False, sites: Sequence[PeriodicSite] | None = None, numerical_tol: float = 1e-08) → list[list[PeriodicNeighbor]][source]
                                                                    +get_all_neighbors(r: float, include_index: bool = False, include_image: bool = False, sites: Sequence[PeriodicSite] | None = None, numerical_tol: float = 1e-08) → list[list[PeriodicNeighbor]][source]

                                                                    Get neighbors for each atom in the unit cell, out to a distance r. Use this method if you are planning on looping over all sites in the crystal. If you only want neighbors for a particular site, use the @@ -10295,12 +10295,12 @@

                                                                    Submodules
                                                                    -get_all_neighbors_old(**kwargs)[source]
                                                                    +get_all_neighbors_old(**kwargs)[source]

                                                                    -get_all_neighbors_py(r: float, include_index: bool = False, include_image: bool = False, sites: Sequence[PeriodicSite] | None = None, numerical_tol: float = 1e-08) → list[list[PeriodicNeighbor]][source]
                                                                    +get_all_neighbors_py(r: float, include_index: bool = False, include_image: bool = False, sites: Sequence[PeriodicSite] | None = None, numerical_tol: float = 1e-08) → list[list[PeriodicNeighbor]][source]

                                                                    Get neighbors for each atom in the unit cell, out to a distance r. Use this method if you are planning on looping over all sites in the crystal. If you only want neighbors for a particular site, use the @@ -10345,7 +10345,7 @@

                                                                    Submodules
                                                                    -get_distance(i: int, j: int, jimage=None) → float[source]
                                                                    +get_distance(i: int, j: int, jimage=None) → float[source]

                                                                    Get distance between site i and j assuming periodic boundary conditions. If the index jimage of two sites atom j is not specified it selects the jimage nearest to the i atom and returns the distance and @@ -10369,7 +10369,7 @@

                                                                    Submodules
                                                                    -get_miller_index_from_site_indexes(site_ids: list[int], round_dp: int = 4, verbose: bool = True) → MillerIndex[source]
                                                                    +get_miller_index_from_site_indexes(site_ids: list[int], round_dp: int = 4, verbose: bool = True) → MillerIndex[source]

                                                                    Get the Miller index of a plane from a set of sites indexes.

                                                                    A minimum of 3 sites are required. If more than 3 sites are given the best plane that minimises the distance to all points will be @@ -10397,7 +10397,7 @@

                                                                    Submodules
                                                                    -get_neighbor_list(r: float, sites: Sequence[PeriodicSite] | None = None, numerical_tol: float = 1e-08, exclude_self: bool = True) → tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray][source]
                                                                    +get_neighbor_list(r: float, sites: Sequence[PeriodicSite] | None = None, numerical_tol: float = 1e-08, exclude_self: bool = True) → tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray][source]

                                                                    Get neighbor lists using numpy array representations without constructing Neighbor objects. If the cython extension is installed, this method will be orders of magnitude faster than get_all_neighbors_old and 2-3x faster @@ -10435,7 +10435,7 @@

                                                                    Submodules
                                                                    -get_neighbors(site: PeriodicSite, r: float, include_index: bool = False, include_image: bool = False) → list[PeriodicNeighbor][source]
                                                                    +get_neighbors(site: PeriodicSite, r: float, include_index: bool = False, include_image: bool = False) → list[PeriodicNeighbor][source]

                                                                    Get all neighbors to a site within a sphere of radius r. Excludes the site itself.

                                                                    @@ -10457,7 +10457,7 @@

                                                                    Submodules
                                                                    -get_neighbors_in_shell(origin: ArrayLike, r: float, dr: float, include_index: bool = False, include_image: bool = False) → list[PeriodicNeighbor][source]
                                                                    +get_neighbors_in_shell(origin: ArrayLike, r: float, dr: float, include_index: bool = False, include_image: bool = False) → list[PeriodicNeighbor][source]

                                                                    Get all sites in a shell centered on origin (coords) between radii r-dr and r+dr.

                                                                    @@ -10481,12 +10481,12 @@

                                                                    Submodules
                                                                    -get_neighbors_old(**kwargs)[source]
                                                                    +get_neighbors_old(**kwargs)[source]

                                                                    -get_orderings(mode: Literal['enum', 'sqs'] = 'enum', **kwargs) → list[Structure][source]
                                                                    +get_orderings(mode: Literal['enum', 'sqs'] = 'enum', **kwargs) → list[Structure][source]

                                                                    Get list of orderings for a disordered structure. If structure does not contain disorder, the default structure is returned.

                                                                    @@ -10512,7 +10512,7 @@

                                                                    Submodules
                                                                    -get_primitive_structure(tolerance: float = 0.25, use_site_props: bool = False, constrain_latt: list | dict | None = None) → Self[source]
                                                                    +get_primitive_structure(tolerance: float = 0.25, use_site_props: bool = False, constrain_latt: list | dict | None = None) → Self[source]

                                                                    Find a smaller unit cell than the input. Sometimes it doesn’t find the smallest possible one, so this method is recursively called until it is unable to find a smaller cell.

                                                                    @@ -10541,7 +10541,7 @@

                                                                    Submodules
                                                                    -get_reduced_structure(reduction_algo: Literal['niggli', 'LLL'] = 'niggli') → Self[source]
                                                                    +get_reduced_structure(reduction_algo: Literal['niggli', 'LLL'] = 'niggli') → Self[source]

                                                                    Get a reduced structure.

                                                                    Parameters:
                                                                    @@ -10559,7 +10559,7 @@

                                                                    Submodules
                                                                    -get_sites_in_sphere(pt: ArrayLike, r: float, include_index: bool = False, include_image: bool = False) → list[PeriodicNeighbor][source]
                                                                    +get_sites_in_sphere(pt: ArrayLike, r: float, include_index: bool = False, include_image: bool = False) → list[PeriodicNeighbor][source]

                                                                    Find all sites within a sphere from the point, including a site (if any) sitting on the point itself. This includes sites in other periodic images.

                                                                    Algorithm:

                                                                    @@ -10592,7 +10592,7 @@

                                                                    Submodules
                                                                    -get_sorted_structure(key: Callable | None = None, reverse: bool = False) → Self | Structure[source]
                                                                    +get_sorted_structure(key: Callable | None = None, reverse: bool = False) → Self | Structure[source]

                                                                    Get a sorted copy of the structure. The parameters have the same meaning as in list.sort. By default, sites are sorted by the electronegativity of the species.

                                                                    @@ -10611,7 +10611,7 @@

                                                                    Submodules
                                                                    -get_space_group_info(symprec: float = 0.01, angle_tolerance: float = 5.0) → tuple[str, int][source]
                                                                    +get_space_group_info(symprec: float = 0.01, angle_tolerance: float = 5.0) → tuple[str, int][source]

                                                                    Get the spacegroup of a structure.

                                                                    Parameters:
                                                                    @@ -10637,7 +10637,7 @@

                                                                    Submodules
                                                                    -get_symmetric_neighbor_list(r: float, sg: str | None, unique: bool = False, numerical_tol: float = 1e-08, exclude_self: bool = True) → tuple[ndarray, ...][source]
                                                                    +get_symmetric_neighbor_list(r: float, sg: str | None, unique: bool = False, numerical_tol: float = 1e-08, exclude_self: bool = True) → tuple[ndarray, ...][source]

                                                                    Similar to ‘get_neighbor_list’ with sites=None, but the neighbors are grouped by symmetry. The returned values are a tuple of numpy arrays (center_indices, points_indices, offset_vectors, distances, symmetry_indices). @@ -10686,7 +10686,7 @@

                                                                    Submodules
                                                                    -interpolate(end_structure: Self | Structure, nimages: int | Iterable = 10, interpolate_lattices: bool = False, pbc: bool = True, autosort_tol: float = 0, end_amplitude: float = 1) → list[Self][source]
                                                                    +interpolate(end_structure: Self | Structure, nimages: int | Iterable = 10, interpolate_lattices: bool = False, pbc: bool = True, autosort_tol: float = 0, end_amplitude: float = 1) → list[Self][source]

                                                                    Interpolate between this structure and end_structure. Useful for construction of NEB inputs. To obtain useful results, the cell setting and order of sites must consistent across the start and end structures.

                                                                    @@ -10727,19 +10727,19 @@

                                                                    Submodules
                                                                    -property is_3d_periodic: bool[source]
                                                                    +property is_3d_periodic: bool[source]

                                                                    Whether the Lattice is periodic in all directions.

                                                                    -property lattice: Lattice[source]
                                                                    +property lattice: Lattice[source]

                                                                    Lattice of the structure.

                                                                    -matches(other: Self | Structure, anonymous: bool = False, **kwargs) → bool[source]
                                                                    +matches(other: Self | Structure, anonymous: bool = False, **kwargs) → bool[source]

                                                                    Check whether this structure is similar to another structure. Basically a convenience method to call structure matching.

                                                                    @@ -10763,20 +10763,20 @@

                                                                    Submodules
                                                                    -property pbc: PbcLike[source]
                                                                    +property pbc: PbcLike[source]

                                                                    The periodicity of the structure.

                                                                    -property properties: dict[source]
                                                                    +property properties: dict[source]

                                                                    Properties associated with the whole Structure. Note that this information is only guaranteed to be saved if serializing to native pymatgen output formats (JSON/YAML).

                                                                    -to(filename: PathLike = '', fmt: FileFormats = '', **kwargs) → str[source]
                                                                    +to(filename: PathLike = '', fmt: FileFormats = '', **kwargs) → str[source]

                                                                    Output the structure to a file or string.

                                                                    Parameters:
                                                                    @@ -10809,7 +10809,7 @@

                                                                    Submodules
                                                                    -to_cell(cell_type: Literal['primitive', 'conventional'], **kwargs) → Structure[source]
                                                                    +to_cell(cell_type: Literal['primitive', 'conventional'], **kwargs) → Structure[source]

                                                                    Get a cell based on the current structure.

                                                                    Parameters:
                                                                    @@ -10830,7 +10830,7 @@

                                                                    Submodules
                                                                    -to_conventional(**kwargs) → Structure[source]
                                                                    +to_conventional(**kwargs) → Structure[source]

                                                                    Get a conventional cell based on the current structure.

                                                                    Parameters:
                                                                    @@ -10848,7 +10848,7 @@

                                                                    Submodules
                                                                    -to_primitive(**kwargs) → Structure[source]
                                                                    +to_primitive(**kwargs) → Structure[source]

                                                                    Get a primitive cell based on the current structure.

                                                                    Parameters:
                                                                    @@ -10866,13 +10866,13 @@

                                                                    Submodules
                                                                    -unset_charge() → None[source]
                                                                    +unset_charge() → None[source]

                                                                    Reset the charge to None. E.g. to compute it dynamically based on oxidation states.

                                                                    -property volume: float[source]
                                                                    +property volume: float[source]

                                                                    The volume of the structure in Angstrom^3.

                                                                    @@ -10880,7 +10880,7 @@

                                                                    Submodules
                                                                    -class Molecule(species: Sequence[SpeciesLike], coords: Sequence[ArrayLike], charge: float = 0.0, spin_multiplicity: int | None = None, validate_proximity: bool = False, site_properties: dict | None = None, labels: Sequence[str | None] | None = None, charge_spin_check: bool = True, properties: dict | None = None)[source]
                                                                    +class Molecule(species: Sequence[SpeciesLike], coords: Sequence[ArrayLike], charge: float = 0.0, spin_multiplicity: int | None = None, validate_proximity: bool = False, site_properties: dict | None = None, labels: Sequence[str | None] | None = None, charge_spin_check: bool = True, properties: dict | None = None)[source]

                                                                    Bases: IMolecule, MutableSequence

                                                                    Mutable Molecule. It has all the methods in IMolecule, and allows a user to perform edits on the molecule.

                                                                    @@ -10918,7 +10918,7 @@

                                                                    Submodules
                                                                    -append(species: CompositionLike, coords: ArrayLike, validate_proximity: bool = False, properties: dict | None = None) → Self[source]
                                                                    +append(species: CompositionLike, coords: ArrayLike, validate_proximity: bool = False, properties: dict | None = None) → Self[source]

                                                                    Append a site to the molecule.

                                                                    Parameters:
                                                                    @@ -10938,7 +10938,7 @@

                                                                    Submodules
                                                                    -apply_operation(symm_op: SymmOp) → Self[source]
                                                                    +apply_operation(symm_op: SymmOp) → Self[source]

                                                                    Apply a symmetry operation to the molecule.

                                                                    Parameters:
                                                                    @@ -10955,7 +10955,7 @@

                                                                    Submodules
                                                                    -calculate(calculator: Literal['gfn2-xtb'] | Calculator = 'gfn2-xtb', verbose: bool = False) → Calculator[source]
                                                                    +calculate(calculator: Literal['gfn2-xtb'] | Calculator = 'gfn2-xtb', verbose: bool = False) → Calculator[source]

                                                                    Perform an ASE calculation.

                                                                    Parameters:
                                                                    @@ -10975,7 +10975,7 @@

                                                                    Submodules
                                                                    -insert(idx: int, species: CompositionLike, coords: ArrayLike, validate_proximity: bool = False, properties: dict | None = None, label: str | None = None) → Self[source]
                                                                    +insert(idx: int, species: CompositionLike, coords: ArrayLike, validate_proximity: bool = False, properties: dict | None = None, label: str | None = None) → Self[source]

                                                                    Insert a site to the molecule.

                                                                    Parameters:
                                                                    @@ -10997,7 +10997,7 @@

                                                                    Submodules
                                                                    -perturb(distance: float) → Self[source]
                                                                    +perturb(distance: float) → Self[source]

                                                                    Perform a random perturbation of the sites in a structure to break symmetries.

                                                                    @@ -11015,7 +11015,7 @@

                                                                    Submodules
                                                                    -relax(calculator: str | Calculator = 'gfn2-xtb', optimizer: str | Optimizer = 'FIRE', steps: int = 500, fmax: float = 0.1, opt_kwargs: dict | None = None, return_trajectory: bool = False, verbose: bool = False) → Self | tuple[Self, TrajectoryObserver][source]
                                                                    +relax(calculator: str | Calculator = 'gfn2-xtb', optimizer: str | Optimizer = 'FIRE', steps: int = 500, fmax: float = 0.1, opt_kwargs: dict | None = None, return_trajectory: bool = False, verbose: bool = False) → Self | tuple[Self, TrajectoryObserver][source]

                                                                    Perform a molecule relaxation using an ASE calculator.

                                                                    Parameters:
                                                                    @@ -11047,7 +11047,7 @@

                                                                    Submodules
                                                                    -remove_sites(indices: Sequence[int]) → Self[source]
                                                                    +remove_sites(indices: Sequence[int]) → Self[source]

                                                                    Delete sites with at indices.

                                                                    Parameters:
                                                                    @@ -11064,7 +11064,7 @@

                                                                    Submodules
                                                                    -remove_species(species: Sequence[SpeciesLike]) → Self[source]
                                                                    +remove_species(species: Sequence[SpeciesLike]) → Self[source]

                                                                    Remove all occurrences of a species from a molecule.

                                                                    Parameters:
                                                                    @@ -11081,7 +11081,7 @@

                                                                    Submodules
                                                                    -rotate_sites(indices: Sequence[int] | None = None, theta: float = 0.0, axis: ArrayLike | None = None, anchor: ArrayLike | None = None) → Self[source]
                                                                    +rotate_sites(indices: Sequence[int] | None = None, theta: float = 0.0, axis: ArrayLike | None = None, anchor: ArrayLike | None = None) → Self[source]

                                                                    Rotate specific sites by some angle around vector at anchor.

                                                                    Parameters:
                                                                    @@ -11104,7 +11104,7 @@

                                                                    Submodules
                                                                    -set_charge_and_spin(charge: float, spin_multiplicity: int | None = None) → Self[source]
                                                                    +set_charge_and_spin(charge: float, spin_multiplicity: int | None = None) → Self[source]

                                                                    Set the charge and spin multiplicity.

                                                                    Parameters:
                                                                    @@ -11127,7 +11127,7 @@

                                                                    Submodules
                                                                    -substitute(index: int, func_group: IMolecule | Self | str, bond_order: int = 1) → Self[source]
                                                                    +substitute(index: int, func_group: IMolecule | Self | str, bond_order: int = 1) → Self[source]

                                                                    Substitute atom at index with a functional group.

                                                                    Parameters:
                                                                    @@ -11164,7 +11164,7 @@

                                                                    Submodules
                                                                    -translate_sites(indices: Sequence[int] | None = None, vector: ArrayLike | None = None) → Self[source]
                                                                    +translate_sites(indices: Sequence[int] | None = None, vector: ArrayLike | None = None) → Self[source]

                                                                    Translate specific sites by some vector, keeping the sites within the unit cell.

                                                                    @@ -11188,7 +11188,7 @@

                                                                    Submodules
                                                                    -class Neighbor(species: Composition, coords: NDArray, properties: dict | None = None, nn_distance: float = 0.0, index: int = 0, label: str | None = None)[source]
                                                                    +class Neighbor(species: Composition, coords: NDArray, properties: dict | None = None, nn_distance: float = 0.0, index: int = 0, label: str | None = None)[source]

                                                                    Bases: Site

                                                                    Simple Site subclass to contain a neighboring atom that skips all the unnecessary checks for speed. Can be used as a fixed-length tuple of size 3 to retain backwards compatibility with past use cases.

                                                                    @@ -11210,13 +11210,13 @@

                                                                    Submodules
                                                                    -as_dict() → dict[source]
                                                                    +as_dict() → dict[source]

                                                                    Note that method calls the super of Site, which is MSONable itself.

                                                                    -classmethod from_dict(dct: dict) → Site[source]
                                                                    +classmethod from_dict(dct: dict) → Site[source]

                                                                    Get a Neighbor from a dict.

                                                                    Parameters:
                                                                    @@ -11232,7 +11232,7 @@

                                                                    Submodules
                                                                    -class PeriodicNeighbor(species: Composition, coords: NDArray, lattice: Lattice, properties: dict | None = None, nn_distance: float = 0.0, index: int = 0, image: tuple = (0, 0, 0), label: str | None = None)[source]
                                                                    +class PeriodicNeighbor(species: Composition, coords: NDArray, lattice: Lattice, properties: dict | None = None, nn_distance: float = 0.0, index: int = 0, image: tuple = (0, 0, 0), label: str | None = None)[source]

                                                                    Bases: PeriodicSite

                                                                    Simple PeriodicSite subclass to contain a neighboring atom that skips all the unnecessary checks for speed. Can be used as a fixed-length tuple of @@ -11258,19 +11258,19 @@

                                                                    Submodules
                                                                    -as_dict() → dict[source]
                                                                    +as_dict() → dict[source]

                                                                    Note that method calls the super of Site, which is MSONable itself.

                                                                    -property coords: NDArray[source]
                                                                    +property coords: NDArray[source]

                                                                    Cartesian coords.

                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]

                                                                    Get a PeriodicNeighbor from a dict.

                                                                    Parameters:
                                                                    @@ -11286,7 +11286,7 @@

                                                                    Submodules
                                                                    -class SiteCollection[source]
                                                                    +class SiteCollection[source]

                                                                    Bases: Sequence, ABC

                                                                    Basic SiteCollection. Essentially a sequence of Sites or PeriodicSites. This serves as a base class for Molecule (a collection of Site, i.e., no @@ -11294,12 +11294,12 @@

                                                                    Submodules
                                                                    -DISTANCE_TOLERANCE = 0.5[source]
                                                                    +DISTANCE_TOLERANCE = 0.5[source]

                                                                    -add_oxidation_state_by_element(oxidation_states: dict[str, float]) → Self[source]
                                                                    +add_oxidation_state_by_element(oxidation_states: dict[str, float]) → Self[source]

                                                                    Add oxidation states.

                                                                    Parameters:
                                                                    @@ -11320,7 +11320,7 @@

                                                                    Submodules
                                                                    -add_oxidation_state_by_guess(**kwargs) → Self[source]
                                                                    +add_oxidation_state_by_guess(**kwargs) → Self[source]

                                                                    Decorates the structure with oxidation state, guessing using Composition.oxi_state_guesses(). If multiple guesses are found we take the first one.

                                                                    @@ -11333,7 +11333,7 @@

                                                                    Submodules
                                                                    -add_oxidation_state_by_site(oxidation_states: list[float]) → Self[source]
                                                                    +add_oxidation_state_by_site(oxidation_states: list[float]) → Self[source]

                                                                    Add oxidation states to a structure by site.

                                                                    Parameters:
                                                                    @@ -11354,7 +11354,7 @@

                                                                    Submodules
                                                                    -add_site_property(property_name: str, values: Sequence | np.ndarray) → Self[source]
                                                                    +add_site_property(property_name: str, values: Sequence | np.ndarray) → Self[source]

                                                                    Add a property to a site. Note: This is the preferred method for adding magnetic moments, selective dynamics, and related site-specific properties to a structure/molecule object.

                                                                    @@ -11383,7 +11383,7 @@

                                                                    Submodules
                                                                    -add_spin_by_element(spins: dict[str, float]) → Self[source]
                                                                    +add_spin_by_element(spins: dict[str, float]) → Self[source]

                                                                    Add spin states to structure.

                                                                    Parameters:
                                                                    @@ -11395,7 +11395,7 @@

                                                                    Submodules
                                                                    -add_spin_by_site(spins: Sequence[float]) → Self[source]
                                                                    +add_spin_by_site(spins: Sequence[float]) → Self[source]

                                                                    Add spin states to structure by site.

                                                                    Parameters:
                                                                    @@ -11406,58 +11406,58 @@

                                                                    Submodules
                                                                    -property alphabetical_formula: str[source]
                                                                    +property alphabetical_formula: str[source]

                                                                    The formula as a string.

                                                                    -property atomic_numbers: tuple[int, ...][source]
                                                                    +property atomic_numbers: tuple[int, ...][source]

                                                                    Tuple of atomic numbers.

                                                                    -property cart_coords: ndarray[source]
                                                                    +property cart_coords: ndarray[source]

                                                                    An np.array of the Cartesian coordinates of sites in the structure.

                                                                    -property charge: float[source]
                                                                    +property charge: float[source]

                                                                    The net charge of the structure based on oxidation states. If Elements are found, a charge of 0 is assumed.

                                                                    -property chemical_system: str[source]
                                                                    +property chemical_system: str[source]

                                                                    The chemical system of the structure.

                                                                    -property chemical_system_set: set[str][source]
                                                                    +property chemical_system_set: set[str][source]

                                                                    The set of chemical systems in the structure. E.g. {“Al”, “Ga”, “In”, “N”} for a AlGaInN quaternary.

                                                                    -property composition: Composition[source]
                                                                    +property composition: Composition[source]

                                                                    The structure’s corresponding Composition object.

                                                                    -abstract copy() → Self[source]
                                                                    +abstract copy() → Self[source]

                                                                    Get a copy of itself. Concrete subclasses should implement this method.

                                                                    -property distance_matrix: ndarray[source]
                                                                    +property distance_matrix: ndarray[source]

                                                                    The distance matrix between all sites in the structure. For periodic structures, this is overwritten to return the nearest image distance.

                                                                    @@ -11465,13 +11465,13 @@

                                                                    Submodules
                                                                    -property elements: list[Element | Species | DummySpecies][source]
                                                                    +property elements: list[Element | Species | DummySpecies][source]

                                                                    The elements in the structure as a list of Element objects.

                                                                    -extract_cluster(target_sites: list[Site], **kwargs) → list[Site][source]
                                                                    +extract_cluster(target_sites: list[Site], **kwargs) → list[Site][source]

                                                                    Extract a cluster of atoms based on bond lengths.

                                                                    Parameters:
                                                                    @@ -11488,13 +11488,13 @@

                                                                    Submodules
                                                                    -property formula: str[source]
                                                                    +property formula: str[source]

                                                                    The formula as a string.

                                                                    -from_ase_atoms(**kwargs) → Structure[source]
                                                                    +from_ase_atoms(**kwargs) → Structure[source]

                                                                    Convert ase.Atoms to pymatgen Structure.

                                                                    Parameters:
                                                                    @@ -11508,19 +11508,19 @@

                                                                    Submodules
                                                                    -abstract classmethod from_file(filename: str) → None[source]
                                                                    +abstract classmethod from_file(filename: str) → None[source]

                                                                    Read in SiteCollection from a filename.

                                                                    -abstract classmethod from_str(input_string: str, fmt: Any) → None[source]
                                                                    +abstract classmethod from_str(input_string: str, fmt: Any) → None[source]

                                                                    Read in SiteCollection from a string.

                                                                    -get_angle(i: int, j: int, k: int) → float[source]
                                                                    +get_angle(i: int, j: int, k: int) → float[source]

                                                                    Get angle specified by three sites.

                                                                    Parameters:
                                                                    @@ -11538,7 +11538,7 @@

                                                                    Submodules
                                                                    -get_dihedral(i: int, j: int, k: int, l: int) → float[source]
                                                                    +get_dihedral(i: int, j: int, k: int, l: int) → float[source]

                                                                    Get dihedral angle specified by four sites.

                                                                    Parameters:
                                                                    @@ -11557,7 +11557,7 @@

                                                                    Submodules
                                                                    -abstract get_distance(i: int, j: int) → float[source]
                                                                    +abstract get_distance(i: int, j: int) → float[source]

                                                                    Get distance between sites at index i and j.

                                                                    Parameters:
                                                                    @@ -11574,27 +11574,27 @@

                                                                    Submodules
                                                                    -group_by_types() → Iterator[Site | PeriodicSite][source]
                                                                    +group_by_types() → Iterator[Site | PeriodicSite][source]

                                                                    Iterate over species grouped by type.

                                                                    -indices_from_symbol(symbol: str) → tuple[int, ...][source]
                                                                    +indices_from_symbol(symbol: str) → tuple[int, ...][source]

                                                                    Get a tuple with the sequential indices of the sites that contain an element with the given chemical symbol.

                                                                    -property is_ordered: bool[source]
                                                                    +property is_ordered: bool[source]

                                                                    Check if structure is ordered, meaning no partial occupancies in any of the sites.

                                                                    -is_valid(tol: float = 0.5) → bool[source]
                                                                    +is_valid(tol: float = 0.5) → bool[source]

                                                                    True if SiteCollection does not contain atoms that are too close together. Note that the distance definition is based on type of SiteCollection. Cartesian distances are used for non-periodic @@ -11614,36 +11614,36 @@

                                                                    Submodules
                                                                    -property labels: list[str | None][source]
                                                                    +property labels: list[str | None][source]

                                                                    Site labels as a list.

                                                                    -property n_elems: int[source]
                                                                    +property n_elems: int[source]

                                                                    Number of types of atoms.

                                                                    -property ntypesp[source]
                                                                    +property ntypesp[source]
                                                                    -property num_sites: int[source]
                                                                    +property num_sites: int[source]

                                                                    Number of sites.

                                                                    -property reduced_formula: str[source]
                                                                    +property reduced_formula: str[source]

                                                                    The reduced formula as a string.

                                                                    -relabel_sites(ignore_uniq: bool = False) → Self[source]
                                                                    +relabel_sites(ignore_uniq: bool = False) → Self[source]

                                                                    Relabel sites to ensure they are unique.

                                                                    Site labels are updated in-place, and relabeled by suffixing _1, _2, …, _n for duplicates. Call Structure.copy().relabel_sites() to avoid modifying the original structure.

                                                                    @@ -11663,13 +11663,13 @@

                                                                    Submodules
                                                                    -remove_oxidation_states() → Self[source]
                                                                    +remove_oxidation_states() → Self[source]

                                                                    Removes oxidation states from a structure.

                                                                    -remove_site_property(property_name: str) → Self[source]
                                                                    +remove_site_property(property_name: str) → Self[source]

                                                                    Removes a property to a site.

                                                                    Parameters:
                                                                    @@ -11686,13 +11686,13 @@

                                                                    Submodules
                                                                    -remove_spin() → Self[source]
                                                                    +remove_spin() → Self[source]

                                                                    Remove spin states from structure.

                                                                    -replace_species(species_mapping: dict[SpeciesLike, SpeciesLike | dict[SpeciesLike, float]], in_place: bool = True) → Self[source]
                                                                    +replace_species(species_mapping: dict[SpeciesLike, SpeciesLike | dict[SpeciesLike, float]], in_place: bool = True) → Self[source]

                                                                    Replace species.

                                                                    Note that this resets the label of any affected site to species_string.

                                                                    @@ -11717,20 +11717,20 @@

                                                                    Submodules
                                                                    -property site_properties: dict[str, Sequence][source]
                                                                    +property site_properties: dict[str, Sequence][source]

                                                                    The site properties as a dict of sequences. E.g. {“magmom”: (5, -5), “charge”: (-4, 4)}.

                                                                    -property sites: list[PeriodicSite] | tuple[PeriodicSite, ...][source]
                                                                    +property sites: list[PeriodicSite] | tuple[PeriodicSite, ...][source]

                                                                    The sites in the Structure.

                                                                    -property species: list[Element | Species][source]
                                                                    +property species: list[Element | Species][source]

                                                                    Only works for ordered structures.

                                                                    Raises:
                                                                    @@ -11747,27 +11747,27 @@

                                                                    Submodules
                                                                    -property species_and_occu: list[Composition][source]
                                                                    +property species_and_occu: list[Composition][source]

                                                                    List of species and occupancies at each site of the structure.

                                                                    -property symbol_set: tuple[str, ...][source]
                                                                    +property symbol_set: tuple[str, ...][source]

                                                                    Tuple with the set of chemical symbols. Note that len(symbol_set) == len(types_of_specie).

                                                                    -abstract to(filename: str = '', fmt: Literal['cif', 'poscar', 'cssr', 'json', 'yaml', 'yml', 'xsf', 'mcsqs', 'res', 'pwmat', ''] = '') → str | None[source]
                                                                    +abstract to(filename: str = '', fmt: Literal['cif', 'poscar', 'cssr', 'json', 'yaml', 'yml', 'xsf', 'mcsqs', 'res', 'pwmat', ''] = '') → str | None[source]

                                                                    Generate string representations (cif, json, poscar, ….) of SiteCollections (e.g., molecules / structures). Should return str or None if written to a file.

                                                                    -to_ase_atoms(**kwargs) → Atoms[source]
                                                                    +to_ase_atoms(**kwargs) → Atoms[source]

                                                                    Convert the structure/molecule to an ase.Atoms object.

                                                                    Parameters:
                                                                    @@ -11781,19 +11781,19 @@

                                                                    Submodules
                                                                    -to_file(filename: str = '', fmt: Literal['cif', 'poscar', 'cssr', 'json', 'yaml', 'yml', 'xsf', 'mcsqs', 'res', 'pwmat', ''] = '') → str | None[source]
                                                                    +to_file(filename: str = '', fmt: Literal['cif', 'poscar', 'cssr', 'json', 'yaml', 'yml', 'xsf', 'mcsqs', 'res', 'pwmat', ''] = '') → str | None[source]

                                                                    A more intuitive alias for .to().

                                                                    -property types_of_specie: tuple[Element | Species | DummySpecies, ...][source]
                                                                    +property types_of_specie: tuple[Element | Species | DummySpecies, ...][source]

                                                                    Specie -> Species rename, to maintain backwards compatibility.

                                                                    -property types_of_species: tuple[Element | Species | DummySpecies, ...][source]
                                                                    +property types_of_species: tuple[Element | Species | DummySpecies, ...][source]

                                                                    Tuple of types of species.

                                                                    @@ -11801,7 +11801,7 @@

                                                                    Submodules
                                                                    -class Structure(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike] | np.ndarray, charge: float | None = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict | None = None, labels: Sequence[str | None] | None = None, properties: dict | None = None)[source]
                                                                    +class Structure(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike] | np.ndarray, charge: float | None = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict | None = None, labels: Sequence[str | None] | None = None, properties: dict | None = None)[source]

                                                                    Bases: IStructure, MutableSequence

                                                                    Mutable version of structure.

                                                                    Create a periodic structure.

                                                                    @@ -11850,7 +11850,7 @@

                                                                    Submodules
                                                                    -append(species: CompositionLike, coords: ArrayLike, coords_are_cartesian: bool = False, validate_proximity: bool = False, properties: dict | None = None) → Self[source]
                                                                    +append(species: CompositionLike, coords: ArrayLike, coords_are_cartesian: bool = False, validate_proximity: bool = False, properties: dict | None = None) → Self[source]

                                                                    Append a site to the structure.

                                                                    Parameters:
                                                                    @@ -11872,7 +11872,7 @@

                                                                    Submodules
                                                                    -apply_operation(symm_op: SymmOp, fractional: bool = False) → Self[source]
                                                                    +apply_operation(symm_op: SymmOp, fractional: bool = False) → Self[source]

                                                                    Apply a symmetry operation to the structure in place and return the modified structure. The lattice is operated on by the rotation matrix only. Coords are operated in full and then transformed to the new lattice.

                                                                    @@ -11896,7 +11896,7 @@

                                                                    Submodules
                                                                    -apply_strain(strain: ArrayLike, inplace: bool = True) → Self[source]
                                                                    +apply_strain(strain: ArrayLike, inplace: bool = True) → Self[source]

                                                                    Apply a strain to the lattice.

                                                                    Parameters:
                                                                    @@ -11921,7 +11921,7 @@

                                                                    Submodules
                                                                    -calculate(calculator: str | Calculator = 'm3gnet', verbose: bool = False) → Calculator[source]
                                                                    +calculate(calculator: str | Calculator = 'm3gnet', verbose: bool = False) → Calculator[source]

                                                                    Perform an ASE calculation.

                                                                    Parameters:
                                                                    @@ -11942,7 +11942,7 @@

                                                                    Submodules
                                                                    -classmethod from_prototype(prototype: str, species: Sequence, **kwargs) → Self[source]
                                                                    +classmethod from_prototype(prototype: str, species: Sequence, **kwargs) → Self[source]

                                                                    Rapidly construct common prototype structures.

                                                                    Parameters:
                                                                    @@ -11964,7 +11964,7 @@

                                                                    Submodules
                                                                    -insert(idx: int, species: CompositionLike, coords: ArrayLike, coords_are_cartesian: bool = False, validate_proximity: bool = False, properties: dict | None = None, label: str | None = None) → Self[source]
                                                                    +insert(idx: int, species: CompositionLike, coords: ArrayLike, coords_are_cartesian: bool = False, validate_proximity: bool = False, properties: dict | None = None, label: str | None = None) → Self[source]

                                                                    Insert a site to the structure.

                                                                    Parameters:
                                                                    @@ -11988,13 +11988,13 @@

                                                                    Submodules
                                                                    -property lattice: Lattice[source]
                                                                    +property lattice: Lattice[source]

                                                                    Lattice associated with structure.

                                                                    -make_supercell(scaling_matrix: ArrayLike, to_unit_cell: bool = True, in_place: bool = True) → Self[source]
                                                                    +make_supercell(scaling_matrix: ArrayLike, to_unit_cell: bool = True, in_place: bool = True) → Self[source]

                                                                    Create a supercell.

                                                                    Parameters:
                                                                    @@ -12031,7 +12031,7 @@

                                                                    Submodules
                                                                    -merge_sites(tol: float = 0.01, mode: Literal['sum', 'delete', 'average'] = 'sum') → Self[source]
                                                                    +merge_sites(tol: float = 0.01, mode: Literal['sum', 'delete', 'average'] = 'sum') → Self[source]

                                                                    Merges sites (adding occupancies) within tol of each other. Removes site properties.

                                                                    @@ -12055,7 +12055,7 @@

                                                                    Submodules
                                                                    -perturb(distance: float, min_distance: float | None = None) → Self[source]
                                                                    +perturb(distance: float, min_distance: float | None = None) → Self[source]

                                                                    Perform a random perturbation of the sites in a structure to break symmetries. Modifies the structure in place.

                                                                    @@ -12079,7 +12079,7 @@

                                                                    Submodules
                                                                    -relax(calculator: str | Calculator = 'm3gnet', relax_cell: bool = True, optimizer: str | Optimizer = 'FIRE', steps: int = 500, fmax: float = 0.1, stress_weight: float = 0.01, opt_kwargs: dict | None = None, return_trajectory: bool = False, verbose: bool = False) → Structure | tuple[Structure, TrajectoryObserver | Trajectory][source]
                                                                    +relax(calculator: str | Calculator = 'm3gnet', relax_cell: bool = True, optimizer: str | Optimizer = 'FIRE', steps: int = 500, fmax: float = 0.1, stress_weight: float = 0.01, opt_kwargs: dict | None = None, return_trajectory: bool = False, verbose: bool = False) → Structure | tuple[Structure, TrajectoryObserver | Trajectory][source]

                                                                    Perform a crystal structure relaxation using an ASE calculator.

                                                                    Parameters:
                                                                    @@ -12114,7 +12114,7 @@

                                                                    Submodules
                                                                    -remove_sites(indices: Sequence[int | None]) → Self[source]
                                                                    +remove_sites(indices: Sequence[int | None]) → Self[source]

                                                                    Delete sites with at indices.

                                                                    Parameters:
                                                                    @@ -12131,7 +12131,7 @@

                                                                    Submodules
                                                                    -remove_species(species: Sequence[SpeciesLike]) → Self[source]
                                                                    +remove_species(species: Sequence[SpeciesLike]) → Self[source]

                                                                    Remove all occurrences of several species from a structure.

                                                                    Parameters:
                                                                    @@ -12148,7 +12148,7 @@

                                                                    Submodules
                                                                    -replace(idx: int, species: CompositionLike, coords: ArrayLike | None = None, coords_are_cartesian: bool = False, properties: dict | None = None, label: str | None = None) → Self[source]
                                                                    +replace(idx: int, species: CompositionLike, coords: ArrayLike | None = None, coords_are_cartesian: bool = False, properties: dict | None = None, label: str | None = None) → Self[source]

                                                                    Replace a single site. Takes either a species or a dict of species and occupations.

                                                                    @@ -12175,7 +12175,7 @@

                                                                    Submodules
                                                                    -rotate_sites(indices: list[int] | None = None, theta: float = 0.0, axis: ArrayLike | None = None, anchor: ArrayLike | None = None, to_unit_cell: bool = True) → Self[source]
                                                                    +rotate_sites(indices: list[int] | None = None, theta: float = 0.0, axis: ArrayLike | None = None, anchor: ArrayLike | None = None, to_unit_cell: bool = True) → Self[source]

                                                                    Rotate specific sites by some angle around vector at anchor. Modifies the structure in place.

                                                                    @@ -12200,7 +12200,7 @@

                                                                    Submodules
                                                                    -scale_lattice(volume: float) → Self[source]
                                                                    +scale_lattice(volume: float) → Self[source]

                                                                    Perform scaling of the lattice vectors so that length proportions and angles are preserved.

                                                                    @@ -12218,7 +12218,7 @@

                                                                    Submodules
                                                                    -set_charge(new_charge: float = 0.0) → Self[source]
                                                                    +set_charge(new_charge: float = 0.0) → Self[source]

                                                                    Set the overall structure charge.

                                                                    Parameters:
                                                                    @@ -12235,7 +12235,7 @@

                                                                    Submodules
                                                                    -sort(key: Callable | None = None, reverse: bool = False) → Self[source]
                                                                    +sort(key: Callable | None = None, reverse: bool = False) → Self[source]

                                                                    Sort a structure in place. The parameters have the same meaning as in list.sort(). By default, sites are sorted by the electronegativity of the species. The difference between this method and @@ -12262,7 +12262,7 @@

                                                                    Submodules
                                                                    -substitute(index: int, func_group: IMolecule | Molecule | str, bond_order: int = 1) → Self[source]
                                                                    +substitute(index: int, func_group: IMolecule | Molecule | str, bond_order: int = 1) → Self[source]

                                                                    Substitute atom at index with a functional group.

                                                                    Parameters:
                                                                    @@ -12299,7 +12299,7 @@

                                                                    Submodules
                                                                    -translate_sites(indices: int | Sequence[int], vector: ArrayLike, frac_coords: bool = True, to_unit_cell: bool = True) → Self[source]
                                                                    +translate_sites(indices: int | Sequence[int], vector: ArrayLike, frac_coords: bool = True, to_unit_cell: bool = True) → Self[source]

                                                                    Translate specific sites by some vector, keeping the sites within the unit cell. Modifies the structure in place.

                                                                    @@ -12327,7 +12327,7 @@

                                                                    Submodules
                                                                    -exception StructureError[source]
                                                                    +exception StructureError[source]

                                                                    Bases: Exception

                                                                    Exception class for Structure. Raised when the structure has problems, e.g. atoms that are too close.

                                                                    @@ -12351,7 +12351,7 @@

                                                                    Submodules
                                                                    -class ReconstructionGenerator(initial_structure: Structure, min_slab_size: float, min_vacuum_size: float, reconstruction_name: str)[source]
                                                                    +class ReconstructionGenerator(initial_structure: Structure, min_slab_size: float, min_vacuum_size: float, reconstruction_name: str)[source]

                                                                    Bases: object

                                                                    Build a reconstructed Slab from a given initial Structure.

                                                                    This class needs a pre-defined dictionary specifying the parameters @@ -12359,7 +12359,7 @@

                                                                    Submodules
                                                                    -slabgen_params[source]
                                                                    +slabgen_params[source]

                                                                    Parameters for the SlabGenerator.

                                                                    Type:
                                                                    @@ -12370,7 +12370,7 @@

                                                                    Submodules
                                                                    -trans_matrix[source]
                                                                    +trans_matrix[source]

                                                                    A 3x3 transformation matrix to generate the reconstructed slab. Only the a and b lattice vectors are actually changed while the c vector remains the same. @@ -12384,7 +12384,7 @@

                                                                    Submodules
                                                                    -reconstruction_json[source]
                                                                    +reconstruction_json[source]

                                                                    The full JSON or dictionary containing the instructions for building the slab.

                                                                    @@ -12497,7 +12497,7 @@

                                                                    Submodules
                                                                    -build_slabs() → list[Slab][source]
                                                                    +build_slabs() → list[Slab][source]
                                                                    Build reconstructed Slabs by:

                                                                    1. Obtaining the unreconstructed Slab using the specified @@ -12520,7 +12520,7 @@

                                                                      Submodules
                                                                      -get_unreconstructed_slabs() → list[Slab][source]
                                                                      +get_unreconstructed_slabs() → list[Slab][source]

                                                                      Generate the unreconstructed (super) Slabs.

                                                                      TODO (@DanielYang59): this should be a private method.

                                                                    @@ -12529,7 +12529,7 @@

                                                                    Submodules
                                                                    -class Slab(lattice: Lattice | np.ndarray, species: Sequence[Any], coords: np.ndarray, miller_index: MillerIndex, oriented_unit_cell: Structure, shift: float, scale_factor: np.ndarray, reorient_lattice: bool = True, validate_proximity: bool = False, to_unit_cell: bool = False, reconstruction: str | None = None, coords_are_cartesian: bool = False, site_properties: dict | None = None, energy: float | None = None)[source]
                                                                    +class Slab(lattice: Lattice | np.ndarray, species: Sequence[Any], coords: np.ndarray, miller_index: MillerIndex, oriented_unit_cell: Structure, shift: float, scale_factor: np.ndarray, reorient_lattice: bool = True, validate_proximity: bool = False, to_unit_cell: bool = False, reconstruction: str | None = None, coords_are_cartesian: bool = False, site_properties: dict | None = None, energy: float | None = None)[source]

                                                                    Bases: Structure

                                                                    Hold information for a Slab, with additional attributes pertaining to slabs, but the init method does not @@ -12590,7 +12590,7 @@

                                                                    Submodules
                                                                    -add_adsorbate_atom(indices: list[int], species: str | Element | Species, distance: float, specie: Species | Element | str | None = None) → Self[source]
                                                                    +add_adsorbate_atom(indices: list[int], species: str | Element | Species, distance: float, specie: Species | Element | str | None = None) → Self[source]

                                                                    Add adsorbate onto the Slab, along the c lattice vector.

                                                                    Parameters:
                                                                    @@ -12614,19 +12614,19 @@

                                                                    Submodules
                                                                    -as_dict(**kwargs) → dict[source]
                                                                    +as_dict(**kwargs) → dict[source]

                                                                    MSONable dict.

                                                                    -property center_of_mass: ndarray[source]
                                                                    +property center_of_mass: ndarray[source]

                                                                    The center of mass of the Slab in fractional coordinates.

                                                                    -copy(site_properties: dict[str, Any] | None = None) → Self[source]
                                                                    +copy(site_properties: dict[str, Any] | None = None) → Self[source]

                                                                    Get a copy of the Slab, with options to update site properties.

                                                                    Parameters:
                                                                    @@ -12642,7 +12642,7 @@

                                                                    Submodules
                                                                    -property dipole: ndarray[source]
                                                                    +property dipole: ndarray[source]

                                                                    The dipole moment of the Slab in the direction of the surface normal.

                                                                    Note that the Slab must be oxidation state decorated for this to work properly. Otherwise, the Slab will always have a dipole moment of 0.

                                                                    @@ -12650,7 +12650,7 @@

                                                                    Submodules
                                                                    -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                    +classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                    Parameters:

                                                                    dct – dict.

                                                                    @@ -12666,7 +12666,7 @@

                                                                    Submodules
                                                                    -get_orthogonal_c_slab() → Self[source]
                                                                    +get_orthogonal_c_slab() → Self[source]

                                                                    Generate a Slab where the normal (c lattice vector) is forced to be orthogonal to the surface a and b lattice vectors.

                                                                    Note that this breaks inherent symmetries in the slab.

                                                                    @@ -12678,7 +12678,7 @@

                                                                    Submodules
                                                                    -get_sorted_structure(key=None, reverse: bool = False) → Self[source]
                                                                    +get_sorted_structure(key=None, reverse: bool = False) → Self[source]

                                                                    Get a sorted copy of the structure. The parameters have the same meaning as in list.sort. By default, sites are sorted by the electronegativity of the species. Note that Slab has to override this @@ -12698,7 +12698,7 @@

                                                                    Submodules
                                                                    -get_surface_sites(tag: bool = False) → dict[str, list][source]
                                                                    +get_surface_sites(tag: bool = False) → dict[str, list][source]

                                                                    Get the surface sites and their indices in a dictionary. Useful for analysis involving broken bonds and for finding adsorption sites.

                                                                    The oriented unit cell of the slab will determine the @@ -12724,7 +12724,7 @@

                                                                    Submodules
                                                                    -get_symmetric_site(point: ArrayLike, cartesian: bool = False) → ArrayLike[source]
                                                                    +get_symmetric_site(point: ArrayLike, cartesian: bool = False) → ArrayLike[source]

                                                                    Use symmetry operations to find an equivalent site on the other side of the slab. Works mainly for slabs with Laue symmetry.

                                                                    This is useful for retaining the non-polar and @@ -12752,7 +12752,7 @@

                                                                    Submodules
                                                                    -get_tasker2_slabs(tol: float = 0.01, same_species_only: bool = True) → list[Self][source]
                                                                    +get_tasker2_slabs(tol: float = 0.01, same_species_only: bool = True) → list[Self][source]

                                                                    Get a list of slabs that have been Tasker 2 corrected.

                                                                    Parameters:
                                                                    @@ -12775,7 +12775,7 @@

                                                                    Submodules
                                                                    -is_polar(tol_dipole_per_unit_area: float = 0.001) → bool[source]
                                                                    +is_polar(tol_dipole_per_unit_area: float = 0.001) → bool[source]

                                                                    Check if the Slab is polar by computing the normalized dipole per unit area. Normalized dipole per unit area is used as it is more reliable than using the absolute value, which varies with surface area.

                                                                    @@ -12791,7 +12791,7 @@

                                                                    Submodules
                                                                    -is_symmetric(symprec: float = 0.1) → bool[source]
                                                                    +is_symmetric(symprec: float = 0.1) → bool[source]
                                                                    Check if Slab is symmetric, i.e., contains inversion, mirror on (hkl) plane,

                                                                    or screw axis (rotation and translation) about [hkl].

                                                                    @@ -12811,19 +12811,19 @@

                                                                    Submodules
                                                                    -property normal: ndarray[source]
                                                                    +property normal: ndarray[source]

                                                                    The surface normal vector of the Slab, normalized to unit length.

                                                                    -property surface_area: float[source]
                                                                    +property surface_area: float[source]

                                                                    The surface area of the Slab.

                                                                    -symmetrically_add_atom(species: str | Element | Species, point: ArrayLike, specie: str | Element | Species | None = None, coords_are_cartesian: bool = False) → None[source]
                                                                    +symmetrically_add_atom(species: str | Element | Species, point: ArrayLike, specie: str | Element | Species | None = None, coords_are_cartesian: bool = False) → None[source]

                                                                    Add a species at a selected site in a Slab. Will also add an equivalent site on the other side to maintain symmetry.

                                                                    @@ -12840,7 +12840,7 @@

                                                                    Submodules
                                                                    -symmetrically_remove_atoms(indices: list[int]) → None[source]
                                                                    +symmetrically_remove_atoms(indices: list[int]) → None[source]

                                                                    Remove sites from a list of indices. Will also remove the equivalent site on the other side of the slab to maintain symmetry.

                                                                    @@ -12857,7 +12857,7 @@

                                                                    Submodules
                                                                    -class SlabGenerator(initial_structure: Structure, miller_index: MillerIndex, min_slab_size: float, min_vacuum_size: float, lll_reduce: bool = False, center_slab: bool = False, in_unit_planes: bool = False, primitive: bool = True, max_normal_search: int | None = None, reorient_lattice: bool = True)[source]
                                                                    +class SlabGenerator(initial_structure: Structure, miller_index: MillerIndex, min_slab_size: float, min_vacuum_size: float, lll_reduce: bool = False, center_slab: bool = False, in_unit_planes: bool = False, primitive: bool = True, max_normal_search: int | None = None, reorient_lattice: bool = True)[source]

                                                                    Bases: object

                                                                    Generate different slabs using shift values determined by where a unique termination can be found, along with other criteria such as where a @@ -12865,7 +12865,7 @@

                                                                    Submodules
                                                                    -oriented_unit_cell[source]
                                                                    +oriented_unit_cell[source]

                                                                    An oriented unit cell of the parent structure.

                                                                    Type:
                                                                    @@ -12876,7 +12876,7 @@

                                                                    Submodules
                                                                    -parent[source]
                                                                    +parent[source]

                                                                    Parent structure from which Slab was derived.

                                                                    Type:
                                                                    @@ -12887,7 +12887,7 @@

                                                                    Submodules
                                                                    -lll_reduce[source]
                                                                    +lll_reduce[source]

                                                                    Whether the slabs will be orthogonalized.

                                                                    Type:
                                                                    @@ -12898,7 +12898,7 @@

                                                                    Submodules
                                                                    -center_slab[source]
                                                                    +center_slab[source]

                                                                    Whether the slabs will be centered in the slab-vacuum system.

                                                                    Type:
                                                                    @@ -12909,7 +12909,7 @@

                                                                    Submodules
                                                                    -slab_scale_factor[source]
                                                                    +slab_scale_factor[source]

                                                                    Scale factor that brings the parent cell to the surface cell.

                                                                    @@ -12921,7 +12921,7 @@

                                                                    Submodules
                                                                    -miller_index[source]
                                                                    +miller_index[source]

                                                                    Miller index of plane parallel to surface.

                                                                    Type:
                                                                    @@ -12932,7 +12932,7 @@

                                                                    Submodules
                                                                    -min_slab_size[source]
                                                                    +min_slab_size[source]

                                                                    Minimum size of layers containing atoms, in angstroms.

                                                                    Type:
                                                                    @@ -12943,7 +12943,7 @@

                                                                    Submodules
                                                                    -min_vac_size[source]
                                                                    +min_vac_size[source]

                                                                    Minimum vacuum layer size, in angstroms.

                                                                    Type:
                                                                    @@ -13002,7 +13002,7 @@

                                                                    Submodules
                                                                    -get_slab(shift: float = 0, tol: float = 0.1, energy: float | None = None) → Slab[source]
                                                                    +get_slab(shift: float = 0, tol: float = 0.1, energy: float | None = None) → Slab[source]
                                                                    [Private method] Generate a slab based on a given termination

                                                                    coordinate along the lattice c direction.

                                                                    @@ -13028,7 +13028,7 @@

                                                                    Submodules
                                                                    -get_slabs(bonds: dict[tuple[Species | Element, Species | Element], float] | None = None, ftol: float = 0.1, tol: float = 0.1, max_broken_bonds: int = 0, symmetrize: bool = False, repair: bool = False, ztol: float = 0) → list[Slab][source]
                                                                    +get_slabs(bonds: dict[tuple[Species | Element, Species | Element], float] | None = None, ftol: float = 0.1, tol: float = 0.1, max_broken_bonds: int = 0, symmetrize: bool = False, repair: bool = False, ztol: float = 0) → list[Slab][source]

                                                                    Generate slabs with shift values calculated from the internal gen_possible_terminations func. If the user decide to avoid breaking any polyhedral bond (by setting bonds), any shift value that do so @@ -13069,7 +13069,7 @@

                                                                    Submodules
                                                                    -move_to_other_side(init_slab: Slab, index_of_sites: list[int]) → Slab[source]
                                                                    +move_to_other_side(init_slab: Slab, index_of_sites: list[int]) → Slab[source]

                                                                    Move surface sites to the opposite surface of the Slab.

                                                                    If a selected site resides on the top half of the Slab, it would be moved to the bottom side, and vice versa. @@ -13099,7 +13099,7 @@

                                                                    Submodules
                                                                    -nonstoichiometric_symmetrized_slab(init_slab: Slab) → list[Slab][source]
                                                                    +nonstoichiometric_symmetrized_slab(init_slab: Slab) → list[Slab][source]

                                                                    Symmetrize the two surfaces of a Slab, but may break the stoichiometry.

                                                                    How it works:

                                                                    1. Check whether two surfaces of the slab are equivalent. @@ -13125,7 +13125,7 @@

                                                                    Submodules
                                                                    -repair_broken_bonds(slab: Slab, bonds: dict[tuple[Species | Element, Species | Element], float]) → Slab[source]
                                                                    +repair_broken_bonds(slab: Slab, bonds: dict[tuple[Species | Element, Species | Element], float]) → Slab[source]

                                                                    Repair broken bonds (specified by the bonds parameter) due to slab cleaving, and repair them by moving undercoordinated atoms to the other surface.

                                                                    @@ -13158,7 +13158,7 @@

                                                                    Submodules
                                                                    -center_slab(slab: Structure) → Structure[source]
                                                                    +center_slab(slab: Structure) → Structure[source]

                                                                    Relocate the slab to the center such that its center (the slab region) is close to z=0.5.

                                                                    This makes it easier to find surface sites and apply @@ -13189,7 +13189,7 @@

                                                                    Submodules
                                                                    -generate_all_slabs(structure: Structure, max_index: int, min_slab_size: float, min_vacuum_size: float, bonds: dict | None = None, tol: float = 0.1, ftol: float = 0.1, max_broken_bonds: int = 0, lll_reduce: bool = False, center_slab: bool = False, primitive: bool = True, max_normal_search: int | None = None, symmetrize: bool = False, repair: bool = False, include_reconstructions: bool = False, in_unit_planes: bool = False) → list[Slab][source]
                                                                    +generate_all_slabs(structure: Structure, max_index: int, min_slab_size: float, min_vacuum_size: float, bonds: dict | None = None, tol: float = 0.1, ftol: float = 0.1, max_broken_bonds: int = 0, lll_reduce: bool = False, center_slab: bool = False, primitive: bool = True, max_normal_search: int | None = None, symmetrize: bool = False, repair: bool = False, include_reconstructions: bool = False, in_unit_planes: bool = False) → list[Slab][source]

                                                                    Find all unique Slabs up to a given Miller index.

                                                                    Slabs oriented along certain Miller indices may be equivalent to other Miller indices under symmetry operations. To avoid @@ -13256,13 +13256,13 @@

                                                                    Submodules
                                                                    -get_d(slab: Slab) → float[source]
                                                                    +get_d(slab: Slab) → float[source]

                                                                    Determine the z-spacing between the bottom two layers for a Slab.

                                                                    -get_slab_regions(slab: Slab, blength: float = 3.5) → list[tuple[float, float]][source]
                                                                    +get_slab_regions(slab: Slab, blength: float = 3.5) → list[tuple[float, float]][source]

                                                                    Find the z-ranges for the slab region.

                                                                    Useful for discerning where the slab ends and vacuum begins if the slab is not fully within the cell.

                                                                    @@ -13282,7 +13282,7 @@

                                                                    Submodules
                                                                    -get_symmetrically_distinct_miller_indices(structure: Structure, max_index: int, return_hkil: bool = False) → list[source]
                                                                    +get_symmetrically_distinct_miller_indices(structure: Structure, max_index: int, return_hkil: bool = False) → list[source]

                                                                    Find all symmetrically distinct indices below a certain max-index for a given structure. Analysis is based on the symmetry of the reciprocal lattice of the structure.

                                                                    @@ -13302,7 +13302,7 @@

                                                                    Submodules
                                                                    -get_symmetrically_equivalent_miller_indices(structure: Structure, miller_index: tuple[int, ...], return_hkil: bool = True, system: CrystalSystem | None = None) → list[source]
                                                                    +get_symmetrically_equivalent_miller_indices(structure: Structure, miller_index: tuple[int, ...], return_hkil: bool = True, system: CrystalSystem | None = None) → list[source]

                                                                    Get indices for all equivalent sites within a given structure. Analysis is based on the symmetry of its reciprocal lattice.

                                                                    @@ -13321,7 +13321,7 @@

                                                                    Submodules
                                                                    -hkl_transformation(transf: np.ndarray, miller_index: MillerIndex) → Tuple3Ints[source]
                                                                    +hkl_transformation(transf: np.ndarray, miller_index: MillerIndex) → Tuple3Ints[source]

                                                                    Transform the Miller index from setting A to B with a transformation matrix.

                                                                    Parameters:
                                                                    @@ -13335,7 +13335,7 @@

                                                                    Submodules
                                                                    -miller_index_from_sites(lattice: Lattice | ArrayLike, coords: ArrayLike, coords_are_cartesian: bool = True, round_dp: int = 4, verbose: bool = True) → Tuple3Ints[source]
                                                                    +miller_index_from_sites(lattice: Lattice | ArrayLike, coords: ArrayLike, coords_are_cartesian: bool = True, round_dp: int = 4, verbose: bool = True) → Tuple3Ints[source]

                                                                    Get the Miller index of a plane, determined by a given set of coordinates.

                                                                    A minimum of 3 sets of coordinates are required. If more than 3 coordinates are given, the plane that minimises the distance to all @@ -13370,7 +13370,7 @@

                                                                    Submodules
                                                                    -class SquareTensor(input_array: NDArray, vscale: NDArray | None = None)[source]
                                                                    +class SquareTensor(input_array: NDArray, vscale: NDArray | None = None)[source]

                                                                    Bases: Tensor

                                                                    Base class for doing useful general operations on second rank tensors (stress, strain etc.).

                                                                    @@ -13389,13 +13389,13 @@

                                                                    Submodules
                                                                    -property det: Self[source]
                                                                    +property det: Self[source]

                                                                    Shorthand for the determinant of the SquareTensor.

                                                                    -get_scaled(scale_factor: float) → Self[source]
                                                                    +get_scaled(scale_factor: float) → Self[source]

                                                                    Scales the tensor by a certain multiplicative scale factor.

                                                                    Parameters:
                                                                    @@ -13407,13 +13407,13 @@

                                                                    Submodules
                                                                    -property inv: Self[source]
                                                                    +property inv: Self[source]

                                                                    Shorthand for matrix inverse on SquareTensor.

                                                                    -is_rotation(tol: float = 0.001, include_improper: bool = True) → bool[source]
                                                                    +is_rotation(tol: float = 0.001, include_improper: bool = True) → bool[source]

                                                                    Test to see if tensor is a valid rotation matrix, performs a test to check whether the inverse is equal to the transpose and if the determinant is equal to one within the specified @@ -13433,13 +13433,13 @@

                                                                    Submodules
                                                                    -polar_decomposition(side: str = 'right') → tuple[source]
                                                                    +polar_decomposition(side: str = 'right') → tuple[source]

                                                                    Calculate matrices for polar decomposition.

                                                                    -property principal_invariants: NDArray[source]
                                                                    +property principal_invariants: NDArray[source]

                                                                    A list of principal invariants for the tensor, which are the values of the coefficients of the characteristic polynomial for the matrix.

                                                                    @@ -13447,7 +13447,7 @@

                                                                    Submodules
                                                                    -refine_rotation() → Self[source]
                                                                    +refine_rotation() → Self[source]

                                                                    Helper method for refining rotation matrix by ensuring that second and third rows are perpendicular to the first. Gets new y vector from an orthogonal projection of x onto y @@ -13464,7 +13464,7 @@

                                                                    Submodules
                                                                    -property trans: Self[source]
                                                                    +property trans: Self[source]

                                                                    Shorthand for transpose on SquareTensor.

                                                                    @@ -13472,7 +13472,7 @@

                                                                    Submodules
                                                                    -class Tensor(input_array: NDArray, vscale: NDArray | None = None, check_rank: int | None = None)[source]
                                                                    +class Tensor(input_array: NDArray, vscale: NDArray | None = None, check_rank: int | None = None)[source]

                                                                    Bases: ndarray, MSONable

                                                                    Base class for doing useful general operations on Nth order tensors, without restrictions on the type (stress, elastic, strain, piezo, etc.).

                                                                    @@ -13493,7 +13493,7 @@

                                                                    Submodules
                                                                    -as_dict(voigt: bool = False) → dict[source]
                                                                    +as_dict(voigt: bool = False) → dict[source]

                                                                    Serializes the tensor object.

                                                                    Parameters:
                                                                    @@ -13511,7 +13511,7 @@

                                                                    Submodules
                                                                    -average_over_unit_sphere(quad: dict | None = None) → Self[source]
                                                                    +average_over_unit_sphere(quad: dict | None = None) → Self[source]

                                                                    Average the tensor projection over the unit with option for custom quadrature.

                                                                    Parameters:
                                                                    @@ -13527,7 +13527,7 @@

                                                                    Submodules
                                                                    -convert_to_ieee(structure: Structure, initial_fit: bool = True, refine_rotation: bool = True) → Self[source]
                                                                    +convert_to_ieee(structure: Structure, initial_fit: bool = True, refine_rotation: bool = True) → Self[source]

                                                                    Given a structure associated with a tensor, attempts a calculation of the tensor in IEEE format according to the 1987 IEEE standards.

                                                                    @@ -13551,13 +13551,13 @@

                                                                    Submodules
                                                                    -einsum_sequence(other_arrays: NDArray, einsum_string: str | None = None) → NDArray[source]
                                                                    +einsum_sequence(other_arrays: NDArray, einsum_string: str | None = None) → NDArray[source]

                                                                    Calculate the result of an einstein summation expression.

                                                                    -fit_to_structure(structure: Structure, symprec: float = 0.1)[source]
                                                                    +fit_to_structure(structure: Structure, symprec: float = 0.1)[source]

                                                                    Get a tensor that is invariant with respect to symmetry operations corresponding to a structure.

                                                                    @@ -13574,7 +13574,7 @@

                                                                    Submodules
                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]

                                                                    Instantiate Tensors from dicts (using MSONable API).

                                                                    Returns:
                                                                    @@ -13588,7 +13588,7 @@

                                                                    Submodules
                                                                    -classmethod from_values_indices(values: list[float], indices: NDArray, populate: bool = False, structure: Structure | None = None, voigt_rank: int | None = None, vsym: bool = True, verbose: bool = False) → Self[source]
                                                                    +classmethod from_values_indices(values: list[float], indices: NDArray, populate: bool = False, structure: Structure | None = None, voigt_rank: int | None = None, vsym: bool = True, verbose: bool = False) → Self[source]

                                                                    Create a tensor from values and indices, with options for populating the remainder of the tensor.

                                                                    @@ -13614,7 +13614,7 @@

                                                                    Submodules
                                                                    -classmethod from_voigt(voigt_input: NDArray) → Self[source]
                                                                    +classmethod from_voigt(voigt_input: NDArray) → Self[source]

                                                                    Constructor based on the voigt notation vector or matrix.

                                                                    Parameters:
                                                                    @@ -13625,7 +13625,7 @@

                                                                    Submodules
                                                                    -get_grouped_indices(voigt: bool = False, **kwargs) → list[list][source]
                                                                    +get_grouped_indices(voigt: bool = False, **kwargs) → list[list][source]

                                                                    Get index sets for equivalent tensor values.

                                                                    Parameters:
                                                                    @@ -13654,7 +13654,7 @@

                                                                    Submodules
                                                                    -static get_ieee_rotation(structure: Structure, refine_rotation: bool = True) → SquareTensor[source]
                                                                    +static get_ieee_rotation(structure: Structure, refine_rotation: bool = True) → SquareTensor[source]

                                                                    Given a structure associated with a tensor, determines the rotation matrix for IEEE conversion according to the 1987 IEEE standards.

                                                                    @@ -13672,7 +13672,7 @@

                                                                    Submodules
                                                                    -get_symbol_dict(voigt: bool = True, zero_index: bool = False, **kwargs) → dict[str, NDArray][source]
                                                                    +get_symbol_dict(voigt: bool = True, zero_index: bool = False, **kwargs) → dict[str, NDArray][source]

                                                                    Create a summary dict for tensor with associated symbol.

                                                                    Parameters:
                                                                    @@ -13704,7 +13704,7 @@

                                                                    Submodules
                                                                    -static get_voigt_dict(rank: int) → dict[tuple[int, ...], tuple[int, ...]][source]
                                                                    +static get_voigt_dict(rank: int) → dict[tuple[int, ...], tuple[int, ...]][source]

                                                                    Get a dictionary that maps indices in the tensor to those in a voigt representation based on input rank.

                                                                    @@ -13716,7 +13716,7 @@

                                                                    Submodules
                                                                    -is_fit_to_structure(structure: Structure, tol: float = 0.01) → bool[source]
                                                                    +is_fit_to_structure(structure: Structure, tol: float = 0.01) → bool[source]

                                                                    Test whether a tensor is invariant with respect to the symmetry operations of a particular structure by testing whether the residual of the symmetric portion is below a @@ -13733,7 +13733,7 @@

                                                                    Submodules
                                                                    -is_symmetric(tol: float = 1e-05) → bool[source]
                                                                    +is_symmetric(tol: float = 1e-05) → bool[source]

                                                                    Test whether a tensor is symmetric or not based on the residual with its symmetric part, from self.symmetrized.

                                                                    @@ -13745,7 +13745,7 @@

                                                                    Submodules
                                                                    -is_voigt_symmetric(tol: float = 1e-06) → bool[source]
                                                                    +is_voigt_symmetric(tol: float = 1e-06) → bool[source]

                                                                    Test symmetry of tensor to that necessary for voigt-conversion by grouping indices into pairs and constructing a sequence of possible permutations to be used in a tensor transpose.

                                                                    @@ -13753,7 +13753,7 @@

                                                                    Submodules
                                                                    -populate(structure: Structure, prec: float = 1e-05, maxiter: int = 200, verbose: bool = False, precond: bool = True, vsym: bool = True) → Self[source]
                                                                    +populate(structure: Structure, prec: float = 1e-05, maxiter: int = 200, verbose: bool = False, precond: bool = True, vsym: bool = True) → Self[source]

                                                                    Takes a partially populated tensor, and populates the non-zero entries according to the following procedure, iterated until the desired convergence (specified via prec) is achieved.

                                                                    @@ -13787,7 +13787,7 @@

                                                                    Submodules
                                                                    -project(n: NDArray) → Self[source]
                                                                    +project(n: NDArray) → Self[source]

                                                                    Project a tensor into a vector. Returns the tensor dotted into a unit vector along the input n.

                                                                    @@ -13809,7 +13809,7 @@

                                                                    Submodules
                                                                    -rotate(matrix: NDArray, tol: float = 0.001) → Self[source]
                                                                    +rotate(matrix: NDArray, tol: float = 0.001) → Self[source]

                                                                    Apply a rotation directly, and tests input matrix to ensure a valid rotation.

                                                                    @@ -13824,7 +13824,7 @@

                                                                    Submodules
                                                                    -round(decimals: int = 0) → Self[source]
                                                                    +round(decimals: int = 0) → Self[source]

                                                                    Wrapper around numpy.round to ensure object of same type is returned.

                                                                    @@ -13844,7 +13844,7 @@

                                                                    Submodules
                                                                    -structure_transform(original_structure: Structure, new_structure: Structure, refine_rotation: bool = True) → Self[source]
                                                                    +structure_transform(original_structure: Structure, new_structure: Structure, refine_rotation: bool = True) → Self[source]

                                                                    Transforms a tensor from one basis for an original structure into a new basis defined by a new structure.

                                                                    @@ -13867,12 +13867,12 @@

                                                                    Submodules
                                                                    -symbol = 'T'[source]
                                                                    +symbol = 'T'[source]

                                                                    -property symmetrized: Self[source]
                                                                    +property symmetrized: Self[source]

                                                                    A generally symmetrized tensor, calculated by taking the sum of the tensor and its transpose with respect to all possible permutations of indices.

                                                                    @@ -13880,7 +13880,7 @@

                                                                    Submodules
                                                                    -transform(symm_op: SymmOp) → Self[source]
                                                                    +transform(symm_op: SymmOp) → Self[source]

                                                                    Apply a transformation (via a symmetry operation) to a tensor.

                                                                    Parameters:
                                                                    @@ -13891,20 +13891,20 @@

                                                                    Submodules
                                                                    -property voigt: NDArray[source]
                                                                    +property voigt: NDArray[source]

                                                                    The tensor in Voigt notation.

                                                                    -property voigt_symmetrized: Self[source]
                                                                    +property voigt_symmetrized: Self[source]

                                                                    A “voigt”-symmetrized tensor, i. e. a Voigt-notation tensor such that it is invariant w.r.t. permutation of indices.

                                                                    -zeroed(tol: float = 0.001) → Self[source]
                                                                    +zeroed(tol: float = 0.001) → Self[source]

                                                                    Get the matrix with all entries below a certain threshold (i.e. tol) set to zero.

                                                                    @@ -13912,7 +13912,7 @@

                                                                    Submodules
                                                                    -class TensorCollection(tensor_list: Sequence, base_class=<class 'pymatgen.core.tensors.Tensor'>)[source]
                                                                    +class TensorCollection(tensor_list: Sequence, base_class=<class 'pymatgen.core.tensors.Tensor'>)[source]

                                                                    Bases: Sequence, MSONable

                                                                    A sequence of tensors that can be used for fitting data or for having a tensor expansion.

                                                                    @@ -13926,7 +13926,7 @@

                                                                    Submodules
                                                                    -as_dict(voigt: bool = False) → dict[source]
                                                                    +as_dict(voigt: bool = False) → dict[source]
                                                                    Parameters:

                                                                    voigt – Whether to use Voigt form.

                                                                    @@ -13939,7 +13939,7 @@

                                                                    Submodules
                                                                    -convert_to_ieee(structure: Structure, initial_fit: bool = True, refine_rotation: bool = True) → Self[source]
                                                                    +convert_to_ieee(structure: Structure, initial_fit: bool = True, refine_rotation: bool = True) → Self[source]

                                                                    Convert all tensors to IEEE.

                                                                    Parameters:
                                                                    @@ -13957,7 +13957,7 @@

                                                                    Submodules
                                                                    -fit_to_structure(structure: Structure, symprec: float = 0.1) → Self[source]
                                                                    +fit_to_structure(structure: Structure, symprec: float = 0.1) → Self[source]

                                                                    Fit all tensors to a Structure.

                                                                    Parameters:
                                                                    @@ -13974,7 +13974,7 @@

                                                                    Submodules
                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                    +classmethod from_dict(dct: dict) → Self[source]

                                                                    Create TensorCollection from dict.

                                                                    Parameters:
                                                                    @@ -13988,7 +13988,7 @@

                                                                    Submodules
                                                                    -classmethod from_voigt(voigt_input_list: list[Tensor], base_class=<class 'pymatgen.core.tensors.Tensor'>) → Self[source]
                                                                    +classmethod from_voigt(voigt_input_list: list[Tensor], base_class=<class 'pymatgen.core.tensors.Tensor'>) → Self[source]

                                                                    Create TensorCollection from voigt form.

                                                                    Parameters:
                                                                    @@ -14005,7 +14005,7 @@

                                                                    Submodules
                                                                    -is_fit_to_structure(structure: Structure, tol: float = 0.01) → bool[source]
                                                                    +is_fit_to_structure(structure: Structure, tol: float = 0.01) → bool[source]
                                                                    Parameters:
                                                                      @@ -14021,7 +14021,7 @@

                                                                      Submodules
                                                                      -is_symmetric(tol: float = 1e-05) → bool[source]
                                                                      +is_symmetric(tol: float = 1e-05) → bool[source]
                                                                      Parameters:

                                                                      tol – tolerance.

                                                                      @@ -14034,7 +14034,7 @@

                                                                      Submodules
                                                                      -is_voigt_symmetric(tol: float = 1e-06) → bool[source]
                                                                      +is_voigt_symmetric(tol: float = 1e-06) → bool[source]
                                                                      Parameters:

                                                                      tol – tolerance.

                                                                      @@ -14047,13 +14047,13 @@

                                                                      Submodules
                                                                      -property ranks: list[source]
                                                                      +property ranks: list[source]

                                                                      Ranks for all tensors.

                                                                      -rotate(matrix, tol: float = 0.001) → Self[source]
                                                                      +rotate(matrix, tol: float = 0.001) → Self[source]

                                                                      Rotates TensorCollection.

                                                                      Parameters:
                                                                      @@ -14070,7 +14070,7 @@

                                                                      Submodules
                                                                      -round(*args, **kwargs) → Self[source]
                                                                      +round(*args, **kwargs) → Self[source]

                                                                      Round all tensors.

                                                                      Parameters:
                                                                      @@ -14087,13 +14087,13 @@

                                                                      Submodules
                                                                      -property symmetrized: Self[source]
                                                                      +property symmetrized: Self[source]

                                                                      TensorCollection where all tensors are symmetrized.

                                                                      -transform(symm_op: SymmOp) → Self[source]
                                                                      +transform(symm_op: SymmOp) → Self[source]

                                                                      Transforms TensorCollection with a symmetry operation.

                                                                      Parameters:
                                                                      @@ -14107,19 +14107,19 @@

                                                                      Submodules
                                                                      -property voigt: list[NDArray][source]
                                                                      +property voigt: list[NDArray][source]

                                                                      TensorCollection where all tensors are in Voigt form.

                                                                      -property voigt_symmetrized: Self[source]
                                                                      +property voigt_symmetrized: Self[source]

                                                                      TensorCollection where all tensors are voigt symmetrized.

                                                                      -zeroed(tol: float = 0.001) → Self[source]
                                                                      +zeroed(tol: float = 0.001) → Self[source]
                                                                      Parameters:

                                                                      tol – Tolerance.

                                                                      @@ -14134,7 +14134,7 @@

                                                                      Submodules
                                                                      -class TensorMapping(tensors: Sequence[Tensor] = (), values: Sequence = (), tol: float = 1e-05)[source]
                                                                      +class TensorMapping(tensors: Sequence[Tensor] = (), values: Sequence = (), tol: float = 1e-05)[source]

                                                                      Bases: MutableMapping

                                                                      Base class for tensor mappings, which function much like a dictionary, but use numpy routines to determine approximate @@ -14159,13 +14159,13 @@

                                                                      Submodules
                                                                      -items()[source]
                                                                      +items()[source]

                                                                      Items in mapping.

                                                                      -values()[source]
                                                                      +values()[source]

                                                                      Values in mapping.

                                                                      @@ -14173,13 +14173,13 @@

                                                                      Submodules
                                                                      -get_uvec(vec: NDArray) → NDArray[source]
                                                                      +get_uvec(vec: NDArray) → NDArray[source]

                                                                      Get a unit vector parallel to input vector.

                                                                      -symmetry_reduce(tensors, structure: Structure, tol: float = 1e-08, **kwargs) → TensorMapping[source]
                                                                      +symmetry_reduce(tensors, structure: Structure, tol: float = 1e-08, **kwargs) → TensorMapping[source]

                                                                      Convert a list of tensors corresponding to a structure and returns a dictionary consisting of unique tensor keys with SymmOp values corresponding to transformations that will result in derivative @@ -14209,7 +14209,7 @@

                                                                      Submodules
                                                                      -class Trajectory(species: list[str | Element | Species | DummySpecies | Composition], coords: list[list[Vector3D]] | np.ndarray | list[np.ndarray], charge: float | None = None, spin_multiplicity: float | None = None, lattice: Lattice | Matrix3D | list[Lattice] | list[Matrix3D] | np.ndarray | None = None, *, site_properties: SitePropsType | None = None, frame_properties: list[dict] | None = None, constant_lattice: bool | None = True, time_step: float | None = None, coords_are_displacement: bool = False, base_positions: list[list[Vector3D]] | np.ndarray | None = None)[source]
                                                                      +class Trajectory(species: list[str | Element | Species | DummySpecies | Composition], coords: list[list[Vector3D]] | np.ndarray | list[np.ndarray], charge: float | None = None, spin_multiplicity: float | None = None, lattice: Lattice | Matrix3D | list[Lattice] | list[Matrix3D] | np.ndarray | None = None, *, site_properties: SitePropsType | None = None, frame_properties: list[dict] | None = None, constant_lattice: bool | None = True, time_step: float | None = None, coords_are_displacement: bool = False, base_positions: list[list[Vector3D]] | np.ndarray | None = None)[source]

                                                                      Bases: MSONable

                                                                      Trajectory of a geometry optimization or molecular dynamics simulation.

                                                                      Provides basic functions such as slicing trajectory, combining trajectories, and @@ -14278,13 +14278,13 @@

                                                                      Submodules
                                                                      -as_dict() → dict[source]
                                                                      +as_dict() → dict[source]

                                                                      Return the trajectory as a MSONable dict.

                                                                      -extend(trajectory: Self) → None[source]
                                                                      +extend(trajectory: Self) → None[source]

                                                                      Append a trajectory to the current one.

                                                                      The lattice, coords, and all other properties are combined.

                                                                      @@ -14296,7 +14296,7 @@

                                                                      Submodules
                                                                      -classmethod from_file(filename: str | Path, constant_lattice: bool = True, **kwargs) → Self[source]
                                                                      +classmethod from_file(filename: str | Path, constant_lattice: bool = True, **kwargs) → Self[source]

                                                                      Create trajectory from XDATCAR, vasprun.xml file, or ASE trajectory (.traj) file.

                                                                      Parameters:
                                                                      @@ -14318,7 +14318,7 @@

                                                                      Submodules
                                                                      -classmethod from_molecules(molecules: list[Molecule], **kwargs) → Self[source]
                                                                      +classmethod from_molecules(molecules: list[Molecule], **kwargs) → Self[source]

                                                                      Create trajectory from a list of molecules.

                                                                      Note: Assumes no atoms removed during simulation.

                                                                      @@ -14336,7 +14336,7 @@

                                                                      Submodules
                                                                      -classmethod from_structures(structures: list[Structure], constant_lattice: bool = True, **kwargs) → Self[source]
                                                                      +classmethod from_structures(structures: list[Structure], constant_lattice: bool = True, **kwargs) → Self[source]

                                                                      Create trajectory from a list of structures.

                                                                      Note: Assumes no atoms removed during simulation.

                                                                      @@ -14356,7 +14356,7 @@

                                                                      Submodules
                                                                      -get_molecule(idx: int) → Molecule[source]
                                                                      +get_molecule(idx: int) → Molecule[source]

                                                                      Get molecule at specified index.

                                                                      Parameters:
                                                                      @@ -14370,7 +14370,7 @@

                                                                      Submodules
                                                                      -get_structure(idx: int) → Structure[source]
                                                                      +get_structure(idx: int) → Structure[source]

                                                                      Get structure at specified index.

                                                                      Parameters:
                                                                      @@ -14384,7 +14384,7 @@

                                                                      Submodules
                                                                      -to_displacements() → None[source]
                                                                      +to_displacements() → None[source]

                                                                      Convert positions of trajectory into displacements between consecutive frames.

                                                                      base_positions and coords should both be in fractional coords. Does not work for absolute coords because the atoms are to be wrapped into the @@ -14394,7 +14394,7 @@

                                                                      Submodules
                                                                      -to_positions() → None[source]
                                                                      +to_positions() → None[source]

                                                                      Convert displacements between consecutive frames into positions.

                                                                      base_positions and coords should both be in fractional coords or absolute coords.

                                                                      @@ -14403,7 +14403,7 @@

                                                                      Submodules
                                                                      -write_Xdatcar(filename: PathLike = 'XDATCAR', system: str | None = None, significant_figures: int = 6) → None[source]
                                                                      +write_Xdatcar(filename: PathLike = 'XDATCAR', system: str | None = None, significant_figures: int = 6) → None[source]

                                                                      Write to Xdatcar file.

                                                                      The supported kwargs are the same as those for the Xdatcar_from_structs.get_str method and are passed through directly.

                                                                      @@ -14438,7 +14438,7 @@

                                                                      Submodules
                                                                      -class ArrayWithUnit(input_array: NDArray, unit: str | Unit, unit_type: str | None = None)[source]
                                                                      +class ArrayWithUnit(input_array: NDArray, unit: str | Unit, unit_type: str | None = None)[source]

                                                                      Bases: ndarray

                                                                      Subclasses numpy.ndarray to attach a unit type. Typically, you should use the pre-defined unit type subclasses such as EnergyArray, @@ -14458,7 +14458,7 @@

                                                                      Submodules
                                                                      -property as_base_units[source]
                                                                      +property as_base_units[source]

                                                                      This ArrayWithUnit in base SI units, including derived units.

                                                                      Returns:
                                                                      @@ -14469,20 +14469,20 @@

                                                                      Submodules
                                                                      -conversions() → str[source]
                                                                      +conversions() → str[source]

                                                                      Get a string showing the available conversions. Useful tool in interactive mode.

                                                                      -property supported_units: dict[source]
                                                                      +property supported_units: dict[source]

                                                                      Supported units for specific unit type.

                                                                      -to(new_unit: str | Unit) → Self[source]
                                                                      +to(new_unit: str | Unit) → Self[source]

                                                                      Convert to a new unit.

                                                                      Parameters:
                                                                      @@ -14500,13 +14500,13 @@

                                                                      Submodules
                                                                      -property unit: Unit[source]
                                                                      +property unit: Unit[source]

                                                                      The unit, e.g. “eV”.

                                                                      -property unit_type: str | None[source]
                                                                      +property unit_type: str | None[source]

                                                                      The type of unit. Energy, Charge, etc.

                                                                      @@ -14514,7 +14514,7 @@

                                                                      Submodules
                                                                      -Charge = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='charge')[source]
                                                                      +Charge = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='charge')[source]

                                                                      A float with a charge unit.

                                                                      Parameters:
                                                                      @@ -14529,7 +14529,7 @@

                                                                      Submodules
                                                                      -Energy = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='energy')[source]
                                                                      +Energy = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='energy')[source]

                                                                      A float with an energy unit.

                                                                      Parameters:
                                                                      @@ -14543,7 +14543,7 @@

                                                                      Submodules
                                                                      -class FloatWithUnit(val, unit: str | Unit, unit_type: str | None = None)[source]
                                                                      +class FloatWithUnit(val, unit: str | Unit, unit_type: str | None = None)[source]

                                                                      Bases: float

                                                                      Subclasses float to attach a unit type. Typically, you should use the pre-defined unit type subclasses such as Energy, Length, etc. instead of @@ -14578,7 +14578,7 @@

                                                                      Submodules
                                                                      -property as_base_units[source]
                                                                      +property as_base_units[source]

                                                                      This FloatWithUnit in base SI units, including derived units.

                                                                      Returns:
                                                                      @@ -14589,7 +14589,7 @@

                                                                      Submodules
                                                                      -classmethod from_str(string: str) → Self[source]
                                                                      +classmethod from_str(string: str) → Self[source]

                                                                      Convert string to FloatWithUnit.

                                                                      Example usage:

                                                                      Memory.from_str(“1. Mb”).

                                                                      @@ -14599,13 +14599,13 @@

                                                                      Submodules
                                                                      -property supported_units: tuple[source]
                                                                      +property supported_units: tuple[source]

                                                                      Supported units for specific unit type.

                                                                      -to(new_unit: str | Unit) → Self[source]
                                                                      +to(new_unit: str | Unit) → Self[source]

                                                                      Convert to a new unit. Right now, only support 1 to 1 mapping of units of each type.

                                                                      @@ -14625,13 +14625,13 @@

                                                                      Submodules
                                                                      -property unit: Unit[source]
                                                                      +property unit: Unit[source]

                                                                      The unit, e.g. “eV”.

                                                                      -property unit_type: str | None[source]
                                                                      +property unit_type: str | None[source]

                                                                      The type of unit. Energy, Charge, etc.

                                                                      @@ -14639,7 +14639,7 @@

                                                                      Submodules
                                                                      -Length = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='length')[source]
                                                                      +Length = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='length')[source]

                                                                      A float with a length unit.

                                                                      Parameters:
                                                                      @@ -14654,7 +14654,7 @@

                                                                      Submodules
                                                                      -Mass = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='mass')[source]
                                                                      +Mass = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='mass')[source]

                                                                      A float with a mass unit.

                                                                      Parameters:
                                                                      @@ -14669,7 +14669,7 @@

                                                                      Submodules
                                                                      -Memory = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='memory')[source]
                                                                      +Memory = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='memory')[source]

                                                                      A float with a memory unit.

                                                                      Parameters:
                                                                      @@ -14684,7 +14684,7 @@

                                                                      Submodules
                                                                      -Temp = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='temperature')[source]
                                                                      +Temp = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='temperature')[source]

                                                                      A float with a temperature unit.

                                                                      Parameters:
                                                                      @@ -14698,7 +14698,7 @@

                                                                      Submodules
                                                                      -Time = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='time')[source]
                                                                      +Time = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='time')[source]

                                                                      A float with a time unit.

                                                                      Parameters:
                                                                      @@ -14713,7 +14713,7 @@

                                                                      Submodules
                                                                      -class Unit(unit_def: str | dict[str, int])[source]
                                                                      +class Unit(unit_def: str | dict[str, int])[source]

                                                                      Bases: Mapping

                                                                      Represent a unit, e.g. “m” for meters, etc. Supports compound units. Only integer powers are supported.

                                                                      @@ -14728,7 +14728,7 @@

                                                                      Submodules
                                                                      -property as_base_units: tuple[dict, float][source]
                                                                      +property as_base_units: tuple[dict, float][source]

                                                                      Convert all units to base SI units, including derived units.

                                                                      Returns:
                                                                      @@ -14746,7 +14746,7 @@

                                                                      Submodules
                                                                      -get_conversion_factor(new_unit: str | Unit) → float[source]
                                                                      +get_conversion_factor(new_unit: str | Unit) → float[source]

                                                                      Get the conversion factor between this unit and a new unit. Compound units are supported, but must have the same powers in each unit type.

                                                                      @@ -14761,14 +14761,14 @@

                                                                      Submodules
                                                                      -exception UnitError[source]
                                                                      +exception UnitError[source]

                                                                      Bases: BaseException

                                                                      Exception class for unit errors.

                                                                      -obj_with_unit(obj: Any, unit: str) → FloatWithUnit | ArrayWithUnit | dict[str, FloatWithUnit | ArrayWithUnit][source]
                                                                      +obj_with_unit(obj: Any, unit: str) → FloatWithUnit | ArrayWithUnit | dict[str, FloatWithUnit | ArrayWithUnit][source]

                                                                      Get a FloatWithUnit instance if obj is scalar, a dictionary of objects with units if obj is a dict, else an instance of ArrayWithUnit.

                                                                      @@ -14784,7 +14784,7 @@

                                                                      Submodules
                                                                      -unitized(unit)[source]
                                                                      +unitized(unit)[source]

                                                                      Decorator to assign units to the output of a function. You can also use it to standardize the output units of a function that already returns a FloatWithUnit or ArrayWithUnit. For sequences, all values in the sequences @@ -14810,7 +14810,7 @@

                                                                      Submodules
                                                                      -class XcFunc(xc: LibxcFunc | None = None, x: LibxcFunc | None = None, c: LibxcFunc | None = None)[source]
                                                                      +class XcFunc(xc: LibxcFunc | None = None, x: LibxcFunc | None = None, c: LibxcFunc | None = None)[source]

                                                                      Bases: MSONable

                                                                      Store information about the XC correlation functional.

                                                                      Client code usually creates the object by calling the class methods:

                                                                      @@ -14867,84 +14867,84 @@

                                                                      Submodules
                                                                      -abinitixc_to_libxc: ClassVar[dict[int, dict[str, LibxcFunc]]] = {1: {'xc': LibxcFunc(name='LDA_XC_TETER93', kind='EXCHANGE_CORRELATION', family='LDA')}, 2: {'c': LibxcFunc(name='LDA_C_PZ', kind='CORRELATION', family='LDA'), 'x': LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA')}, 4: {'c': LibxcFunc(name='LDA_C_WIGNER', kind='CORRELATION', family='LDA'), 'x': LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA')}, 5: {'c': LibxcFunc(name='LDA_C_HL', kind='CORRELATION', family='LDA'), 'x': LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA')}, 7: {'c': LibxcFunc(name='LDA_C_PW', kind='CORRELATION', family='LDA'), 'x': LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA')}, 11: {'c': LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA'), 'x': LibxcFunc(name='GGA_X_PBE', kind='EXCHANGE', family='GGA')}, 14: {'c': LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA'), 'x': LibxcFunc(name='GGA_X_PBE_R', kind='EXCHANGE', family='GGA')}, 15: {'c': LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA'), 'x': LibxcFunc(name='GGA_X_RPBE', kind='EXCHANGE', family='GGA')}}[source]
                                                                      +abinitixc_to_libxc: ClassVar[dict[int, dict[str, LibxcFunc]]] = {1: {'xc': LibxcFunc(name='LDA_XC_TETER93', kind='EXCHANGE_CORRELATION', family='LDA')}, 2: {'c': LibxcFunc(name='LDA_C_PZ', kind='CORRELATION', family='LDA'), 'x': LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA')}, 4: {'c': LibxcFunc(name='LDA_C_WIGNER', kind='CORRELATION', family='LDA'), 'x': LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA')}, 5: {'c': LibxcFunc(name='LDA_C_HL', kind='CORRELATION', family='LDA'), 'x': LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA')}, 7: {'c': LibxcFunc(name='LDA_C_PW', kind='CORRELATION', family='LDA'), 'x': LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA')}, 11: {'c': LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA'), 'x': LibxcFunc(name='GGA_X_PBE', kind='EXCHANGE', family='GGA')}, 14: {'c': LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA'), 'x': LibxcFunc(name='GGA_X_PBE_R', kind='EXCHANGE', family='GGA')}, 15: {'c': LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA'), 'x': LibxcFunc(name='GGA_X_RPBE', kind='EXCHANGE', family='GGA')}}[source]

                                                                      -classmethod aliases() → list[str][source]
                                                                      +classmethod aliases() → list[str][source]

                                                                      List of registered names.

                                                                      -as_dict() → dict[source]
                                                                      +as_dict() → dict[source]

                                                                      Serialize to MSONable dict representation e.g. to write to disk as JSON.

                                                                      -classmethod asxc(obj) → Self[source]
                                                                      +classmethod asxc(obj) → Self[source]

                                                                      Convert to XcFunc.

                                                                      -defined_aliases: ClassVar[dict[tuple[LibxcFunc, LibxcFunc], type_name]] = {(LibxcFunc(name='GGA_X_AM05', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_AM05', kind='CORRELATION', family='GGA')): ('GGA', 'AM05'), (LibxcFunc(name='GGA_X_B88', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_LYP', kind='CORRELATION', family='GGA')): ('GGA', 'BLYP'), (LibxcFunc(name='GGA_X_PBE', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA')): ('GGA', 'PBE'), (LibxcFunc(name='GGA_X_PBE_R', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA')): ('GGA', 'revPBE'), (LibxcFunc(name='GGA_X_PBE_SOL', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PBE_SOL', kind='CORRELATION', family='GGA')): ('GGA', 'PBEsol'), (LibxcFunc(name='GGA_X_PW91', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PW91', kind='CORRELATION', family='GGA')): ('GGA', 'PW91'), (LibxcFunc(name='GGA_X_RPBE', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA')): ('GGA', 'RPBE'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_GL', kind='CORRELATION', family='LDA')): ('LDA', 'GL'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_HL', kind='CORRELATION', family='LDA')): ('LDA', 'HL'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_PW', kind='CORRELATION', family='LDA')): ('LDA', 'PW'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_PW_MOD', kind='CORRELATION', family='LDA')): ('LDA', 'PW_MOD'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_PZ', kind='CORRELATION', family='LDA')): ('LDA', 'PZ'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_VWN', kind='CORRELATION', family='LDA')): ('LDA', 'VWN'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_WIGNER', kind='CORRELATION', family='LDA')): ('LDA', 'W')}[source]
                                                                      +defined_aliases: ClassVar[dict[tuple[LibxcFunc, LibxcFunc], type_name]] = {(LibxcFunc(name='GGA_X_AM05', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_AM05', kind='CORRELATION', family='GGA')): ('GGA', 'AM05'), (LibxcFunc(name='GGA_X_B88', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_LYP', kind='CORRELATION', family='GGA')): ('GGA', 'BLYP'), (LibxcFunc(name='GGA_X_PBE', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA')): ('GGA', 'PBE'), (LibxcFunc(name='GGA_X_PBE_R', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA')): ('GGA', 'revPBE'), (LibxcFunc(name='GGA_X_PBE_SOL', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PBE_SOL', kind='CORRELATION', family='GGA')): ('GGA', 'PBEsol'), (LibxcFunc(name='GGA_X_PW91', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PW91', kind='CORRELATION', family='GGA')): ('GGA', 'PW91'), (LibxcFunc(name='GGA_X_RPBE', kind='EXCHANGE', family='GGA'), LibxcFunc(name='GGA_C_PBE', kind='CORRELATION', family='GGA')): ('GGA', 'RPBE'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_GL', kind='CORRELATION', family='LDA')): ('LDA', 'GL'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_HL', kind='CORRELATION', family='LDA')): ('LDA', 'HL'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_PW', kind='CORRELATION', family='LDA')): ('LDA', 'PW'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_PW_MOD', kind='CORRELATION', family='LDA')): ('LDA', 'PW_MOD'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_PZ', kind='CORRELATION', family='LDA')): ('LDA', 'PZ'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_VWN', kind='CORRELATION', family='LDA')): ('LDA', 'VWN'), (LibxcFunc(name='LDA_X', kind='EXCHANGE', family='LDA'), LibxcFunc(name='LDA_C_WIGNER', kind='CORRELATION', family='LDA')): ('LDA', 'W')}[source]
                                                                      -classmethod from_abinit_ixc(ixc: int) → Self | None[source]
                                                                      +classmethod from_abinit_ixc(ixc: int) → Self | None[source]

                                                                      Build the object from Abinit ixc (integer).

                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                      +classmethod from_dict(dct: dict) → Self[source]

                                                                      Deserialize from MSONable dict representation.

                                                                      -classmethod from_name(name: str) → Self[source]
                                                                      +classmethod from_name(name: str) → Self[source]

                                                                      Build the object from one of the registered names.

                                                                      -classmethod from_type_name(typ: str | None, name: str) → Self[source]
                                                                      +classmethod from_type_name(typ: str | None, name: str) → Self[source]

                                                                      Build the object from (type, name).

                                                                      -name()[source]
                                                                      +name()[source]

                                                                      The name of the functional. If the functional is not found in the aliases, the string has the form X_NAME+C_NAME.

                                                                      -type()[source]
                                                                      +type()[source]

                                                                      The type of the functional.

                                                                      -class type_name(type: Literal['LDA', 'GGA'], name: str)[source]
                                                                      +class type_name(type: Literal['LDA', 'GGA'], name: str)[source]

                                                                      Bases: NamedTuple

                                                                      Type and name of the XcFunc.

                                                                      Create new instance of type_name(type, name)

                                                                      -name: str[source]
                                                                      +name: str[source]

                                                                      Alias for field number 1

                                                                      -type: Literal['LDA', 'GGA'][source]
                                                                      +type: Literal['LDA', 'GGA'][source]

                                                                      Alias for field number 0

                                                                      @@ -14952,7 +14952,7 @@

                                                                      Submodules
                                                                      -xcf[source]
                                                                      +xcf[source]

                                                                      alias of LibxcFunc

                                                                      diff --git a/docs/pymatgen.electronic_structure.html b/docs/pymatgen.electronic_structure.html index 0bf865a3fe4..f563ea5c9fa 100644 --- a/docs/pymatgen.electronic_structure.html +++ b/docs/pymatgen.electronic_structure.html @@ -4,7 +4,7 @@ - pymatgen.electronic_structure package — pymatgen 2024.6.4 documentation + pymatgen.electronic_structure package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                      - 2024.6.4 + 2024.6.10
                                                                      @@ -458,13 +458,13 @@

                                                                      Submodules
                                                                      -class BandStructure(kpoints: ndarray, eigenvals: dict[Spin, ndarray], lattice: Lattice, efermi: float, labels_dict=None, coords_are_cartesian: bool = False, structure: Structure | None = None, projections: dict[Spin, ndarray] | None = None)[source]
                                                                      +class BandStructure(kpoints: ndarray, eigenvals: dict[Spin, ndarray], lattice: Lattice, efermi: float, labels_dict=None, coords_are_cartesian: bool = False, structure: Structure | None = None, projections: dict[Spin, ndarray] | None = None)[source]

                                                                      Bases: object

                                                                      This is the most generic band structure data possible it’s defined by a list of kpoints + energies for each of them.

                                                                      -kpoints[source]
                                                                      +kpoints[source]

                                                                      The list of kpoints (as Kpoint objects) in the band structure.

                                                                      Type:
                                                                      @@ -475,7 +475,7 @@

                                                                      Submodules
                                                                      -lattice_rec[source]
                                                                      +lattice_rec[source]

                                                                      The reciprocal lattice of the band structure.

                                                                      Type:
                                                                      @@ -486,7 +486,7 @@

                                                                      Submodules
                                                                      -efermi[source]
                                                                      +efermi[source]

                                                                      The Fermi energy.

                                                                      Type:
                                                                      @@ -497,7 +497,7 @@

                                                                      Submodules
                                                                      -is_spin_polarized[source]
                                                                      +is_spin_polarized[source]

                                                                      True if the band structure is spin-polarized.

                                                                      Type:
                                                                      @@ -508,7 +508,7 @@

                                                                      Submodules
                                                                      -bands[source]
                                                                      +bands[source]

                                                                      The energy eigenvalues as a {spin: array}. Note that the use of an array is necessary for computational as well as memory efficiency due to the large amount of numerical data. The indices of the array are [band_index, kpoint_index].

                                                                      @@ -521,7 +521,7 @@

                                                                      Submodules
                                                                      -nb_bands[source]
                                                                      +nb_bands[source]

                                                                      Returns the number of bands in the band structure.

                                                                      Type:
                                                                      @@ -532,7 +532,7 @@

                                                                      Submodules
                                                                      -structure[source]
                                                                      +structure[source]

                                                                      Returns the structure.

                                                                      Type:
                                                                      @@ -543,7 +543,7 @@

                                                                      Submodules
                                                                      -projections[source]
                                                                      +projections[source]

                                                                      The projections as a {spin: array}. Note that the use of an array is necessary for computational as well as memory efficiency due to the large amount of numerical data. The indices of the array are [band_index, kpoint_index, @@ -585,13 +585,13 @@

                                                                      Submodules
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      JSON-serializable dict representation of BandStructure.

                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                      +classmethod from_dict(dct: dict) → Self[source]

                                                                      Create from dict.

                                                                      Parameters:
                                                                      @@ -605,7 +605,7 @@

                                                                      Submodules
                                                                      -classmethod from_old_dict(dct) → Self[source]
                                                                      +classmethod from_old_dict(dct) → Self[source]
                                                                      Parameters:

                                                                      dct (dict) – A dict with all data for a band structure symmetry line object.

                                                                      @@ -618,7 +618,7 @@

                                                                      Submodules
                                                                      -get_band_gap()[source]
                                                                      +get_band_gap()[source]

                                                                      Get band gap data.

                                                                      Returns:
                                                                      @@ -634,7 +634,7 @@

                                                                      Submodules
                                                                      -get_cbm()[source]
                                                                      +get_cbm()[source]

                                                                      Get data about the CBM.

                                                                      Returns:
                                                                      @@ -667,7 +667,7 @@

                                                                      Submodules
                                                                      -get_direct_band_gap()[source]
                                                                      +get_direct_band_gap()[source]

                                                                      Get the direct band gap.

                                                                      Returns:
                                                                      @@ -678,7 +678,7 @@

                                                                      Submodules
                                                                      -get_direct_band_gap_dict()[source]
                                                                      +get_direct_band_gap_dict()[source]

                                                                      Get a dictionary of information about the direct band gap.

                                                                      @@ -691,7 +691,7 @@

                                                                      Submodules
                                                                      -get_kpoint_degeneracy(kpoint, cartesian=False, tol: float = 0.01)[source]
                                                                      +get_kpoint_degeneracy(kpoint, cartesian=False, tol: float = 0.01)[source]

                                                                      Get degeneracy of a given k-point based on structure symmetry.

                                                                      Parameters:
                                                                      @@ -712,7 +712,7 @@

                                                                      Submodules
                                                                      -get_projection_on_elements()[source]
                                                                      +get_projection_on_elements()[source]

                                                                      Get a dictionary of projections on elements.

                                                                      Returns:
                                                                      @@ -729,7 +729,7 @@

                                                                      Submodules
                                                                      -get_projections_on_elements_and_orbitals(el_orb_spec: dict[str, list[str]])[source]
                                                                      +get_projections_on_elements_and_orbitals(el_orb_spec: dict[str, list[str]])[source]

                                                                      Get a dictionary of projections on elements and specific orbitals.

                                                                      Parameters:
                                                                      @@ -747,7 +747,7 @@

                                                                      Submodules
                                                                      -get_sym_eq_kpoints(kpoint, cartesian=False, tol: float = 0.01)[source]
                                                                      +get_sym_eq_kpoints(kpoint, cartesian=False, tol: float = 0.01)[source]

                                                                      Get a list of unique symmetrically equivalent k-points.

                                                                      Parameters:
                                                                      @@ -768,7 +768,7 @@

                                                                      Submodules
                                                                      -get_vbm()[source]
                                                                      +get_vbm()[source]

                                                                      Get data about the VBM.

                                                                      Returns:
                                                                      @@ -797,7 +797,7 @@

                                                                      Submodules
                                                                      -is_metal(efermi_tol=0.0001) → bool[source]
                                                                      +is_metal(efermi_tol=0.0001) → bool[source]

                                                                      Check if the band structure indicates a metal by looking if the fermi level crosses a band.

                                                                      @@ -814,7 +814,7 @@

                                                                      Submodules
                                                                      -class BandStructureSymmLine(kpoints, eigenvals, lattice, efermi, labels_dict, coords_are_cartesian=False, structure=None, projections=None)[source]
                                                                      +class BandStructureSymmLine(kpoints, eigenvals, lattice, efermi, labels_dict, coords_are_cartesian=False, structure=None, projections=None)[source]

                                                                      Bases: BandStructure, MSONable

                                                                      Store band structures along selected (symmetry) lines in the Brillouin zone. We call the different symmetry lines (ex: \Gamma to Z) “branches”.

                                                                      @@ -848,7 +848,7 @@

                                                                      Submodules
                                                                      -apply_scissor(new_band_gap)[source]
                                                                      +apply_scissor(new_band_gap)[source]

                                                                      Apply a scissor operator (shift of the CBM) to fit the given band gap. If it’s a metal, we look for the band crossing the Fermi level and shift this one up. This will not work all the time for metals!

                                                                      @@ -867,13 +867,13 @@

                                                                      Submodules
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      JSON-serializable dict representation of BandStructureSymmLine.

                                                                      -get_branch(index)[source]
                                                                      +get_branch(index)[source]

                                                                      Get in what branch(es) is the kpoint. There can be several branches.

                                                                      @@ -891,7 +891,7 @@

                                                                      Submodules
                                                                      -get_equivalent_kpoints(index)[source]
                                                                      +get_equivalent_kpoints(index)[source]

                                                                      Get the list of kpoint indices equivalent (meaning they are the same frac coords) to the given one.

                                                                      @@ -910,7 +910,7 @@

                                                                      Submodules
                                                                      -class Kpoint(coords: ndarray, lattice: Lattice, to_unit_cell: bool = False, coords_are_cartesian: bool = False, label: str | None = None)[source]
                                                                      +class Kpoint(coords: ndarray, lattice: Lattice, to_unit_cell: bool = False, coords_are_cartesian: bool = False, label: str | None = None)[source]

                                                                      Bases: MSONable

                                                                      Store kpoint objects. A kpoint is defined with a lattice and frac or Cartesian coordinates syntax similar than the site object in @@ -932,43 +932,43 @@

                                                                      Submodules
                                                                      -property a: float[source]
                                                                      +property a: float[source]

                                                                      Fractional a coordinate of the kpoint.

                                                                      -as_dict() → dict[str, Any][source]
                                                                      +as_dict() → dict[str, Any][source]

                                                                      JSON-serializable dict representation of a kpoint.

                                                                      -property b: float[source]
                                                                      +property b: float[source]

                                                                      Fractional b coordinate of the kpoint.

                                                                      -property c: float[source]
                                                                      +property c: float[source]

                                                                      Fractional c coordinate of the kpoint.

                                                                      -property cart_coords: ndarray[source]
                                                                      +property cart_coords: ndarray[source]

                                                                      The Cartesian coordinates of the kpoint as a numpy array.

                                                                      -property frac_coords: ndarray[source]
                                                                      +property frac_coords: ndarray[source]

                                                                      The fractional coordinates of the kpoint as a numpy array.

                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                      +classmethod from_dict(dct: dict) → Self[source]

                                                                      Create from dict.

                                                                      Parameters:
                                                                      @@ -982,13 +982,13 @@

                                                                      Submodules
                                                                      -property label: str | None[source]
                                                                      +property label: str | None[source]

                                                                      The label associated with the kpoint.

                                                                      -property lattice: Lattice[source]
                                                                      +property lattice: Lattice[source]

                                                                      The lattice associated with the kpoint. It’s a pymatgen.core.Lattice object.

                                                                      @@ -997,7 +997,7 @@

                                                                      Submodules
                                                                      -class LobsterBandStructureSymmLine(kpoints, eigenvals, lattice, efermi, labels_dict, coords_are_cartesian=False, structure=None, projections=None)[source]
                                                                      +class LobsterBandStructureSymmLine(kpoints, eigenvals, lattice, efermi, labels_dict, coords_are_cartesian=False, structure=None, projections=None)[source]

                                                                      Bases: BandStructureSymmLine

                                                                      Lobster subclass of BandStructure with customized functions.

                                                                      @@ -1030,13 +1030,13 @@

                                                                      Submodules
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      JSON-serializable dict representation of BandStructureSymmLine.

                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                      Parameters:

                                                                      dct (dict) – A dict with all data for a band structure symmetry line @@ -1050,7 +1050,7 @@

                                                                      Submodules
                                                                      -classmethod from_old_dict(dct) → Self[source]
                                                                      +classmethod from_old_dict(dct) → Self[source]
                                                                      Parameters:

                                                                      dct (dict) – A dict with all data for a band structure symmetry line @@ -1064,7 +1064,7 @@

                                                                      Submodules
                                                                      -get_projection_on_elements()[source]
                                                                      +get_projection_on_elements()[source]

                                                                      Get a dictionary of projections on elements. It sums over all available orbitals for each element.

                                                                      @@ -1082,7 +1082,7 @@

                                                                      Submodules
                                                                      -get_projections_on_elements_and_orbitals(el_orb_spec)[source]
                                                                      +get_projections_on_elements_and_orbitals(el_orb_spec)[source]

                                                                      Return a dictionary of projections on elements and specific orbitals.

                                                                      Parameters:
                                                                      @@ -1104,7 +1104,7 @@

                                                                      Submodules
                                                                      -get_reconstructed_band_structure(list_bs, efermi=None)[source]
                                                                      +get_reconstructed_band_structure(list_bs, efermi=None)[source]

                                                                      Take a list of band structures and reconstructs one band structure object from all of them.

                                                                      This is typically very useful when you split non self consistent @@ -1144,7 +1144,7 @@

                                                                      Submodules
                                                                      -class BoltztrapAnalyzer(gap=None, mu_steps=None, cond=None, seebeck=None, kappa=None, hall=None, doping=None, mu_doping=None, seebeck_doping=None, cond_doping=None, kappa_doping=None, hall_doping=None, intrans=None, dos=None, dos_partial=None, carrier_conc=None, vol=None, warning=None, bz_bands=None, bz_kpoints=None, fermi_surface_data=None)[source]
                                                                      +class BoltztrapAnalyzer(gap=None, mu_steps=None, cond=None, seebeck=None, kappa=None, hall=None, doping=None, mu_doping=None, seebeck_doping=None, cond_doping=None, kappa_doping=None, hall_doping=None, intrans=None, dos=None, dos_partial=None, carrier_conc=None, vol=None, warning=None, bz_bands=None, bz_kpoints=None, fermi_surface_data=None)[source]

                                                                      Bases: object

                                                                      Store all the data from a boltztrap run.

                                                                      Constructor taking directly all the data generated by Boltztrap. You @@ -1232,13 +1232,13 @@

                                                                      Submodules
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      MSONable dict.

                                                                      -static check_acc_bzt_bands(sbs_bz, sbs_ref, warn_thr=(0.03, 0.03))[source]
                                                                      +static check_acc_bzt_bands(sbs_bz, sbs_ref, warn_thr=(0.03, 0.03))[source]

                                                                      Compare sbs_bz BandStructureSymmLine calculated with boltztrap with the sbs_ref BandStructureSymmLine as reference (from MP for instance), computing correlation and energy difference for eight bands @@ -1271,7 +1271,7 @@

                                                                      Submodules
                                                                      -classmethod from_dict(data: dict) → Self[source]
                                                                      +classmethod from_dict(data: dict) → Self[source]
                                                                      Parameters:

                                                                      data – Dict representation.

                                                                      @@ -1284,7 +1284,7 @@

                                                                      Submodules
                                                                      -classmethod from_files(path_dir: str, dos_spin: Literal[-1, 1] = 1) → Self[source]
                                                                      +classmethod from_files(path_dir: str, dos_spin: Literal[-1, 1] = 1) → Self[source]

                                                                      Get a BoltztrapAnalyzer object from a set of files.

                                                                      Parameters:
                                                                      @@ -1301,7 +1301,7 @@

                                                                      Submodules
                                                                      -get_average_eff_mass(output='eigs', doping_levels=True)[source]
                                                                      +get_average_eff_mass(output='eigs', doping_levels=True)[source]

                                                                      Get the average effective mass tensor. We call it average because it takes into account all the bands and regions in the Brillouin zone. This is different than the standard @@ -1355,7 +1355,7 @@

                                                                      Submodules
                                                                      -get_carrier_concentration()[source]
                                                                      +get_carrier_concentration()[source]

                                                                      Get the carrier concentration (in cm^-3).

                                                                      Returns:
                                                                      @@ -1371,7 +1371,7 @@

                                                                      Submodules
                                                                      -get_complete_dos(structure: Structure, analyzer_for_second_spin=None)[source]
                                                                      +get_complete_dos(structure: Structure, analyzer_for_second_spin=None)[source]

                                                                      Get a CompleteDos object with the DOS from the interpolated projected band structure.

                                                                      Parameters:
                                                                      @@ -1399,7 +1399,7 @@

                                                                      Submodules
                                                                      -get_complexity_factor(output: Literal['average', 'tensor'] = 'average', temp=300, doping_levels=False, Lambda=0.5)[source]
                                                                      +get_complexity_factor(output: Literal['average', 'tensor'] = 'average', temp=300, doping_levels=False, Lambda=0.5)[source]

                                                                      Fermi surface complexity factor respect to calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor from ab initio band structure calculations. @@ -1433,7 +1433,7 @@

                                                                      Submodules
                                                                      -get_conductivity(output='eigs', doping_levels=True, relaxation_time=1e-14)[source]
                                                                      +get_conductivity(output='eigs', doping_levels=True, relaxation_time=1e-14)[source]

                                                                      Get the conductivity (1/Ohm*m) in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If doping_levels=True, the results are given at @@ -1476,7 +1476,7 @@

                                                                      Submodules
                                                                      -get_extreme(target_prop, maximize=True, min_temp=None, max_temp=None, min_doping=None, max_doping=None, isotropy_tolerance=0.05, use_average=True)[source]
                                                                      +get_extreme(target_prop, maximize=True, min_temp=None, max_temp=None, min_doping=None, max_doping=None, isotropy_tolerance=0.05, use_average=True)[source]

                                                                      Use eigenvalues over a range of carriers, temperatures, and doping levels, to estimate the “best” value that can be achieved for the given target_property. Note that this method searches the doping dict only, not the full mu dict.

                                                                      @@ -1504,7 +1504,7 @@

                                                                      Submodules
                                                                      -get_hall_carrier_concentration()[source]
                                                                      +get_hall_carrier_concentration()[source]

                                                                      Get the Hall carrier concentration (in cm^-3). This is the trace of the Hall tensor (see Boltztrap source code) Hall carrier concentration are not always exactly the same than carrier concentration.

                                                                      @@ -1522,7 +1522,7 @@

                                                                      Submodules
                                                                      -get_mu_bounds(temp=300)[source]
                                                                      +get_mu_bounds(temp=300)[source]
                                                                      Parameters:

                                                                      temp – Temperature.

                                                                      @@ -1535,7 +1535,7 @@

                                                                      Submodules
                                                                      -get_power_factor(output='eigs', doping_levels=True, relaxation_time=1e-14)[source]
                                                                      +get_power_factor(output='eigs', doping_levels=True, relaxation_time=1e-14)[source]

                                                                      Get the power factor (Seebeck^2 * conductivity) in units microW/(m*K^2) in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If @@ -1579,7 +1579,7 @@

                                                                      Submodules
                                                                      -get_seebeck(output='eigs', doping_levels=True)[source]
                                                                      +get_seebeck(output='eigs', doping_levels=True)[source]

                                                                      Get the seebeck coefficient (microV/K) in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If doping_levels=True, the results are given at @@ -1620,7 +1620,7 @@

                                                                      Submodules
                                                                      -get_seebeck_eff_mass(output='average', temp=300, doping_levels=False, Lambda=0.5)[source]
                                                                      +get_seebeck_eff_mass(output='average', temp=300, doping_levels=False, Lambda=0.5)[source]

                                                                      Seebeck effective mass calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor from ab initio band structure calculations. @@ -1654,7 +1654,7 @@

                                                                      Submodules
                                                                      -get_symm_bands(structure: Structure, efermi, kpt_line=None, labels_dict=None)[source]
                                                                      +get_symm_bands(structure: Structure, efermi, kpt_line=None, labels_dict=None)[source]

                                                                      Useful to read bands from Boltztrap output and get a BandStructureSymmLine object comparable with that one from a DFT calculation (if the same kpt_line is provided). Default kpt_line and labels_dict is the standard path of high symmetry @@ -1666,7 +1666,7 @@

                                                                      Submodules
                                                                      -get_thermal_conductivity(output='eigs', doping_levels=True, k_el=True, relaxation_time=1e-14)[source]
                                                                      +get_thermal_conductivity(output='eigs', doping_levels=True, k_el=True, relaxation_time=1e-14)[source]

                                                                      Get the electronic part of the thermal conductivity in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If @@ -1711,7 +1711,7 @@

                                                                      Submodules
                                                                      -get_zt(output='eigs', doping_levels=True, relaxation_time=1e-14, k_l=1)[source]
                                                                      +get_zt(output='eigs', doping_levels=True, relaxation_time=1e-14, k_l=1)[source]

                                                                      Get the ZT coefficient (S^2*cond*T/thermal cond) in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If @@ -1756,7 +1756,7 @@

                                                                      Submodules
                                                                      -static parse_cond_and_hall(path_dir, doping_levels=None)[source]
                                                                      +static parse_cond_and_hall(path_dir, doping_levels=None)[source]

                                                                      Parse the conductivity and Hall tensors.

                                                                      Parameters:
                                                                      @@ -1775,7 +1775,7 @@

                                                                      Submodules
                                                                      -static parse_intrans(path_dir)[source]
                                                                      +static parse_intrans(path_dir)[source]

                                                                      Parse boltztrap.intrans mainly to extract the value of scissor applied to the bands or some other inputs.

                                                                      @@ -1793,7 +1793,7 @@

                                                                      Submodules
                                                                      -static parse_outputtrans(path_dir)[source]
                                                                      +static parse_outputtrans(path_dir)[source]

                                                                      Parse .outputtrans file.

                                                                      Parameters:
                                                                      @@ -1807,7 +1807,7 @@

                                                                      Submodules
                                                                      -static parse_struct(path_dir)[source]
                                                                      +static parse_struct(path_dir)[source]

                                                                      Parse boltztrap.struct file (only the volume).

                                                                      Parameters:
                                                                      @@ -1824,7 +1824,7 @@

                                                                      Submodules
                                                                      -static parse_transdos(path_dir, efermi, dos_spin=1, trim_dos=False)[source]
                                                                      +static parse_transdos(path_dir, efermi, dos_spin=1, trim_dos=False)[source]

                                                                      Parse .transdos (total DOS) and .transdos_x_y (partial DOS) files.

                                                                      Parameters:
                                                                      @@ -1845,7 +1845,7 @@

                                                                      Submodules
                                                                      -exception BoltztrapError[source]
                                                                      +exception BoltztrapError[source]

                                                                      Bases: Exception

                                                                      Exception class for boltztrap. Raised when the boltztrap gives an error.

                                                                      @@ -1853,7 +1853,7 @@

                                                                      Submodules
                                                                      -class BoltztrapRunner(bs, nelec, dos_type='HISTO', energy_grid=0.005, lpfac=10, run_type='BOLTZ', band_nb=None, tauref=0, tauexp=0, tauen=0, soc=False, doping=None, energy_span_around_fermi=1.5, scissor=0.0, kpt_line=None, spin=None, cond_band=False, tmax=1300, tgrid=50, symprec=0.001, cb_cut=10, timeout=7200)[source]
                                                                      +class BoltztrapRunner(bs, nelec, dos_type='HISTO', energy_grid=0.005, lpfac=10, run_type='BOLTZ', band_nb=None, tauref=0, tauexp=0, tauen=0, soc=False, doping=None, energy_span_around_fermi=1.5, scissor=0.0, kpt_line=None, spin=None, cond_band=False, tmax=1300, tgrid=50, symprec=0.001, cb_cut=10, timeout=7200)[source]

                                                                      Bases: MSONable

                                                                      This class is used to run Boltztrap on a band structure object.

                                                                      @@ -1928,25 +1928,25 @@

                                                                      Submodules
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      MSONable dict.

                                                                      -property bs[source]
                                                                      +property bs[source]

                                                                      The BandStructure.

                                                                      -property nelec[source]
                                                                      +property nelec[source]

                                                                      Number of electrons.

                                                                      -run(path_dir=None, convergence=True, write_input=True, clear_dir=False, max_lpfac=150, min_egrid=5e-05)[source]
                                                                      +run(path_dir=None, convergence=True, write_input=True, clear_dir=False, max_lpfac=150, min_egrid=5e-05)[source]

                                                                      Write inputs (optional), run BoltzTraP, and ensure convergence (optional).

                                                                      @@ -1970,7 +1970,7 @@

                                                                      Submodules
                                                                      -write_def(output_file) → None[source]
                                                                      +write_def(output_file) → None[source]

                                                                      Write the def to an output file.

                                                                      Parameters:
                                                                      @@ -1981,7 +1981,7 @@

                                                                      Submodules
                                                                      -write_energy(output_file) → None[source]
                                                                      +write_energy(output_file) → None[source]

                                                                      Write the energy to an output file.

                                                                      Parameters:
                                                                      @@ -1992,7 +1992,7 @@

                                                                      Submodules
                                                                      -write_input(output_dir) → None[source]
                                                                      +write_input(output_dir) → None[source]

                                                                      Write the input files.

                                                                      Parameters:
                                                                      @@ -2003,7 +2003,7 @@

                                                                      Submodules
                                                                      -write_intrans(output_file) → None[source]
                                                                      +write_intrans(output_file) → None[source]

                                                                      Write the intrans to an output file.

                                                                      Parameters:
                                                                      @@ -2014,7 +2014,7 @@

                                                                      Submodules
                                                                      -write_proj(output_file_proj: str, output_file_def: str) → None[source]
                                                                      +write_proj(output_file_proj: str, output_file_def: str) → None[source]

                                                                      Write the projections to an output file.

                                                                      Parameters:
                                                                      @@ -2028,7 +2028,7 @@

                                                                      Submodules
                                                                      -write_struct(output_file) → None[source]
                                                                      +write_struct(output_file) → None[source]

                                                                      Write the structure to an output file.

                                                                      Parameters:
                                                                      @@ -2041,7 +2041,7 @@

                                                                      Submodules
                                                                      -compare_sym_bands(bands_obj, bands_ref_obj, nb=None)[source]
                                                                      +compare_sym_bands(bands_obj, bands_ref_obj, nb=None)[source]

                                                                      Compute the mean of correlation between bzt and vasp bandstructure on sym line, for all bands and locally (for each branches) the difference squared (%) if nb is specified.

                                                                      @@ -2049,7 +2049,7 @@

                                                                      Submodules
                                                                      -eta_from_seebeck(seeb, Lambda) → float[source]
                                                                      +eta_from_seebeck(seeb, Lambda) → float[source]

                                                                      It takes a value of seebeck and adjusts the analytic seebeck until it’s equal.

                                                                      Returns:
                                                                      @@ -2063,7 +2063,7 @@

                                                                      Submodules
                                                                      -read_cube_file(filename)[source]
                                                                      +read_cube_file(filename)[source]
                                                                      Parameters:

                                                                      filename – Cube filename.

                                                                      @@ -2076,14 +2076,14 @@

                                                                      Submodules
                                                                      -seebeck_eff_mass_from_carr(eta, n, T, Lambda) → float[source]
                                                                      +seebeck_eff_mass_from_carr(eta, n, T, Lambda) → float[source]

                                                                      Calculate seebeck effective mass at a certain carrier concentration eta in kB*T units, n in cm-3, T in K, returns mass in m0 units.

                                                                      -seebeck_eff_mass_from_seebeck_carr(seeb, n, T, Lambda) → float[source]
                                                                      +seebeck_eff_mass_from_seebeck_carr(seeb, n, T, Lambda) → float[source]

                                                                      Find the chemical potential where analytic and calculated seebeck are identical and then calculate the seebeck effective mass at that chemical potential and a certain carrier concentration n.

                                                                      @@ -2091,7 +2091,7 @@

                                                                      Submodules
                                                                      -seebeck_spb(eta, Lambda=0.5)[source]
                                                                      +seebeck_spb(eta, Lambda=0.5)[source]

                                                                      Seebeck analytic formula in the single parabolic model.

                                                                      @@ -2111,7 +2111,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -class Cohp(efermi, energies, cohp, are_coops=False, are_cobis=False, are_multi_center_cobis=False, icohp=None)[source]
                                                                      +class Cohp(efermi, energies, cohp, are_coops=False, are_cobis=False, are_multi_center_cobis=False, icohp=None)[source]

                                                                      Bases: MSONable

                                                                      Basic COHP object.

                                                                      @@ -2129,19 +2129,19 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      JSON-serializable dict representation of COHP.

                                                                      -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                      +classmethod from_dict(dct: dict[str, Any]) → Self[source]

                                                                      Get a COHP object from a dict representation of the COHP.

                                                                      -get_cohp(spin=None, integrated=False)[source]
                                                                      +get_cohp(spin=None, integrated=False)[source]

                                                                      Get the COHP or ICOHP for a particular spin.

                                                                      Parameters:
                                                                      @@ -2161,13 +2161,13 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -get_icohp(spin=None)[source]
                                                                      +get_icohp(spin=None)[source]

                                                                      Convenient alternative to get the ICOHP for a particular spin.

                                                                      -get_interpolated_value(energy, integrated=False)[source]
                                                                      +get_interpolated_value(energy, integrated=False)[source]

                                                                      Get the COHP for a particular energy.

                                                                      Parameters:
                                                                      @@ -2181,7 +2181,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -has_antibnd_states_below_efermi(spin=None, limit=0.01)[source]
                                                                      +has_antibnd_states_below_efermi(spin=None, limit=0.01)[source]

                                                                      Get dict indicating if there are antibonding states below the Fermi level depending on the spin spin: Spin limit: -COHP smaller -limit will be considered.

                                                                      @@ -2191,12 +2191,12 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -class CompleteCohp(structure, avg_cohp, cohp_dict, bonds=None, are_coops=False, are_cobis=False, are_multi_center_cobis=False, orb_res_cohp=None)[source]
                                                                      +class CompleteCohp(structure, avg_cohp, cohp_dict, bonds=None, are_coops=False, are_cobis=False, are_multi_center_cobis=False, orb_res_cohp=None)[source]

                                                                      Bases: Cohp

                                                                      A wrapper class that defines an average COHP, and individual COHPs.

                                                                      -are_coops[source]
                                                                      +are_coops[source]

                                                                      Indicates whether the object is consisting of COOPs.

                                                                      Type:
                                                                      @@ -2207,7 +2207,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -are_cobis[source]
                                                                      +are_cobis[source]

                                                                      Indicates whether the object is consisting of COBIs.

                                                                      Type:
                                                                      @@ -2218,7 +2218,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -efermi[source]
                                                                      +efermi[source]

                                                                      Fermi energy.

                                                                      Type:
                                                                      @@ -2229,7 +2229,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -energies[source]
                                                                      +energies[source]

                                                                      Sequence of energies.

                                                                      Type:
                                                                      @@ -2240,7 +2240,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -structure[source]
                                                                      +structure[source]

                                                                      Structure associated with the COHPs.

                                                                      Type:
                                                                      @@ -2251,7 +2251,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -cohp[source]
                                                                      +cohp[source]

                                                                      The average COHP.

                                                                      Type:
                                                                      @@ -2262,7 +2262,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -icohp[source]
                                                                      +icohp[source]

                                                                      The average ICOHP.

                                                                      Type:
                                                                      @@ -2273,7 +2273,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -all_cohps[source]
                                                                      +all_cohps[source]

                                                                      A dict of COHPs for individual bonds of the form {label: COHP}.

                                                                      Type:
                                                                      @@ -2284,7 +2284,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -orb_res_cohp[source]
                                                                      +orb_res_cohp[source]

                                                                      Orbital-resolved COHPs.

                                                                      Type:
                                                                      @@ -2317,19 +2317,19 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      JSON-serializable dict representation of CompleteCohp.

                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                      +classmethod from_dict(dct: dict) → Self[source]

                                                                      Get CompleteCohp object from dict representation.

                                                                      -classmethod from_file(fmt, filename=None, structure_file=None, are_coops=False, are_cobis=False, are_multi_center_cobis=False) → Self[source]
                                                                      +classmethod from_file(fmt, filename=None, structure_file=None, are_coops=False, are_cobis=False, are_multi_center_cobis=False) → Self[source]

                                                                      Creates a CompleteCohp object from an output file of a COHP calculation. Valid formats are either LMTO (for the Stuttgart LMTO-ASA code) or LOBSTER (for the LOBSTER code).

                                                                      @@ -2360,7 +2360,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -get_cohp_by_label(label, summed_spin_channels=False)[source]
                                                                      +get_cohp_by_label(label, summed_spin_channels=False)[source]

                                                                      Get specific COHP object.

                                                                      Parameters:
                                                                      @@ -2377,7 +2377,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -get_orbital_resolved_cohp(label, orbitals, summed_spin_channels=False)[source]
                                                                      +get_orbital_resolved_cohp(label, orbitals, summed_spin_channels=False)[source]

                                                                      Get orbital-resolved COHP.

                                                                      Parameters:
                                                                      @@ -2403,7 +2403,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -get_summed_cohp_by_label_and_orbital_list(label_list, orbital_list, divisor=1, summed_spin_channels=False)[source]
                                                                      +get_summed_cohp_by_label_and_orbital_list(label_list, orbital_list, divisor=1, summed_spin_channels=False)[source]

                                                                      Get a COHP object that includes a summed COHP divided by divisor.

                                                                      Parameters:
                                                                      @@ -2423,7 +2423,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -get_summed_cohp_by_label_list(label_list, divisor=1, summed_spin_channels=False)[source]
                                                                      +get_summed_cohp_by_label_list(label_list, divisor=1, summed_spin_channels=False)[source]

                                                                      Get a COHP object that includes a summed COHP divided by divisor.

                                                                      Parameters:
                                                                      @@ -2443,12 +2443,12 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -class IcohpCollection(list_labels, list_atom1, list_atom2, list_length, list_translation, list_num, list_icohp, is_spin_polarized, list_orb_icohp=None, are_coops=False, are_cobis=False)[source]
                                                                      +class IcohpCollection(list_labels, list_atom1, list_atom2, list_length, list_translation, list_num, list_icohp, is_spin_polarized, list_orb_icohp=None, are_coops=False, are_cobis=False)[source]

                                                                      Bases: MSONable

                                                                      Store IcohpValues.

                                                                      -are_coops[source]
                                                                      +are_coops[source]

                                                                      Boolean to indicate if these are ICOOPs.

                                                                      Type:
                                                                      @@ -2459,7 +2459,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -are_cobis[source]
                                                                      +are_cobis[source]

                                                                      Boolean to indicate if these are ICOOPs.

                                                                      Type:
                                                                      @@ -2470,7 +2470,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -is_spin_polarized[source]
                                                                      +is_spin_polarized[source]

                                                                      Boolean to indicate if the Lobster calculation was done spin polarized or not.

                                                                      Type:
                                                                      @@ -2500,19 +2500,19 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -property are_cobis: bool[source]
                                                                      +property are_cobis: bool[source]

                                                                      Whether this a cobi.

                                                                      -property are_coops: bool[source]
                                                                      +property are_coops: bool[source]

                                                                      Whether this is a coop.

                                                                      -extremum_icohpvalue(summed_spin_channels=True, spin=Spin.up)[source]
                                                                      +extremum_icohpvalue(summed_spin_channels=True, spin=Spin.up)[source]

                                                                      Get ICOHP/ICOOP of strongest bond.

                                                                      Parameters:
                                                                      @@ -2529,7 +2529,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -get_icohp_by_label(label, summed_spin_channels=True, spin=Spin.up, orbitals=None) → float[source]
                                                                      +get_icohp_by_label(label, summed_spin_channels=True, spin=Spin.up, orbitals=None) → float[source]

                                                                      Get an icohp value for a certain bond as indicated by the label (bond labels starting by “1” as in ICOHPLIST/ICOOPLIST).

                                                                      @@ -2552,7 +2552,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -get_icohp_dict_by_bondlengths(minbondlength=0.0, maxbondlength=8.0)[source]
                                                                      +get_icohp_dict_by_bondlengths(minbondlength=0.0, maxbondlength=8.0)[source]

                                                                      Get a dict of IcohpValues corresponding to certain bond lengths.

                                                                      Parameters:
                                                                      @@ -2569,7 +2569,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -get_icohp_dict_of_site(site, minsummedicohp=None, maxsummedicohp=None, minbondlength=0.0, maxbondlength=8.0, only_bonds_to=None)[source]
                                                                      +get_icohp_dict_of_site(site, minsummedicohp=None, maxsummedicohp=None, minbondlength=0.0, maxbondlength=8.0, only_bonds_to=None)[source]

                                                                      Get a dict of IcohpValue for a certain site (indicated by integer).

                                                                      Parameters:
                                                                      @@ -2592,7 +2592,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -get_summed_icohp_by_label_list(label_list, divisor=1.0, summed_spin_channels=True, spin=Spin.up) → float[source]
                                                                      +get_summed_icohp_by_label_list(label_list, divisor=1.0, summed_spin_channels=True, spin=Spin.up) → float[source]

                                                                      Get the sum of several ICOHP values that are indicated by a list of labels (labels of the bonds are the same as in ICOHPLIST/ICOOPLIST).

                                                                      @@ -2615,7 +2615,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -property is_spin_polarized: bool[source]
                                                                      +property is_spin_polarized: bool[source]

                                                                      Whether it is spin polarized.

                                                                      @@ -2623,12 +2623,12 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -class IcohpValue(label, atom1, atom2, length, translation, num, icohp, are_coops=False, are_cobis=False, orbitals=None)[source]
                                                                      +class IcohpValue(label, atom1, atom2, length, translation, num, icohp, are_coops=False, are_cobis=False, orbitals=None)[source]

                                                                      Bases: MSONable

                                                                      Store information on an ICOHP or ICOOP value.

                                                                      -energies[source]
                                                                      +energies[source]

                                                                      Energy values for the COHP/ICOHP/COOP/ICOOP.

                                                                      Type:
                                                                      @@ -2639,7 +2639,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -densities[source]
                                                                      +densities[source]

                                                                      Density of states values for the COHP/ICOHP/COOP/ICOOP.

                                                                      Type:
                                                                      @@ -2650,7 +2650,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -energies_are_cartesian[source]
                                                                      +energies_are_cartesian[source]

                                                                      Whether the energies are cartesian or not.

                                                                      Type:
                                                                      @@ -2661,7 +2661,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -are_coops[source]
                                                                      +are_coops[source]

                                                                      Whether the object is a COOP/ICOOP or not.

                                                                      Type:
                                                                      @@ -2672,7 +2672,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -are_cobis[source]
                                                                      +are_cobis[source]

                                                                      Whether the object is a COBIS/ICOBIS or not.

                                                                      Type:
                                                                      @@ -2683,7 +2683,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -icohp[source]
                                                                      +icohp[source]

                                                                      A dictionary of the ICOHP/COHP values. The keys are Spin.up and Spin.down.

                                                                      Type:
                                                                      @@ -2694,7 +2694,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -summed_icohp[source]
                                                                      +summed_icohp[source]

                                                                      The summed ICOHP/COHP values.

                                                                      Type:
                                                                      @@ -2705,7 +2705,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -num_bonds[source]
                                                                      +num_bonds[source]

                                                                      The number of bonds used for the average COHP (relevant for Lobster versions <3.0).

                                                                      Type:
                                                                      @@ -2733,7 +2733,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -property are_cobis: bool[source]
                                                                      +property are_cobis: bool[source]

                                                                      Tells if ICOBIs or not.

                                                                      Returns:
                                                                      @@ -2744,7 +2744,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -property are_coops: bool[source]
                                                                      +property are_coops: bool[source]

                                                                      Tells if ICOOPs or not.

                                                                      Returns:
                                                                      @@ -2755,7 +2755,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -property icohp[source]
                                                                      +property icohp[source]

                                                                      Dict with ICOHPs for spin up and spin down.

                                                                      Returns:
                                                                      @@ -2769,7 +2769,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -icohpvalue(spin=Spin.up)[source]
                                                                      +icohpvalue(spin=Spin.up)[source]
                                                                      Parameters:

                                                                      spin – Spin.up or Spin.down.

                                                                      @@ -2785,7 +2785,7 @@

                                                                      pymatgen.electronic_structure.boltztrap2 module
                                                                      -icohpvalue_orbital(orbitals, spin=Spin.up) → float[source]
                                                                      +icohpvalue_orbital(orbitals, spin=Spin.up) → float[source]
                                                                      Parameters:
                                                                        @@ -2804,7 +2804,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -property is_spin_polarized: bool[source]
                                                                        +property is_spin_polarized: bool[source]

                                                                        Tells if spin polarized calculation or not.

                                                                        Returns:
                                                                        @@ -2815,7 +2815,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -property num_bonds[source]
                                                                        +property num_bonds[source]

                                                                        Tells the number of bonds for which the ICOHP value is an average.

                                                                        Returns:
                                                                        @@ -2826,7 +2826,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -property summed_icohp[source]
                                                                        +property summed_icohp[source]

                                                                        Sums ICOHPs of both spin channels for spin polarized compounds.

                                                                        Returns:
                                                                        @@ -2840,7 +2840,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -property summed_orbital_icohp[source]
                                                                        +property summed_orbital_icohp[source]

                                                                        Sums orbital-resolved ICOHPs of both spin channels for spin-polarized compounds.

                                                                        Returns:
                                                                        @@ -2856,7 +2856,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_integrated_cohp_in_energy_range(cohp, label, orbital=None, energy_range=None, relative_E_Fermi=True, summed_spin_channels=True)[source]
                                                                        +get_integrated_cohp_in_energy_range(cohp, label, orbital=None, energy_range=None, relative_E_Fermi=True, summed_spin_channels=True)[source]

                                                                        Integrate CompleteCohp objects which include data on integrated COHPs :param cohp: CompleteCohp object :param label: label of the COHP data @@ -2887,7 +2887,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class Magmom(moment: float | Sequence[float] | np.ndarray | Magmom, saxis: Sequence[float] = (0, 0, 1))[source]
                                                                        +class Magmom(moment: float | Sequence[float] | np.ndarray | Magmom, saxis: Sequence[float] = (0, 0, 1))[source]

                                                                        Bases: MSONable

                                                                        New class in active development. Use with caution, feedback is appreciated.

                                                                        @@ -2938,7 +2938,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -static are_collinear(magmoms) → bool[source]
                                                                        +static are_collinear(magmoms) → bool[source]

                                                                        Check if a set of magnetic moments are collinear with each other.

                                                                        Parameters:
                                                                        @@ -2952,7 +2952,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -classmethod from_global_moment_and_saxis(global_moment, saxis) → Self[source]
                                                                        +classmethod from_global_moment_and_saxis(global_moment, saxis) → Self[source]

                                                                        Convenience method to initialize Magmom from a given global magnetic moment, i.e. magnetic moment with saxis=(0,0,1), and provided saxis.

                                                                        @@ -2970,7 +2970,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -classmethod from_moment_relative_to_crystal_axes(moment: list[float], lattice: Lattice) → Self[source]
                                                                        +classmethod from_moment_relative_to_crystal_axes(moment: list[float], lattice: Lattice) → Self[source]

                                                                        Obtaining a Magmom object from a magnetic moment provided relative to crystal axes.

                                                                        Used for obtaining moments from magCIF file.

                                                                        @@ -2989,7 +2989,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_00t_magmom_with_xyz_saxis()[source]
                                                                        +get_00t_magmom_with_xyz_saxis()[source]

                                                                        For internal implementation reasons, in non-collinear calculations VASP prefers the following.

                                                                        MAGMOM = 0 0 total_magnetic_moment @@ -3015,7 +3015,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -static get_consistent_set_and_saxis(magmoms, saxis=None)[source]
                                                                        +static get_consistent_set_and_saxis(magmoms, saxis=None)[source]

                                                                        Ensure a list of magmoms use the same spin axis. Returns a tuple of a list of Magmoms and their global spin axis.

                                                                        @@ -3036,7 +3036,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_moment(saxis=(0, 0, 1))[source]
                                                                        +get_moment(saxis=(0, 0, 1))[source]

                                                                        Get magnetic moment relative to a given spin quantization axis. If no axis is provided, moment will be given relative to the Magmom’s internal spin quantization axis, i.e. equivalent to @@ -3053,7 +3053,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_moment_relative_to_crystal_axes(lattice)[source]
                                                                        +get_moment_relative_to_crystal_axes(lattice)[source]

                                                                        If scalar magmoms, moments will be given arbitrarily along z. Used for writing moments to magCIF file.

                                                                        @@ -3068,7 +3068,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -static get_suggested_saxis(magmoms)[source]
                                                                        +static get_suggested_saxis(magmoms)[source]

                                                                        Get a suggested spin axis for a set of magmoms, taking the largest magnetic moment as the reference. For calculations with collinear spins, this would give a sensible saxis for a ncl @@ -3085,7 +3085,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_xyz_magmom_with_001_saxis()[source]
                                                                        +get_xyz_magmom_with_001_saxis()[source]

                                                                        Get a Magmom in the default setting of saxis = [0, 0, 1] and the magnetic moment rotated as required.

                                                                        @@ -3097,13 +3097,13 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -property global_moment: ndarray[source]
                                                                        +property global_moment: ndarray[source]

                                                                        The magnetic moment defined in an arbitrary global reference frame as an np.array of length 3.

                                                                        -static have_consistent_saxis(magmoms) → bool[source]
                                                                        +static have_consistent_saxis(magmoms) → bool[source]

                                                                        Check that all Magmom objects in a list have a consistent spin quantization axis. To write MAGMOM tags to a VASP INCAR, a global SAXIS value for all magmoms has to be used. If saxis are inconsistent, can create consistent set with: @@ -3120,7 +3120,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -property projection[source]
                                                                        +property projection[source]

                                                                        Projects moment along spin quantization axis. Useful for obtaining collinear approximation for slightly non-collinear magmoms.

                                                                        @@ -3134,138 +3134,138 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class Orbital(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                        +class Orbital(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                        Bases: Enum

                                                                        Enum type for specific orbitals. The indices are the order in which the orbitals are reported in VASP and has no special meaning.

                                                                        -dx2 = 8[source]
                                                                        +dx2 = 8[source]
                                                                        -dxy = 4[source]
                                                                        +dxy = 4[source]
                                                                        -dxz = 7[source]
                                                                        +dxz = 7[source]
                                                                        -dyz = 5[source]
                                                                        +dyz = 5[source]
                                                                        -dz2 = 6[source]
                                                                        +dz2 = 6[source]
                                                                        -f0 = 12[source]
                                                                        +f0 = 12[source]
                                                                        -f1 = 13[source]
                                                                        +f1 = 13[source]
                                                                        -f2 = 14[source]
                                                                        +f2 = 14[source]
                                                                        -f3 = 15[source]
                                                                        +f3 = 15[source]
                                                                        -f_1 = 11[source]
                                                                        +f_1 = 11[source]
                                                                        -f_2 = 10[source]
                                                                        +f_2 = 10[source]
                                                                        -f_3 = 9[source]
                                                                        +f_3 = 9[source]
                                                                        -property orbital_type[source]
                                                                        +property orbital_type[source]

                                                                        OrbitalType of an orbital.

                                                                        -px = 3[source]
                                                                        +px = 3[source]
                                                                        -py = 1[source]
                                                                        +py = 1[source]
                                                                        -pz = 2[source]
                                                                        +pz = 2[source]
                                                                        -s = 0[source]
                                                                        +s = 0[source]

                                                                        -class OrbitalType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                        +class OrbitalType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                        Bases: Enum

                                                                        Enum type for orbital type. Indices are the azimuthal quantum number l.

                                                                        -d = 2[source]
                                                                        +d = 2[source]
                                                                        -f = 3[source]
                                                                        +f = 3[source]
                                                                        -p = 1[source]
                                                                        +p = 1[source]
                                                                        -s = 0[source]
                                                                        +s = 0[source]
                                                                        -class Spin(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                        +class Spin(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                        Bases: Enum

                                                                        Enum type for Spin. Only up and down. Usage: Spin.up, Spin.down.

                                                                        -down = -1[source]
                                                                        +down = -1[source]
                                                                        -up = 1[source]
                                                                        +up = 1[source]
                                                                        @@ -3276,7 +3276,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class CompleteDos(structure: Structure, total_dos: Dos, pdoss: Mapping[PeriodicSite, Mapping[Orbital, Mapping[Spin, ArrayLike]]], normalize: bool = False)[source]
                                                                        +class CompleteDos(structure: Structure, total_dos: Dos, pdoss: Mapping[PeriodicSite, Mapping[Orbital, Mapping[Spin, ArrayLike]]], normalize: bool = False)[source]

                                                                        Bases: Dos

                                                                        This wrapper class defines a total dos, and also provides a list of PDos. Mainly used by pymatgen.io.vasp.Vasprun to create a complete Dos from @@ -3284,7 +3284,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -structure[source]
                                                                        +structure[source]

                                                                        Structure associated with the CompleteDos.

                                                                        Type:
                                                                        @@ -3295,7 +3295,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -pdos[source]
                                                                        +pdos[source]

                                                                        Dict of partial densities of the form {Site:{Orbital:{Spin:Densities}}}.

                                                                        Type:
                                                                        @@ -3318,13 +3318,13 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -as_dict() → dict[source]
                                                                        +as_dict() → dict[source]

                                                                        JSON-serializable dict representation of CompleteDos.

                                                                        -static fp_to_dict(fp: NamedTuple) → dict[source]
                                                                        +static fp_to_dict(fp: NamedTuple) → dict[source]

                                                                        Convert a fingerprint into a dictionary.

                                                                        Parameters:
                                                                        @@ -3341,13 +3341,13 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        Get CompleteDos object from dict representation.

                                                                        -get_band_center(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]
                                                                        +get_band_center(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]

                                                                        Compute the orbital-projected band center, defined as the first moment relative to the Fermi level

                                                                        @@ -3379,7 +3379,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_band_filling(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None) → float[source]
                                                                        +get_band_filling(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None) → float[source]

                                                                        Compute the orbital-projected band filling, defined as the zeroth moment up to the Fermi level.

                                                                        @@ -3402,7 +3402,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_band_kurtosis(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]
                                                                        +get_band_kurtosis(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]
                                                                        Get the orbital-projected kurtosis, defined as the fourth standardized moment

                                                                        int_{-inf}^{+inf} rho(E)*(E-E_center)^4 dE/int_{-inf}^{+inf} rho(E) dE) / @@ -3434,7 +3434,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_band_skewness(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]
                                                                        +get_band_skewness(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]
                                                                        Get the orbital-projected skewness, defined as the third standardized moment

                                                                        int_{-inf}^{+inf} rho(E)*(E-E_center)^3 dE/int_{-inf}^{+inf} rho(E) dE) / @@ -3466,7 +3466,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_band_width(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]
                                                                        +get_band_width(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]
                                                                        Get the orbital-projected band width, defined as the square root of the second moment

                                                                        sqrt(int_{-inf}^{+inf} rho(E)*(E-E_center)^2 dE/int_{-inf}^{+inf} rho(E) dE)

                                                                        @@ -3496,7 +3496,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_dos_fp(type: str = 'summed_pdos', binning: bool = True, min_e: float | None = None, max_e: float | None = None, n_bins: int = 256, normalize: bool = True) → NamedTuple[source]
                                                                        +get_dos_fp(type: str = 'summed_pdos', binning: bool = True, min_e: float | None = None, max_e: float | None = None, n_bins: int = 256, normalize: bool = True) → NamedTuple[source]

                                                                        Generate the DOS fingerprint.

                                                                        Based on work of:

                                                                        F. Knoop, T. A. r Purcell, M. Scheffler, C. Carbogno, J. Open Source Softw. 2020, 5, 2671. @@ -3533,7 +3533,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -static get_dos_fp_similarity(fp1: NamedTuple, fp2: NamedTuple, col: int = 1, pt: int | str = 'All', normalize: bool = False, tanimoto: bool = False) → float[source]
                                                                        +static get_dos_fp_similarity(fp1: NamedTuple, fp2: NamedTuple, col: int = 1, pt: int | str = 'All', normalize: bool = False, tanimoto: bool = False) → float[source]

                                                                        Calculate the similarity index (dot product) of two fingerprints.

                                                                        Parameters:
                                                                        @@ -3560,7 +3560,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_element_dos() → dict[SpeciesLike, Dos][source]
                                                                        +get_element_dos() → dict[SpeciesLike, Dos][source]

                                                                        Get element projected Dos.

                                                                        Returns:
                                                                        @@ -3571,7 +3571,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_element_spd_dos(el: SpeciesLike) → dict[OrbitalType, Dos][source]
                                                                        +get_element_spd_dos(el: SpeciesLike) → dict[OrbitalType, Dos][source]

                                                                        Get element and spd projected Dos.

                                                                        Parameters:
                                                                        @@ -3588,7 +3588,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_hilbert_transform(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None) → Dos[source]
                                                                        +get_hilbert_transform(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None) → Dos[source]

                                                                        Return the Hilbert transform of the orbital-projected density of states, often plotted for a Newns-Anderson analysis.

                                                                        @@ -3607,7 +3607,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_n_moment(n: int, band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None, center: bool = True) → float[source]
                                                                        +get_n_moment(n: int, band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None, center: bool = True) → float[source]
                                                                        Get the nth moment of the DOS centered around the orbital-projected band center, defined as

                                                                        int_{-inf}^{+inf} rho(E)*(E-E_center)^n dE/int_{-inf}^{+inf} rho(E) dE

                                                                        @@ -3636,13 +3636,13 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_normalized() → CompleteDos[source]
                                                                        +get_normalized() → CompleteDos[source]

                                                                        Get a normalized version of the CompleteDos.

                                                                        -get_site_dos(site: PeriodicSite) → Dos[source]
                                                                        +get_site_dos(site: PeriodicSite) → Dos[source]

                                                                        Get the total Dos for a site (all orbitals).

                                                                        Parameters:
                                                                        @@ -3656,7 +3656,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_site_orbital_dos(site: PeriodicSite, orbital: Orbital) → Dos[source]
                                                                        +get_site_orbital_dos(site: PeriodicSite, orbital: Orbital) → Dos[source]

                                                                        Get the Dos for a particular orbital of a particular site.

                                                                        Parameters:
                                                                        @@ -3673,7 +3673,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_site_spd_dos(site: PeriodicSite) → dict[OrbitalType, Dos][source]
                                                                        +get_site_spd_dos(site: PeriodicSite) → dict[OrbitalType, Dos][source]

                                                                        Get orbital projected Dos of a particular site.

                                                                        Parameters:
                                                                        @@ -3690,7 +3690,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_site_t2g_eg_resolved_dos(site: PeriodicSite) → dict[str, Dos][source]
                                                                        +get_site_t2g_eg_resolved_dos(site: PeriodicSite) → dict[str, Dos][source]

                                                                        Get the t2g, eg projected DOS for a particular site.

                                                                        Parameters:
                                                                        @@ -3707,7 +3707,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_spd_dos() → dict[OrbitalType, Dos][source]
                                                                        +get_spd_dos() → dict[OrbitalType, Dos][source]

                                                                        Get orbital projected Dos.

                                                                        Returns:
                                                                        @@ -3721,7 +3721,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_upper_band_edge(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]
                                                                        +get_upper_band_edge(band: OrbitalType = OrbitalType.d, elements: list[SpeciesLike] | None = None, sites: list[PeriodicSite] | None = None, spin: Spin | None = None, erange: list[float] | None = None) → float[source]

                                                                        Get the orbital-projected upper band edge. The definition by Xin et al. Phys. Rev. B, 89, 115114 (2014) is used, which is the highest peak position of the Hilbert transform of the orbital-projected DOS.

                                                                        @@ -3744,7 +3744,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -property spin_polarization: float | None[source]
                                                                        +property spin_polarization: float | None[source]

                                                                        Calculate spin polarization at Fermi level. If the calculation is not spin-polarized, None will be returned.

                                                                        See Sanvito et al., doi: 10.1126/sciadv.1602241 for an example usage.

                                                                        @@ -3766,13 +3766,13 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class DOS(energies: ArrayLike, densities: ArrayLike, efermi: float)[source]
                                                                        +class DOS(energies: ArrayLike, densities: ArrayLike, efermi: float)[source]

                                                                        Bases: Spectrum

                                                                        Replacement basic DOS object. All other DOS objects are extended versions of this object. Work in progress.

                                                                        -energies[source]
                                                                        +energies[source]

                                                                        The sequence of energies.

                                                                        Type:
                                                                        @@ -3783,7 +3783,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -densities[source]
                                                                        +densities[source]

                                                                        A dict of spin densities, e.g. {Spin.up: […], Spin.down: […]}.

                                                                        Type:
                                                                        @@ -3794,7 +3794,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -efermi[source]
                                                                        +efermi[source]

                                                                        Fermi level.

                                                                        Type:
                                                                        @@ -3816,17 +3816,17 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -XLABEL = 'Energy'[source]
                                                                        +XLABEL = 'Energy'[source]

                                                                        -YLABEL = 'Density'[source]
                                                                        +YLABEL = 'Density'[source]
                                                                        -get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin=None) → tuple[float, float][source]
                                                                        +get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin=None) → tuple[float, float][source]

                                                                        Expects a DOS object and finds the cbm and vbm.

                                                                        Parameters:
                                                                        @@ -3849,7 +3849,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_gap(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None)[source]
                                                                        +get_gap(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None)[source]

                                                                        Expects a DOS object and finds the gap.

                                                                        Parameters:
                                                                        @@ -3869,7 +3869,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None)[source]
                                                                        +get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None)[source]

                                                                        Expects a DOS object and finds the gap.

                                                                        Parameters:
                                                                        @@ -3895,13 +3895,13 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class Dos(efermi: float, energies: ArrayLike, densities: Mapping[Spin, ArrayLike], norm_vol: float | None = None)[source]
                                                                        +class Dos(efermi: float, energies: ArrayLike, densities: Mapping[Spin, ArrayLike], norm_vol: float | None = None)[source]

                                                                        Bases: MSONable

                                                                        Basic DOS object. All other DOS objects are extended versions of this object.

                                                                        -energies[source]
                                                                        +energies[source]

                                                                        The sequence of energies.

                                                                        Type:
                                                                        @@ -3912,7 +3912,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -densities[source]
                                                                        +densities[source]

                                                                        A dict of spin densities, e.g. {Spin.up: […], Spin.down: […]}.

                                                                        Type:
                                                                        @@ -3923,7 +3923,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -efermi[source]
                                                                        +efermi[source]

                                                                        Fermi level.

                                                                        Type:
                                                                        @@ -3946,19 +3946,19 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -as_dict() → dict[source]
                                                                        +as_dict() → dict[source]

                                                                        JSON-serializable dict representation of Dos.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        Get Dos object from dict representation of Dos.

                                                                        -get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None) → tuple[float, float][source]
                                                                        +get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None) → tuple[float, float][source]

                                                                        Expects a DOS object and finds the cbm and vbm.

                                                                        Parameters:
                                                                        @@ -3981,7 +3981,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_densities(spin: Spin | None = None)[source]
                                                                        +get_densities(spin: Spin | None = None)[source]

                                                                        Get the density of states for a particular spin.

                                                                        Parameters:
                                                                        @@ -3996,7 +3996,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_gap(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None)[source]
                                                                        +get_gap(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None)[source]

                                                                        Expects a DOS object and finds the gap.

                                                                        Parameters:
                                                                        @@ -4016,7 +4016,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None) → Tuple3Floats[source]
                                                                        +get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None) → Tuple3Floats[source]

                                                                        Expects a DOS object and finds the gap.

                                                                        Parameters:
                                                                        @@ -4040,7 +4040,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_interpolated_value(energy: float) → dict[Spin, float][source]
                                                                        +get_interpolated_value(energy: float) → dict[Spin, float][source]

                                                                        Get interpolated density for a particular energy.

                                                                        Parameters:
                                                                        @@ -4057,7 +4057,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_smeared_densities(sigma: float)[source]
                                                                        +get_smeared_densities(sigma: float)[source]

                                                                        Get the Dict representation of the densities, {Spin: densities}, but with a Gaussian smearing of std dev sigma.

                                                                        @@ -4074,7 +4074,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class FermiDos(dos: Dos, structure: Structure | None = None, nelecs: float | None = None, bandgap: float | None = None)[source]
                                                                        +class FermiDos(dos: Dos, structure: Structure | None = None, nelecs: float | None = None, bandgap: float | None = None)[source]

                                                                        Bases: Dos, MSONable

                                                                        This wrapper class helps relate the density of states, doping levels (i.e. carrier concentrations) and corresponding fermi levels. A negative @@ -4098,19 +4098,19 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -as_dict() → dict[source]
                                                                        +as_dict() → dict[source]

                                                                        JSON-serializable dict representation of Dos.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        Get Dos object from dict representation of Dos.

                                                                        -get_doping(fermi_level: float, temperature: float) → float[source]
                                                                        +get_doping(fermi_level: float, temperature: float) → float[source]

                                                                        Calculate the doping (majority carrier concentration) at a given Fermi level and temperature. A simple Left Riemann sum is used for integrating the density of states over energy & equilibrium Fermi-Dirac @@ -4133,7 +4133,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_fermi(concentration: float, temperature: float, rtol: float = 0.01, nstep: int = 50, step: float = 0.1, precision: int = 8) → float[source]
                                                                        +get_fermi(concentration: float, temperature: float, rtol: float = 0.01, nstep: int = 50, step: float = 0.1, precision: int = 8) → float[source]

                                                                        Find the Fermi level at which the doping concentration at the given temperature (T) is equal to concentration. A greedy algorithm is used where the relative error is minimized by calculating the doping at a @@ -4163,7 +4163,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_fermi_interextrapolated(concentration: float, temperature: float, warn: bool = True, c_ref: float = 10000000000.0, **kwargs) → float[source]
                                                                        +get_fermi_interextrapolated(concentration: float, temperature: float, warn: bool = True, c_ref: float = 10000000000.0, **kwargs) → float[source]

                                                                        Similar to get_fermi except that when get_fermi fails to converge, an interpolated or extrapolated fermi is returned with the assumption that the Fermi level changes linearly with log(abs(concentration)).

                                                                        @@ -4192,7 +4192,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class LobsterCompleteDos(structure: Structure, total_dos: Dos, pdoss: Mapping[PeriodicSite, Mapping[Orbital, Mapping[Spin, ArrayLike]]], normalize: bool = False)[source]
                                                                        +class LobsterCompleteDos(structure: Structure, total_dos: Dos, pdoss: Mapping[PeriodicSite, Mapping[Orbital, Mapping[Spin, ArrayLike]]], normalize: bool = False)[source]

                                                                        Bases: CompleteDos

                                                                        Extended CompleteDOS for Lobster.

                                                                        @@ -4209,13 +4209,13 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        Hydrate CompleteDos object from dict representation.

                                                                        -get_element_spd_dos(el: SpeciesLike) → dict[str, Dos][source]
                                                                        +get_element_spd_dos(el: SpeciesLike) → dict[str, Dos][source]

                                                                        Get element and spd projected Dos.

                                                                        Parameters:
                                                                        @@ -4232,7 +4232,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_site_orbital_dos(site: PeriodicSite, orbital: str) → Dos[source]
                                                                        +get_site_orbital_dos(site: PeriodicSite, orbital: str) → Dos[source]

                                                                        Get the Dos for a particular orbital of a particular site.

                                                                        Parameters:
                                                                        @@ -4253,7 +4253,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_site_t2g_eg_resolved_dos(site: PeriodicSite) → dict[str, Dos][source]
                                                                        +get_site_t2g_eg_resolved_dos(site: PeriodicSite) → dict[str, Dos][source]

                                                                        Get the t2g, eg projected DOS for a particular site.

                                                                        Parameters:
                                                                        @@ -4271,7 +4271,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_spd_dos() → dict[str, Dos][source]
                                                                        +get_spd_dos() → dict[str, Dos][source]

                                                                        Get orbital projected Dos. For example, if 3s and 4s are included in the basis of some element, they will be both summed in the orbital projected DOS.

                                                                        @@ -4289,7 +4289,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -add_densities(density1: Mapping[Spin, ArrayLike], density2: Mapping[Spin, ArrayLike]) → dict[Spin, np.ndarray][source]
                                                                        +add_densities(density1: Mapping[Spin, ArrayLike], density2: Mapping[Spin, ArrayLike]) → dict[Spin, np.ndarray][source]

                                                                        Sum two densities.

                                                                        Parameters:
                                                                        @@ -4306,7 +4306,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -f0(E, fermi, T) → float[source]
                                                                        +f0(E, fermi, T) → float[source]

                                                                        Fermi-Dirac distribution function.

                                                                        Parameters:
                                                                        @@ -4331,7 +4331,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class BSDOSPlotter(bs_projection: Literal['elements'] | None = 'elements', dos_projection: str = 'elements', vb_energy_range: float = 4, cb_energy_range: float = 4, fixed_cb_energy: bool = False, egrid_interval: float = 1, font: str = 'Times New Roman', axis_fontsize: float = 20, tick_fontsize: float = 15, legend_fontsize: float = 14, bs_legend: str = 'best', dos_legend: str = 'best', rgb_legend: bool = True, fig_size: tuple[float, float] = (11, 8.5))[source]
                                                                        +class BSDOSPlotter(bs_projection: Literal['elements'] | None = 'elements', dos_projection: str = 'elements', vb_energy_range: float = 4, cb_energy_range: float = 4, fixed_cb_energy: bool = False, egrid_interval: float = 1, font: str = 'Times New Roman', axis_fontsize: float = 20, tick_fontsize: float = 15, legend_fontsize: float = 14, bs_legend: str = 'best', dos_legend: str = 'best', rgb_legend: bool = True, fig_size: tuple[float, float] = (11, 8.5))[source]

                                                                        Bases: object

                                                                        A joint, aligned band structure and density of states plot. Contributions from Jan Pohls as well as the online example from Germain Salvato-Vallverdu: @@ -4360,7 +4360,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_plot(bs: BandStructureSymmLine, dos: Dos | CompleteDos | None = None) → plt.Axes | tuple[plt.Axes, plt.Axes][source]
                                                                        +get_plot(bs: BandStructureSymmLine, dos: Dos | CompleteDos | None = None) → plt.Axes | tuple[plt.Axes, plt.Axes][source]

                                                                        Get a matplotlib plot object.

                                                                        Parameters:
                                                                        @@ -4384,7 +4384,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class BSPlotter(bs: BandStructureSymmLine)[source]
                                                                        +class BSPlotter(bs: BandStructureSymmLine)[source]

                                                                        Bases: object

                                                                        Plot or get data to facilitate the plotting of band structure.

                                                                        @@ -4394,13 +4394,13 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -add_bs(bs: BandStructureSymmLine | list[BandStructureSymmLine]) → None[source]
                                                                        +add_bs(bs: BandStructureSymmLine | list[BandStructureSymmLine]) → None[source]

                                                                        Add bands objects to the BSPlotter.

                                                                        -bs_plot_data(zero_to_efermi=True, bs=None, bs_ref=None, split_branches=True)[source]
                                                                        +bs_plot_data(zero_to_efermi=True, bs=None, bs_ref=None, split_branches=True)[source]

                                                                        Get the data nicely formatted for a plot.

                                                                        Parameters:
                                                                        @@ -4444,7 +4444,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_plot(zero_to_efermi=True, ylim=None, smooth=False, vbm_cbm_marker=False, smooth_tol=0, smooth_k=3, smooth_np=100, bs_labels=None)[source]
                                                                        +get_plot(zero_to_efermi=True, ylim=None, smooth=False, vbm_cbm_marker=False, smooth_tol=0, smooth_k=3, smooth_np=100, bs_labels=None)[source]

                                                                        Get a matplotlib object for the bandstructures plot. Multiple bandstructure objs are plotted together if they have the same high symm path.

                                                                        @@ -4472,7 +4472,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_ticks()[source]
                                                                        +get_ticks()[source]

                                                                        Get all ticks and labels for a band structure plot.

                                                                        Returns:
                                                                        @@ -4488,7 +4488,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_ticks_old()[source]
                                                                        +get_ticks_old()[source]

                                                                        Get all ticks and labels for a band structure plot.

                                                                        Returns:
                                                                        @@ -4504,7 +4504,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_brillouin()[source]
                                                                        +plot_brillouin()[source]

                                                                        Plot the Brillouin zone.

                                                                        Returns:
                                                                        @@ -4518,7 +4518,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_compare(other_plotter, legend=True) → Axes[source]
                                                                        +plot_compare(other_plotter, legend=True) → Axes[source]

                                                                        Plot two band structure for comparison. One is in red the other in blue (no difference in spins). The two band structures need to be defined on the same symmetry lines! and the distance between symmetry lines is @@ -4541,7 +4541,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -save_plot(filename: str, ylim=None, zero_to_efermi=True, smooth=False) → None[source]
                                                                        +save_plot(filename: str, ylim=None, zero_to_efermi=True, smooth=False) → None[source]

                                                                        Save matplotlib plot to a file.

                                                                        Parameters:
                                                                        @@ -4558,7 +4558,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -show(zero_to_efermi=True, ylim=None, smooth=False, smooth_tol=None) → None[source]
                                                                        +show(zero_to_efermi=True, ylim=None, smooth=False, smooth_tol=None) → None[source]

                                                                        Show the plot using matplotlib.

                                                                        Parameters:
                                                                        @@ -4580,7 +4580,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class BSPlotterProjected(bs: BandStructureSymmLine)[source]
                                                                        +class BSPlotterProjected(bs: BandStructureSymmLine)[source]

                                                                        Bases: BSPlotter

                                                                        Plot or get data to facilitate plotting of projected band structure along orbitals, elements or sites.

                                                                        @@ -4594,7 +4594,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_elt_projected_plots(zero_to_efermi: bool = True, ylim: tuple[float, float] | None = None, vbm_cbm_marker: bool = False, band_linewidth: float = 1.0) → Axes[source]
                                                                        +get_elt_projected_plots(zero_to_efermi: bool = True, ylim: tuple[float, float] | None = None, vbm_cbm_marker: bool = False, band_linewidth: float = 1.0) → Axes[source]

                                                                        Generate a plot with subplots for different elements.

                                                                        The blue and red colors are for spin up and spin down The size of the dot in the plot corresponds to the value @@ -4615,7 +4615,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_elt_projected_plots_color(zero_to_efermi: bool = True, elt_ordered: list | None = None, band_linewidth: float = 3) → Axes[source]
                                                                        +get_elt_projected_plots_color(zero_to_efermi: bool = True, elt_ordered: list | None = None, band_linewidth: float = 3) → Axes[source]

                                                                        Generate a pyplot plot where the band structure line color depends on the element of the band. where each element is associated with red, green or blue.

                                                                        @@ -4645,7 +4645,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_projected_plots_dots(dictio: dict[str, list], zero_to_efermi: bool = True, ylim: tuple[float, float] | None = None, vbm_cbm_marker: bool = False, band_linewidth: float = 1.0, marker_size: float = 15.0) → Axes[source]
                                                                        +get_projected_plots_dots(dictio: dict[str, list], zero_to_efermi: bool = True, ylim: tuple[float, float] | None = None, vbm_cbm_marker: bool = False, band_linewidth: float = 1.0, marker_size: float = 15.0) → Axes[source]

                                                                        Generate a plot with subplots for each element-orbital pair.

                                                                        The orbitals are named as in the FATBAND file, e.g. “2p” or “2p_x”.

                                                                        he blue and red colors are for spin up and spin down @@ -4674,7 +4674,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_projected_plots_dots_patom_pmorb(dictio, dictpa, sum_atoms=None, sum_morbs=None, zero_to_efermi=True, ylim=None, vbm_cbm_marker=False, selected_branches=None, w_h_size=(12, 8), num_column=None)[source]
                                                                        +get_projected_plots_dots_patom_pmorb(dictio, dictpa, sum_atoms=None, sum_morbs=None, zero_to_efermi=True, ylim=None, vbm_cbm_marker=False, selected_branches=None, w_h_size=(12, 8), num_column=None)[source]

                                                                        Return a plot composed of subplots for different atoms and orbitals (subshell orbitals such as ‘s’, ‘p’, ‘d’ and ‘f’ defined by azimuthal quantum numbers l = 0, 1, 2 and 3, respectively or individual orbitals like ‘px’, ‘py’ and ‘pz’ defined @@ -4749,7 +4749,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class BoltztrapPlotter(bz)[source]
                                                                        +class BoltztrapPlotter(bz)[source]

                                                                        Bases: object

                                                                        Plot Boltztrap data.

                                                                        @@ -4759,7 +4759,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_carriers(temp=300)[source]
                                                                        +plot_carriers(temp=300)[source]

                                                                        Plot the carrier concentration in function of Fermi level.

                                                                        Parameters:
                                                                        @@ -4773,7 +4773,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_complexity_factor_mu(temps=(300,), output='average', Lambda=0.5)[source]
                                                                        +plot_complexity_factor_mu(temps=(300,), output='average', Lambda=0.5)[source]

                                                                        Plot respect to the chemical potential of the Fermi surface complexity factor calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor @@ -4799,7 +4799,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_conductivity_dop(temps='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]
                                                                        +plot_conductivity_dop(temps='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]

                                                                        Plot the conductivity in function of doping levels for different temperatures.

                                                                        @@ -4820,7 +4820,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_conductivity_mu(temp: float = 600, output: str = 'eig', relaxation_time: float = 1e-14, xlim: Sequence[float] | None = None)[source]
                                                                        +plot_conductivity_mu(temp: float = 600, output: str = 'eig', relaxation_time: float = 1e-14, xlim: Sequence[float] | None = None)[source]

                                                                        Plot the conductivity in function of Fermi level. Semi-log plot.

                                                                        Parameters:
                                                                        @@ -4840,7 +4840,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_conductivity_temp(doping='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]
                                                                        +plot_conductivity_temp(doping='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]

                                                                        Plot the conductivity in function of temperature for different doping levels.

                                                                        Parameters:
                                                                        @@ -4860,7 +4860,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_dos(sigma=0.05)[source]
                                                                        +plot_dos(sigma=0.05)[source]

                                                                        Plot dos.

                                                                        Parameters:
                                                                        @@ -4874,7 +4874,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_eff_mass_dop(temps='all', output: Literal['average', 'eigs'] = 'average')[source]
                                                                        +plot_eff_mass_dop(temps='all', output: Literal['average', 'eigs'] = 'average')[source]

                                                                        Plot the average effective mass in function of doping levels for different temperatures.

                                                                        @@ -4895,7 +4895,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_eff_mass_temp(doping='all', output: Literal['average', 'eigs'] = 'average')[source]
                                                                        +plot_eff_mass_temp(doping='all', output: Literal['average', 'eigs'] = 'average')[source]

                                                                        Plot the average effective mass in function of temperature for different doping levels.

                                                                        @@ -4915,7 +4915,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_hall_carriers(temp=300)[source]
                                                                        +plot_hall_carriers(temp=300)[source]

                                                                        Plot the Hall carrier concentration in function of Fermi level.

                                                                        Parameters:
                                                                        @@ -4929,7 +4929,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_power_factor_dop(temps='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]
                                                                        +plot_power_factor_dop(temps='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]

                                                                        Plot the Power Factor in function of doping levels for different temperatures.

                                                                        Parameters:
                                                                        @@ -4949,7 +4949,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_power_factor_mu(temp: float = 600, output: str = 'eig', relaxation_time: float = 1e-14, xlim: Sequence[float] | None = None)[source]
                                                                        +plot_power_factor_mu(temp: float = 600, output: str = 'eig', relaxation_time: float = 1e-14, xlim: Sequence[float] | None = None)[source]

                                                                        Plot the power factor in function of Fermi level. Semi-log plot.

                                                                        Parameters:
                                                                        @@ -4969,7 +4969,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_power_factor_temp(doping='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]
                                                                        +plot_power_factor_temp(doping='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]

                                                                        Plot the Power Factor in function of temperature for different doping levels.

                                                                        Parameters:
                                                                        @@ -4989,7 +4989,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_seebeck_dop(temps='all', output: Literal['average', 'eigs'] = 'average')[source]
                                                                        +plot_seebeck_dop(temps='all', output: Literal['average', 'eigs'] = 'average')[source]

                                                                        Plot the Seebeck in function of doping levels for different temperatures.

                                                                        Parameters:
                                                                        @@ -5008,7 +5008,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_seebeck_eff_mass_mu(temps=(300,), output='average', Lambda=0.5)[source]
                                                                        +plot_seebeck_eff_mass_mu(temps=(300,), output='average', Lambda=0.5)[source]

                                                                        Plot respect to the chemical potential of the Seebeck effective mass calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor @@ -5034,7 +5034,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_seebeck_mu(temp: float = 600, output: str = 'eig', xlim: Sequence[float] | None = None)[source]
                                                                        +plot_seebeck_mu(temp: float = 600, output: str = 'eig', xlim: Sequence[float] | None = None)[source]

                                                                        Plot the seebeck coefficient in function of Fermi level.

                                                                        Parameters:
                                                                        @@ -5052,7 +5052,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_seebeck_temp(doping='all', output: Literal['average', 'eigs'] = 'average')[source]
                                                                        +plot_seebeck_temp(doping='all', output: Literal['average', 'eigs'] = 'average')[source]

                                                                        Plot the Seebeck coefficient in function of temperature for different doping levels.

                                                                        @@ -5072,7 +5072,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_zt_dop(temps='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]
                                                                        +plot_zt_dop(temps='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]

                                                                        Plot the figure of merit zT in function of doping levels for different temperatures.

                                                                        @@ -5093,7 +5093,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_zt_mu(temp: float = 600, output: str = 'eig', relaxation_time: float = 1e-14, xlim: Sequence[float] | None = None) → plt.Axes[source]
                                                                        +plot_zt_mu(temp: float = 600, output: str = 'eig', relaxation_time: float = 1e-14, xlim: Sequence[float] | None = None) → plt.Axes[source]

                                                                        Plot the ZT as function of Fermi level.

                                                                        Parameters:
                                                                        @@ -5116,7 +5116,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_zt_temp(doping='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]
                                                                        +plot_zt_temp(doping='all', output: Literal['average', 'eigs'] = 'average', relaxation_time=1e-14)[source]

                                                                        Plot the figure of merit zT in function of temperature for different doping levels.

                                                                        Parameters:
                                                                        @@ -5141,7 +5141,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class CohpPlotter(zero_at_efermi=True, are_coops=False, are_cobis=False)[source]
                                                                        +class CohpPlotter(zero_at_efermi=True, are_coops=False, are_cobis=False)[source]

                                                                        Bases: object

                                                                        Plot crystal orbital Hamilton populations (COHPs) or crystal orbital overlap populations (COOPs). It is modeled after the DosPlotter object.

                                                                        @@ -5159,7 +5159,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -add_cohp(label, cohp) → None[source]
                                                                        +add_cohp(label, cohp) → None[source]

                                                                        Add a COHP for plotting.

                                                                        Parameters:
                                                                        @@ -5173,7 +5173,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -add_cohp_dict(cohp_dict, key_sort_func=None) → None[source]
                                                                        +add_cohp_dict(cohp_dict, key_sort_func=None) → None[source]

                                                                        Add a dictionary of COHPs with an optional sorting function for the keys.

                                                                        @@ -5188,7 +5188,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_cohp_dict()[source]
                                                                        +get_cohp_dict()[source]

                                                                        Get the added COHPs as a json-serializable dict. Note that if you have specified smearing for the COHP plot, the populations returned will be the smeared and not the original populations.

                                                                        @@ -5205,7 +5205,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_plot(xlim=None, ylim=None, plot_negative=None, integrated=False, invert_axes=True)[source]
                                                                        +get_plot(xlim=None, ylim=None, plot_negative=None, integrated=False, invert_axes=True)[source]

                                                                        Get a matplotlib plot showing the COHP.

                                                                        Parameters:
                                                                        @@ -5231,7 +5231,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -save_plot(filename: str, xlim=None, ylim=None) → None[source]
                                                                        +save_plot(filename: str, xlim=None, ylim=None) → None[source]

                                                                        Save matplotlib plot to a file.

                                                                        Parameters:
                                                                        @@ -5248,7 +5248,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -show(xlim=None, ylim=None) → None[source]
                                                                        +show(xlim=None, ylim=None) → None[source]

                                                                        Show the plot using matplotlib.

                                                                        Parameters:
                                                                        @@ -5266,7 +5266,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -class DosPlotter(zero_at_efermi: bool = True, stack: bool = False, sigma: float | None = None)[source]
                                                                        +class DosPlotter(zero_at_efermi: bool = True, stack: bool = False, sigma: float | None = None)[source]

                                                                        Bases: object

                                                                        Plot DOSs. The interface is extremely flexible given there are many different ways in which people want to view DOS. @@ -5295,7 +5295,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -add_dos(label: str, dos: Dos) → None[source]
                                                                        +add_dos(label: str, dos: Dos) → None[source]

                                                                        Add a DOS for plotting.

                                                                        Parameters:
                                                                        @@ -5309,7 +5309,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -add_dos_dict(dos_dict, key_sort_func=None) → None[source]
                                                                        +add_dos_dict(dos_dict, key_sort_func=None) → None[source]

                                                                        Add a dictionary of DOSs, with an optional sorting function for the keys.

                                                                        @@ -5324,7 +5324,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_dos_dict()[source]
                                                                        +get_dos_dict()[source]

                                                                        Get the added doses as a json-serializable dict. Note that if you have specified smearing for the DOS plot, the densities returned will be the smeared densities, not the original densities.

                                                                        @@ -5341,7 +5341,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -get_plot(xlim: tuple[float, float] | None = None, ylim: tuple[float, float] | None = None, invert_axes: bool = False, beta_dashed: bool = False) → plt.Axes[source]
                                                                        +get_plot(xlim: tuple[float, float] | None = None, ylim: tuple[float, float] | None = None, invert_axes: bool = False, beta_dashed: bool = False) → plt.Axes[source]

                                                                        Get a matplotlib plot showing the DOS.

                                                                        Parameters:
                                                                        @@ -5365,7 +5365,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -save_plot(filename: str, xlim=None, ylim=None, invert_axes=False, beta_dashed=False) → None[source]
                                                                        +save_plot(filename: str, xlim=None, ylim=None, invert_axes=False, beta_dashed=False) → None[source]

                                                                        Save matplotlib plot to a file.

                                                                        Parameters:
                                                                        @@ -5384,7 +5384,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -show(xlim=None, ylim=None, invert_axes=False, beta_dashed=False) → None[source]
                                                                        +show(xlim=None, ylim=None, invert_axes=False, beta_dashed=False) → None[source]

                                                                        Show the plot using matplotlib.

                                                                        Parameters:
                                                                        @@ -5404,7 +5404,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -fold_point(p, lattice, coords_are_cartesian=False)[source]
                                                                        +fold_point(p, lattice, coords_are_cartesian=False)[source]

                                                                        Folds a point with coordinates p inside the first Brillouin zone of the lattice.

                                                                        Parameters:
                                                                        @@ -5423,7 +5423,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_brillouin_zone(bz_lattice, lines=None, labels=None, kpoints=None, fold=False, coords_are_cartesian: bool = False, ax: Axes = None, **kwargs)[source]
                                                                        +plot_brillouin_zone(bz_lattice, lines=None, labels=None, kpoints=None, fold=False, coords_are_cartesian: bool = False, ax: Axes = None, **kwargs)[source]

                                                                        Plots a 3D representation of the Brillouin zone of the structure. Can add to the plot paths, labels and kpoints.

                                                                        @@ -5487,7 +5487,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_brillouin_zone_from_kpath(kpath, ax: Axes = None, **kwargs) → Axes[source]
                                                                        +plot_brillouin_zone_from_kpath(kpath, ax: Axes = None, **kwargs) → Axes[source]
                                                                        Get the plot (as a matplotlib object) of the symmetry line path in

                                                                        the Brillouin Zone.

                                                                        @@ -5549,7 +5549,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_ellipsoid(hessian, center, lattice=None, rescale=1.0, ax: Axes = None, coords_are_cartesian=False, arrows=False, **kwargs)[source]
                                                                        +plot_ellipsoid(hessian, center, lattice=None, rescale=1.0, ax: Axes = None, coords_are_cartesian=False, arrows=False, **kwargs)[source]

                                                                        Plots a 3D ellipsoid rappresenting the Hessian matrix in input. Useful to get a graphical visualization of the effective mass of a band in a single k-point.

                                                                        @@ -5582,7 +5582,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_fermi_surface(data, structure, cbm, energy_levels=None, multiple_figure=True, mlab_figure=None, kpoints_dict=None, colors=None, transparency_factor=None, labels_scale_factor=0.05, points_scale_factor=0.02, interactive=True)[source]
                                                                        +plot_fermi_surface(data, structure, cbm, energy_levels=None, multiple_figure=True, mlab_figure=None, kpoints_dict=None, colors=None, transparency_factor=None, labels_scale_factor=0.05, points_scale_factor=0.02, interactive=True)[source]

                                                                        Plot the Fermi surface at specific energy value using Boltztrap 1 FERMI mode.

                                                                        The easiest way to use this plotter is:

                                                                        @@ -5651,7 +5651,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_labels(labels, lattice=None, coords_are_cartesian=False, ax: Axes = None, **kwargs)[source]
                                                                        +plot_labels(labels, lattice=None, coords_are_cartesian=False, ax: Axes = None, **kwargs)[source]

                                                                        Add labels to a matplotlib Axes.

                                                                        Parameters:
                                                                        @@ -5674,7 +5674,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_lattice_vectors(lattice, ax: Axes = None, **kwargs)[source]
                                                                        +plot_lattice_vectors(lattice, ax: Axes = None, **kwargs)[source]

                                                                        Add the basis vectors of the lattice provided to a matplotlib Axes.

                                                                        Parameters:
                                                                        @@ -5693,7 +5693,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_path(line, lattice=None, coords_are_cartesian=False, ax: Axes = None, **kwargs)[source]
                                                                        +plot_path(line, lattice=None, coords_are_cartesian=False, ax: Axes = None, **kwargs)[source]

                                                                        Add a line passing through the coordinates listed in ‘line’ to a matplotlib Axes.

                                                                        Parameters:
                                                                        @@ -5716,7 +5716,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_points(points, lattice=None, coords_are_cartesian=False, fold=False, ax: Axes = None, **kwargs)[source]
                                                                        +plot_points(points, lattice=None, coords_are_cartesian=False, fold=False, ax: Axes = None, **kwargs)[source]

                                                                        Add Points to a matplotlib Axes.

                                                                        Parameters:
                                                                        @@ -5740,7 +5740,7 @@

                                                                        pymatgen.electronic_structure.boltztrap2 module
                                                                        -plot_wigner_seitz(lattice, ax: Axes = None, **kwargs)[source]
                                                                        +plot_wigner_seitz(lattice, ax: Axes = None, **kwargs)[source]

                                                                        Add the skeleton of the Wigner-Seitz cell of the lattice to a matplotlib Axes.

                                                                        Parameters:
                                                                        diff --git a/docs/pymatgen.entries.html b/docs/pymatgen.entries.html index c12792b1c1e..496fe8bf9cf 100644 --- a/docs/pymatgen.entries.html +++ b/docs/pymatgen.entries.html @@ -4,7 +4,7 @@ - pymatgen.entries package — pymatgen 2024.6.4 documentation + pymatgen.entries package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                        - 2024.6.4 + 2024.6.10
                                                                        @@ -248,7 +248,7 @@ and PDEntry inherit from this class.

                                                                        -class Entry(composition: Composition | str | dict[str, float], energy: float)[source]
                                                                        +class Entry(composition: Composition | str | dict[str, float], energy: float)[source]

                                                                        Bases: MSONable, ABC

                                                                        A lightweight object containing the energy associated with a specific chemical composition. This base class is not @@ -267,49 +267,49 @@

                                                                        -as_dict() → dict[source]
                                                                        +as_dict() → dict[source]

                                                                        MSONable dict.

                                                                        -property composition: Composition[source]
                                                                        +property composition: Composition[source]

                                                                        The composition of the entry.

                                                                        -property elements: list[Element | Species | DummySpecies][source]
                                                                        +property elements: list[Element | Species | DummySpecies][source]

                                                                        The set of elements in the entry.

                                                                        -abstract property energy: float[source]
                                                                        +abstract property energy: float[source]

                                                                        The energy of the entry.

                                                                        -property energy_per_atom: float[source]
                                                                        +property energy_per_atom: float[source]

                                                                        The energy per atom of the entry.

                                                                        -property formula: str[source]
                                                                        +property formula: str[source]

                                                                        The formula of the entry.

                                                                        -property is_element: bool[source]
                                                                        +property is_element: bool[source]

                                                                        Whether composition of entry is an element.

                                                                        -normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → Entry[source]
                                                                        +normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → Entry[source]

                                                                        Normalize the entry’s composition and energy.

                                                                        Parameters:
                                                                        @@ -321,7 +321,7 @@
                                                                        -property reduced_formula: str[source]
                                                                        +property reduced_formula: str[source]

                                                                        The reduced formula of the entry.

                                                                        @@ -336,7 +336,7 @@

                                                                        Submodules
                                                                        -class AnionCorrection(*args, **kwargs)[source]
                                                                        +class AnionCorrection(*args, **kwargs)[source]

                                                                        Bases: AnionCorrection

                                                                        Correct anion energies to obtain the right formation energies. Note that this depends on calculations being run within the same input set.

                                                                        @@ -354,7 +354,7 @@

                                                                        Submodules
                                                                        -class AqueousCorrection(*args, **kwargs)[source]
                                                                        +class AqueousCorrection(*args, **kwargs)[source]

                                                                        Bases: AqueousCorrection

                                                                        This class implements aqueous phase compound corrections for elements and H2O.

                                                                        @@ -371,14 +371,14 @@

                                                                        Submodules
                                                                        -class Compatibility[source]
                                                                        +class Compatibility[source]

                                                                        Bases: MSONable, ABC

                                                                        Abstract Compatibility class, not intended for direct use. Compatibility classes are used to correct the energies of an entry or a set of entries. All Compatibility classes must implement get_adjustments() method.

                                                                        -static explain(entry)[source]
                                                                        +static explain(entry)[source]

                                                                        Prints an explanation of the energy adjustments applied by the Compatibility class. Inspired by the “explain” methods in many database methodologies.

                                                                        @@ -391,7 +391,7 @@

                                                                        Submodules
                                                                        -abstract get_adjustments(entry: ComputedEntry | ComputedStructureEntry) → list[EnergyAdjustment][source]
                                                                        +abstract get_adjustments(entry: ComputedEntry | ComputedStructureEntry) → list[EnergyAdjustment][source]

                                                                        Get the energy adjustments for a ComputedEntry.

                                                                        This method must generate a list of EnergyAdjustment objects of the appropriate type (constant, composition-based, or temperature-based) @@ -419,7 +419,7 @@

                                                                        Submodules
                                                                        -process_entries(entries: AnyComputedEntry | list[AnyComputedEntry], clean: bool = True, verbose: bool = False, inplace: bool = True, on_error: Literal['ignore', 'warn', 'raise'] = 'ignore') → list[AnyComputedEntry][source]
                                                                        +process_entries(entries: AnyComputedEntry | list[AnyComputedEntry], clean: bool = True, verbose: bool = False, inplace: bool = True, on_error: Literal['ignore', 'warn', 'raise'] = 'ignore') → list[AnyComputedEntry][source]

                                                                        Process a sequence of entries with the chosen Compatibility scheme.

                                                                        Warning: This method changes entries in place! All changes can be undone and original entries restored by setting entry.energy_adjustments = [].

                                                                        @@ -453,7 +453,7 @@

                                                                        Submodules
                                                                        -process_entry(entry: ComputedEntry, **kwargs) → ComputedEntry | None[source]
                                                                        +process_entry(entry: ComputedEntry, **kwargs) → ComputedEntry | None[source]

                                                                        Process a single entry with the chosen Corrections. Note that this method will change the data of the original entry.

                                                                        @@ -473,7 +473,7 @@

                                                                        Submodules
                                                                        -exception CompatibilityError[source]
                                                                        +exception CompatibilityError[source]

                                                                        Bases: Exception

                                                                        Exception class for Compatibility. Raised by attempting correction on incompatible calculation.

                                                                        @@ -481,7 +481,7 @@

                                                                        Submodules
                                                                        -class Correction[source]
                                                                        +class Correction[source]

                                                                        Bases: ABC

                                                                        A Correction class is a pre-defined scheme for correction a computed entry based on the type and chemistry of the structure and the @@ -489,7 +489,7 @@

                                                                        Submodules
                                                                        -correct_entry(entry)[source]
                                                                        +correct_entry(entry)[source]

                                                                        Corrects a single entry.

                                                                        Parameters:
                                                                        @@ -506,7 +506,7 @@

                                                                        Submodules
                                                                        -abstract get_correction(entry: ComputedEntry | ComputedStructureEntry) → EnergyAdjustment[source]
                                                                        +abstract get_correction(entry: ComputedEntry | ComputedStructureEntry) → EnergyAdjustment[source]

                                                                        Get correction and uncertainty for a single entry.

                                                                        Parameters:
                                                                        @@ -525,7 +525,7 @@

                                                                        Submodules
                                                                        -class CorrectionsList(corrections: Sequence[Correction], run_types: list[str] | None = None)[source]
                                                                        +class CorrectionsList(corrections: Sequence[Correction], run_types: list[str] | None = None)[source]

                                                                        Bases: Compatibility

                                                                        The CorrectionsList class combines a list of corrections to be applied to an entry or a set of entries. Note that some of the Corrections have @@ -547,7 +547,7 @@

                                                                        Submodules
                                                                        -explain(entry)[source]
                                                                        +explain(entry)[source]

                                                                        Prints an explanation of the corrections that are being applied for a given compatibility scheme. Inspired by the “explain” methods in many database methodologies.

                                                                        @@ -560,13 +560,13 @@

                                                                        Submodules
                                                                        -get_adjustments(entry: ComputedEntry | ComputedStructureEntry) → list[EnergyAdjustment][source]
                                                                        +get_adjustments(entry: ComputedEntry | ComputedStructureEntry) → list[EnergyAdjustment][source]

                                                                        Get the list of energy adjustments to be applied to an entry.

                                                                        -get_corrections_dict(entry: ComputedEntry | ComputedStructureEntry) → tuple[dict[str, float], dict[str, float]][source]
                                                                        +get_corrections_dict(entry: ComputedEntry | ComputedStructureEntry) → tuple[dict[str, float], dict[str, float]][source]

                                                                        Get the correction values and uncertainties applied to a particular entry.

                                                                        Parameters:
                                                                        @@ -587,7 +587,7 @@

                                                                        Submodules
                                                                        -get_explanation_dict(entry)[source]
                                                                        +get_explanation_dict(entry)[source]

                                                                        Explain the corrections applied for a given compatibility scheme. Inspired by the “explain” methods in many database methodologies.

                                                                        @@ -616,7 +616,7 @@

                                                                        Submodules
                                                                        -class GasCorrection(*args, **kwargs)[source]
                                                                        +class GasCorrection(*args, **kwargs)[source]

                                                                        Bases: GasCorrection

                                                                        Correct gas energies to obtain the right formation energies. Note that this depends on calculations being run within the same input set. @@ -630,7 +630,7 @@

                                                                        Submodules
                                                                        -class MITAqueousCompatibility(compat_type: Literal['GGA', 'Advanced'] = 'Advanced', correct_peroxide: bool = True, check_potcar_hash: bool = False)[source]
                                                                        +class MITAqueousCompatibility(compat_type: Literal['GGA', 'Advanced'] = 'Advanced', correct_peroxide: bool = True, check_potcar_hash: bool = False)[source]

                                                                        Bases: CorrectionsList

                                                                        This class implements the GGA/GGA+U mixing scheme, which allows mixing of entries. Note that this should only be used for VASP calculations using the @@ -656,7 +656,7 @@

                                                                        Submodules
                                                                        -class MITCompatibility(compat_type: Literal['GGA', 'Advanced'] = 'Advanced', correct_peroxide: bool = True, check_potcar_hash: bool = False)[source]
                                                                        +class MITCompatibility(compat_type: Literal['GGA', 'Advanced'] = 'Advanced', correct_peroxide: bool = True, check_potcar_hash: bool = False)[source]

                                                                        Bases: CorrectionsList

                                                                        This class implements the GGA/GGA+U mixing scheme, which allows mixing of entries. Note that this should only be used for VASP calculations using the @@ -682,7 +682,7 @@

                                                                        Submodules
                                                                        -class MaterialsProject2020Compatibility(*args, **kwargs)[source]
                                                                        +class MaterialsProject2020Compatibility(*args, **kwargs)[source]

                                                                        Bases: MaterialsProject2020Compatibility

                                                                        This class implements the Materials Project 2020 energy correction scheme, which incorporates uncertainty quantification and allows for mixing of GGA and GGA+U entries @@ -757,7 +757,7 @@

                                                                        Submodules
                                                                        -class MaterialsProjectAqueousCompatibility(*args, **kwargs)[source]
                                                                        +class MaterialsProjectAqueousCompatibility(*args, **kwargs)[source]

                                                                        Bases: MaterialsProjectAqueousCompatibility

                                                                        This class implements the Aqueous energy referencing scheme for constructing Pourbaix diagrams from DFT energies, as described in Persson et al.

                                                                        @@ -810,7 +810,7 @@

                                                                        Submodules
                                                                        -class MaterialsProjectCompatibility(compat_type: str = 'Advanced', correct_peroxide: bool = True, check_potcar_hash: bool = False)[source]
                                                                        +class MaterialsProjectCompatibility(compat_type: str = 'Advanced', correct_peroxide: bool = True, check_potcar_hash: bool = False)[source]

                                                                        Bases: CorrectionsList

                                                                        This class implements the GGA/GGA+U mixing scheme, which allows mixing of entries. Note that this should only be used for VASP calculations using the @@ -837,7 +837,7 @@

                                                                        Submodules
                                                                        -class PotcarCorrection(input_set: type[VaspInputSet], check_potcar: bool = True, check_hash: bool = False)[source]
                                                                        +class PotcarCorrection(input_set: type[VaspInputSet], check_potcar: bool = True, check_hash: bool = False)[source]

                                                                        Bases: Correction

                                                                        Check that POTCARs are valid within a pre-defined input set. This ensures that calculations performed using different InputSets are not @@ -864,7 +864,7 @@

                                                                        Submodules
                                                                        -get_correction(entry: ComputedEntry | ComputedStructureEntry) → ufloat[source]
                                                                        +get_correction(entry: ComputedEntry | ComputedStructureEntry) → ufloat[source]
                                                                        Parameters:

                                                                        entry (AnyComputedEntry) – ComputedEntry or ComputedStructureEntry.

                                                                        @@ -888,7 +888,7 @@

                                                                        Submodules
                                                                        -class UCorrection(*args, **kwargs)[source]
                                                                        +class UCorrection(*args, **kwargs)[source]

                                                                        Bases: UCorrection

                                                                        This class implements the GGA/GGA+U mixing scheme, which allows mixing of entries. Entry.parameters must contain a “hubbards” key which is a dict @@ -920,7 +920,7 @@

                                                                        Submodules
                                                                        -needs_u_correction(comp: CompositionLike, u_config: dict[str, dict[str, float]] = {'F': {'Co': -1.638, 'Cr': -1.999, 'Fe': -2.256, 'Mn': -1.668, 'Mo': -3.202, 'Ni': -2.541, 'V': -1.7, 'W': -4.438}, 'O': {'Co': -1.638, 'Cr': -1.999, 'Fe': -2.256, 'Mn': -1.668, 'Mo': -3.202, 'Ni': -2.541, 'V': -1.7, 'W': -4.438}}) → set[str][source]
                                                                        +needs_u_correction(comp: CompositionLike, u_config: dict[str, dict[str, float]] = {'F': {'Co': -1.638, 'Cr': -1.999, 'Fe': -2.256, 'Mn': -1.668, 'Mo': -3.202, 'Ni': -2.541, 'V': -1.7, 'W': -4.438}, 'O': {'Co': -1.638, 'Cr': -1.999, 'Fe': -2.256, 'Mn': -1.668, 'Mo': -3.202, 'Ni': -2.541, 'V': -1.7, 'W': -4.438}}) → set[str][source]

                                                                        Check if a composition is Hubbard U-corrected in the Materials Project 2020 GGA/GGA+U mixing scheme.

                                                                        @@ -954,7 +954,7 @@

                                                                        Submodules
                                                                        -class CompositionEnergyAdjustment(adj_per_atom, n_atoms, uncertainty_per_atom=nan, name='', cls=None, description='Composition-based energy adjustment')[source]
                                                                        +class CompositionEnergyAdjustment(adj_per_atom, n_atoms, uncertainty_per_atom=nan, name='', cls=None, description='Composition-based energy adjustment')[source]

                                                                        Bases: EnergyAdjustment

                                                                        An energy adjustment applied to a ComputedEntry based on the atomic composition. Used in various DFT energy correction schemes.

                                                                        @@ -975,13 +975,13 @@

                                                                        Submodules
                                                                        -property explain[source]
                                                                        +property explain[source]

                                                                        An explanation of how the energy adjustment is calculated.

                                                                        -normalize(factor: float) → None[source]
                                                                        +normalize(factor: float) → None[source]

                                                                        Normalize energy adjustment (in place), dividing value/uncertainty by a factor.

                                                                        @@ -993,13 +993,13 @@

                                                                        Submodules
                                                                        -property uncertainty[source]
                                                                        +property uncertainty[source]

                                                                        The value of the energy adjustment in eV.

                                                                        -property value[source]
                                                                        +property value[source]

                                                                        The value of the energy adjustment in eV.

                                                                        @@ -1007,7 +1007,7 @@

                                                                        Submodules
                                                                        -class ComputedEntry(composition: Composition | str | dict[str, float], energy: float, correction: float = 0.0, energy_adjustments: list | None = None, parameters: dict | None = None, data: dict | None = None, entry_id: str | None = None)[source]
                                                                        +class ComputedEntry(composition: Composition | str | dict[str, float], energy: float, correction: float = 0.0, energy_adjustments: list | None = None, parameters: dict | None = None, data: dict | None = None, entry_id: str | None = None)[source]

                                                                        Bases: Entry

                                                                        Lightweight Entry object for computed data. Contains facilities for applying corrections to the energy attribute and for storing @@ -1037,53 +1037,53 @@

                                                                        Submodules
                                                                        -as_dict() → dict[source]
                                                                        +as_dict() → dict[source]

                                                                        MSONable dict.

                                                                        -copy() → ComputedEntry[source]
                                                                        +copy() → ComputedEntry[source]

                                                                        Get a copy of the ComputedEntry.

                                                                        -property correction: float[source]
                                                                        +property correction: float[source]

                                                                        Returns: float: the total energy correction / adjustment applied to the entry in eV.

                                                                        -property correction_per_atom: float[source]
                                                                        +property correction_per_atom: float[source]

                                                                        Returns: float: the total energy correction / adjustment applied to the entry in eV/atom.

                                                                        -property correction_uncertainty: float[source]
                                                                        +property correction_uncertainty: float[source]

                                                                        Returns: float: the uncertainty of the energy adjustments applied to the entry in eV.

                                                                        -property correction_uncertainty_per_atom: float[source]
                                                                        +property correction_uncertainty_per_atom: float[source]

                                                                        Returns: float: the uncertainty of the energy adjustments applied to the entry in eV/atom.

                                                                        -property energy: float[source]
                                                                        +property energy: float[source]

                                                                        The corrected energy of the entry.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]
                                                                        Parameters:

                                                                        dct (dict) – Dict representation.

                                                                        @@ -1096,7 +1096,7 @@

                                                                        Submodules
                                                                        -normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → ComputedEntry[source]
                                                                        +normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → ComputedEntry[source]

                                                                        Normalize the entry’s composition and energy.

                                                                        Parameters:
                                                                        @@ -1108,14 +1108,14 @@

                                                                        Submodules
                                                                        -property uncorrected_energy: float[source]
                                                                        +property uncorrected_energy: float[source]

                                                                        Returns: float: the uncorrected energy of the entry.

                                                                        -property uncorrected_energy_per_atom: float[source]
                                                                        +property uncorrected_energy_per_atom: float[source]

                                                                        Returns: float: the uncorrected energy of the entry, normalized by atoms in eV/atom.

                                                                        @@ -1124,7 +1124,7 @@

                                                                        Submodules
                                                                        -class ComputedStructureEntry(structure: Structure, energy: float, correction: float = 0.0, composition: Composition | str | dict[str, float] | None = None, energy_adjustments: list | None = None, parameters: dict | None = None, data: dict | None = None, entry_id: str | None = None)[source]
                                                                        +class ComputedStructureEntry(structure: Structure, energy: float, correction: float = 0.0, composition: Composition | str | dict[str, float] | None = None, energy_adjustments: list | None = None, parameters: dict | None = None, data: dict | None = None, entry_id: str | None = None)[source]

                                                                        Bases: ComputedEntry

                                                                        A heavier version of ComputedEntry which contains a structure as well. The structure is needed for some analyses.

                                                                        @@ -1154,19 +1154,19 @@

                                                                        Submodules
                                                                        -as_dict() → dict[source]
                                                                        +as_dict() → dict[source]

                                                                        MSONable dict.

                                                                        -copy() → ComputedStructureEntry[source]
                                                                        +copy() → ComputedStructureEntry[source]

                                                                        Get a copy of the ComputedStructureEntry.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]
                                                                        Parameters:

                                                                        dct (dict) – Dict representation.

                                                                        @@ -1179,7 +1179,7 @@

                                                                        Submodules
                                                                        -normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → ComputedStructureEntry[source]
                                                                        +normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → ComputedStructureEntry[source]

                                                                        Normalize the entry’s composition and energy. The structure remains unchanged.

                                                                        Parameters:
                                                                        @@ -1191,7 +1191,7 @@

                                                                        Submodules
                                                                        -property structure: Structure[source]
                                                                        +property structure: Structure[source]

                                                                        The structure of the entry.

                                                                        @@ -1199,7 +1199,7 @@

                                                                        Submodules
                                                                        -class ConstantEnergyAdjustment(value, uncertainty=nan, name='Constant energy adjustment', cls=None, description='Constant energy adjustment')[source]
                                                                        +class ConstantEnergyAdjustment(value, uncertainty=nan, name='Constant energy adjustment', cls=None, description='Constant energy adjustment')[source]

                                                                        Bases: EnergyAdjustment

                                                                        A constant energy adjustment applied to a ComputedEntry. Useful in energy referencing schemes such as the Aqueous energy referencing scheme.

                                                                        @@ -1218,13 +1218,13 @@

                                                                        Submodules
                                                                        -property explain[source]
                                                                        +property explain[source]

                                                                        An explanation of how the energy adjustment is calculated.

                                                                        -normalize(factor: float) → None[source]
                                                                        +normalize(factor: float) → None[source]

                                                                        Normalize energy adjustment (in place), dividing value/uncertainty by a factor.

                                                                        @@ -1238,7 +1238,7 @@

                                                                        Submodules
                                                                        -class EnergyAdjustment(value, uncertainty=nan, name='Manual adjustment', cls=None, description='')[source]
                                                                        +class EnergyAdjustment(value, uncertainty=nan, name='Manual adjustment', cls=None, description='')[source]

                                                                        Bases: MSONable

                                                                        Lightweight class to contain information about an energy adjustment or energy correction.

                                                                        @@ -1256,13 +1256,13 @@

                                                                        Submodules
                                                                        -abstract property explain[source]
                                                                        +abstract property explain[source]

                                                                        Return an explanation of how the energy adjustment is calculated.

                                                                        -abstract normalize(factor)[source]
                                                                        +abstract normalize(factor)[source]

                                                                        Scale the value of the current energy adjustment by factor in-place.

                                                                        This method is utilized in ComputedEntry.normalize() to scale the energies to a formula unit basis (e.g. E_Fe6O9 = 3 x E_Fe2O3).

                                                                        @@ -1270,13 +1270,13 @@

                                                                        Submodules
                                                                        -property uncertainty[source]
                                                                        +property uncertainty[source]

                                                                        The uncertainty in the value of the energy adjustment in eV.

                                                                        -property value[source]
                                                                        +property value[source]

                                                                        The value of the energy correction in eV.

                                                                        @@ -1284,7 +1284,7 @@

                                                                        Submodules
                                                                        -class GibbsComputedStructureEntry(structure: Structure, formation_enthalpy_per_atom: float, temp: float = 300, gibbs_model: Literal['SISSO'] = 'SISSO', composition: Composition | None = None, correction: float = 0.0, energy_adjustments: list | None = None, parameters: dict | None = None, data: dict | None = None, entry_id: str | None = None)[source]
                                                                        +class GibbsComputedStructureEntry(structure: Structure, formation_enthalpy_per_atom: float, temp: float = 300, gibbs_model: Literal['SISSO'] = 'SISSO', composition: Composition | None = None, correction: float = 0.0, energy_adjustments: list | None = None, parameters: dict | None = None, data: dict | None = None, entry_id: str | None = None)[source]

                                                                        Bases: ComputedStructureEntry

                                                                        An extension to ComputedStructureEntry which includes the estimated Gibbs free energy of formation via a machine-learned model.

                                                                        @@ -1314,13 +1314,13 @@

                                                                        Submodules
                                                                        -as_dict() → dict[source]
                                                                        +as_dict() → dict[source]

                                                                        MSONable dict.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]
                                                                        Parameters:

                                                                        dct (dict) – Dict representation.

                                                                        @@ -1333,7 +1333,7 @@

                                                                        Submodules
                                                                        -classmethod from_entries(entries, temp=300, gibbs_model='SISSO') → list[Self][source]
                                                                        +classmethod from_entries(entries, temp=300, gibbs_model='SISSO') → list[Self][source]

                                                                        Constructor method for initializing GibbsComputedStructureEntry objects from T = 0 K ComputedStructureEntry objects, as acquired from a thermochemical database e.g. The Materials Project.

                                                                        @@ -1362,7 +1362,7 @@

                                                                        Submodules
                                                                        -classmethod from_pd(pd, temp=300, gibbs_model='SISSO') → list[Self][source]
                                                                        +classmethod from_pd(pd, temp=300, gibbs_model='SISSO') → list[Self][source]

                                                                        Constructor method for initializing a list of GibbsComputedStructureEntry objects from an existing T = 0 K phase diagram composed of ComputedStructureEntry objects, as acquired from a thermochemical database; @@ -1392,7 +1392,7 @@

                                                                        Submodules
                                                                        -gf_sisso() → float[source]
                                                                        +gf_sisso() → float[source]

                                                                        Gibbs Free Energy of formation as calculated by SISSO descriptor from Bartel et al. (2018). Units: eV (not normalized).

                                                                        WARNING: This descriptor only applies to solids. The implementation here @@ -1420,7 +1420,7 @@

                                                                        Submodules
                                                                        -class ManualEnergyAdjustment(value)[source]
                                                                        +class ManualEnergyAdjustment(value)[source]

                                                                        Bases: ConstantEnergyAdjustment

                                                                        A manual energy adjustment applied to a ComputedEntry.

                                                                        @@ -1432,7 +1432,7 @@

                                                                        Submodules
                                                                        -class TemperatureEnergyAdjustment(adj_per_deg, temp, n_atoms, uncertainty_per_deg=nan, name='', cls=None, description='Temperature-based energy adjustment')[source]
                                                                        +class TemperatureEnergyAdjustment(adj_per_deg, temp, n_atoms, uncertainty_per_deg=nan, name='', cls=None, description='Temperature-based energy adjustment')[source]

                                                                        Bases: EnergyAdjustment

                                                                        An energy adjustment applied to a ComputedEntry based on the temperature. Used, for example, to add entropy to DFT energies.

                                                                        @@ -1454,13 +1454,13 @@

                                                                        Submodules
                                                                        -property explain[source]
                                                                        +property explain[source]

                                                                        An explanation of how the energy adjustment is calculated.

                                                                        -normalize(factor: float) → None[source]
                                                                        +normalize(factor: float) → None[source]

                                                                        Normalize energy adjustment (in place), dividing value/uncertainty by a factor.

                                                                        @@ -1472,13 +1472,13 @@

                                                                        Submodules
                                                                        -property uncertainty[source]
                                                                        +property uncertainty[source]

                                                                        The value of the energy adjustment in eV.

                                                                        -property value[source]
                                                                        +property value[source]

                                                                        The value of the energy correction in eV.

                                                                        @@ -1491,44 +1491,44 @@

                                                                        Submodules
                                                                        -class CorrectionCalculator(species: list[str] | None = None, max_error: float = 0.1, allow_unstable: float | bool = 0.1, exclude_polyanions: list[str] | None = None)[source]
                                                                        +class CorrectionCalculator(species: list[str] | None = None, max_error: float = 0.1, allow_unstable: float | bool = 0.1, exclude_polyanions: list[str] | None = None)[source]

                                                                        Bases: object

                                                                        A CorrectionCalculator contains experimental and computed entries which it uses to compute corrections.

                                                                        It graphs residual errors after applying the computed corrections and creates the MPCompatibility.yaml file the Correction classes use.

                                                                        -species[source]
                                                                        +species[source]

                                                                        list of species that corrections are being calculated for

                                                                        -exp_compounds[source]
                                                                        +exp_compounds[source]

                                                                        list of dictionaries which each contain a compound’s formula and experimental data

                                                                        -calc_compounds[source]
                                                                        +calc_compounds[source]

                                                                        dictionary of ComputedEntry objects

                                                                        -corrections[source]
                                                                        +corrections[source]

                                                                        list of corrections in same order as species list

                                                                        -corrections_std_error[source]
                                                                        +corrections_std_error[source]

                                                                        list of the variances of the corrections in same order as species list

                                                                        -corrections_dict[source]
                                                                        +corrections_dict[source]

                                                                        dictionary of format {‘species’: (value, uncertainty)} for easier correction lookup

                                                                        @@ -1551,7 +1551,7 @@

                                                                        Submodules
                                                                        -compute_corrections(exp_entries: list, calc_entries: dict) → dict[source]
                                                                        +compute_corrections(exp_entries: list, calc_entries: dict) → dict[source]

                                                                        Compute the corrections and fills in correction, corrections_std_error, and corrections_dict.

                                                                        Parameters:
                                                                        @@ -1575,7 +1575,7 @@

                                                                        Submodules
                                                                        -compute_from_files(exp_gz: str, comp_gz: str) → dict[source]
                                                                        +compute_from_files(exp_gz: str, comp_gz: str) → dict[source]
                                                                        Parameters:
                                                                        -graph_residual_error_per_species(specie: str) → Figure[source]
                                                                        +graph_residual_error_per_species(specie: str) → Figure[source]

                                                                        Graphs the residual errors for each compound that contains specie after applying computed corrections.

                                                                        Parameters:
                                                                        @@ -1612,7 +1612,7 @@

                                                                        Submodules
                                                                        -make_yaml(name: str = 'MP2020', dir: str | None = None) → None[source]
                                                                        +make_yaml(name: str = 'MP2020', dir: str | None = None) → None[source]

                                                                        Create the _name_Compatibility.yaml that stores corrections as well as _name_CompatibilityUncertainties.yaml for correction uncertainties.

                                                                        @@ -1636,7 +1636,7 @@

                                                                        Submodules
                                                                        -class EntrySet(entries: Iterable[PDEntry | ComputedEntry | ComputedStructureEntry])[source]
                                                                        +class EntrySet(entries: Iterable[PDEntry | ComputedEntry | ComputedStructureEntry])[source]

                                                                        Bases: MutableSet, MSONable

                                                                        A convenient container for manipulating entries. Allows for generating subsets, dumping into files, etc.

                                                                        @@ -1647,7 +1647,7 @@

                                                                        Submodules
                                                                        -add(element)[source]
                                                                        +add(element)[source]

                                                                        Add an entry.

                                                                        Parameters:
                                                                        @@ -1658,20 +1658,20 @@

                                                                        Submodules
                                                                        -as_dict() → dict[Literal['entries'], list[Entry]][source]
                                                                        +as_dict() → dict[Literal['entries'], list[Entry]][source]

                                                                        Get MSONable dict.

                                                                        -property chemsys: set[source]
                                                                        +property chemsys: set[source]

                                                                        Returns: set representing the chemical system, e.g. {“Li”, “Fe”, “P”, “O”}.

                                                                        -discard(element)[source]
                                                                        +discard(element)[source]

                                                                        Discard an entry.

                                                                        Parameters:
                                                                        @@ -1682,7 +1682,7 @@

                                                                        Submodules
                                                                        -classmethod from_csv(filename: str) → Self[source]
                                                                        +classmethod from_csv(filename: str) → Self[source]

                                                                        Imports PDEntries from a csv.

                                                                        Parameters:
                                                                        @@ -1696,7 +1696,7 @@

                                                                        Submodules
                                                                        -get_subset_in_chemsys(chemsys: list[str])[source]
                                                                        +get_subset_in_chemsys(chemsys: list[str])[source]

                                                                        Get an EntrySet containing only the set of entries belonging to a particular chemical system (in this definition, it includes all sub systems). For example, if the entries are from the @@ -1715,27 +1715,27 @@

                                                                        Submodules
                                                                        -property ground_states: set[source]
                                                                        +property ground_states: set[source]

                                                                        A set containing only the entries that are ground states, i.e., the lowest energy per atom entry at each composition.

                                                                        -is_ground_state(entry) → bool[source]
                                                                        +is_ground_state(entry) → bool[source]

                                                                        Boolean indicating whether a given Entry is a ground state.

                                                                        -remove_non_ground_states()[source]
                                                                        +remove_non_ground_states()[source]

                                                                        Removes all non-ground state entries, i.e., only keep the lowest energy per atom entry at each composition.

                                                                        -to_csv(filename: str, latexify_names: bool = False) → None[source]
                                                                        +to_csv(filename: str, latexify_names: bool = False) → None[source]

                                                                        Exports PDEntries to a csv.

                                                                        Parameters:
                                                                        @@ -1753,7 +1753,7 @@

                                                                        Submodules
                                                                        -group_entries_by_composition(entries, sort_by_e_per_atom=True)[source]
                                                                        +group_entries_by_composition(entries, sort_by_e_per_atom=True)[source]
                                                                        Given a sequence of Entry-like objects, group them by composition and

                                                                        optionally sort by energy above hull.

                                                                        @@ -1775,7 +1775,7 @@

                                                                        Submodules
                                                                        -group_entries_by_structure(entries, species_to_remove=None, ltol=0.2, stol=0.4, angle_tol=5, primitive_cell=True, scale=True, comparator=None, ncpus=None)[source]
                                                                        +group_entries_by_structure(entries, species_to_remove=None, ltol=0.2, stol=0.4, angle_tol=5, primitive_cell=True, scale=True, comparator=None, ncpus=None)[source]

                                                                        Given a sequence of ComputedStructureEntries, use structure fitter to group them by structural similarity.

                                                                        @@ -1812,7 +1812,7 @@

                                                                        Submodules
                                                                        -class ExpEntry(composition, thermodata, temperature=298)[source]
                                                                        +class ExpEntry(composition, thermodata, temperature=298)[source]

                                                                        Bases: PDEntry, MSONable

                                                                        An lightweight ExpEntry object containing experimental data for a composition for many purposes. Extends a PDEntry so that it can be used for @@ -1832,13 +1832,13 @@

                                                                        Submodules
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        MSONable dict.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]
                                                                        Parameters:

                                                                        dct (dict) – Dict representation.

                                                                        @@ -1858,7 +1858,7 @@

                                                                        Submodules
                                                                        -class MaterialsProjectDFTMixingScheme(structure_matcher: ~pymatgen.analysis.structure_matcher.StructureMatcher | None = None, run_type_1: str = 'GGA(+U)', run_type_2: str = 'R2SCAN', compat_1: ~pymatgen.entries.compatibility.Compatibility | None = <pymatgen.entries.compatibility.cached_class.<locals>._decorated object>, compat_2: ~pymatgen.entries.compatibility.Compatibility | None = None, fuzzy_matching: bool = True, check_potcar: bool = True)[source]
                                                                        +class MaterialsProjectDFTMixingScheme(structure_matcher: ~pymatgen.analysis.structure_matcher.StructureMatcher | None = None, run_type_1: str = 'GGA(+U)', run_type_2: str = 'R2SCAN', compat_1: ~pymatgen.entries.compatibility.Compatibility | None = <pymatgen.entries.compatibility.cached_class.<locals>._decorated object>, compat_2: ~pymatgen.entries.compatibility.Compatibility | None = None, fuzzy_matching: bool = True, check_potcar: bool = True)[source]

                                                                        Bases: Compatibility

                                                                        This class implements the Materials Project mixing scheme, which allows mixing of energies from different DFT functionals. Note that this should only be used for @@ -1915,13 +1915,13 @@

                                                                        Submodules
                                                                        -static display_entries(entries)[source]
                                                                        +static display_entries(entries)[source]

                                                                        Generate a pretty printout of key properties of a list of ComputedEntry.

                                                                        -get_adjustments(entry, mixing_state_data: DataFrame | None = None)[source]
                                                                        +get_adjustments(entry, mixing_state_data: DataFrame | None = None)[source]

                                                                        Get the corrections applied to a particular entry. Note that get_adjustments is not intended to be called directly in the R2SCAN mixing scheme. Call process_entries instead, and it will pass the required arguments to get_adjustments.

                                                                        @@ -1954,7 +1954,7 @@

                                                                        Submodules
                                                                        -get_mixing_state_data(entries: list[ComputedStructureEntry])[source]
                                                                        +get_mixing_state_data(entries: list[ComputedStructureEntry])[source]

                                                                        Generate internal state data to be passed to get_adjustments.

                                                                        Parameters:
                                                                        @@ -1995,7 +1995,7 @@

                                                                        Submodules
                                                                        -process_entries(entries: ComputedEntry | ComputedStructureEntry | list[ComputedEntry | ComputedStructureEntry], clean: bool = True, verbose: bool = False, inplace: bool = True, mixing_state_data=None) → list[ComputedEntry | ComputedStructureEntry][source]
                                                                        +process_entries(entries: ComputedEntry | ComputedStructureEntry | list[ComputedEntry | ComputedStructureEntry], clean: bool = True, verbose: bool = False, inplace: bool = True, mixing_state_data=None) → list[ComputedEntry | ComputedStructureEntry][source]

                                                                        Process a sequence of entries with the DFT mixing scheme. Note that this method will change the data of the original entries.

                                                                        diff --git a/docs/pymatgen.ext.html b/docs/pymatgen.ext.html index 28fff7b4288..f50ff27ff78 100644 --- a/docs/pymatgen.ext.html +++ b/docs/pymatgen.ext.html @@ -4,7 +4,7 @@ - pymatgen.ext namespace — pymatgen 2024.6.4 documentation + pymatgen.ext namespace — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                        - 2024.6.4 + 2024.6.10
                                                                        @@ -168,12 +168,12 @@

                                                                        Submodules
                                                                        -class COD[source]
                                                                        +class COD[source]

                                                                        Bases: object

                                                                        An interface to the Crystallography Open Database.

                                                                        -get_cod_ids(formula) → list[int][source]
                                                                        +get_cod_ids(formula) → list[int][source]

                                                                        Query the COD for all cod ids associated with a formula. Requires mysql executable to be in the path.

                                                                        @@ -188,7 +188,7 @@

                                                                        Submodules
                                                                        -get_structure_by_formula(formula: str, **kwargs) → list[dict[str, str | int | Structure]][source]
                                                                        +get_structure_by_formula(formula: str, **kwargs) → list[dict[str, str | int | Structure]][source]

                                                                        Query the COD for structures by formula. Requires mysql executable to be in the path.

                                                                        @@ -209,7 +209,7 @@

                                                                        Submodules
                                                                        -get_structure_by_id(cod_id: int, timeout: int = 600, **kwargs) → Structure[source]
                                                                        +get_structure_by_id(cod_id: int, timeout: int = 600, **kwargs) → Structure[source]

                                                                        Query the COD for a structure by id.

                                                                        Parameters:
                                                                        @@ -227,7 +227,7 @@

                                                                        Submodules
                                                                        -query(sql: str) → str[source]
                                                                        +query(sql: str) → str[source]

                                                                        Perform a query.

                                                                        Parameters:
                                                                        @@ -241,7 +241,7 @@

                                                                        Submodules
                                                                        -url = 'www.crystallography.net'[source]
                                                                        +url = 'www.crystallography.net'[source]

                                                                        @@ -257,14 +257,14 @@

                                                                        Submoduleshttps://materialsproject.org/dashboard.

                                                                        -exception MPRestError[source]
                                                                        +exception MPRestError[source]

                                                                        Bases: Exception

                                                                        Exception class for legacy MPRestAdaptor. Raised when query is malformed.

                                                                        -class MPRester(*args, **kwargs)[source]
                                                                        +class MPRester(*args, **kwargs)[source]

                                                                        Bases: object

                                                                        A class to conveniently interface with the new and legacy Materials Project REST interface.

                                                                        The recommended way to use MPRester is as a context manager to ensure @@ -300,91 +300,91 @@

                                                                        Submodules
                                                                        -exception MPRestError[source]
                                                                        +exception MPRestError[source]

                                                                        Bases: Exception

                                                                        Exception class for legacy MPRestAdaptor. Raised when query is malformed.

                                                                        -class TaskType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                        +class TaskType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                        Bases: Enum

                                                                        task types available in legacy MP data.

                                                                        -GGAU_DEF = 'GGA+U Deformation'[source]
                                                                        +GGAU_DEF = 'GGA+U Deformation'[source]
                                                                        -GGAU_LINE = 'GGA+U NSCF Line'[source]
                                                                        +GGAU_LINE = 'GGA+U NSCF Line'[source]
                                                                        -GGAU_OPT = 'GGA+U Structure Optimization'[source]
                                                                        +GGAU_OPT = 'GGA+U Structure Optimization'[source]
                                                                        -GGAU_STATIC = 'GGA+U Static'[source]
                                                                        +GGAU_STATIC = 'GGA+U Static'[source]
                                                                        -GGAU_STATIC_DIEL = 'GGA+U Static Dielectric'[source]
                                                                        +GGAU_STATIC_DIEL = 'GGA+U Static Dielectric'[source]
                                                                        -GGAU_UNIFORM = 'GGA+U NSCF Uniform'[source]
                                                                        +GGAU_UNIFORM = 'GGA+U NSCF Uniform'[source]
                                                                        -GGA_DEF = 'GGA Deformation'[source]
                                                                        +GGA_DEF = 'GGA Deformation'[source]
                                                                        -GGA_LINE = 'GGA NSCF Line'[source]
                                                                        +GGA_LINE = 'GGA NSCF Line'[source]
                                                                        -GGA_OPT = 'GGA Structure Optimization'[source]
                                                                        +GGA_OPT = 'GGA Structure Optimization'[source]
                                                                        -GGA_STATIC = 'GGA Static'[source]
                                                                        +GGA_STATIC = 'GGA Static'[source]
                                                                        -GGA_STATIC_DIEL = 'GGA Static Dielectric'[source]
                                                                        +GGA_STATIC_DIEL = 'GGA Static Dielectric'[source]
                                                                        -GGA_UNIFORM = 'GGA NSCF Uniform'[source]
                                                                        +GGA_UNIFORM = 'GGA NSCF Uniform'[source]
                                                                        -LDA_STATIC_DIEL = 'LDA Static Dielectric'[source]
                                                                        +LDA_STATIC_DIEL = 'LDA Static Dielectric'[source]
                                                                        -SCAN_OPT = 'SCAN Structure Optimization'[source]
                                                                        +SCAN_OPT = 'SCAN Structure Optimization'[source]
                                                                        -get_chunks(sequence: Sequence[Any], size=1)[source]
                                                                        +get_chunks(sequence: Sequence[Any], size=1)[source]
                                                                        Parameters:
                                                                        -describe()[source]
                                                                        +describe()[source]

                                                                        Human-readable information about the resources being searched by the OptimadeRester.

                                                                        -get_snls(elements: list[str] | str | None = None, nelements: int | None = None, nsites: int | None = None, chemical_formula_anonymous: str | None = None, chemical_formula_hill: str | None = None, additional_response_fields: str | list[str] | set[str] | None = None) → dict[str, dict[str, StructureNL]][source]
                                                                        +get_snls(elements: list[str] | str | None = None, nelements: int | None = None, nsites: int | None = None, chemical_formula_anonymous: str | None = None, chemical_formula_hill: str | None = None, additional_response_fields: str | list[str] | set[str] | None = None) → dict[str, dict[str, StructureNL]][source]

                                                                        Retrieve StructureNL from OPTIMADE providers.

                                                                        A StructureNL is an object provided by pymatgen which combines Structure with associated metadata, such as the URL is was downloaded from and any additional namespaced @@ -499,7 +499,7 @@

                                                                        Submodules
                                                                        -get_snls_with_filter(optimade_filter: str, additional_response_fields: str | list[str] | set[str] | None = None) → dict[str, dict[str, StructureNL]][source]
                                                                        +get_snls_with_filter(optimade_filter: str, additional_response_fields: str | list[str] | set[str] | None = None) → dict[str, dict[str, StructureNL]][source]

                                                                        Get structures satisfying a given OPTIMADE filter.

                                                                        Parameters:
                                                                        @@ -519,7 +519,7 @@

                                                                        Submodules
                                                                        -get_structures(elements: list[str] | str | None = None, nelements: int | None = None, nsites: int | None = None, chemical_formula_anonymous: str | None = None, chemical_formula_hill: str | None = None) → dict[str, dict[str, Structure]][source]
                                                                        +get_structures(elements: list[str] | str | None = None, nelements: int | None = None, nsites: int | None = None, chemical_formula_anonymous: str | None = None, chemical_formula_hill: str | None = None) → dict[str, dict[str, Structure]][source]

                                                                        Retrieve Structures from OPTIMADE providers.

                                                                        Not all functionality of OPTIMADE is currently exposed in this convenience method. To use a custom filter, call get_structures_with_filter().

                                                                        @@ -550,7 +550,7 @@

                                                                        Submodules
                                                                        -get_structures_with_filter(optimade_filter: str) → dict[str, dict[str, Structure]][source]
                                                                        +get_structures_with_filter(optimade_filter: str) → dict[str, dict[str, Structure]][source]

                                                                        Get structures satisfying a given OPTIMADE filter.

                                                                        Parameters:
                                                                        @@ -567,12 +567,12 @@

                                                                        Submodules
                                                                        -mandatory_response_fields = ('lattice_vectors', 'cartesian_site_positions', 'species', 'species_at_sites')[source]
                                                                        +mandatory_response_fields = ('lattice_vectors', 'cartesian_site_positions', 'species', 'species_at_sites')[source]

                                                                        -refresh_aliases(providers_url='https://providers.optimade.org/providers.json')[source]
                                                                        +refresh_aliases(providers_url='https://providers.optimade.org/providers.json')[source]

                                                                        Update available OPTIMADE structure resources based on the current list of OPTIMADE providers.

                                                                        @@ -581,37 +581,37 @@

                                                                        Submodules
                                                                        -class Provider(name: str, base_url: str, description: str, homepage: str, prefix: str)[source]
                                                                        +class Provider(name: str, base_url: str, description: str, homepage: str, prefix: str)[source]

                                                                        Bases: NamedTuple

                                                                        TODO: Import optimade-python-tool’s data structures will make more sense.

                                                                        Create new instance of Provider(name, base_url, description, homepage, prefix)

                                                                        -base_url: str[source]
                                                                        +base_url: str[source]

                                                                        Alias for field number 1

                                                                        -description: str[source]
                                                                        +description: str[source]

                                                                        Alias for field number 2

                                                                        -homepage: str[source]
                                                                        +homepage: str[source]

                                                                        Alias for field number 3

                                                                        -name: str[source]
                                                                        +name: str[source]

                                                                        Alias for field number 0

                                                                        -prefix: str[source]
                                                                        +prefix: str[source]

                                                                        Alias for field number 4

                                                                        diff --git a/docs/pymatgen.html b/docs/pymatgen.html index 503d3863494..dec0600faae 100644 --- a/docs/pymatgen.html +++ b/docs/pymatgen.html @@ -4,7 +4,7 @@ - pymatgen namespace — pymatgen 2024.6.4 documentation + pymatgen namespace — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -36,7 +36,7 @@
                                                                        - 2024.6.4 + 2024.6.10
                                                                        @@ -718,15 +718,7 @@

                                                                        Subpackagespymatgen.analysis.solar package
                                                                      • pymatgen.analysis.structure_prediction package

                                                                        • -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        Build from dict.

                                                                        -property nspden[source]
                                                                        +property nspden[source]

                                                                        Number of independent density components.

                                                                        -property nspinor[source]
                                                                        +property nspinor[source]

                                                                        Number of independent spinor components.

                                                                        -property nsppol: int[source]
                                                                        +property nsppol: int[source]

                                                                        Number of independent spin polarizations.

                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Return dictionary with Abinit variables.

                                                                        @@ -613,7 +613,7 @@

                                                                        Submodules
                                                                        -class ElectronsAlgorithm(*args, **kwargs)[source]
                                                                        +class ElectronsAlgorithm(*args, **kwargs)[source]

                                                                        Bases: dict, AbivarAble, MSONable

                                                                        Variables controlling the SCF/NSCF algorithm.

                                                                        @@ -634,19 +634,19 @@

                                                                        Submodules
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        Get JSON-able dict representation.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        Build from dict.

                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Dictionary with Abinit input variables.

                                                                        @@ -654,7 +654,7 @@

                                                                        Submodules
                                                                        -class ExcHamiltonian(bs_loband, nband, mbpt_sciss, coulomb_mode, ecuteps, spin_mode='polarized', mdf_epsinf=None, exc_type='TDA', algo='haydock', with_lf=True, bs_freq_mesh=None, zcut=None, **kwargs)[source]
                                                                        +class ExcHamiltonian(bs_loband, nband, mbpt_sciss, coulomb_mode, ecuteps, spin_mode='polarized', mdf_epsinf=None, exc_type='TDA', algo='haydock', with_lf=True, bs_freq_mesh=None, zcut=None, **kwargs)[source]

                                                                        Bases: AbivarAble

                                                                        Contain parameters for the solution of the Bethe-Salpeter equation.

                                                                        @@ -678,31 +678,31 @@

                                                                        Submodules
                                                                        -property inclvkb[source]
                                                                        +property inclvkb[source]

                                                                        Treatment of the dipole matrix element (NC pseudos, default is 2).

                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Get a dictionary with the abinit variables.

                                                                        -property use_cg[source]
                                                                        +property use_cg[source]

                                                                        True if we are using the conjugate gradient method.

                                                                        -property use_direct_diago[source]
                                                                        +property use_direct_diago[source]

                                                                        True if we are performing the direct diagonalization of the BSE Hamiltonian.

                                                                        -property use_haydock[source]
                                                                        +property use_haydock[source]

                                                                        True if we are using the Haydock iterative technique.

                                                                        @@ -710,7 +710,7 @@

                                                                        Submodules
                                                                        -class HilbertTransform(nomegasf, domegasf=None, spmeth=1, nfreqre=None, freqremax=None, nfreqim=None, freqremin=None)[source]
                                                                        +class HilbertTransform(nomegasf, domegasf=None, spmeth=1, nfreqre=None, freqremax=None, nfreqim=None, freqremin=None)[source]

                                                                        Bases: AbivarAble

                                                                        Parameters for the Hilbert-transform method (Screening code) i.e. the parameters defining the frequency mesh used for the spectral function @@ -730,7 +730,7 @@

                                                                        Submodules
                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Get a dictionary with the abinit variables.

                                                                        @@ -738,7 +738,7 @@

                                                                        Submodules
                                                                        -class KSampling(mode=KSamplingModes.monkhorst, num_kpts=0, kpts=((1, 1, 1),), kpt_shifts=(0.5, 0.5, 0.5), kpts_weights=None, use_symmetries=True, use_time_reversal=True, chksymbreak=None, comment=None)[source]
                                                                        +class KSampling(mode=KSamplingModes.monkhorst, num_kpts=0, kpts=((1, 1, 1),), kpt_shifts=(0.5, 0.5, 0.5), kpts_weights=None, use_symmetries=True, use_time_reversal=True, chksymbreak=None, comment=None)[source]

                                                                        Bases: AbivarAble, MSONable

                                                                        Input variables defining the K-point sampling.

                                                                        Highly flexible constructor for KSampling objects. The flexibility comes @@ -783,13 +783,13 @@

                                                                        Submodules
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        Get JSON-able dict representation.

                                                                        -classmethod automatic_density(structure, kppa, chksymbreak=None, use_symmetries=True, use_time_reversal=True, shifts=(0.5, 0.5, 0.5))[source]
                                                                        +classmethod automatic_density(structure, kppa, chksymbreak=None, use_symmetries=True, use_time_reversal=True, shifts=(0.5, 0.5, 0.5))[source]

                                                                        Get an automatic Kpoint object based on a structure and a kpoint density. Uses Gamma centered meshes for hexagonal cells and Monkhorst-Pack grids otherwise.

                                                                        @@ -809,19 +809,19 @@

                                                                        Submodules
                                                                        -classmethod explicit_path(ndivsm, kpath_bounds)[source]
                                                                        +classmethod explicit_path(ndivsm, kpath_bounds)[source]

                                                                        See _path for the meaning of the variables.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        Build from dict.

                                                                        -classmethod gamma_centered(kpts=(1, 1, 1), use_symmetries=True, use_time_reversal=True)[source]
                                                                        +classmethod gamma_centered(kpts=(1, 1, 1), use_symmetries=True, use_time_reversal=True)[source]

                                                                        Convenient static constructor for an automatic Gamma centered Kpoint grid.

                                                                        Parameters:
                                                                        @@ -841,19 +841,19 @@

                                                                        Submodules
                                                                        -classmethod gamma_only()[source]
                                                                        +classmethod gamma_only()[source]

                                                                        Gamma-only sampling.

                                                                        -property is_homogeneous: bool[source]
                                                                        +property is_homogeneous: bool[source]

                                                                        Homogeneous sampling.

                                                                        -classmethod monkhorst(ngkpt, shiftk=(0.5, 0.5, 0.5), chksymbreak=None, use_symmetries=True, use_time_reversal=True, comment=None)[source]
                                                                        +classmethod monkhorst(ngkpt, shiftk=(0.5, 0.5, 0.5), chksymbreak=None, use_symmetries=True, use_time_reversal=True, comment=None)[source]

                                                                        Convenient static constructor for a Monkhorst-Pack mesh.

                                                                        Parameters:
                                                                        @@ -872,7 +872,7 @@

                                                                        Submodules
                                                                        -classmethod monkhorst_automatic(structure, ngkpt, use_symmetries=True, use_time_reversal=True, chksymbreak=None, comment=None)[source]
                                                                        +classmethod monkhorst_automatic(structure, ngkpt, use_symmetries=True, use_time_reversal=True, chksymbreak=None, comment=None)[source]

                                                                        Convenient static constructor for an automatic Monkhorst-Pack mesh.

                                                                        Parameters:
                                                                        @@ -891,13 +891,13 @@

                                                                        Submodules
                                                                        -classmethod path_from_structure(ndivsm, structure) → Self[source]
                                                                        +classmethod path_from_structure(ndivsm, structure) → Self[source]

                                                                        See _path for the meaning of the variables.

                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Dictionary with Abinit variables.

                                                                        @@ -905,29 +905,29 @@

                                                                        Submodules
                                                                        -class KSamplingModes(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                        +class KSamplingModes(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                        Bases: Enum

                                                                        Enum if the different samplings of the BZ.

                                                                        -automatic = 3[source]
                                                                        +automatic = 3[source]
                                                                        -monkhorst = 1[source]
                                                                        +monkhorst = 1[source]
                                                                        -path = 2[source]
                                                                        +path = 2[source]

                                                                        -class ModelDielectricFunction(mdf_epsinf)[source]
                                                                        +class ModelDielectricFunction(mdf_epsinf)[source]

                                                                        Bases: AbivarAble

                                                                        Model dielectric function used for BSE calculation.

                                                                        @@ -937,7 +937,7 @@

                                                                        Submodules
                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Return dictionary with abinit variables.

                                                                        @@ -945,7 +945,7 @@

                                                                        Submodules
                                                                        -class PPModel(mode='godby', plasmon_freq=None)[source]
                                                                        +class PPModel(mode='godby', plasmon_freq=None)[source]

                                                                        Bases: AbivarAble, MSONable

                                                                        Parameters defining the plasmon-pole technique. The common way to instantiate a PPModel object is via the class method PPModel.as_ppmodel(string).

                                                                        @@ -959,13 +959,13 @@

                                                                        Submodules
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        Get JSON-able dict representation.

                                                                        -classmethod as_ppmodel(obj)[source]
                                                                        +classmethod as_ppmodel(obj)[source]

                                                                        Constructs an instance of PPModel from obj.

                                                                        Accepts obj in the form:
                                                                        -classmethod get_noppmodel()[source]
                                                                        +classmethod get_noppmodel()[source]

                                                                        Calculation without plasmon-pole model.

                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Return dictionary with Abinit variables.

                                                                        @@ -998,39 +998,39 @@

                                                                        Submodules
                                                                        -class PPModelModes(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                        +class PPModelModes(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                        Bases: Enum

                                                                        Different kind of plasmon-pole models.

                                                                        -farid = 4[source]
                                                                        +farid = 4[source]
                                                                        -godby = 1[source]
                                                                        +godby = 1[source]
                                                                        -hybersten = 2[source]
                                                                        +hybersten = 2[source]
                                                                        -linden = 3[source]
                                                                        +linden = 3[source]
                                                                        -noppmodel = 0[source]
                                                                        +noppmodel = 0[source]

                                                                        -class RelaxationMethod(*args, **kwargs)[source]
                                                                        +class RelaxationMethod(*args, **kwargs)[source]

                                                                        Bases: AbivarAble, MSONable

                                                                        This object stores the variables for the (constrained) structural optimization ionmov and optcell specify the type of relaxation. @@ -1055,53 +1055,53 @@

                                                                        Submodules
                                                                        -IONMOV_DEFAULT = 3[source]
                                                                        +IONMOV_DEFAULT = 3[source]

                                                                        -OPTCELL_DEFAULT = 2[source]
                                                                        +OPTCELL_DEFAULT = 2[source]
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        Convert to dictionary.

                                                                        -classmethod atoms_and_cell(atoms_constraints=None)[source]
                                                                        +classmethod atoms_and_cell(atoms_constraints=None)[source]

                                                                        Relax atomic positions as well as unit cell.

                                                                        -classmethod atoms_only(atoms_constraints=None)[source]
                                                                        +classmethod atoms_only(atoms_constraints=None)[source]

                                                                        Relax atomic positions, keep unit cell fixed.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        Build from dictionary.

                                                                        -property move_atoms[source]
                                                                        +property move_atoms[source]

                                                                        True if atoms must be moved.

                                                                        -property move_cell[source]
                                                                        +property move_cell[source]

                                                                        True if lattice parameters must be optimized.

                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Get a dictionary with the abinit variables.

                                                                        @@ -1109,7 +1109,7 @@

                                                                        Submodules
                                                                        -class Screening(ecuteps, nband, w_type='RPA', sc_mode='one_shot', hilbert=None, ecutwfn=None, inclvkb=2)[source]
                                                                        +class Screening(ecuteps, nband, w_type='RPA', sc_mode='one_shot', hilbert=None, ecutwfn=None, inclvkb=2)[source]

                                                                        Bases: AbivarAble

                                                                        This object defines the parameters used for the computation of the screening function.

                                                                        @@ -1128,13 +1128,13 @@

                                                                        Submodules
                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Get a dictionary with the abinit variables.

                                                                        -property use_hilbert[source]
                                                                        +property use_hilbert[source]

                                                                        True if we are using the Hilbert transform method.

                                                                        @@ -1142,7 +1142,7 @@

                                                                        Submodules
                                                                        -class SelfEnergy(se_type, sc_mode, nband, ecutsigx, screening, gw_qprange=1, ppmodel=None, ecuteps=None, ecutwfn=None, gwpara=2)[source]
                                                                        +class SelfEnergy(se_type, sc_mode, nband, ecutsigx, screening, gw_qprange=1, ppmodel=None, ecuteps=None, ecutwfn=None, gwpara=2)[source]

                                                                        Bases: AbivarAble

                                                                        Define the parameters used for the computation of the self-energy.

                                                                        @@ -1164,25 +1164,25 @@

                                                                        Submodules
                                                                        -property gwcalctyp[source]
                                                                        +property gwcalctyp[source]

                                                                        The value of the gwcalctyp input variable.

                                                                        -property symsigma[source]
                                                                        +property symsigma[source]

                                                                        1 if symmetries can be used to reduce the number of q-points.

                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Get a dictionary with the abinit variables.

                                                                        -property use_ppmodel[source]
                                                                        +property use_ppmodel[source]

                                                                        True if we are using the plasmon-pole approximation.

                                                                        @@ -1190,7 +1190,7 @@

                                                                        Submodules
                                                                        -class Smearing(occopt, tsmear)[source]
                                                                        +class Smearing(occopt, tsmear)[source]

                                                                        Bases: AbivarAble, MSONable

                                                                        Variables defining the smearing technique. The preferred way to instantiate a Smearing object is via the class method Smearing.as_smearing(string).

                                                                        @@ -1204,13 +1204,13 @@

                                                                        Submodules
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        JSON-friendly dict representation of Smearing.

                                                                        -classmethod as_smearing(obj)[source]
                                                                        +classmethod as_smearing(obj)[source]

                                                                        Constructs an instance of Smearing from obj. Accepts obj in the form:

                                                                        -property mode[source]
                                                                        +property mode[source]

                                                                        String with smearing technique.

                                                                        -static nosmearing()[source]
                                                                        +static nosmearing()[source]

                                                                        For calculations without smearing.

                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Return dictionary with Abinit variables.

                                                                        @@ -1250,7 +1250,7 @@

                                                                        Submodules
                                                                        -class SpinMode(mode, nsppol, nspinor, nspden)[source]
                                                                        +class SpinMode(mode, nsppol, nspinor, nspden)[source]

                                                                        Bases: SpinMode, AbivarAble, MSONable

                                                                        Different configurations of the electron density as implemented in abinit: One can use as_spinmode to construct the object via SpinMode.as_spinmode @@ -1267,25 +1267,25 @@

                                                                        Submodules
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        JSON-friendly dict representation of SpinMode.

                                                                        -classmethod as_spinmode(obj)[source]
                                                                        +classmethod as_spinmode(obj)[source]

                                                                        Convert obj into a SpinMode instance.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        Build from dict.

                                                                        -to_abivars()[source]
                                                                        +to_abivars()[source]

                                                                        Dictionary with Abinit input variables.

                                                                        @@ -1293,14 +1293,14 @@

                                                                        Submodules
                                                                        -contract(string)[source]
                                                                        +contract(string)[source]

                                                                        assert contract(“1 1 1 2 2 3”) == “3*1 2*2 1*3” assert contract(“1 1 3 2 3”) == “2*1 1*3 1*2 1*3”

                                                                        -lattice_from_abivars(cls=None, *args, **kwargs)[source]
                                                                        +lattice_from_abivars(cls=None, *args, **kwargs)[source]

                                                                        Get a Lattice object from a dictionary with the Abinit variables acell and either rprim in Bohr or angdeg. If acell is not given, the Abinit default of [1, 1, 1] Bohr is used.

                                                                        @@ -1315,7 +1315,7 @@

                                                                        Submodules
                                                                        -species_by_znucl(structure: Structure) → list[Species][source]
                                                                        +species_by_znucl(structure: Structure) → list[Species][source]

                                                                        Get list of unique specie found in structure ordered according to sites.

                                                                        Example

                                                                        Site0: 0.5 0 0 O @@ -1325,7 +1325,7 @@

                                                                        Submodules
                                                                        -structure_from_abivars(cls=None, *args, **kwargs) → Structure[source]
                                                                        +structure_from_abivars(cls=None, *args, **kwargs) → Structure[source]

                                                                        Build a Structure object from a dictionary with ABINIT variables.

                                                                        Parameters:
                                                                        @@ -1348,7 +1348,7 @@

                                                                        Submodules
                                                                        -structure_to_abivars(structure: Structure, enforce_znucl: list | None = None, enforce_typat: list | None = None, **kwargs)[source]
                                                                        +structure_to_abivars(structure: Structure, enforce_znucl: list | None = None, enforce_typat: list | None = None, **kwargs)[source]

                                                                        Receives a structure and returns a dictionary with ABINIT variables.

                                                                        Parameters:
                                                                        @@ -1369,7 +1369,7 @@

                                                                        Submodules
                                                                        -class AbinitTimer(sections, info, cpu_time, wall_time)[source]
                                                                        +class AbinitTimer(sections, info, cpu_time, wall_time)[source]

                                                                        Bases: object

                                                                        Container class storing the timing results.

                                                                        @@ -1384,7 +1384,7 @@

                                                                        Submodules
                                                                        -cpuwall_histogram(ax: Axes = None, **kwargs)[source]
                                                                        +cpuwall_histogram(ax: Axes = None, **kwargs)[source]

                                                                        Plot histogram with cpu- and wall-time on axis ax.

                                                                        Parameters:
                                                                        @@ -1438,44 +1438,44 @@

                                                                        Submodules
                                                                        -get_dataframe(sort_key='wall_time', **kwargs)[source]
                                                                        +get_dataframe(sort_key='wall_time', **kwargs)[source]

                                                                        Return a pandas DataFrame with entries sorted according to sort_key.

                                                                        -get_section(section_name)[source]
                                                                        +get_section(section_name)[source]

                                                                        Return section associated to section_name.

                                                                        -get_values(keys)[source]
                                                                        +get_values(keys)[source]

                                                                        Return a list of values associated to a particular list of keys.

                                                                        -names_and_values(key, minval=None, minfract=None, sorted=True)[source]
                                                                        +names_and_values(key, minval=None, minfract=None, sorted=True)[source]

                                                                        Select the entries whose value[key] is >= minval or whose fraction[key] is >= minfract Return the names of the sections and the corresponding values.

                                                                        -property ncpus[source]
                                                                        +property ncpus[source]

                                                                        Total number of CPUs employed.

                                                                        -order_sections(key, reverse=True)[source]
                                                                        +order_sections(key, reverse=True)[source]

                                                                        Sort sections according to the value of key.

                                                                        -pie(key='wall_time', minfract=0.05, ax: Axes = None, **kwargs)[source]
                                                                        +pie(key='wall_time', minfract=0.05, ax: Axes = None, **kwargs)[source]

                                                                        Plot pie chart for this timer.

                                                                        Parameters:
                                                                        @@ -1533,7 +1533,7 @@

                                                                        Submodules
                                                                        -scatter_hist(ax: Axes = None, **kwargs)[source]
                                                                        +scatter_hist(ax: Axes = None, **kwargs)[source]

                                                                        Scatter plot + histogram.

                                                                        Parameters:
                                                                        @@ -1587,25 +1587,25 @@

                                                                        Submodules
                                                                        -sum_sections(keys)[source]
                                                                        +sum_sections(keys)[source]

                                                                        Sum value of keys.

                                                                        -to_csv(fileobj=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)[source]
                                                                        +to_csv(fileobj=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)[source]

                                                                        Write data on file fileobj using CSV format.

                                                                        -to_table(sort_key='wall_time', stop=None)[source]
                                                                        +to_table(sort_key='wall_time', stop=None)[source]

                                                                        Return a table (list of lists) with timer data.

                                                                        -totable(sort_key='wall_time', stop=None)[source]
                                                                        +totable(sort_key='wall_time', stop=None)[source]

                                                                        Return a table (list of lists) with timer data.

                                                                        @@ -1613,14 +1613,14 @@

                                                                        Submodules
                                                                        -exception AbinitTimerParseError[source]
                                                                        +exception AbinitTimerParseError[source]

                                                                        Bases: ParseError

                                                                        Errors raised by AbinitTimerParser.

                                                                        -class AbinitTimerParser[source]
                                                                        +class AbinitTimerParser[source]

                                                                        Bases: Iterable

                                                                        Responsible for parsing a list of output files, extracting the timing results and analyzing the results. @@ -1634,36 +1634,36 @@

                                                                        Submodules
                                                                        -BEGIN_TAG = '-<BEGIN_TIMER'[source]
                                                                        +BEGIN_TAG = '-<BEGIN_TIMER'[source]

                                                                        -END_TAG = '-<END_TIMER>'[source]
                                                                        +END_TAG = '-<END_TIMER>'[source]
                                                                        -Error[source]
                                                                        +Error[source]

                                                                        alias of AbinitTimerParseError

                                                                        -property filenames[source]
                                                                        +property filenames[source]

                                                                        List of files that have been parsed successfully.

                                                                        -get_sections(section_name)[source]
                                                                        +get_sections(section_name)[source]

                                                                        Get the list of sections stored in self.timers() given section_name A fake section is returned if the timer does not have section_name.

                                                                        -parse(filenames)[source]
                                                                        +parse(filenames)[source]

                                                                        Read and parse a filename or a list of filenames. Files that cannot be opened are ignored. A single filename may also be given.

                                                                        @@ -1675,7 +1675,7 @@

                                                                        Submodules
                                                                        -pefficiency()[source]
                                                                        +pefficiency()[source]

                                                                        Analyze the parallel efficiency.

                                                                        Returns:
                                                                        @@ -1686,13 +1686,13 @@

                                                                        Submodules
                                                                        -plot_all(show=True, **kwargs)[source]
                                                                        +plot_all(show=True, **kwargs)[source]

                                                                        Call all plot methods provided by the parser.

                                                                        -plot_efficiency(key='wall_time', what='good+bad', nmax=5, ax: Axes = None, **kwargs)[source]
                                                                        +plot_efficiency(key='wall_time', what='good+bad', nmax=5, ax: Axes = None, **kwargs)[source]

                                                                        Plot the parallel efficiency.

                                                                        Parameters:
                                                                        @@ -1766,7 +1766,7 @@

                                                                        Submodules
                                                                        -plot_pie(key='wall_time', minfract=0.05, **kwargs)[source]
                                                                        +plot_pie(key='wall_time', minfract=0.05, **kwargs)[source]

                                                                        Plot pie charts of the different timers.

                                                                        Parameters:
                                                                        @@ -1820,7 +1820,7 @@

                                                                        Submodules
                                                                        -plot_stacked_hist(key='wall_time', nmax=5, ax: Axes = None, **kwargs)[source]
                                                                        +plot_stacked_hist(key='wall_time', nmax=5, ax: Axes = None, **kwargs)[source]

                                                                        Plot stacked histogram of the different timers.

                                                                        Parameters:
                                                                        @@ -1877,26 +1877,26 @@

                                                                        Submodules
                                                                        -section_names(ordkey='wall_time')[source]
                                                                        +section_names(ordkey='wall_time')[source]

                                                                        Get the names of sections ordered by ordkey. For the time being, the values are taken from the first timer.

                                                                        -summarize(**kwargs)[source]
                                                                        +summarize(**kwargs)[source]

                                                                        Return pandas DataFrame with the most important results stored in the timers.

                                                                        -timers(filename=None, mpi_rank='0')[source]
                                                                        +timers(filename=None, mpi_rank='0')[source]

                                                                        Return the list of timers associated to the given filename and MPI rank mpi_rank.

                                                                        -classmethod walk(top='.', ext='.abo')[source]
                                                                        +classmethod walk(top='.', ext='.abo')[source]

                                                                        Scan directory tree starting from top, look for files with extension ext and parse timing data.

                                                                        @@ -1919,7 +1919,7 @@

                                                                        Submodules
                                                                        -class AbinitTimerSection(name, cpu_time, cpu_fract, wall_time, wall_fract, ncalls, gflops)[source]
                                                                        +class AbinitTimerSection(name, cpu_time, cpu_fract, wall_time, wall_fract, ncalls, gflops)[source]

                                                                        Bases: object

                                                                        Record with the timing results associated to a section of code.

                                                                        @@ -1937,40 +1937,40 @@

                                                                        Submodules
                                                                        -FIELDS = ('name', 'wall_time', 'wall_fract', 'cpu_time', 'cpu_fract', 'ncalls', 'gflops')[source]
                                                                        +FIELDS = ('name', 'wall_time', 'wall_fract', 'cpu_time', 'cpu_fract', 'ncalls', 'gflops')[source]

                                                                        -NUMERIC_FIELDS = ('wall_time', 'wall_fract', 'cpu_time', 'cpu_fract', 'ncalls', 'gflops')[source]
                                                                        +NUMERIC_FIELDS = ('wall_time', 'wall_fract', 'cpu_time', 'cpu_fract', 'ncalls', 'gflops')[source]
                                                                        -STR_FIELDS = ('name',)[source]
                                                                        +STR_FIELDS = ('name',)[source]
                                                                        -classmethod fake()[source]
                                                                        +classmethod fake()[source]

                                                                        Return a fake section. Mainly used to fill missing entries if needed.

                                                                        -to_csvline(with_header=False)[source]
                                                                        +to_csvline(with_header=False)[source]

                                                                        Return a string with data in CSV format. Add header if with_header.

                                                                        -to_dict()[source]
                                                                        +to_dict()[source]

                                                                        Get the values as a dictionary.

                                                                        -to_tuple()[source]
                                                                        +to_tuple()[source]

                                                                        Get the values as a tuple.

                                                                        @@ -1978,7 +1978,7 @@

                                                                        Submodules
                                                                        -class ParallelEfficiency(filenames, ref_idx, *args, **kwargs)[source]
                                                                        +class ParallelEfficiency(filenames, ref_idx, *args, **kwargs)[source]

                                                                        Bases: dict

                                                                        Store results concerning the parallel efficiency of the job.

                                                                        @@ -1991,19 +1991,19 @@

                                                                        Submodules
                                                                        -bad_sections(key='wall_time', criterion='mean', nmax=5)[source]
                                                                        +bad_sections(key='wall_time', criterion='mean', nmax=5)[source]

                                                                        Return first nmax sections with worst value of key key using criterion criterion.

                                                                        -good_sections(key='wall_time', criterion='mean', nmax=5)[source]
                                                                        +good_sections(key='wall_time', criterion='mean', nmax=5)[source]

                                                                        Return first nmax sections with best value of key key using criterion criterion.

                                                                        -totable(stop=None, reverse=True)[source]
                                                                        +totable(stop=None, reverse=True)[source]

                                                                        Get table (list of lists) with timing results.

                                                                        Parameters:
                                                                        @@ -2019,7 +2019,7 @@

                                                                        Submodules
                                                                        -alternate(*iterables)[source]
                                                                        +alternate(*iterables)[source]

                                                                        [a[0], b[0], … , a[1], b[1], …, a[n], b[n] …] >>> alternate([1, 4], [2, 5], [3, 6]) [1, 2, 3, 4, 5, 6].

                                                                        @@ -2033,18 +2033,18 @@

                                                                        Submodules
                                                                        -class AbstractInput[source]
                                                                        +class AbstractInput[source]

                                                                        Bases: MutableMapping, ABC

                                                                        Abstract class defining the methods that must be implemented by Input objects.

                                                                        -deepcopy()[source]
                                                                        +deepcopy()[source]

                                                                        Deep copy of the input.

                                                                        -pop_vars(keys)[source]
                                                                        +pop_vars(keys)[source]

                                                                        Remove the variables listed in keys. Return dictionary with the variables that have been removed. Unlike remove_vars, no exception is raised if the variables are not in the input.

                                                                        @@ -2059,7 +2059,7 @@

                                                                        Submodules
                                                                        -remove_vars(keys: Sequence[str], strict: bool = True) → dict[str, InputVariable][source]
                                                                        +remove_vars(keys: Sequence[str], strict: bool = True) → dict[str, InputVariable][source]

                                                                        Remove the variables listed in keys. Return dictionary with the variables that have been removed.

                                                                        @@ -2074,7 +2074,7 @@

                                                                        Submodules
                                                                        -set_vars(*args, **kwargs)[source]
                                                                        +set_vars(*args, **kwargs)[source]

                                                                        Set the value of the variables. Return dict with the variables added to the input.

                                                                        Example

                                                                        @@ -2083,7 +2083,7 @@

                                                                        Submodules
                                                                        -set_vars_ifnotin(*args, **kwargs)[source]
                                                                        +set_vars_ifnotin(*args, **kwargs)[source]

                                                                        Set the value of the variables but only if the variable is not already present. Return dict with the variables added to the input.

                                                                        Example

                                                                        @@ -2092,19 +2092,19 @@

                                                                        Submodules
                                                                        -abstract to_str()[source]
                                                                        +abstract to_str()[source]

                                                                        Get a string with the input.

                                                                        -abstract property vars[source]
                                                                        +abstract property vars[source]

                                                                        Dictionary with the input variables. Used to implement dict-like interface.

                                                                        -write(filepath='run.abi')[source]
                                                                        +write(filepath='run.abi')[source]

                                                                        Write the input file to file to filepath.

                                                                        @@ -2112,7 +2112,7 @@

                                                                        Submodules
                                                                        -class BasicAbinitInput(structure, pseudos: str | list[str] | list[Pseudo] | PseudoTable, pseudo_dir=None, comment=None, abi_args=None, abi_kwargs=None)[source]
                                                                        +class BasicAbinitInput(structure, pseudos: str | list[str] | list[Pseudo] | PseudoTable, pseudo_dir=None, comment=None, abi_args=None, abi_kwargs=None)[source]

                                                                        Bases: AbstractInput, MSONable

                                                                        Store the ABINIT variables for a single dataset.

                                                                        @@ -2133,49 +2133,49 @@

                                                                        Submodules
                                                                        -Error[source]
                                                                        +Error[source]

                                                                        alias of BasicAbinitInputError

                                                                        -add_abiobjects(*abi_objects)[source]
                                                                        +add_abiobjects(*abi_objects)[source]

                                                                        For a list of AbiVarable objects, add the corresponding variables to the input.

                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        JSON interface used in pymatgen for easier serialization.

                                                                        -property comment[source]
                                                                        +property comment[source]

                                                                        Optional string with comment. None if comment is not set.

                                                                        -classmethod from_dict(dct: dict) → Self[source]
                                                                        +classmethod from_dict(dct: dict) → Self[source]

                                                                        JSON interface used in pymatgen for easier serialization.

                                                                        -property isnc[source]
                                                                        +property isnc[source]

                                                                        True if norm-conserving calculation.

                                                                        -property ispaw[source]
                                                                        +property ispaw[source]

                                                                        True if PAW calculation.

                                                                        -new_with_vars(*args, **kwargs)[source]
                                                                        +new_with_vars(*args, **kwargs)[source]

                                                                        Get a new input with the given variables.

                                                                        Example

                                                                        new = input.new_with_vars(ecut=20)

                                                                        @@ -2183,39 +2183,39 @@

                                                                        Submodules
                                                                        -pop_irdvars()[source]
                                                                        +pop_irdvars()[source]

                                                                        Remove all the ird* variables present in self. Return dictionary with the variables that have been removed.

                                                                        -pop_tolerances()[source]
                                                                        +pop_tolerances()[source]

                                                                        Remove all the tolerance variables present in self. Return dictionary with the variables that have been removed.

                                                                        -property pseudos[source]
                                                                        +property pseudos[source]

                                                                        List of |Pseudo| objects.

                                                                        -set_comment(comment)[source]
                                                                        +set_comment(comment)[source]

                                                                        Set a comment to be included at the top of the file.

                                                                        -set_gamma_sampling()[source]
                                                                        +set_gamma_sampling()[source]

                                                                        Gamma-only sampling of the BZ.

                                                                        -set_kmesh(ngkpt, shiftk, kptopt=1)[source]
                                                                        +set_kmesh(ngkpt, shiftk, kptopt=1)[source]

                                                                        Set the variables for the sampling of the BZ.

                                                                        Parameters:
                                                                        @@ -2230,7 +2230,7 @@

                                                                        Submodules
                                                                        -set_kpath(ndivsm, kptbounds=None, iscf=-2)[source]
                                                                        +set_kpath(ndivsm, kptbounds=None, iscf=-2)[source]

                                                                        Set the variables for the computation of the electronic band structure.

                                                                        Parameters:
                                                                        @@ -2245,7 +2245,7 @@

                                                                        Submodules
                                                                        -set_spin_mode(spin_mode)[source]
                                                                        +set_spin_mode(spin_mode)[source]

                                                                        Set the variables used to the treat the spin degree of freedom. Return dictionary with the variables that have been removed.

                                                                        @@ -2264,19 +2264,19 @@

                                                                        Submodules
                                                                        -set_structure(structure: Structure)[source]
                                                                        +set_structure(structure: Structure)[source]

                                                                        Set structure.

                                                                        -property structure[source]
                                                                        +property structure[source]

                                                                        The |Structure| object associated to this input.

                                                                        -to_str(post=None, with_structure=True, with_pseudos=True, exclude=None)[source]
                                                                        +to_str(post=None, with_structure=True, with_pseudos=True, exclude=None)[source]

                                                                        String representation.

                                                                        Parameters:
                                                                        @@ -2298,7 +2298,7 @@

                                                                        Submodules
                                                                        -property vars[source]
                                                                        +property vars[source]

                                                                        Dictionary with variables.

                                                                        @@ -2306,14 +2306,14 @@

                                                                        Submodules
                                                                        -exception BasicAbinitInputError[source]
                                                                        +exception BasicAbinitInputError[source]

                                                                        Bases: Exception

                                                                        Base error class for exceptions raised by BasicAbinitInput.

                                                                        -class BasicMultiDataset(structure: Structure | Sequence[Structure], pseudos, pseudo_dir='', ndtset=1)[source]
                                                                        +class BasicMultiDataset(structure: Structure | Sequence[Structure], pseudos, pseudo_dir='', ndtset=1)[source]

                                                                        Bases: object

                                                                        This object is essentially a list of BasicAbinitInputs. that provides an easy-to-use interface to apply global changes to the @@ -2366,85 +2366,85 @@

                                                                        Submodules
                                                                        -Error[source]
                                                                        +Error[source]

                                                                        alias of BasicAbinitInputError

                                                                        -addnew_from(dtindex)[source]
                                                                        +addnew_from(dtindex)[source]

                                                                        Add a new entry in the multidataset by copying the input with index dtindex.

                                                                        -append(abinit_input)[source]
                                                                        +append(abinit_input)[source]

                                                                        Add a BasicAbinitInput to the list.

                                                                        -deepcopy()[source]
                                                                        +deepcopy()[source]

                                                                        Deep copy of the BasicMultiDataset.

                                                                        -extend(abinit_inputs)[source]
                                                                        +extend(abinit_inputs)[source]

                                                                        Extends self with a list of BasicAbinitInputs.

                                                                        -classmethod from_inputs(inputs: list[BasicAbinitInput]) → Self[source]
                                                                        +classmethod from_inputs(inputs: list[BasicAbinitInput]) → Self[source]

                                                                        Construct a multidataset from a list of BasicAbinitInputs.

                                                                        -property has_same_structures[source]
                                                                        +property has_same_structures[source]

                                                                        True if all inputs in BasicMultiDataset are equal.

                                                                        -property isnc[source]
                                                                        +property isnc[source]

                                                                        True if norm-conserving calculation.

                                                                        -property ispaw[source]
                                                                        +property ispaw[source]

                                                                        True if PAW calculation.

                                                                        -property ndtset[source]
                                                                        +property ndtset[source]

                                                                        Number of inputs in self.

                                                                        -property pseudos[source]
                                                                        +property pseudos[source]

                                                                        Abinit pseudopotentials.

                                                                        -classmethod replicate_input(input, ndtset)[source]
                                                                        +classmethod replicate_input(input, ndtset)[source]

                                                                        Construct a multidataset with ndtset from the BasicAbinitInput input.

                                                                        -split_datasets()[source]
                                                                        +split_datasets()[source]

                                                                        Return list of BasicAbinitInputs.

                                                                        -to_str(with_pseudos=True)[source]
                                                                        +to_str(with_pseudos=True)[source]

                                                                        String representation i.e. the input file read by Abinit.

                                                                        Parameters:
                                                                        @@ -2455,7 +2455,7 @@

                                                                        Submodules
                                                                        -write(filepath='run.abi')[source]
                                                                        +write(filepath='run.abi')[source]

                                                                        Write ndset input files to disk. The name of the file is constructed from the dataset index e.g. run0.abi.

                                                                        @@ -2464,7 +2464,7 @@

                                                                        Submodules
                                                                        -class ShiftMode(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                        +class ShiftMode(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                        Bases: Enum

                                                                        Mode used to generate the shifts for the k-point sampling. G: Gamma centered @@ -2476,27 +2476,27 @@

                                                                        Submodules
                                                                        -GammaCentered = 'G'[source]
                                                                        +GammaCentered = 'G'[source]

                                                                        -MonkhorstPack = 'M'[source]
                                                                        +MonkhorstPack = 'M'[source]
                                                                        -OneSymmetric = 'O'[source]
                                                                        +OneSymmetric = 'O'[source]
                                                                        -Symmetric = 'S'[source]
                                                                        +Symmetric = 'S'[source]
                                                                        -classmethod from_object(obj) → Self[source]
                                                                        +classmethod from_object(obj) → Self[source]

                                                                        Get an instance of ShiftMode based on the type of object passed. Converts strings to ShiftMode depending on the initial letter of the string. G for GammaCentered, M for MonkhorstPack, S for Symmetric, O for OneSymmetric. @@ -2507,7 +2507,7 @@

                                                                        Submodules
                                                                        -as_structure(obj)[source]
                                                                        +as_structure(obj)[source]

                                                                        Convert obj into a Structure. Accepts:

                                                                          @@ -2520,7 +2520,7 @@

                                                                          Submodules
                                                                          -calc_shiftk(structure, symprec: float = 0.01, angle_tolerance=5)[source]
                                                                          +calc_shiftk(structure, symprec: float = 0.01, angle_tolerance=5)[source]

                                                                          Find the values of shiftk and nshiftk appropriated for the sampling of the Brillouin zone.

                                                                          When the primitive vectors of the lattice do NOT form a FCC or a BCC lattice, the usual (shifted) Monkhorst-Pack grids are formed by using nshiftk=1 and shiftk 0.5 0.5 0.5 . @@ -2577,7 +2577,7 @@

                                                                          Submodules
                                                                          -ebands_input(structure, pseudos, kppa=None, nscf_nband=None, ndivsm=15, ecut=None, pawecutdg=None, scf_nband=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None, dos_kppa=None)[source]
                                                                          +ebands_input(structure, pseudos, kppa=None, nscf_nband=None, ndivsm=15, ecut=None, pawecutdg=None, scf_nband=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None, dos_kppa=None)[source]

                                                                          Get a |BasicMultiDataset| object for band structure calculations.

                                                                          Parameters:
                                                                          @@ -2607,7 +2607,7 @@

                                                                          Submodules
                                                                          -gs_input(structure, pseudos, kppa=None, ecut=None, pawecutdg=None, scf_nband=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None)[source]
                                                                          +gs_input(structure, pseudos, kppa=None, ecut=None, pawecutdg=None, scf_nband=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None)[source]

                                                                          Get a BasicAbinitInput for ground-state calculation.

                                                                          Parameters:
                                                                          @@ -2632,7 +2632,7 @@

                                                                          Submodules
                                                                          -ion_ioncell_relax_input(structure, pseudos, kppa=None, nband=None, ecut=None, pawecutdg=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None, shift_mode='Monkhorst-pack')[source]
                                                                          +ion_ioncell_relax_input(structure, pseudos, kppa=None, nband=None, ecut=None, pawecutdg=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None, shift_mode='Monkhorst-pack')[source]

                                                                          Get a |BasicMultiDataset| for a structural relaxation. The first dataset optimizes the atomic positions at fixed unit cell. The second datasets optimizes both ions and unit cell parameters.

                                                                          @@ -2654,7 +2654,7 @@

                                                                          Submodules
                                                                          -num_valence_electrons(structure, pseudos) → float[source]
                                                                          +num_valence_electrons(structure, pseudos) → float[source]

                                                                          Get the number of valence electrons.

                                                                          Parameters:
                                                                          @@ -2669,7 +2669,7 @@

                                                                          Submodules
                                                                          -class AbinitHeader(*args, **kwargs)[source]
                                                                          +class AbinitHeader(*args, **kwargs)[source]

                                                                          Bases: AttrDict

                                                                          Stores the values reported in the Abinit header.

                                                                          @@ -2682,7 +2682,7 @@

                                                                          Submodules
                                                                          -to_str(verbose=0, title=None, **kwargs)[source]
                                                                          +to_str(verbose=0, title=None, **kwargs)[source]

                                                                          String representation. kwargs are passed to pprint.pformat.

                                                                          Parameters:
                                                                          @@ -2696,7 +2696,7 @@

                                                                          Submodules
                                                                          -to_string(verbose=0, title=None, **kwargs)[source]
                                                                          +to_string(verbose=0, title=None, **kwargs)[source]

                                                                          String representation. kwargs are passed to pprint.pformat.

                                                                          Parameters:
                                                                          @@ -2712,39 +2712,39 @@

                                                                          Submodules
                                                                          -class EtsfReader(path)[source]
                                                                          +class EtsfReader(path)[source]

                                                                          Bases: NetcdfReader

                                                                          This object reads data from a file written according to the ETSF-IO specifications.

                                                                          We assume that the netcdf file contains at least the crystallographic section.

                                                                          Open the Netcdf file specified by path (read mode).

                                                                          -chemical_symbols()[source]
                                                                          +chemical_symbols()[source]

                                                                          Chemical symbols char [number of atom species][symbol length].

                                                                          -read_abinit_hdr()[source]
                                                                          +read_abinit_hdr()[source]

                                                                          Read the variables associated to the Abinit header.

                                                                          Return AbinitHeader

                                                                          -read_abinit_xcfunc()[source]
                                                                          +read_abinit_xcfunc()[source]

                                                                          Read ixc from an Abinit file. Return XcFunc object.

                                                                          -read_structure(cls=<class 'pymatgen.core.structure.Structure'>)[source]
                                                                          +read_structure(cls=<class 'pymatgen.core.structure.Structure'>)[source]

                                                                          Get the crystalline structure stored in the rootgrp.

                                                                          -type_idx_from_symbol(symbol)[source]
                                                                          +type_idx_from_symbol(symbol)[source]

                                                                          Get the type index from the chemical symbol. Note python convention.

                                                                          @@ -2752,14 +2752,14 @@

                                                                          Submodules
                                                                          -class NO_DEFAULT[source]
                                                                          +class NO_DEFAULT[source]

                                                                          Bases: object

                                                                          Signal that read_value should raise an Error.

                                                                          -class NetcdfReader(path)[source]
                                                                          +class NetcdfReader(path)[source]

                                                                          Bases: object

                                                                          Wraps and extends netCDF4.Dataset. Read only mode. Supports with statements.

                                                                          @@ -2769,25 +2769,25 @@

                                                                          Submodules
                                                                          -Error[source]
                                                                          +Error[source]

                                                                          alias of NetcdfReaderError

                                                                          -close()[source]
                                                                          +close()[source]

                                                                          Close the file.

                                                                          -print_tree()[source]
                                                                          +print_tree()[source]

                                                                          Print all the groups in the file.

                                                                          -read_dimvalue(dimname, path='/', default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]
                                                                          +read_dimvalue(dimname, path='/', default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]

                                                                          Get the value of a dimension.

                                                                          Parameters:
                                                                          @@ -2803,14 +2803,14 @@

                                                                          Submodules
                                                                          -read_keys(keys, dict_cls=<class 'monty.collections.AttrDict'>, path='/')[source]
                                                                          +read_keys(keys, dict_cls=<class 'monty.collections.AttrDict'>, path='/')[source]

                                                                          Read a list of variables/dimensions from file. If a key is not present the corresponding entry in the output dictionary is set to None.

                                                                          -read_value(varname, path='/', cmode=None, default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]
                                                                          +read_value(varname, path='/', cmode=None, default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]

                                                                          Get the values of variable with name varname in the group specified by path.

                                                                          Parameters:
                                                                          @@ -2831,19 +2831,19 @@

                                                                          Submodules
                                                                          -read_variable(varname, path='/')[source]
                                                                          +read_variable(varname, path='/')[source]

                                                                          Get the variable with name varname in the group specified by path.

                                                                          -read_varnames(path='/')[source]
                                                                          +read_varnames(path='/')[source]

                                                                          List of variable names stored in the group specified by path.

                                                                          -walk_tree(top=None)[source]
                                                                          +walk_tree(top=None)[source]

                                                                          Navigate all the groups in the file starting from top. If top is None, the root group is used.

                                                                          @@ -2852,20 +2852,20 @@

                                                                          Submodules
                                                                          -exception NetcdfReaderError[source]
                                                                          +exception NetcdfReaderError[source]

                                                                          Bases: Exception

                                                                          Base error class for NetcdfReader.

                                                                          -as_etsfreader(file)[source]
                                                                          +as_etsfreader(file)[source]

                                                                          Return an EtsfReader. Accepts filename or EtsfReader.

                                                                          -as_ncreader(file)[source]
                                                                          +as_ncreader(file)[source]

                                                                          Convert file into a NetcdfReader instance. Returns reader, close_it where close_it is set to True if we have to close the file before leaving the procedure.

                                                                          @@ -2873,7 +2873,7 @@

                                                                          Submodules
                                                                          -structure_from_ncdata(ncdata, site_properties=None, cls=<class 'pymatgen.core.structure.Structure'>)[source]
                                                                          +structure_from_ncdata(ncdata, site_properties=None, cls=<class 'pymatgen.core.structure.Structure'>)[source]

                                                                          Read and return a pymatgen structure from a NetCDF file containing crystallographic data in the ETSF-IO format.

                                                                          @@ -2894,14 +2894,14 @@

                                                                          Submodules
                                                                          -class AbinitHeader[source]
                                                                          +class AbinitHeader[source]

                                                                          Bases: dict

                                                                          Dictionary whose keys can be also accessed as attributes.

                                                                          -class AbinitPseudo(path, header)[source]
                                                                          +class AbinitPseudo(path, header)[source]

                                                                          Bases: Pseudo

                                                                          An AbinitPseudo is a pseudopotential whose file contains an abinit header.

                                                                          @@ -2914,37 +2914,37 @@

                                                                          Submodules
                                                                          -property Z[source]
                                                                          +property Z[source]

                                                                          The atomic number of the atom.

                                                                          -property Z_val[source]
                                                                          +property Z_val[source]

                                                                          Valence charge.

                                                                          -property l_local[source]
                                                                          +property l_local[source]

                                                                          Angular momentum used for the local part.

                                                                          -property l_max[source]
                                                                          +property l_max[source]

                                                                          Maximum angular momentum.

                                                                          -property summary[source]
                                                                          +property summary[source]

                                                                          Summary line reported in the ABINIT header.

                                                                          -property supports_soc[source]
                                                                          +property supports_soc[source]

                                                                          True if the pseudo can be used in a calculation with spin-orbit coupling. Base classes should provide a concrete implementation that computes this value.

                                                                          @@ -2953,19 +2953,19 @@

                                                                          Submodules
                                                                          -class Hint(ecut, pawecutdg=None)[source]
                                                                          +class Hint(ecut, pawecutdg=None)[source]

                                                                          Bases: object

                                                                          Suggested value for the cutoff energy [Hartree units] and the cutoff energy for the dense grid (only for PAW pseudos).

                                                                          -as_dict()[source]
                                                                          +as_dict()[source]

                                                                          Return dictionary for MSONable protocol.

                                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                                          +classmethod from_dict(dct: dict) → Self[source]

                                                                          Build instance from dictionary (MSONable protocol).

                                                                          @@ -2973,12 +2973,12 @@

                                                                          Submodules
                                                                          -class NcAbinitHeader(summary, **kwargs)[source]
                                                                          +class NcAbinitHeader(summary, **kwargs)[source]

                                                                          Bases: AbinitHeader

                                                                          The abinit header found in the NC pseudopotential files.

                                                                          -static fhi_header(filename, ppdesc)[source]
                                                                          +static fhi_header(filename, ppdesc)[source]

                                                                          Parse the FHI abinit header. Example:

                                                                          Troullier-Martins psp for element Sc Thu Oct 27 17:33:22 EDT 1994

                                                                          21.00000 3.00000 940714 zatom, zion, pspdat @@ -2990,7 +2990,7 @@

                                                                          Submodules
                                                                          -static gth_header(filename, ppdesc)[source]
                                                                          +static gth_header(filename, ppdesc)[source]

                                                                          Parse the GTH abinit header. Example:

                                                                          Goedecker-Teter-Hutter Wed May 8 14:27:44 EDT 1996 1 1 960508 zatom,zion,pspdat @@ -3005,7 +3005,7 @@

                                                                          Submodules
                                                                          -static hgh_header(filename, ppdesc)[source]
                                                                          +static hgh_header(filename, ppdesc)[source]

                                                                          Parse the HGH abinit header. Example:

                                                                          Hartwigsen-Goedecker-Hutter psp for Ne, from PRB58, 3641 (1998)

                                                                          10 8 010605 zatom,zion,pspdat @@ -3016,7 +3016,7 @@

                                                                          Submodules
                                                                          -static oncvpsp_header(filename, ppdesc)[source]
                                                                          +static oncvpsp_header(filename, ppdesc)[source]

                                                                          Parse the ONCVPSP abinit header. Example:

                                                                          Li ONCVPSP r_core= 2.01 3.02
                                                                          @@ -3043,7 +3043,7 @@

                                                                          Submodules
                                                                          -static tm_header(filename, ppdesc)[source]
                                                                          +static tm_header(filename, ppdesc)[source]

                                                                          Parse the TM abinit header. Example:

                                                                          Troullier-Martins psp for element Fm Thu Oct 27 17:28:39 EDT 1994 100.00000 14.00000 940714 zatom, zion, pspdat

                                                                          @@ -3065,7 +3065,7 @@

                                                                          Submodules
                                                                          -class NcAbinitPseudo(path, header)[source]
                                                                          +class NcAbinitPseudo(path, header)[source]

                                                                          Bases: NcPseudo, AbinitPseudo

                                                                          Norm-conserving pseudopotential in the Abinit format.

                                                                          @@ -3078,38 +3078,38 @@

                                                                          Submodules
                                                                          -property Z[source]
                                                                          +property Z[source]

                                                                          The atomic number of the atom.

                                                                          -property Z_val[source]
                                                                          +property Z_val[source]

                                                                          Number of valence electrons.

                                                                          -property l_local[source]
                                                                          +property l_local[source]

                                                                          Angular momentum used for the local part.

                                                                          -property l_max[source]
                                                                          +property l_max[source]

                                                                          Maximum angular momentum.

                                                                          -property nlcc_radius[source]
                                                                          +property nlcc_radius[source]

                                                                          Radius at which the core charge vanish (i.e. cut-off in a.u.). Returns 0.0 if nlcc is not used.

                                                                          -property summary[source]
                                                                          +property summary[source]

                                                                          Summary line reported in the ABINIT header.

                                                                          @@ -3117,26 +3117,26 @@

                                                                          Submodules
                                                                          -class NcPseudo[source]
                                                                          +class NcPseudo[source]

                                                                          Bases: ABC

                                                                          Abstract class defining the methods that must be implemented by the concrete classes representing norm-conserving pseudopotentials.

                                                                          -property has_nlcc[source]
                                                                          +property has_nlcc[source]

                                                                          True if the pseudo is generated with non-linear core correction.

                                                                          -abstract property nlcc_radius[source]
                                                                          +abstract property nlcc_radius[source]

                                                                          Radius at which the core charge vanish (i.e. cut-off in a.u.). Returns 0.0 if nlcc is not used.

                                                                          -property rcore[source]
                                                                          +property rcore[source]

                                                                          Radius of the pseudization sphere in a.u.

                                                                          @@ -3144,12 +3144,12 @@

                                                                          Submodules
                                                                          -class PawAbinitHeader(summary, **kwargs)[source]
                                                                          +class PawAbinitHeader(summary, **kwargs)[source]

                                                                          Bases: AbinitHeader

                                                                          The abinit header found in the PAW pseudopotential files.

                                                                          -static paw_header(filename, ppdesc)[source]
                                                                          +static paw_header(filename, ppdesc)[source]

                                                                          Parse the PAW abinit header. Examples:

                                                                          Paw atomic data for element Ni - Generated by AtomPAW (N. Holzwarth) + AtomPAW2Abinit v3.0.5
                                                                          @@ -3225,7 +3225,7 @@

                                                                          Submodules
                                                                          -class PawAbinitPseudo(path, header)[source]
                                                                          +class PawAbinitPseudo(path, header)[source]

                                                                          Bases: PawPseudo, AbinitPseudo

                                                                          Paw pseudopotential in the Abinit format.

                                                                          @@ -3238,13 +3238,13 @@

                                                                          Submodules
                                                                          -property paw_radius[source]
                                                                          +property paw_radius[source]

                                                                          Radius of the PAW sphere in a.u.

                                                                          -property supports_soc[source]
                                                                          +property supports_soc[source]

                                                                          True if the pseudo can be used in a calculation with spin-orbit coupling. Base classes should provide a concrete implementation that computes this value.

                                                                          @@ -3253,19 +3253,19 @@

                                                                          Submodules
                                                                          -class PawPseudo[source]
                                                                          +class PawPseudo[source]

                                                                          Bases: ABC

                                                                          Abstract class that defines the methods that must be implemented by the concrete classes representing PAW pseudopotentials.

                                                                          -abstract property paw_radius[source]
                                                                          +abstract property paw_radius[source]

                                                                          Radius of the PAW sphere in a.u.

                                                                          -property rcore[source]
                                                                          +property rcore[source]

                                                                          Alias of paw_radius.

                                                                          @@ -3273,7 +3273,7 @@

                                                                          Submodules
                                                                          -class PawXmlSetup(filepath)[source]
                                                                          +class PawXmlSetup(filepath)[source]

                                                                          Bases: Pseudo, PawPseudo

                                                                          Setup class for PawXml.

                                                                          @@ -3283,49 +3283,49 @@

                                                                          Submodules
                                                                          -property Z[source]
                                                                          +property Z[source]

                                                                          The atomic number of the atom.

                                                                          -property Z_val[source]
                                                                          +property Z_val[source]

                                                                          Number of valence electrons.

                                                                          -ae_core_density()[source]
                                                                          +ae_core_density()[source]

                                                                          The all-electron radial density.

                                                                          -ae_partial_waves()[source]
                                                                          +ae_partial_waves()[source]

                                                                          Dictionary with the AE partial waves indexed by state.

                                                                          -property l_local[source]
                                                                          +property l_local[source]

                                                                          Angular momentum used for the local part.

                                                                          -property l_max[source]
                                                                          +property l_max[source]

                                                                          Maximum angular momentum.

                                                                          -property paw_radius[source]
                                                                          +property paw_radius[source]

                                                                          Radius of the PAW sphere in a.u.

                                                                          -plot_densities(ax: plt.Axes = None, **kwargs)[source]
                                                                          +plot_densities(ax: plt.Axes = None, **kwargs)[source]

                                                                          Plot the PAW densities.

                                                                          Parameters:
                                                                          @@ -3376,7 +3376,7 @@

                                                                          Submodules
                                                                          -plot_projectors(ax: plt.Axes = None, fontsize=12, **kwargs)[source]
                                                                          +plot_projectors(ax: plt.Axes = None, fontsize=12, **kwargs)[source]

                                                                          Plot the PAW projectors.

                                                                          Parameters:
                                                                          @@ -3430,7 +3430,7 @@

                                                                          Submodules
                                                                          -plot_waves(ax: plt.Axes = None, fontsize=12, **kwargs)[source]
                                                                          +plot_waves(ax: plt.Axes = None, fontsize=12, **kwargs)[source]

                                                                          Plot the AE and the pseudo partial waves.

                                                                          Parameters:
                                                                          @@ -3487,43 +3487,43 @@

                                                                          Submodules
                                                                          -projector_functions()[source]
                                                                          +projector_functions()[source]

                                                                          Dictionary with the PAW projectors indexed by state.

                                                                          -pseudo_core_density()[source]
                                                                          +pseudo_core_density()[source]

                                                                          The pseudized radial density.

                                                                          -property pseudo_partial_waves[source]
                                                                          +property pseudo_partial_waves[source]

                                                                          Dictionary with the pseudo partial waves indexed by state.

                                                                          -root()[source]
                                                                          +root()[source]

                                                                          Root tree of XML.

                                                                          -property summary[source]
                                                                          +property summary[source]

                                                                          String summarizing the most important properties.

                                                                          -property supports_soc[source]
                                                                          +property supports_soc[source]

                                                                          Here I assume that the ab-initio code can treat the SOC within the on-site approximation.

                                                                          -yield_figs(**kwargs)[source]
                                                                          +yield_figs(**kwargs)[source]

                                                                          This function generates a predefined list of matplotlib figures with minimal input from the user.

                                                                          @@ -3531,31 +3531,31 @@

                                                                          Submodules
                                                                          -class Pseudo[source]
                                                                          +class Pseudo[source]

                                                                          Bases: MSONable, ABC

                                                                          Abstract base class defining the methods that must be implemented by the concrete pseudo-potential sub-classes.

                                                                          -abstract property Z: int[source]
                                                                          +abstract property Z: int[source]

                                                                          The atomic number of the atom.

                                                                          -abstract property Z_val: int[source]
                                                                          +abstract property Z_val: int[source]

                                                                          Valence charge.

                                                                          -as_dict(**kwargs)[source]
                                                                          +as_dict(**kwargs)[source]

                                                                          Return dictionary for MSONable protocol.

                                                                          -classmethod as_pseudo(obj)[source]
                                                                          +classmethod as_pseudo(obj)[source]

                                                                          Convert obj into a pseudo. Accepts:

                                                                            @@ -3567,7 +3567,7 @@

                                                                            Submodules
                                                                            -as_tmpfile(tmpdir=None)[source]
                                                                            +as_tmpfile(tmpdir=None)[source]

                                                                            Copy the pseudopotential to a temporary a file and returns a new pseudopotential object. Useful for unit tests in which we have to change the content of the file.

                                                                            @@ -3580,43 +3580,43 @@

                                                                            Submodules
                                                                            -property basename: str[source]
                                                                            +property basename: str[source]

                                                                            File basename.

                                                                            -compute_md5()[source]
                                                                            +compute_md5()[source]

                                                                            Compute and return MD5 hash value.

                                                                            -property djrepo_path[source]
                                                                            +property djrepo_path[source]

                                                                            The path of the djrepo file. None if file does not exist.

                                                                            -property element: Element[source]
                                                                            +property element: Element[source]

                                                                            Pymatgen Element.

                                                                            -property filepath: str[source]
                                                                            +property filepath: str[source]

                                                                            Absolute path to pseudopotential file.

                                                                            -classmethod from_dict(dct: dict) → Self[source]
                                                                            +classmethod from_dict(dct: dict) → Self[source]

                                                                            Build instance from dictionary (MSONable protocol).

                                                                            -classmethod from_file(filename: str) → Self[source]
                                                                            +classmethod from_file(filename: str) → Self[source]

                                                                            Build an instance of a concrete Pseudo subclass from filename. Note: the parser knows the concrete class that should be instantiated Client code should rely on the abstract interface provided by Pseudo.

                                                                            @@ -3624,19 +3624,19 @@

                                                                            Submodules
                                                                            -property has_dojo_report[source]
                                                                            +property has_dojo_report[source]

                                                                            True if the pseudo has an associated DOJO_REPORT section.

                                                                            -property has_hints[source]
                                                                            +property has_hints[source]

                                                                            True if self provides hints on the cutoff energy.

                                                                            -hint_for_accuracy(accuracy='normal')[source]
                                                                            +hint_for_accuracy(accuracy='normal')[source]

                                                                            Get a Hint object with the suggested value of ecut [Ha] and pawecutdg [Ha] for the given accuracy. ecut and pawecutdg are set to zero if no hint is available.

                                                                            @@ -3649,37 +3649,37 @@

                                                                            Submodules
                                                                            -property isnc: bool[source]
                                                                            +property isnc: bool[source]

                                                                            True if norm-conserving pseudopotential.

                                                                            -property ispaw: bool[source]
                                                                            +property ispaw: bool[source]

                                                                            True if PAW pseudopotential.

                                                                            -abstract property l_local: int[source]
                                                                            +abstract property l_local: int[source]

                                                                            Angular momentum used for the local part.

                                                                            -abstract property l_max: int[source]
                                                                            +abstract property l_max: int[source]

                                                                            Maximum angular momentum.

                                                                            -md5()[source]
                                                                            +md5()[source]

                                                                            MD5 hash value.

                                                                            -open_pspsfile(ecut=20, pawecutdg=None)[source]
                                                                            +open_pspsfile(ecut=20, pawecutdg=None)[source]

                                                                            Calls Abinit to compute the internal tables for the application of the pseudopotential part. Returns PspsFile object providing methods to plot and analyze the data or None if file is not found or it’s not readable.

                                                                            @@ -3695,32 +3695,32 @@

                                                                            Submodules
                                                                            -abstract property summary: str[source]
                                                                            +abstract property summary: str[source]

                                                                            String summarizing the most important properties.

                                                                            -abstract property supports_soc[source]
                                                                            +abstract property supports_soc[source]

                                                                            True if the pseudo can be used in a calculation with spin-orbit coupling. Base classes should provide a concrete implementation that computes this value.

                                                                            -property symbol: str[source]
                                                                            +property symbol: str[source]

                                                                            Element symbol.

                                                                            -to_str(verbose=0) → str[source]
                                                                            +to_str(verbose=0) → str[source]

                                                                            String representation.

                                                                            -property type: str[source]
                                                                            +property type: str[source]

                                                                            Type of pseudo.

                                                                            @@ -3728,14 +3728,14 @@

                                                                            Submodules
                                                                            -exception PseudoParseError[source]
                                                                            +exception PseudoParseError[source]

                                                                            Bases: ParseError

                                                                            Base Error class for the exceptions raised by PseudoParser.

                                                                          -class PseudoParser[source]
                                                                          +class PseudoParser[source]

                                                                          Bases: object

                                                                          Responsible for parsing pseudopotential files and returning pseudopotential objects.

                                                                          @@ -3744,13 +3744,13 @@

                                                                          Submodules
                                                                          -Error[source]
                                                                          +Error[source]

                                                                          alias of PseudoParseError

                                                                          -parse(filename)[source]
                                                                          +parse(filename)[source]

                                                                          Read and parse a pseudopotential file. Main entry point for client code.

                                                                          Returns:
                                                                          @@ -3761,31 +3761,31 @@

                                                                          Submodules
                                                                          -class ppdesc(pspcod: int, name: str, psp_type: str, format: None)[source]
                                                                          +class ppdesc(pspcod: int, name: str, psp_type: str, format: None)[source]

                                                                          Bases: NamedTuple

                                                                          Supported values of pspcod.

                                                                          Create new instance of ppdesc(pspcod, name, psp_type, format)

                                                                          -format: None[source]
                                                                          +format: None[source]

                                                                          Alias for field number 3

                                                                          -name: str[source]
                                                                          +name: str[source]

                                                                          Alias for field number 1

                                                                          -psp_type: str[source]
                                                                          +psp_type: str[source]

                                                                          Alias for field number 2

                                                                          -pspcod: int[source]
                                                                          +pspcod: int[source]

                                                                          Alias for field number 0

                                                                          @@ -3793,7 +3793,7 @@

                                                                          Submodules
                                                                          -read_ppdesc(filename)[source]
                                                                          +read_ppdesc(filename)[source]

                                                                          Read the pseudopotential descriptor from filename.

                                                                          Returns:
                                                                          @@ -3807,7 +3807,7 @@

                                                                          Submodules
                                                                          -scan_directory(dirname, exclude_exts=(), exclude_fnames=())[source]
                                                                          +scan_directory(dirname, exclude_exts=(), exclude_fnames=())[source]

                                                                          Analyze the files contained in directory dirname.

                                                                          Parameters:
                                                                          @@ -3827,7 +3827,7 @@

                                                                          Submodules
                                                                          -class PseudoTable(pseudos: Sequence[Pseudo])[source]
                                                                          +class PseudoTable(pseudos: Sequence[Pseudo])[source]

                                                                          Bases: Sequence, MSONable

                                                                          Define the pseudopotentials from the element table. Individidual elements are accessed by name, symbol or atomic number.

                                                                          @@ -3844,7 +3844,7 @@

                                                                          Submodules
                                                                          -all_combinations_for_elements(element_symbols)[source]
                                                                          +all_combinations_for_elements(element_symbols)[source]

                                                                          Get a list with all the possible combination of pseudos for the given list of element_symbols. Each item is a list of pseudopotential objects.

                                                                          @@ -3854,37 +3854,37 @@

                                                                          Submodules
                                                                          -property allnc: bool[source]
                                                                          +property allnc: bool[source]

                                                                          True if all pseudos are norm-conserving.

                                                                          -property allpaw[source]
                                                                          +property allpaw[source]

                                                                          True if all pseudos are PAW.

                                                                          -as_dict(**kwargs)[source]
                                                                          +as_dict(**kwargs)[source]

                                                                          Return dictionary for MSONable protocol.

                                                                          -classmethod as_table(items)[source]
                                                                          +classmethod as_table(items)[source]

                                                                          Return an instance of PseudoTable from the iterable items.

                                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                                          +classmethod from_dict(dct: dict) → Self[source]

                                                                          Build instance from dictionary (MSONable protocol).

                                                                          -classmethod from_dir(top, exts=None, exclude_dirs='_*') → Self | None[source]
                                                                          +classmethod from_dir(top, exts=None, exclude_dirs='_*') → Self | None[source]

                                                                          Find all pseudos in the directory tree starting from top.

                                                                          Parameters:
                                                                          @@ -3903,7 +3903,7 @@

                                                                          Submodules
                                                                          -get_pseudos_for_structure(structure: Structure)[source]
                                                                          +get_pseudos_for_structure(structure: Structure)[source]

                                                                          Get the list of Pseudo objects to be used for this Structure.

                                                                          Parameters:
                                                                          @@ -3920,13 +3920,13 @@

                                                                          Submodules
                                                                          -is_complete(zmax=118) → bool[source]
                                                                          +is_complete(zmax=118) → bool[source]

                                                                          True if table is complete i.e. all elements with Z < zmax have at least on pseudopotential.

                                                                          -print_table(stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, filter_function=None)[source]
                                                                          +print_table(stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, filter_function=None)[source]

                                                                          A pretty ASCII printer for the periodic table, based on some filter_function.

                                                                          Parameters:
                                                                          @@ -3942,7 +3942,7 @@

                                                                          Submodules
                                                                          -pseudo_with_symbol(symbol, allow_multi=False)[source]
                                                                          +pseudo_with_symbol(symbol, allow_multi=False)[source]

                                                                          Get the pseudo with the given chemical symbol.

                                                                          Parameters:
                                                                          @@ -3960,7 +3960,7 @@

                                                                          Submodules
                                                                          -pseudos_with_symbols(symbols)[source]
                                                                          +pseudos_with_symbols(symbols)[source]

                                                                          Get the pseudos with the given chemical symbols.

                                                                          Raises:
                                                                          @@ -3971,7 +3971,7 @@

                                                                          Submodules
                                                                          -select(condition) → PseudoTable[source]
                                                                          +select(condition) → PseudoTable[source]

                                                                          Select only those pseudopotentials for which condition is True.

                                                                          Parameters:
                                                                          @@ -3988,20 +3988,20 @@

                                                                          Submodules
                                                                          -select_family(family)[source]
                                                                          +select_family(family)[source]

                                                                          Return PseudoTable with element belonging to the specified family, e.g. family=”alkaline”.

                                                                          -select_rows(rows)[source]
                                                                          +select_rows(rows)[source]

                                                                          Get new class:PseudoTable object with pseudos in the given rows of the periodic table. rows can be either a int or a list of integers.

                                                                          -select_symbols(symbols, ret_list=False)[source]
                                                                          +select_symbols(symbols, ret_list=False)[source]

                                                                          Get a PseudoTable with the pseudopotentials with the given list of chemical symbols.

                                                                          Parameters:
                                                                          @@ -4016,13 +4016,13 @@

                                                                          Submodules
                                                                          -sort_by_z()[source]
                                                                          +sort_by_z()[source]

                                                                          Return a new PseudoTable with pseudos sorted by Z.

                                                                          -sorted(attrname, reverse=False)[source]
                                                                          +sorted(attrname, reverse=False)[source]

                                                                          Sort the table according to the value of attribute attrname.

                                                                          Returns:
                                                                          @@ -4036,19 +4036,19 @@

                                                                          Submodules
                                                                          -to_table(filter_function=None)[source]
                                                                          +to_table(filter_function=None)[source]

                                                                          Return string with data in tabular form.

                                                                          -with_dojo_report()[source]
                                                                          +with_dojo_report()[source]

                                                                          Select pseudos containing the DOJO_REPORT section. Return new class:PseudoTable object.

                                                                          -property zlist[source]
                                                                          +property zlist[source]

                                                                          Ordered list with the atomic numbers available in the table.

                                                                          @@ -4056,20 +4056,20 @@

                                                                          Submodules
                                                                          -class RadialFunction(mesh: Any, values: NDArray)[source]
                                                                          +class RadialFunction(mesh: Any, values: NDArray)[source]

                                                                          Bases: NamedTuple

                                                                          Radial Function class.

                                                                          TODO: use RadialFunction from pseudo_dojo.

                                                                          Create new instance of RadialFunction(mesh, values)

                                                                          -mesh: Any[source]
                                                                          +mesh: Any[source]

                                                                          Alias for field number 0

                                                                          -values: NDArray[source]
                                                                          +values: NDArray[source]

                                                                          Alias for field number 1

                                                                          @@ -4077,13 +4077,13 @@

                                                                          Submodules
                                                                          -l2str(l_ang_mom)[source]
                                                                          +l2str(l_ang_mom)[source]

                                                                          Convert the angular momentum l (int) to string.

                                                                          -str2l(s)[source]
                                                                          +str2l(s)[source]

                                                                          Convert a string to the angular momentum l (int).

                                                                          @@ -4093,7 +4093,7 @@

                                                                          Submodules
                                                                          -class InputVariable(name: str, value, units: str = '', valperline: int = 3)[source]
                                                                          +class InputVariable(name: str, value, units: str = '', valperline: int = 3)[source]

                                                                          Bases: object

                                                                          An Abinit input variable.

                                                                          @@ -4108,51 +4108,51 @@

                                                                          Submodules
                                                                          -property basename[source]
                                                                          +property basename[source]

                                                                          The name trimmed of any dataset index.

                                                                          -property dataset[source]
                                                                          +property dataset[source]

                                                                          The dataset index in string form.

                                                                          -format_list(values, float_decimal=0)[source]
                                                                          +format_list(values, float_decimal=0)[source]

                                                                          Format a list of values into a string. The result might be spread among several lines.

                                                                          -static format_list2d(values, float_decimal=0)[source]
                                                                          +static format_list2d(values, float_decimal=0)[source]

                                                                          Format a list of lists.

                                                                          -static format_scalar(val, float_decimal=0)[source]
                                                                          +static format_scalar(val, float_decimal=0)[source]

                                                                          Format a single numerical value into a string with the appropriate number of decimal.

                                                                          -get_value()[source]
                                                                          +get_value()[source]

                                                                          Return the value.

                                                                          -property name[source]
                                                                          +property name[source]

                                                                          Name of the variable.

                                                                          -property units[source]
                                                                          +property units[source]

                                                                          The units.

                                                                          @@ -4160,7 +4160,7 @@

                                                                          Submodules
                                                                          -flatten(iterable)[source]
                                                                          +flatten(iterable)[source]

                                                                          Make an iterable flat, i.e. a 1d iterable object.

                                                                          diff --git a/docs/pymatgen.io.aims.html b/docs/pymatgen.io.aims.html index d1a1b982098..da5a7ab5c9a 100644 --- a/docs/pymatgen.io.aims.html +++ b/docs/pymatgen.io.aims.html @@ -4,7 +4,7 @@ - pymatgen.io.aims package — pymatgen 2024.6.4 documentation + pymatgen.io.aims package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                          - 2024.6.4 + 2024.6.10
                                                                          @@ -348,12 +348,12 @@

                                                                          Submodules
                                                                          -class AimsControlIn(_parameters: dict[str, Any] = <factory>)[source]
                                                                          +class AimsControlIn(_parameters: dict[str, Any] = <factory>)[source]

                                                                          Bases: MSONable

                                                                          An FHI-aims control.in file.

                                                                          -_parameters[source]
                                                                          +_parameters[source]

                                                                          The parameters dictionary containing all input flags (key) and values for the control.in file

                                                                          @@ -365,13 +365,13 @@

                                                                          Submodules
                                                                          -as_dict() → dict[str, Any][source]
                                                                          +as_dict() → dict[str, Any][source]

                                                                          Get a dictionary representation of the geometry.in file.

                                                                          -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                          +classmethod from_dict(dct: dict[str, Any]) → Self[source]

                                                                          Initialize from dictionary.

                                                                          Parameters:
                                                                          @@ -385,7 +385,7 @@

                                                                          Submodules
                                                                          -get_aims_control_parameter_str(key: str, value: Any, fmt: str) → str[source]
                                                                          +get_aims_control_parameter_str(key: str, value: Any, fmt: str) → str[source]

                                                                          Get the string needed to add a parameter to the control.in file

                                                                          Parameters:
                                                                          @@ -406,7 +406,7 @@

                                                                          Submodules
                                                                          -get_content(structure: Structure | Molecule, verbose_header: bool = False, directory: str | Path | None = None) → str[source]
                                                                          +get_content(structure: Structure | Molecule, verbose_header: bool = False, directory: str | Path | None = None) → str[source]

                                                                          Get the content of the file

                                                                          Parameters:
                                                                          @@ -428,7 +428,7 @@

                                                                          Submodules
                                                                          -get_species_block(structure: Structure | Molecule, species_dir: str | Path) → str[source]
                                                                          +get_species_block(structure: Structure | Molecule, species_dir: str | Path) → str[source]

                                                                          Get the basis set information for a structure

                                                                          Parameters:
                                                                          @@ -448,13 +448,13 @@

                                                                          Submodules
                                                                          -property parameters: dict[str, Any][source]
                                                                          +property parameters: dict[str, Any][source]

                                                                          The dictionary of input parameters for control.in

                                                                          -write_file(structure: Structure | Molecule, directory: str | Path | None = None, verbose_header: bool = False, overwrite: bool = False) → None[source]
                                                                          +write_file(structure: Structure | Molecule, directory: str | Path | None = None, verbose_header: bool = False, overwrite: bool = False) → None[source]

                                                                          Write the control.in file

                                                                          Parameters:
                                                                          @@ -480,12 +480,12 @@

                                                                          Submodules
                                                                          -class AimsCube(type: str = <factory>, origin: Sequence[float] | Tuple3Floats = <factory>, edges: Sequence[Sequence[float]] = <factory>, points: Sequence[int] | Tuple3Ints = <factory>, format: str = 'cube', spin_state: int | None = None, kpoint: int | None = None, filename: str | None = None, elf_type: int | None = None)[source]
                                                                          +class AimsCube(type: str = <factory>, origin: Sequence[float] | Tuple3Floats = <factory>, edges: Sequence[Sequence[float]] = <factory>, points: Sequence[int] | Tuple3Ints = <factory>, format: str = 'cube', spin_state: int | None = None, kpoint: int | None = None, filename: str | None = None, elf_type: int | None = None)[source]

                                                                          Bases: MSONable

                                                                          The FHI-aims cubes

                                                                          -type[source]
                                                                          +type[source]

                                                                          The value to be outputted as a cube file

                                                                          Type:
                                                                          @@ -496,7 +496,7 @@

                                                                          Submodules
                                                                          -origin[source]
                                                                          +origin[source]

                                                                          The origin of the cube

                                                                          Type:
                                                                          @@ -507,7 +507,7 @@

                                                                          Submodules
                                                                          -edges[source]
                                                                          +edges[source]

                                                                          Specifies the edges of a cube: dx, dy, dz dx (float): The length of the step in the x direction dy (float): The length of the step in the y direction @@ -521,7 +521,7 @@

                                                                          Submodules
                                                                          -points[source]
                                                                          +points[source]

                                                                          The number of points along each edge

                                                                          @@ -533,7 +533,7 @@

                                                                          Submodules
                                                                          -spin_state[source]
                                                                          +spin_state[source]

                                                                          The spin-channel to use either 1 or 2

                                                                          Type:
                                                                          @@ -544,7 +544,7 @@

                                                                          Submodules
                                                                          -kpoint[source]
                                                                          +kpoint[source]

                                                                          The k-point to use (the index of the list printed from output k_point_list)

                                                                          @@ -556,7 +556,7 @@

                                                                          Submodules
                                                                          -filename[source]
                                                                          +filename[source]

                                                                          The filename to use

                                                                          Type:
                                                                          @@ -567,7 +567,7 @@

                                                                          Submodules
                                                                          -format[source]
                                                                          +format[source]

                                                                          The format to output the cube file in: cube, gOpenMol, or xsf

                                                                          Type:
                                                                          @@ -578,7 +578,7 @@

                                                                          Submodules
                                                                          -elf_type[source]
                                                                          +elf_type[source]

                                                                          The type of electron localization function to use ( see FHI-aims manual)

                                                                          @@ -590,39 +590,39 @@

                                                                          Submodules
                                                                          -as_dict() → dict[str, Any][source]
                                                                          +as_dict() → dict[str, Any][source]

                                                                          Get a dictionary representation of the geometry.in file.

                                                                          -property control_block: str[source]
                                                                          +property control_block: str[source]

                                                                          The block of text for the control.in file of the Cube

                                                                          -edges: Sequence[Sequence[float]][source]
                                                                          +edges: Sequence[Sequence[float]][source]
                                                                          -elf_type: int | None = None[source]
                                                                          +elf_type: int | None = None[source]
                                                                          -filename: str | None = None[source]
                                                                          +filename: str | None = None[source]
                                                                          -format: str = 'cube'[source]
                                                                          +format: str = 'cube'[source]
                                                                          -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                          +classmethod from_dict(dct: dict[str, Any]) → Self[source]

                                                                          Initialize from dictionary.

                                                                          Parameters:
                                                                          @@ -636,39 +636,39 @@

                                                                          Submodules
                                                                          -kpoint: int | None = None[source]
                                                                          +kpoint: int | None = None[source]

                                                                          -origin: Sequence[float] | Tuple3Floats[source]
                                                                          +origin: Sequence[float] | Tuple3Floats[source]
                                                                          -points: Sequence[int] | Tuple3Ints[source]
                                                                          +points: Sequence[int] | Tuple3Ints[source]
                                                                          -spin_state: int | None = None[source]
                                                                          +spin_state: int | None = None[source]
                                                                          -type: str[source]
                                                                          +type: str[source]
                                                                          -class AimsGeometryIn(_content: str, _structure: Structure | Molecule)[source]
                                                                          +class AimsGeometryIn(_content: str, _structure: Structure | Molecule)[source]

                                                                          Bases: MSONable

                                                                          Representation of an aims geometry.in file

                                                                          -_content[source]
                                                                          +_content[source]

                                                                          The content of the input file

                                                                          Type:
                                                                          @@ -679,7 +679,7 @@

                                                                          Submodules
                                                                          -_structure[source]
                                                                          +_structure[source]

                                                                          The structure or molecule representation of the file

                                                                          @@ -691,19 +691,19 @@

                                                                          Submodules
                                                                          -as_dict() → dict[str, Any][source]
                                                                          +as_dict() → dict[str, Any][source]

                                                                          Get a dictionary representation of the geometry.in file.

                                                                          -property content: str[source]
                                                                          +property content: str[source]

                                                                          Access the contents of the file

                                                                          -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                          +classmethod from_dict(dct: dict[str, Any]) → Self[source]

                                                                          Initialize from dictionary.

                                                                          Parameters:
                                                                          @@ -717,7 +717,7 @@

                                                                          Submodules
                                                                          -classmethod from_file(filepath: str | Path) → Self[source]
                                                                          +classmethod from_file(filepath: str | Path) → Self[source]

                                                                          Create an AimsGeometryIn from an input file.

                                                                          Parameters:
                                                                          @@ -734,7 +734,7 @@

                                                                          Submodules
                                                                          -classmethod from_str(contents: str) → Self[source]
                                                                          +classmethod from_str(contents: str) → Self[source]

                                                                          Create an input from the content of an input file

                                                                          Parameters:
                                                                          @@ -748,7 +748,7 @@

                                                                          Submodules
                                                                          -classmethod from_structure(structure: Structure | Molecule) → Self[source]
                                                                          +classmethod from_structure(structure: Structure | Molecule) → Self[source]

                                                                          Construct an input file from an input structure.

                                                                          Parameters:
                                                                          @@ -765,13 +765,13 @@

                                                                          Submodules
                                                                          -property structure: Structure | Molecule[source]
                                                                          +property structure: Structure | Molecule[source]

                                                                          Access structure for the file

                                                                          -write_file(directory: str | Path | None = None, overwrite: bool = False) → None[source]
                                                                          +write_file(directory: str | Path | None = None, overwrite: bool = False) → None[source]

                                                                          Write the geometry.in file

                                                                          Parameters:
                                                                          @@ -791,7 +791,7 @@

                                                                          Submodules
                                                                          -class AimsOutput(results: Molecule | Structure | Sequence[Molecule | Structure], metadata: dict[str, Any], structure_summary: dict[str, Any])[source]
                                                                          +class AimsOutput(results: Molecule | Structure | Sequence[Molecule | Structure], metadata: dict[str, Any], structure_summary: dict[str, Any])[source]

                                                                          Bases: MSONable

                                                                          The main output file for FHI-aims.

                                                                          @@ -808,73 +808,73 @@

                                                                          Submodules
                                                                          -property aims_version: str[source]
                                                                          +property aims_version: str[source]

                                                                          The version of FHI-aims used for the calculation.

                                                                          -property all_forces: list[list[Vector3D]][source]
                                                                          +property all_forces: list[list[Vector3D]][source]

                                                                          The forces for all images in the calculation.

                                                                          -as_dict() → dict[str, Any][source]
                                                                          +as_dict() → dict[str, Any][source]

                                                                          Create a dict representation of the outputs for MSONable.

                                                                          -property band_gap: float[source]
                                                                          +property band_gap: float[source]

                                                                          The band gap for the final structure in the calculation.

                                                                          -property cbm: float[source]
                                                                          +property cbm: float[source]

                                                                          The LUMO level for the final structure in the calculation.

                                                                          -property completed: bool[source]
                                                                          +property completed: bool[source]

                                                                          Did the calculation complete.

                                                                          -property direct_band_gap: float[source]
                                                                          +property direct_band_gap: float[source]

                                                                          The direct band gap for the final structure in the calculation.

                                                                          -property fermi_energy: float[source]
                                                                          +property fermi_energy: float[source]

                                                                          The Fermi energy for the final structure in the calculation.

                                                                          -property final_energy: float[source]
                                                                          +property final_energy: float[source]

                                                                          The total energy for the final structure in the calculation.

                                                                          -property final_structure: Structure | Molecule[source]
                                                                          +property final_structure: Structure | Molecule[source]

                                                                          The final structure for the calculation.

                                                                          -property forces: Sequence[Vector3D] | None[source]
                                                                          +property forces: Sequence[Vector3D] | None[source]

                                                                          The forces for the final image of the calculation.

                                                                          -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                          +classmethod from_dict(dct: dict[str, Any]) → Self[source]

                                                                          Construct an AimsOutput from a dictionary.

                                                                          Parameters:
                                                                          @@ -888,7 +888,7 @@

                                                                          Submodules
                                                                          -classmethod from_outfile(outfile: str | Path) → Self[source]
                                                                          +classmethod from_outfile(outfile: str | Path) → Self[source]

                                                                          Construct an AimsOutput from an output file.

                                                                          Parameters:
                                                                          @@ -902,7 +902,7 @@

                                                                          Submodules
                                                                          -classmethod from_str(content: str) → Self[source]
                                                                          +classmethod from_str(content: str) → Self[source]

                                                                          Construct an AimsOutput from an output file.

                                                                          Parameters:
                                                                          @@ -916,7 +916,7 @@

                                                                          Submodules
                                                                          -get_results_for_image(image_ind: int) → Structure | Molecule[source]
                                                                          +get_results_for_image(image_ind: int) → Structure | Molecule[source]

                                                                          Get the results dictionary for a particular image or slice of images.

                                                                          Parameters:
                                                                          @@ -930,49 +930,49 @@

                                                                          Submodules
                                                                          -property initial_structure: Structure | Molecule[source]
                                                                          +property initial_structure: Structure | Molecule[source]

                                                                          The initial structure for the calculations.

                                                                          -property metadata: dict[str, Any][source]
                                                                          +property metadata: dict[str, Any][source]

                                                                          The system metadata.

                                                                          -property n_images: int[source]
                                                                          +property n_images: int[source]

                                                                          The number of images in results.

                                                                          -property stress: Matrix3D[source]
                                                                          +property stress: Matrix3D[source]

                                                                          The stress for the final image of the calculation.

                                                                          -property stresses: Sequence[Matrix3D] | None[source]
                                                                          +property stresses: Sequence[Matrix3D] | None[source]

                                                                          The atomic virial stresses for the final image of the calculation.

                                                                          -property structure_summary: dict[str, Any][source]
                                                                          +property structure_summary: dict[str, Any][source]

                                                                          The summary of the material/molecule that the calculations represent.

                                                                          -property structures: Sequence[Structure | Molecule][source]
                                                                          +property structures: Sequence[Structure | Molecule][source]

                                                                          All images in the output file.

                                                                          -property vbm: float[source]
                                                                          +property vbm: float[source]

                                                                          The HOMO level for the final structure in the calculation.

                                                                          @@ -984,7 +984,7 @@

                                                                          Submodules
                                                                          -class AimsOutCalcChunk(lines: list[str], header: AimsOutHeaderChunk)[source]
                                                                          +class AimsOutCalcChunk(lines: list[str], header: AimsOutHeaderChunk)[source]

                                                                          Bases: AimsOutChunk

                                                                          A part of the aims.out file corresponding to a single structure.

                                                                          Construct the AimsOutCalcChunk.

                                                                          @@ -999,223 +999,223 @@

                                                                          Submodules
                                                                          -property E_f: float | None[source]
                                                                          +property E_f: float | None[source]

                                                                          The Fermi energy

                                                                          -property cbm: float[source]
                                                                          +property cbm: float[source]

                                                                          The conduction band minimnum

                                                                          -property converged: bool[source]
                                                                          +property converged: bool[source]

                                                                          True if the calculation is converged

                                                                          -property coords: list[Vector3D][source]
                                                                          +property coords: list[Vector3D][source]

                                                                          The cartesian coordinates of the atoms

                                                                          -property dielectric_tensor: Matrix3D | None[source]
                                                                          +property dielectric_tensor: Matrix3D | None[source]

                                                                          The dielectric tensor from the aims.out file.

                                                                          -property dipole: Vector3D | None[source]
                                                                          +property dipole: Vector3D | None[source]

                                                                          The electric dipole moment from the aims.out file.

                                                                          -property direct_gap: float[source]
                                                                          +property direct_gap: float[source]

                                                                          The direct bandgap

                                                                          -property electronic_temperature: float[source]
                                                                          +property electronic_temperature: float[source]

                                                                          The electronic temperature for the chunk.

                                                                          -property energy: float[source]
                                                                          +property energy: float[source]

                                                                          The energy from the aims.out file.

                                                                          -property forces: np.array[Vector3D] | None[source]
                                                                          +property forces: np.array[Vector3D] | None[source]

                                                                          The forces from the aims.out file.

                                                                          -property free_energy: float | None[source]
                                                                          +property free_energy: float | None[source]

                                                                          The free energy of the calculation

                                                                          -property gap: float[source]
                                                                          +property gap: float[source]

                                                                          The band gap

                                                                          -property hirshfeld_atomic_dipoles: Sequence[Vector3D] | None[source]
                                                                          +property hirshfeld_atomic_dipoles: Sequence[Vector3D] | None[source]

                                                                          The Hirshfeld atomic dipoles of the system

                                                                          -property hirshfeld_charges: Sequence[float] | None[source]
                                                                          +property hirshfeld_charges: Sequence[float] | None[source]

                                                                          The Hirshfeld charges of the system

                                                                          -property hirshfeld_dipole: None | Vector3D[source]
                                                                          +property hirshfeld_dipole: None | Vector3D[source]

                                                                          The Hirshfeld dipole of the system

                                                                          -property hirshfeld_volumes: Sequence[float] | None[source]
                                                                          +property hirshfeld_volumes: Sequence[float] | None[source]

                                                                          The Hirshfeld atomic dipoles of the system

                                                                          -property initial_lattice: Lattice | None[source]
                                                                          +property initial_lattice: Lattice | None[source]

                                                                          The initial Lattice of the structure

                                                                          -property initial_structure: Structure | Molecule[source]
                                                                          +property initial_structure: Structure | Molecule[source]

                                                                          The initial structure for the calculation

                                                                          -property is_metallic: bool[source]
                                                                          +property is_metallic: bool[source]

                                                                          Is the system is metallic.

                                                                          -property k_point_weights: Sequence[float][source]
                                                                          +property k_point_weights: Sequence[float][source]

                                                                          The k-point weights for the calculation.

                                                                          -property k_points: Sequence[Vector3D][source]
                                                                          +property k_points: Sequence[Vector3D][source]

                                                                          All k-points listed in the calculation.

                                                                          -property lattice: Lattice[source]
                                                                          +property lattice: Lattice[source]

                                                                          The Lattice object for the structure

                                                                          -property magmom: float | None[source]
                                                                          +property magmom: float | None[source]

                                                                          The magnetic moment of the structure

                                                                          -property n_atoms: int[source]
                                                                          +property n_atoms: int[source]

                                                                          The number of atoms in the structure

                                                                          -property n_bands: int[source]
                                                                          +property n_bands: int[source]

                                                                          The number of Kohn-Sham states for the chunk.

                                                                          -property n_electrons: int[source]
                                                                          +property n_electrons: int[source]

                                                                          The number of electrons for the chunk.

                                                                          -property n_iter: int | None[source]
                                                                          +property n_iter: int | None[source]

                                                                          The number of steps needed to converge the SCF cycle for the chunk.

                                                                          -property n_k_points: int[source]
                                                                          +property n_k_points: int[source]

                                                                          The number of k_ppoints for the calculation.

                                                                          -property n_spins: int[source]
                                                                          +property n_spins: int[source]

                                                                          The number of spin channels for the chunk.

                                                                          -property polarization: Vector3D | None[source]
                                                                          +property polarization: Vector3D | None[source]

                                                                          The polarization vector from the aims.out file.

                                                                          -property results: dict[str, Any][source]
                                                                          +property results: dict[str, Any][source]

                                                                          Convert an AimsOutChunk to a Results Dictionary.

                                                                          -property species: list[str][source]
                                                                          +property species: list[str][source]

                                                                          The list of atomic symbols for all atoms in the structure

                                                                          -property stress: Matrix3D | None[source]
                                                                          +property stress: Matrix3D | None[source]

                                                                          The stress from the aims.out file and convert to kbar.

                                                                          -property stresses: np.array[Matrix3D] | None[source]
                                                                          +property stresses: np.array[Matrix3D] | None[source]

                                                                          The stresses from the aims.out file and convert to kbar.

                                                                          -property structure: Structure | Molecule[source]
                                                                          +property structure: Structure | Molecule[source]

                                                                          The pytmagen SiteCollection of the chunk.

                                                                          -property vbm: float[source]
                                                                          +property vbm: float[source]

                                                                          The valance band maximum

                                                                          -property velocities: list[Vector3D][source]
                                                                          +property velocities: list[Vector3D][source]

                                                                          The velocities of the atoms

                                                                          @@ -1223,12 +1223,12 @@

                                                                          Submodules
                                                                          -class AimsOutChunk(lines: list[str] = <factory>)[source]
                                                                          +class AimsOutChunk(lines: list[str] = <factory>)[source]

                                                                          Bases: object

                                                                          Base class for AimsOutChunks.

                                                                          -lines[source]
                                                                          +lines[source]

                                                                          The list of all lines in the chunk

                                                                          Type:
                                                                          @@ -1239,12 +1239,12 @@

                                                                          Submodules
                                                                          -lines: list[str][source]
                                                                          +lines: list[str][source]

                                                                          -parse_scalar(property: str) → float | None[source]
                                                                          +parse_scalar(property: str) → float | None[source]

                                                                          Parse a scalar property from the chunk.

                                                                          Parameters:
                                                                          @@ -1258,7 +1258,7 @@

                                                                          Submodules
                                                                          -reverse_search_for(keys: list[str], line_start: int = 0) → int[source]
                                                                          +reverse_search_for(keys: list[str], line_start: int = 0) → int[source]

                                                                          Find the last time one of the keys appears in self.lines.

                                                                          Parameters:
                                                                          @@ -1275,7 +1275,7 @@

                                                                          Submodules
                                                                          -search_for_all(key: str, line_start: int = 0, line_end: int = -1) → list[int][source]
                                                                          +search_for_all(key: str, line_start: int = 0, line_end: int = -1) → list[int][source]

                                                                          Find the all times the key appears in self.lines.

                                                                          Parameters:
                                                                          @@ -1295,84 +1295,84 @@

                                                                          Submodules
                                                                          -class AimsOutHeaderChunk(lines: list[str] = <factory>, _cache: dict[str, Any] = <factory>)[source]
                                                                          +class AimsOutHeaderChunk(lines: list[str] = <factory>, _cache: dict[str, Any] = <factory>)[source]

                                                                          Bases: AimsOutChunk

                                                                          The header of the aims.out file containing general information.

                                                                          -property aims_uuid: str[source]
                                                                          +property aims_uuid: str[source]

                                                                          The aims-uuid for the calculation.

                                                                          -property build_type: list[str][source]
                                                                          +property build_type: list[str][source]

                                                                          The optional build flags passed to cmake.

                                                                          -property c_compiler: str | None[source]
                                                                          +property c_compiler: str | None[source]

                                                                          The C compiler used to make FHI-aims.

                                                                          -property c_compiler_flags: str | None[source]
                                                                          +property c_compiler_flags: str | None[source]

                                                                          The C compiler flags used to make FHI-aims.

                                                                          -property commit_hash: str[source]
                                                                          +property commit_hash: str[source]

                                                                          The commit hash for the FHI-aims version.

                                                                          -property electronic_temperature: float[source]
                                                                          +property electronic_temperature: float[source]

                                                                          The electronic temperature for the chunk.

                                                                          -property fortran_compiler: str | None[source]
                                                                          +property fortran_compiler: str | None[source]

                                                                          The fortran compiler used to make FHI-aims.

                                                                          -property fortran_compiler_flags: str | None[source]
                                                                          +property fortran_compiler_flags: str | None[source]

                                                                          The fortran compiler flags used to make FHI-aims.

                                                                          -property header_summary: dict[str, Any][source]
                                                                          +property header_summary: dict[str, Any][source]

                                                                          Dictionary summarizing the information inside the header.

                                                                          -property initial_charges: Sequence[float][source]
                                                                          +property initial_charges: Sequence[float][source]

                                                                          The initial charges for the structure

                                                                          -property initial_lattice: Lattice | None[source]
                                                                          +property initial_lattice: Lattice | None[source]

                                                                          The initial lattice vectors from the aims.out file.

                                                                          -property initial_magnetic_moments: Sequence[float][source]
                                                                          +property initial_magnetic_moments: Sequence[float][source]

                                                                          The initial magnetic Moments

                                                                          -property initial_structure: Structure | Molecule[source]
                                                                          +property initial_structure: Structure | Molecule[source]

                                                                          The initial structure

                                                                          Using the FHI-aims output file recreate the initial structure for the calculation.

                                                                          @@ -1380,78 +1380,78 @@

                                                                          Submodules
                                                                          -property is_md: bool[source]
                                                                          +property is_md: bool[source]

                                                                          Is the output for a molecular dynamics calculation?

                                                                          -property is_relaxation: bool[source]
                                                                          +property is_relaxation: bool[source]

                                                                          Is the output for a relaxation?

                                                                          -property k_point_weights: Sequence[float][source]
                                                                          +property k_point_weights: Sequence[float][source]

                                                                          The k-point weights for the calculation.

                                                                          -property k_points: Sequence[Vector3D][source]
                                                                          +property k_points: Sequence[Vector3D][source]

                                                                          All k-points listed in the calculation.

                                                                          -lines: list[str][source]
                                                                          +lines: list[str][source]
                                                                          -property linked_against: list[str][source]
                                                                          +property linked_against: list[str][source]

                                                                          All libraries used to link the FHI-aims executable.

                                                                          -property metadata_summary: dict[str, list[str] | str | None][source]
                                                                          +property metadata_summary: dict[str, list[str] | str | None][source]

                                                                          Dictionary containing all metadata for FHI-aims build.

                                                                          -property n_atoms: int[source]
                                                                          +property n_atoms: int[source]

                                                                          The number of atoms for the material.

                                                                          -property n_bands: int | None[source]
                                                                          +property n_bands: int | None[source]

                                                                          The number of Kohn-Sham states for the chunk.

                                                                          -property n_electrons: int | None[source]
                                                                          +property n_electrons: int | None[source]

                                                                          The number of electrons for the chunk.

                                                                          -property n_k_points: int | None[source]
                                                                          +property n_k_points: int | None[source]

                                                                          The number of k_ppoints for the calculation.

                                                                          -property n_spins: int | None[source]
                                                                          +property n_spins: int | None[source]

                                                                          The number of spin channels for the chunk.

                                                                          -property version_number: str[source]
                                                                          +property version_number: str[source]

                                                                          The commit hash for the FHI-aims version.

                                                                          @@ -1459,7 +1459,7 @@

                                                                          Submodules
                                                                          -exception AimsParseError(message: str)[source]
                                                                          +exception AimsParseError(message: str)[source]

                                                                          Bases: Exception

                                                                          Exception raised if an error occurs when parsing an Aims output file.

                                                                          Initialize the error with the message, message

                                                                          @@ -1467,14 +1467,14 @@

                                                                          Submodules
                                                                          -exception ParseError[source]
                                                                          +exception ParseError[source]

                                                                          Bases: Exception

                                                                          Parse error during reading of a file

                                                                          -check_convergence(chunks: list[AimsOutCalcChunk], non_convergence_ok: bool = False) → bool[source]
                                                                          +check_convergence(chunks: list[AimsOutCalcChunk], non_convergence_ok: bool = False) → bool[source]

                                                                          Check if the aims output file is for a converged calculation.

                                                                          Parameters:
                                                                          @@ -1493,7 +1493,7 @@

                                                                          Submodules
                                                                          -get_aims_out_chunks(content: str | TextIOWrapper, header_chunk: AimsOutHeaderChunk) → Generator[source]
                                                                          +get_aims_out_chunks(content: str | TextIOWrapper, header_chunk: AimsOutHeaderChunk) → Generator[source]

                                                                          Yield unprocessed chunks (header, lines) for each AimsOutChunk image.

                                                                          Parameters:
                                                                          @@ -1510,7 +1510,7 @@

                                                                          Submodules
                                                                          -get_header_chunk(content: str | TextIOWrapper) → AimsOutHeaderChunk[source]
                                                                          +get_header_chunk(content: str | TextIOWrapper) → AimsOutHeaderChunk[source]

                                                                          Get the header chunk for an output

                                                                          Parameters:
                                                                          @@ -1524,7 +1524,7 @@

                                                                          Submodules
                                                                          -get_lines(content: str | TextIOWrapper) → list[str][source]
                                                                          +get_lines(content: str | TextIOWrapper) → list[str][source]

                                                                          Get a list of lines from a str or file of content

                                                                          Parameters:
                                                                          @@ -1538,7 +1538,7 @@

                                                                          Submodules
                                                                          -read_aims_header_info(filename: str | Path) → tuple[dict[str, None | list[str] | str], dict[str, Any]][source]
                                                                          +read_aims_header_info(filename: str | Path) → tuple[dict[str, None | list[str] | str], dict[str, Any]][source]

                                                                          Read the FHI-aims header information.

                                                                          Parameters:
                                                                          @@ -1552,7 +1552,7 @@

                                                                          Submodules
                                                                          -read_aims_header_info_from_content(content: str) → tuple[dict[str, list[str] | None | str], dict[str, Any]][source]
                                                                          +read_aims_header_info_from_content(content: str) → tuple[dict[str, list[str] | None | str], dict[str, Any]][source]

                                                                          Read the FHI-aims header information.

                                                                          Parameters:
                                                                          @@ -1566,7 +1566,7 @@

                                                                          Submodules
                                                                          -read_aims_output(filename: str | Path, index: int | slice = -1, non_convergence_ok: bool = False) → Structure | Molecule | Sequence[Structure | Molecule][source]
                                                                          +read_aims_output(filename: str | Path, index: int | slice = -1, non_convergence_ok: bool = False) → Structure | Molecule | Sequence[Structure | Molecule][source]

                                                                          Import FHI-aims output files with all data available.

                                                                          Includes all structures for relaxations and MD runs with FHI-aims

                                                                          @@ -1585,7 +1585,7 @@

                                                                          Submodules
                                                                          -read_aims_output_from_content(content: str, index: int | slice = -1, non_convergence_ok: bool = False) → Structure | Molecule | Sequence[Structure | Molecule][source]
                                                                          +read_aims_output_from_content(content: str, index: int | slice = -1, non_convergence_ok: bool = False) → Structure | Molecule | Sequence[Structure | Molecule][source]

                                                                          Read and aims output file from the content of a file

                                                                          Parameters:
                                                                          diff --git a/docs/pymatgen.io.aims.sets.html b/docs/pymatgen.io.aims.sets.html index 251933db200..ce9746cb982 100644 --- a/docs/pymatgen.io.aims.sets.html +++ b/docs/pymatgen.io.aims.sets.html @@ -4,7 +4,7 @@ - pymatgen.io.aims.sets package — pymatgen 2024.6.4 documentation + pymatgen.io.aims.sets package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                          - 2024.6.4 + 2024.6.10
                                                                          @@ -164,12 +164,12 @@

                                                                          Submodules
                                                                          -class AimsInputGenerator(user_params: dict[str, ~typing.Any] = <factory>, user_kpoints_settings: dict[str, ~typing.Any] = <factory>)[source]
                                                                          +class AimsInputGenerator(user_params: dict[str, ~typing.Any] = <factory>, user_kpoints_settings: dict[str, ~typing.Any] = <factory>)[source]

                                                                          Bases: InputGenerator

                                                                          A class to generate Aims input sets.

                                                                          -user_params[source]
                                                                          +user_params[source]

                                                                          Updates the default parameters for the FHI-aims calculator

                                                                          @@ -181,7 +181,7 @@

                                                                          Submodules
                                                                          -user_kpoints_settings[source]
                                                                          +user_kpoints_settings[source]

                                                                          The settings used to create the k-grid parameters for FHI-aims

                                                                          @@ -193,7 +193,7 @@

                                                                          Submodules
                                                                          -d2k(structure: Structure, kptdensity: float | list[float] = 5.0, even: bool = True) → Iterable[float][source]
                                                                          +d2k(structure: Structure, kptdensity: float | list[float] = 5.0, even: bool = True) → Iterable[float][source]

                                                                          Convert k-point density to Monkhorst-Pack grid size.

                                                                          inspired by [ase.calculators.calculator.kptdensity2monkhorstpack]

                                                                          @@ -217,7 +217,7 @@

                                                                          Submodules
                                                                          -static d2k_recipcell(recipcell: np.ndarray, pbc: Sequence[bool], kptdensity: float | Sequence[float] = 5.0, even: bool = True) → Sequence[int][source]
                                                                          +static d2k_recipcell(recipcell: np.ndarray, pbc: Sequence[bool], kptdensity: float | Sequence[float] = 5.0, even: bool = True) → Sequence[int][source]

                                                                          Convert k-point density to Monkhorst-Pack grid size.

                                                                          Parameters:
                                                                          @@ -243,7 +243,7 @@

                                                                          Submodules
                                                                          -get_input_set(structure: Structure | Molecule | None = None, prev_dir: str | Path | None = None, properties: list[str] | None = None) → AimsInputSet[source]
                                                                          +get_input_set(structure: Structure | Molecule | None = None, prev_dir: str | Path | None = None, properties: list[str] | None = None) → AimsInputSet[source]

                                                                          Generate an AimsInputSet object.

                                                                          Parameters:
                                                                          @@ -265,7 +265,7 @@

                                                                          Submodules
                                                                          -get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[str, Any][source]
                                                                          +get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[str, Any][source]

                                                                          Update the parameters for a given calculation type.

                                                                          Parameters:
                                                                          @@ -285,7 +285,7 @@

                                                                          Submodules
                                                                          -k2d(structure: Structure, k_grid: ndarray[int])[source]
                                                                          +k2d(structure: Structure, k_grid: ndarray[int])[source]

                                                                          Generate the kpoint density in each direction from given k_grid.

                                                                          Parameters:
                                                                          @@ -307,19 +307,19 @@

                                                                          Submodules
                                                                          -user_kpoints_settings: dict[str, Any][source]
                                                                          +user_kpoints_settings: dict[str, Any][source]

                                                                          -user_params: dict[str, Any][source]
                                                                          +user_params: dict[str, Any][source]

                                                                          -class AimsInputSet(parameters: dict[str, Any], structure: Structure | Molecule, properties: Sequence[str] = ('energy', 'free_energy'))[source]
                                                                          +class AimsInputSet(parameters: dict[str, Any], structure: Structure | Molecule, properties: Sequence[str] = ('energy', 'free_energy'))[source]

                                                                          Bases: InputSet

                                                                          A class to represent a set of Aims inputs.

                                                                          Construct the AimsInputSet.

                                                                          @@ -335,19 +335,19 @@

                                                                          Submodules
                                                                          -property control_in: str | slice | InputFile[source]
                                                                          +property control_in: str | slice | InputFile[source]

                                                                          The control.in file contents.

                                                                          -property geometry_in: str | slice | InputFile[source]
                                                                          +property geometry_in: str | slice | InputFile[source]

                                                                          The geometry.in file contents.

                                                                          -get_input_files() → tuple[str, str][source]
                                                                          +get_input_files() → tuple[str, str][source]

                                                                          Get the input file contents for the calculation.

                                                                          Returns:
                                                                          @@ -361,13 +361,13 @@

                                                                          Submodules
                                                                          -property params_json: str | slice | InputFile[source]
                                                                          +property params_json: str | slice | InputFile[source]

                                                                          The JSON representation of the parameters dict.

                                                                          -remove_parameters(keys: Iterable[str] | str, strict: bool = True) → dict[str, Any][source]
                                                                          +remove_parameters(keys: Iterable[str] | str, strict: bool = True) → dict[str, Any][source]

                                                                          Remove the aims parameters listed in keys.

                                                                          This removes the aims variables from the parameters object.

                                                                          @@ -390,7 +390,7 @@

                                                                          Submodules
                                                                          -set_parameters(*args, **kwargs) → dict[str, Any][source]
                                                                          +set_parameters(*args, **kwargs) → dict[str, Any][source]

                                                                          Set the parameters object for the AimsTemplate.

                                                                          This sets the parameters object that is passed to an AimsTemplate and resets the control.in file

                                                                          @@ -409,7 +409,7 @@

                                                                          Submodules
                                                                          -set_structure(structure: Structure | Molecule)[source]
                                                                          +set_structure(structure: Structure | Molecule)[source]

                                                                          Set the structure object for this input set.

                                                                          Parameters:
                                                                          @@ -423,7 +423,7 @@

                                                                          Submodules
                                                                          -recursive_update(dct: dict, up: dict) → dict[source]
                                                                          +recursive_update(dct: dict, up: dict) → dict[source]

                                                                          Update a dictionary recursively and return it.

                                                                          Parameters:
                                                                          @@ -451,12 +451,12 @@

                                                                          Submodules
                                                                          -class BandStructureSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'bands', k_point_density: float = 20)[source]
                                                                          +class BandStructureSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'bands', k_point_density: float = 20)[source]

                                                                          Bases: AimsInputGenerator

                                                                          A generator for the band structure calculation input set.

                                                                          -calc_type[source]
                                                                          +calc_type[source]

                                                                          The type of calculations

                                                                          Type:
                                                                          @@ -467,7 +467,7 @@

                                                                          Submodules
                                                                          -k_point_density[source]
                                                                          +k_point_density[source]

                                                                          The number of k_points per angstrom

                                                                          Type:
                                                                          @@ -478,12 +478,12 @@

                                                                          Submodules
                                                                          -calc_type: str = 'bands'[source]
                                                                          +calc_type: str = 'bands'[source]

                                                                          -get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[str, Sequence[str]][source]
                                                                          +get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[str, Sequence[str]][source]

                                                                          Get the parameter updates for the calculation.

                                                                          Parameters:
                                                                          @@ -503,19 +503,19 @@

                                                                          Submodules
                                                                          -k_point_density: float = 20[source]
                                                                          +k_point_density: float = 20[source]

                                                                          -class GWSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'GW', k_point_density: float = 20)[source]
                                                                          +class GWSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'GW', k_point_density: float = 20)[source]

                                                                          Bases: AimsInputGenerator

                                                                          A generator for the input set for calculations employing GW self-energy correction.

                                                                          -calc_type[source]
                                                                          +calc_type[source]

                                                                          The type of calculations

                                                                          Type:
                                                                          @@ -526,7 +526,7 @@

                                                                          Submodules
                                                                          -k_point_density[source]
                                                                          +k_point_density[source]

                                                                          The number of k_points per angstrom

                                                                          Type:
                                                                          @@ -537,12 +537,12 @@

                                                                          Submodules
                                                                          -calc_type: str = 'GW'[source]
                                                                          +calc_type: str = 'GW'[source]

                                                                          -get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[str, Any][source]
                                                                          +get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[str, Any][source]

                                                                          Get the parameter updates for the calculation.

                                                                          Parameters:
                                                                          @@ -562,14 +562,14 @@

                                                                          Submodules
                                                                          -k_point_density: float = 20[source]
                                                                          +k_point_density: float = 20[source]

                                                                          -prepare_band_input(structure: Structure, density: float = 20)[source]
                                                                          +prepare_band_input(structure: Structure, density: float = 20)[source]

                                                                          Prepare the band information needed for the FHI-aims control.in file.

                                                                          Parameters:
                                                                          @@ -587,12 +587,12 @@

                                                                          Submodules
                                                                          -class RelaxSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'relaxation', relax_cell: bool = True, max_force: float = 0.001, method: str = 'trm')[source]
                                                                          +class RelaxSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'relaxation', relax_cell: bool = True, max_force: float = 0.001, method: str = 'trm')[source]

                                                                          Bases: AimsInputGenerator

                                                                          Generate FHI-aims relax sets for optimizing internal coordinates and lattice params.

                                                                          -calc_type[source]
                                                                          +calc_type[source]

                                                                          The type of calculation

                                                                          Type:
                                                                          @@ -603,7 +603,7 @@

                                                                          Submodules
                                                                          -relax_cell[source]
                                                                          +relax_cell[source]

                                                                          If True then relax the unit cell from the structure

                                                                          Type:
                                                                          @@ -614,7 +614,7 @@

                                                                          Submodules
                                                                          -max_force[source]
                                                                          +max_force[source]

                                                                          Maximum allowed force in the calculation

                                                                          Type:
                                                                          @@ -625,7 +625,7 @@

                                                                          Submodules
                                                                          -method[source]
                                                                          +method[source]

                                                                          Method used for the geometry optimization

                                                                          Type:
                                                                          @@ -636,12 +636,12 @@

                                                                          Submodules
                                                                          -calc_type: str = 'relaxation'[source]
                                                                          +calc_type: str = 'relaxation'[source]

                                                                          -get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[source]
                                                                          +get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[source]

                                                                          Get the parameter updates for the calculation.

                                                                          Parameters:
                                                                          @@ -661,29 +661,29 @@

                                                                          Submodules
                                                                          -max_force: float = 0.001[source]
                                                                          +max_force: float = 0.001[source]

                                                                          -method: str = 'trm'[source]
                                                                          +method: str = 'trm'[source]
                                                                          -relax_cell: bool = True[source]
                                                                          +relax_cell: bool = True[source]
                                                                          -class SocketIOSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'multi_scf', host: str = 'localhost', port: int = 12345)[source]
                                                                          +class SocketIOSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'multi_scf', host: str = 'localhost', port: int = 12345)[source]

                                                                          Bases: AimsInputGenerator

                                                                          Generate FHI-aims input sets for running with the socket.

                                                                          -calc_type[source]
                                                                          +calc_type[source]

                                                                          The type of calculation

                                                                          Type:
                                                                          @@ -694,7 +694,7 @@

                                                                          Submodules
                                                                          -host[source]
                                                                          +host[source]

                                                                          The hostname for the server the socket is on

                                                                          Type:
                                                                          @@ -705,7 +705,7 @@

                                                                          Submodules
                                                                          -port[source]
                                                                          +port[source]

                                                                          The port the socket server is listening on

                                                                          Type:
                                                                          @@ -716,12 +716,12 @@

                                                                          Submodules
                                                                          -calc_type: str = 'multi_scf'[source]
                                                                          +calc_type: str = 'multi_scf'[source]

                                                                          -get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[source]
                                                                          +get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[source]

                                                                          Get the parameter updates for the calculation.

                                                                          Parameters:
                                                                          @@ -741,24 +741,24 @@

                                                                          Submodules
                                                                          -host: str = 'localhost'[source]
                                                                          +host: str = 'localhost'[source]

                                                                          -port: int = 12345[source]
                                                                          +port: int = 12345[source]
                                                                          -class StaticSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'static')[source]
                                                                          +class StaticSetGenerator(user_params: dict[str, Any] = <factory>, user_kpoints_settings: dict[str, Any] = <factory>, calc_type: str = 'static')[source]

                                                                          Bases: AimsInputGenerator

                                                                          Common class for ground-state generators.

                                                                          -calc_type[source]
                                                                          +calc_type[source]

                                                                          The type of calculation

                                                                          Type:
                                                                          @@ -769,12 +769,12 @@

                                                                          Submodules
                                                                          -calc_type: str = 'static'[source]
                                                                          +calc_type: str = 'static'[source]

                                                                          -get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[str, Any][source]
                                                                          +get_parameter_updates(structure: Structure | Molecule, prev_parameters: dict[str, Any]) → dict[str, Any][source]

                                                                          Get the parameter updates for the calculation.

                                                                          Parameters:
                                                                          diff --git a/docs/pymatgen.io.cp2k.html b/docs/pymatgen.io.cp2k.html index 0aadee004df..014d47417ac 100644 --- a/docs/pymatgen.io.cp2k.html +++ b/docs/pymatgen.io.cp2k.html @@ -4,7 +4,7 @@ - pymatgen.io.cp2k package — pymatgen 2024.6.4 documentation + pymatgen.io.cp2k package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                          - 2024.6.4 + 2024.6.10
                                                                          @@ -449,12 +449,12 @@

                                                                          Submodules
                                                                          -class AtomicMetadata(info: BasisInfo | PotentialInfo | None = None, element: Element | None = None, potential: Literal['All Electron', 'Pseudopotential'] | None = None, name: str | None = None, alias_names: list = <factory>, filename: str | None = None, version: str | None = None)[source]
                                                                          +class AtomicMetadata(info: BasisInfo | PotentialInfo | None = None, element: Element | None = None, potential: Literal['All Electron', 'Pseudopotential'] | None = None, name: str | None = None, alias_names: list = <factory>, filename: str | None = None, version: str | None = None)[source]

                                                                          Bases: MSONable

                                                                          Metadata for basis sets and potentials in cp2k.

                                                                          -info[source]
                                                                          +info[source]

                                                                          Info about this object

                                                                          Type:
                                                                          @@ -465,7 +465,7 @@

                                                                          Submodules
                                                                          -element[source]
                                                                          +element[source]

                                                                          Element for this object

                                                                          Type:
                                                                          @@ -476,7 +476,7 @@

                                                                          Submodules
                                                                          -potential[source]
                                                                          +potential[source]

                                                                          The potential for this object

                                                                          Type:
                                                                          @@ -487,7 +487,7 @@

                                                                          Submodules
                                                                          -name[source]
                                                                          +name[source]

                                                                          Name of the object

                                                                          Type:
                                                                          @@ -498,7 +498,7 @@

                                                                          Submodules
                                                                          -alias_names[source]
                                                                          +alias_names[source]

                                                                          Optional aliases

                                                                          Type:
                                                                          @@ -509,7 +509,7 @@

                                                                          Submodules
                                                                          -filename[source]
                                                                          +filename[source]

                                                                          Name of the file containing this object

                                                                          Type:
                                                                          @@ -520,7 +520,7 @@

                                                                          Submodules
                                                                          -version[source]
                                                                          +version[source]

                                                                          Version

                                                                          Type:
                                                                          @@ -531,49 +531,49 @@

                                                                          Submodules
                                                                          -alias_names: list[source]
                                                                          +alias_names: list[source]

                                                                          -element: Element | None = None[source]
                                                                          +element: Element | None = None[source]
                                                                          -filename: str | None = None[source]
                                                                          +filename: str | None = None[source]
                                                                          -get_hash() → str[source]
                                                                          +get_hash() → str[source]

                                                                          Get a hash of this object.

                                                                          -get_str() → str[source]
                                                                          +get_str() → str[source]

                                                                          Get string representation.

                                                                          -info: BasisInfo | PotentialInfo | None = None[source]
                                                                          +info: BasisInfo | PotentialInfo | None = None[source]
                                                                          -name: str | None = None[source]
                                                                          +name: str | None = None[source]
                                                                          -potential: Literal['All Electron', 'Pseudopotential'] | None = None[source]
                                                                          +potential: Literal['All Electron', 'Pseudopotential'] | None = None[source]
                                                                          -softmatch(other)[source]
                                                                          +softmatch(other)[source]

                                                                          Soft matching to see if a desired basis/potential matches requirements.

                                                                          Does soft matching on the “info” attribute first. Then soft matches against the element and name/aliases.

                                                                          @@ -581,14 +581,14 @@

                                                                          Submodules
                                                                          -version: str | None = None[source]
                                                                          +version: str | None = None[source]

                                                                          -class BandStructure(kpoint_sets: Sequence[KpointSet], filename: str = 'BAND.bs', added_mos: int = -1, keywords: dict | None = None, subsections: dict | None = None)[source]
                                                                          +class BandStructure(kpoint_sets: Sequence[KpointSet], filename: str = 'BAND.bs', added_mos: int = -1, keywords: dict | None = None, subsections: dict | None = None)[source]

                                                                          Bases: Section

                                                                          Specify high symmetry paths for outputting the band structure in CP2K.

                                                                          @@ -604,7 +604,7 @@

                                                                          Submodules
                                                                          -classmethod from_kpoints(kpoints: VaspKpoints, kpoints_line_density: int = 20) → Self[source]
                                                                          +classmethod from_kpoints(kpoints: VaspKpoints, kpoints_line_density: int = 20) → Self[source]

                                                                          Initialize band structure section from a line-mode Kpoint object.

                                                                          Parameters:
                                                                          @@ -620,7 +620,7 @@

                                                                          Submodules
                                                                          -class Band_Structure(*args, **kwargs)[source]
                                                                          +class Band_Structure(*args, **kwargs)[source]

                                                                          Bases: BandStructure

                                                                          Parameters:
                                                                          @@ -637,12 +637,12 @@

                                                                          Submodules
                                                                          -class BasisFile(objects: Sequence | None = None)[source]
                                                                          +class BasisFile(objects: Sequence | None = None)[source]

                                                                          Bases: DataFile

                                                                          Data file for basis sets only.

                                                                          -classmethod from_str(string: str) → Self[source]
                                                                          +classmethod from_str(string: str) → Self[source]

                                                                          Initialize from a string representation.

                                                                          @@ -650,12 +650,12 @@

                                                                          Submodules
                                                                          -class BasisInfo(electrons: int | None = None, core: int | None = None, valence: int | None = None, polarization: int | None = None, diffuse: int | None = None, cc: bool | None = False, pc: bool | None = False, sr: bool | None = False, molopt: bool | None = False, admm: bool | None = False, lri: bool | None = False, contracted: bool | None = None, xc: str | None = None)[source]
                                                                          +class BasisInfo(electrons: int | None = None, core: int | None = None, valence: int | None = None, polarization: int | None = None, diffuse: int | None = None, cc: bool | None = False, pc: bool | None = False, sr: bool | None = False, molopt: bool | None = False, admm: bool | None = False, lri: bool | None = False, contracted: bool | None = None, xc: str | None = None)[source]

                                                                          Bases: MSONable

                                                                          Summary info about a basis set.

                                                                          -electrons[source]
                                                                          +electrons[source]

                                                                          Number of electrons

                                                                          Type:
                                                                          @@ -666,7 +666,7 @@

                                                                          Submodules
                                                                          -core[source]
                                                                          +core[source]

                                                                          Number of basis functions per core electron

                                                                          Type:
                                                                          @@ -677,7 +677,7 @@

                                                                          Submodules
                                                                          -valence[source]
                                                                          +valence[source]

                                                                          Number of basis functions per valence electron OR number of exp if it is a FIT formatted admm basis

                                                                          @@ -689,7 +689,7 @@

                                                                          Submodules
                                                                          -polarization[source]
                                                                          +polarization[source]

                                                                          Number of polarization functions

                                                                          Type:
                                                                          @@ -700,7 +700,7 @@

                                                                          Submodules
                                                                          -diffuse[source]
                                                                          +diffuse[source]

                                                                          Number of added, diffuse/augmentation functions

                                                                          Type:
                                                                          @@ -711,7 +711,7 @@

                                                                          Submodules
                                                                          -cc[source]
                                                                          +cc[source]

                                                                          Correlation consistent

                                                                          Type:
                                                                          @@ -722,7 +722,7 @@

                                                                          Submodules
                                                                          -pc[source]
                                                                          +pc[source]

                                                                          Polarization consistent

                                                                          Type:
                                                                          @@ -733,7 +733,7 @@

                                                                          Submodules
                                                                          -sr[source]
                                                                          +sr[source]

                                                                          Short-range optimized

                                                                          Type:
                                                                          @@ -744,7 +744,7 @@

                                                                          Submodules
                                                                          -molopt[source]
                                                                          +molopt[source]

                                                                          Optimized for molecules/solids

                                                                          Type:
                                                                          @@ -755,7 +755,7 @@

                                                                          Submodules
                                                                          -admm[source]
                                                                          +admm[source]

                                                                          Whether this is an auxiliary basis set for ADMM

                                                                          Type:
                                                                          @@ -766,7 +766,7 @@

                                                                          Submodules
                                                                          -lri[source]
                                                                          +lri[source]

                                                                          Whether this is a local resolution of identity auxiliary basis

                                                                          Type:
                                                                          @@ -777,7 +777,7 @@

                                                                          Submodules
                                                                          -contracted[source]
                                                                          +contracted[source]

                                                                          Whether this basis set is contracted

                                                                          Type:
                                                                          @@ -788,7 +788,7 @@

                                                                          Submodules
                                                                          -xc[source]
                                                                          +xc[source]

                                                                          Exchange correlation functional used for creating this potential

                                                                          Type:
                                                                          @@ -799,87 +799,87 @@

                                                                          Submodules
                                                                          -admm: bool | None = False[source]
                                                                          +admm: bool | None = False[source]

                                                                          -cc: bool | None = False[source]
                                                                          +cc: bool | None = False[source]
                                                                          -contracted: bool | None = None[source]
                                                                          +contracted: bool | None = None[source]
                                                                          -core: int | None = None[source]
                                                                          +core: int | None = None[source]
                                                                          -diffuse: int | None = None[source]
                                                                          +diffuse: int | None = None[source]
                                                                          -electrons: int | None = None[source]
                                                                          +electrons: int | None = None[source]
                                                                          -classmethod from_str(string: str) → Self[source]
                                                                          +classmethod from_str(string: str) → Self[source]

                                                                          Get summary info from a string.

                                                                          -lri: bool | None = False[source]
                                                                          +lri: bool | None = False[source]
                                                                          -molopt: bool | None = False[source]
                                                                          +molopt: bool | None = False[source]
                                                                          -pc: bool | None = False[source]
                                                                          +pc: bool | None = False[source]
                                                                          -polarization: int | None = None[source]
                                                                          +polarization: int | None = None[source]
                                                                          -softmatch(other)[source]
                                                                          +softmatch(other)[source]

                                                                          Soft matching to see if two basis sets match.

                                                                          Will only match those attributes which are defined for this basis info object (one way checking)

                                                                          -sr: bool | None = False[source]
                                                                          +sr: bool | None = False[source]
                                                                          -valence: int | None = None[source]
                                                                          +valence: int | None = None[source]
                                                                          -xc: str | None = None[source]
                                                                          +xc: str | None = None[source]

                                                                          -class BrokenSymmetry(l_alpha: Sequence = (-1,), n_alpha: Sequence = (0,), nel_alpha: Sequence = (-1,), l_beta: Sequence = (-1,), n_beta: Sequence = (0,), nel_beta: Sequence = (-1,))[source]
                                                                          +class BrokenSymmetry(l_alpha: Sequence = (-1,), n_alpha: Sequence = (0,), nel_alpha: Sequence = (-1,), l_beta: Sequence = (-1,), n_beta: Sequence = (0,), nel_beta: Sequence = (-1,))[source]

                                                                          Bases: Section

                                                                          Define the required atomic orbital occupation assigned in initialization of the density matrix, by adding or subtracting electrons from specific @@ -901,7 +901,7 @@

                                                                          Submodules
                                                                          -classmethod from_el(el: Element, oxi_state: int = 0, spin: int = 0) → Self[source]
                                                                          +classmethod from_el(el: Element, oxi_state: int = 0, spin: int = 0) → Self[source]

                                                                          Create section from element, oxidation state, and spin.

                                                                          @@ -909,7 +909,7 @@

                                                                          Submodules
                                                                          -class Cell(lattice: Lattice, keywords: dict | None = None, **kwargs)[source]
                                                                          +class Cell(lattice: Lattice, keywords: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls the cell/lattice parameters for the simulation.

                                                                          Initialize the cell section.

                                                                          @@ -925,7 +925,7 @@

                                                                          Submodules
                                                                          -class Coord(structure: Structure | Molecule, aliases: dict | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class Coord(structure: Structure | Molecule, aliases: dict | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Specify the coordinates of the atoms using a pymatgen structure object.

                                                                          @@ -943,7 +943,7 @@

                                                                          Submodules
                                                                          -class Cp2kInput(name: str = 'CP2K_INPUT', subsections: dict | None = None, **kwargs)[source]
                                                                          +class Cp2kInput(name: str = 'CP2K_INPUT', subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Special instance of ‘Section’ class that is meant to represent the overall cp2k input. Distinguishes itself from Section by overriding get_str() to not print this section’s @@ -951,31 +951,31 @@

                                                                          Submodules
                                                                          -classmethod from_file(filename: str | Path) → Self[source]
                                                                          +classmethod from_file(filename: str | Path) → Self[source]

                                                                          Initialize from a file.

                                                                          -classmethod from_lines(lines: list | tuple) → Self[source]
                                                                          +classmethod from_lines(lines: list | tuple) → Self[source]

                                                                          Helper method to read lines of file.

                                                                          -classmethod from_str(s: str) → Self[source]
                                                                          +classmethod from_str(s: str) → Self[source]

                                                                          Initialize from a string.

                                                                          -get_str()[source]
                                                                          +get_str()[source]

                                                                          Get string representation of the Cp2kInput.

                                                                          -write_file(input_filename: str = 'cp2k.inp', output_dir: str = '.', make_dir_if_not_present: bool = True)[source]
                                                                          +write_file(input_filename: str = 'cp2k.inp', output_dir: str = '.', make_dir_if_not_present: bool = True)[source]

                                                                          Write input to a file.

                                                                          Parameters:
                                                                          @@ -992,7 +992,7 @@

                                                                          Submodules
                                                                          -class DOS(ndigits: int = 6, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class DOS(ndigits: int = 6, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls printing of the density of states.

                                                                          Initialize the DOS section.

                                                                          @@ -1010,35 +1010,35 @@

                                                                          Submodules
                                                                          -class DataFile(objects: Sequence | None = None)[source]
                                                                          +class DataFile(objects: Sequence | None = None)[source]

                                                                          Bases: MSONable

                                                                          A data file for a cp2k calc.

                                                                          -classmethod from_file(filename) → Self[source]
                                                                          +classmethod from_file(filename) → Self[source]

                                                                          Load from a file, reserved for child classes.

                                                                          -abstract classmethod from_str(string: str) → None[source]
                                                                          +abstract classmethod from_str(string: str) → None[source]

                                                                          Initialize from a string.

                                                                          -get_str() → str[source]
                                                                          +get_str() → str[source]

                                                                          Get string representation.

                                                                          -objects: Sequence | None = None[source]
                                                                          +objects: Sequence | None = None[source]
                                                                          -write_file(filename)[source]
                                                                          +write_file(filename)[source]

                                                                          Write to a file.

                                                                          @@ -1046,7 +1046,7 @@

                                                                          Submodules
                                                                          -class Davidson(new_prec_each: int = 20, preconditioner: str = 'FULL_SINGLE_INVERSE', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class Davidson(new_prec_each: int = 20, preconditioner: str = 'FULL_SINGLE_INVERSE', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Parameters for davidson diagonalization.

                                                                          @@ -1082,7 +1082,7 @@

                                                                          Submodules
                                                                          -class Dft(basis_set_filenames: Iterable = ('BASIS_MOLOPT',), potential_filename='GTH_POTENTIALS', uks: bool = True, wfn_restart_file_name: str | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class Dft(basis_set_filenames: Iterable = ('BASIS_MOLOPT',), potential_filename='GTH_POTENTIALS', uks: bool = True, wfn_restart_file_name: str | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls the DFT parameters in Cp2k.

                                                                          Initialize the DFT section.

                                                                          @@ -1105,7 +1105,7 @@

                                                                          Submodules
                                                                          -class DftPlusU(eps_u_ramping=1e-05, init_u_ramping_each_scf=False, l=-1, u_minus_j=0, u_ramping=0, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class DftPlusU(eps_u_ramping=1e-05, init_u_ramping_each_scf=False, l=-1, u_minus_j=0, u_ramping=0, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls DFT+U for an atom kind.

                                                                          Initialize the DftPlusU section.

                                                                          @@ -1126,7 +1126,7 @@

                                                                          Submodules
                                                                          -class Diagonalization(eps_adapt: float = 0, eps_iter: float = 1e-08, eps_jacobi: float = 0, jacobi_threshold: float = 1e-07, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class Diagonalization(eps_adapt: float = 0, eps_iter: float = 1e-08, eps_jacobi: float = 0, jacobi_threshold: float = 1e-07, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls diagonalization settings (if using traditional diagonalization).

                                                                          Initialize the diagonalization section.

                                                                          @@ -1134,7 +1134,7 @@

                                                                          Submodules
                                                                          -class EDensityCube(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class EDensityCube(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls printing of the electron density cube file.

                                                                          Basic object representing a CP2K Section. Sections activate different parts of the @@ -1177,7 +1177,7 @@

                                                                          Submodules
                                                                          -class E_Density_Cube(*args, **kwargs)[source]
                                                                          +class E_Density_Cube(*args, **kwargs)[source]

                                                                          Bases: EDensityCube

                                                                          Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate @@ -1219,7 +1219,7 @@

                                                                          Submodules
                                                                          -class ForceEval(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class ForceEval(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls the calculation of energy and forces in Cp2k.

                                                                          Initialize the ForceEval section.

                                                                          @@ -1227,12 +1227,12 @@

                                                                          Submodules
                                                                          -class GaussianTypeOrbitalBasisSet(info: BasisInfo | None = None, element: Element | None = None, potential: Literal['All Electron', 'Pseudopotential'] | None = None, name: str | None = None, alias_names: list = <factory>, filename: str | None = None, version: str | None = None, nset: int | None = None, n: list[int] | None = None, lmax: list[int] | None = None, lmin: list[int] | None = None, nshell: list[dict[int, int]] | None = None, exponents: list[list[float]] | None = None, coefficients: list[dict[int, dict[int, dict[int, float]]]] | None = None)[source]
                                                                          +class GaussianTypeOrbitalBasisSet(info: BasisInfo | None = None, element: Element | None = None, potential: Literal['All Electron', 'Pseudopotential'] | None = None, name: str | None = None, alias_names: list = <factory>, filename: str | None = None, version: str | None = None, nset: int | None = None, n: list[int] | None = None, lmax: list[int] | None = None, lmin: list[int] | None = None, nshell: list[dict[int, int]] | None = None, exponents: list[list[float]] | None = None, coefficients: list[dict[int, dict[int, dict[int, float]]]] | None = None)[source]

                                                                          Bases: AtomicMetadata

                                                                          Model definition of a GTO basis set.

                                                                          -info[source]
                                                                          +info[source]

                                                                          Cardinality of this basis

                                                                          Type:
                                                                          @@ -1243,7 +1243,7 @@

                                                                          Submodules
                                                                          -nset[source]
                                                                          +nset[source]

                                                                          Number of exponent sets

                                                                          Type:
                                                                          @@ -1254,7 +1254,7 @@

                                                                          Submodules
                                                                          -n[source]
                                                                          +n[source]

                                                                          Principle quantum number for each set

                                                                          Type:
                                                                          @@ -1265,7 +1265,7 @@

                                                                          Submodules
                                                                          -lmax[source]
                                                                          +lmax[source]

                                                                          Maximum angular momentum quantum number for each set

                                                                          Type:
                                                                          @@ -1276,7 +1276,7 @@

                                                                          Submodules
                                                                          -lmin[source]
                                                                          +lmin[source]

                                                                          Minimum angular momentum quantum number for each set

                                                                          Type:
                                                                          @@ -1287,7 +1287,7 @@

                                                                          Submodules
                                                                          -nshell[source]
                                                                          +nshell[source]

                                                                          Number of shells for angular momentum l for each set

                                                                          Type:
                                                                          @@ -1298,7 +1298,7 @@

                                                                          Submodules
                                                                          -exponents[source]
                                                                          +exponents[source]

                                                                          Exponents for each set

                                                                          Type:
                                                                          @@ -1309,7 +1309,7 @@

                                                                          Submodules
                                                                          -coefficients[source]
                                                                          +coefficients[source]

                                                                          Contraction coefficients for each set. Dict[exp->l->shell]

                                                                          Type:
                                                                          @@ -1320,73 +1320,73 @@

                                                                          Submodules
                                                                          -coefficients: list[dict[int, dict[int, dict[int, float]]]] | None = None[source]
                                                                          +coefficients: list[dict[int, dict[int, dict[int, float]]]] | None = None[source]

                                                                          -exponents: list[list[float]] | None = None[source]
                                                                          +exponents: list[list[float]] | None = None[source]
                                                                          -classmethod from_str(string: str) → Self[source]
                                                                          +classmethod from_str(string: str) → Self[source]

                                                                          Read from standard cp2k GTO formatted string.

                                                                          -get_keyword() → Keyword[source]
                                                                          +get_keyword() → Keyword[source]

                                                                          Convert basis to keyword object.

                                                                          -get_str() → str[source]
                                                                          +get_str() → str[source]

                                                                          Get standard cp2k GTO formatted string.

                                                                          -info: BasisInfo | None = None[source]
                                                                          +info: BasisInfo | None = None[source]
                                                                          -lmax: list[int] | None = None[source]
                                                                          +lmax: list[int] | None = None[source]
                                                                          -lmin: list[int] | None = None[source]
                                                                          +lmin: list[int] | None = None[source]
                                                                          -n: list[int] | None = None[source]
                                                                          +n: list[int] | None = None[source]
                                                                          -property nexp[source]
                                                                          +property nexp[source]

                                                                          Number of exponents.

                                                                          -nset: int | None = None[source]
                                                                          +nset: int | None = None[source]
                                                                          -nshell: list[dict[int, int]] | None = None[source]
                                                                          +nshell: list[dict[int, int]] | None = None[source]

                                                                          -class Global(project_name: str = 'CP2K', run_type: str = 'ENERGY_FORCE', keywords: dict | None = None, **kwargs)[source]
                                                                          +class Global(project_name: str = 'CP2K', run_type: str = 'ENERGY_FORCE', keywords: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls ‘global’ settings for cp2k execution such as RUN_TYPE and PROJECT_NAME.

                                                                          Initialize the global section.

                                                                          @@ -1403,12 +1403,12 @@

                                                                          Submodules
                                                                          -class GthPotential(info: PotentialInfo = None, element: Element | None = None, potential: Literal['All Electron', 'Pseudopotential'] | None = None, name: str | None = None, alias_names: list = <factory>, filename: str | None = None, version: str | None = None, n_elecs: dict[int, int] | None = None, r_loc: float | None = None, nexp_ppl: int | None = None, c_exp_ppl: Sequence | None = None, radii: dict[int, float] | None = None, nprj: int | None = None, nprj_ppnl: dict[int, int] | None = None, hprj_ppnl: dict[int, dict[int, dict[int, float]]] | None = None)[source]
                                                                          +class GthPotential(info: PotentialInfo = None, element: Element | None = None, potential: Literal['All Electron', 'Pseudopotential'] | None = None, name: str | None = None, alias_names: list = <factory>, filename: str | None = None, version: str | None = None, n_elecs: dict[int, int] | None = None, r_loc: float | None = None, nexp_ppl: int | None = None, c_exp_ppl: Sequence | None = None, radii: dict[int, float] | None = None, nprj: int | None = None, nprj_ppnl: dict[int, int] | None = None, hprj_ppnl: dict[int, dict[int, dict[int, float]]] | None = None)[source]

                                                                          Bases: AtomicMetadata

                                                                          Representation of GTH-type (pseudo)potential.

                                                                          -info[source]
                                                                          +info[source]

                                                                          Info about this potential

                                                                          Type:
                                                                          @@ -1419,7 +1419,7 @@

                                                                          Submodules
                                                                          -n_elecs[source]
                                                                          +n_elecs[source]

                                                                          Number of electrons for each quantum number

                                                                          Type:
                                                                          @@ -1430,7 +1430,7 @@

                                                                          Submodules
                                                                          -r_loc[source]
                                                                          +r_loc[source]

                                                                          Radius of local projectors

                                                                          Type:
                                                                          @@ -1441,7 +1441,7 @@

                                                                          Submodules
                                                                          -nexp_ppl[source]
                                                                          +nexp_ppl[source]

                                                                          Number of the local pseudopotential functions

                                                                          Type:
                                                                          @@ -1452,7 +1452,7 @@

                                                                          Submodules
                                                                          -c_exp_ppl[source]
                                                                          +c_exp_ppl[source]

                                                                          Sequence = field(None, description=”Coefficients of the local pseudopotential functions

                                                                          Type:
                                                                          @@ -1463,7 +1463,7 @@

                                                                          Submodules
                                                                          -radii[source]
                                                                          +radii[source]

                                                                          Radius of the nonlocal part for angular momentum quantum number l defined by the Gaussian function exponents alpha_prj_ppnl

                                                                          @@ -1475,7 +1475,7 @@

                                                                          Submodules
                                                                          -nprj[source]
                                                                          +nprj[source]

                                                                          Number of projectors

                                                                          Type:
                                                                          @@ -1486,7 +1486,7 @@

                                                                          Submodules
                                                                          -nprj_ppnl[source]
                                                                          +nprj_ppnl[source]

                                                                          Number of the non-local projectors for the angular momentum quantum number

                                                                          Type:
                                                                          @@ -1497,7 +1497,7 @@

                                                                          Submodules
                                                                          -hprj_ppnl[source]
                                                                          +hprj_ppnl[source]

                                                                          Coefficients of the non-local projector functions. Coeff ij for ang momentum l

                                                                          Type:
                                                                          @@ -1513,79 +1513,79 @@

                                                                          Submodules
                                                                          -c_exp_ppl: Sequence | None = None[source]
                                                                          +c_exp_ppl: Sequence | None = None[source]

                                                                          -classmethod from_section(section: Section) → Self[source]
                                                                          +classmethod from_section(section: Section) → Self[source]

                                                                          Extract GTH-formatted string from a section and convert it to model.

                                                                          -classmethod from_str(string: str) → Self[source]
                                                                          +classmethod from_str(string: str) → Self[source]

                                                                          Initialize model from a GTH formatted string.

                                                                          -get_keyword() → Keyword[source]
                                                                          +get_keyword() → Keyword[source]

                                                                          Get keyword object for the potential.

                                                                          -get_section() → Section[source]
                                                                          +get_section() → Section[source]

                                                                          Convert model to a GTH-formatted section object for input files.

                                                                          -get_str() → str[source]
                                                                          +get_str() → str[source]

                                                                          Convert model to a GTH-formatted string.

                                                                          -hprj_ppnl: dict[int, dict[int, dict[int, float]]] | None = None[source]
                                                                          +hprj_ppnl: dict[int, dict[int, dict[int, float]]] | None = None[source]
                                                                          -n_elecs: dict[int, int] | None = None[source]
                                                                          +n_elecs: dict[int, int] | None = None[source]
                                                                          -nexp_ppl: int | None = None[source]
                                                                          +nexp_ppl: int | None = None[source]
                                                                          -nprj: int | None = None[source]
                                                                          +nprj: int | None = None[source]
                                                                          -nprj_ppnl: dict[int, int] | None = None[source]
                                                                          +nprj_ppnl: dict[int, int] | None = None[source]
                                                                          -r_loc: float | None = None[source]
                                                                          +r_loc: float | None = None[source]
                                                                          -radii: dict[int, float] | None = None[source]
                                                                          +radii: dict[int, float] | None = None[source]

                                                                          -class Keyword(name: str, *values, description: str | None = None, units: str | None = None, verbose: bool | None = True, repeats: bool | None = False)[source]
                                                                          +class Keyword(name: str, *values, description: str | None = None, units: str | None = None, verbose: bool | None = True, repeats: bool | None = False)[source]

                                                                          Bases: MSONable

                                                                          A keyword argument in CP2K. Within CP2K Sections, which activate features of the CP2K code, the keywords are arguments that control the functionality of that feature. @@ -1613,19 +1613,19 @@

                                                                          Submodules
                                                                          -as_dict()[source]
                                                                          +as_dict()[source]

                                                                          Get a dictionary representation of the Keyword.

                                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                                          +classmethod from_dict(dct: dict) → Self[source]

                                                                          Initialize from dictionary.

                                                                          -classmethod from_str(s: str) → Self[source]
                                                                          +classmethod from_str(s: str) → Self[source]

                                                                          Initialize from a string.

                                                                          Keywords must be labeled with strings. If the post-processor finds that the keywords is a number, then None is return (used by @@ -1639,13 +1639,13 @@

                                                                          Submodules
                                                                          -get_str() → str[source]
                                                                          +get_str() → str[source]

                                                                          String representation of Keyword.

                                                                          -verbosity(v)[source]
                                                                          +verbosity(v)[source]

                                                                          Change the printing of this keyword’s description.

                                                                          @@ -1653,7 +1653,7 @@

                                                                          Submodules
                                                                          -class KeywordList(keywords: Sequence[Keyword])[source]
                                                                          +class KeywordList(keywords: Sequence[Keyword])[source]

                                                                          Bases: MSONable

                                                                          Some keywords can be repeated, which makes accessing them via the normal dictionary methods a little unnatural. This class deals with this by defining a collection @@ -1666,25 +1666,25 @@

                                                                          Submodules
                                                                          -append(item)[source]
                                                                          +append(item)[source]

                                                                          Append the keyword list.

                                                                          -extend(lst: Sequence[Keyword]) → None[source]
                                                                          +extend(lst: Sequence[Keyword]) → None[source]

                                                                          Extend the keyword list.

                                                                          -get_str(indent: int = 0) → str[source]
                                                                          +get_str(indent: int = 0) → str[source]

                                                                          String representation of Keyword.

                                                                          -verbosity(verbosity)[source]
                                                                          +verbosity(verbosity)[source]

                                                                          Silence all keywords in keyword list.

                                                                          @@ -1692,7 +1692,7 @@

                                                                          Submodules
                                                                          -class Kind(specie: str, alias: str | None = None, magnetization: float = 0.0, basis_set: GaussianTypeOrbitalBasisSet | str | None = 'GTH_BASIS', potential: GthPotential | str | None = 'GTH_POTENTIALS', ghost: bool = False, aux_basis: GaussianTypeOrbitalBasisSet | str | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class Kind(specie: str, alias: str | None = None, magnetization: float = 0.0, basis_set: GaussianTypeOrbitalBasisSet | str | None = 'GTH_BASIS', potential: GthPotential | str | None = 'GTH_POTENTIALS', ghost: bool = False, aux_basis: GaussianTypeOrbitalBasisSet | str | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Specify the information for the different atom types being simulated.

                                                                          Initialize a KIND section.

                                                                          @@ -1722,7 +1722,7 @@

                                                                          Submodules
                                                                          -class KpointSet(npoints: int, kpoints: Iterable, units: str = 'B_VECTOR')[source]
                                                                          +class KpointSet(npoints: int, kpoints: Iterable, units: str = 'B_VECTOR')[source]

                                                                          Bases: Section

                                                                          Specify a kpoint line to be calculated between special points.

                                                                          @@ -1744,7 +1744,7 @@

                                                                          Submodules
                                                                          -class Kpoint_Set(*args, **kwargs)[source]
                                                                          +class Kpoint_Set(*args, **kwargs)[source]

                                                                          Bases: KpointSet

                                                                          Parameters:
                                                                          @@ -1765,7 +1765,7 @@

                                                                          Submodules
                                                                          -class Kpoints(kpts: Sequence | Sequence[Sequence[int]], weights: Sequence | None = None, eps_geo: float = 1e-06, full_grid: bool = False, parallel_group_size: int = -1, scheme: str = 'MONKHORST-PACK', symmetry: bool = False, units: str = 'B_VECTOR', verbose: bool = False, wavefunctions: str = 'COMPLEX')[source]
                                                                          +class Kpoints(kpts: Sequence | Sequence[Sequence[int]], weights: Sequence | None = None, eps_geo: float = 1e-06, full_grid: bool = False, parallel_group_size: int = -1, scheme: str = 'MONKHORST-PACK', symmetry: bool = False, units: str = 'B_VECTOR', verbose: bool = False, wavefunctions: str = 'COMPLEX')[source]

                                                                          Bases: Section

                                                                          Description of the k-points to use for the calculation.

                                                                          @@ -1799,7 +1799,7 @@

                                                                          Submodules
                                                                          -classmethod from_kpoints(kpoints: VaspKpoints, structure=None) → Self[source]
                                                                          +classmethod from_kpoints(kpoints: VaspKpoints, structure=None) → Self[source]

                                                                          Initialize the section from a Kpoints object (pymatgen.io.vasp.inputs). CP2K does not have an automatic gamma-point constructor, so this is generally used to get the number of divisions from a kpoint static constructor and then @@ -1822,7 +1822,7 @@

                                                                          Submodules
                                                                          -class LDOS(index: int = 1, alias: str | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class LDOS(index: int = 1, alias: str | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls printing of the LDOS (List-Density of states). i.e. projects onto specific atoms.

                                                                          Initialize the LDOS section.

                                                                          @@ -1840,7 +1840,7 @@

                                                                          Submodules
                                                                          -class MOCubes(write_cube: bool = False, nhomo: int = 1, nlumo: int = 1, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class MOCubes(write_cube: bool = False, nhomo: int = 1, nlumo: int = 1, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls printing of the molecular orbital eigenvalues.

                                                                          Initialize the MO_CUBES section.

                                                                          @@ -1848,14 +1848,14 @@

                                                                          Submodules
                                                                          -class MO_Cubes(*args, **kwargs)[source]
                                                                          +class MO_Cubes(*args, **kwargs)[source]

                                                                          Bases: MOCubes

                                                                          Initialize the MO_CUBES section.

                                                                          -class Mgrid(cutoff: float = 1200, rel_cutoff: float = 80, ngrids: int = 5, progression_factor: int = 3, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class Mgrid(cutoff: float = 1200, rel_cutoff: float = 80, ngrids: int = 5, progression_factor: int = 3, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls the multigrid for numerical integration.

                                                                          Initialize the MGRID section.

                                                                          @@ -1879,7 +1879,7 @@

                                                                          Submodules
                                                                          -class OrbitalTransformation(minimizer: str = 'CG', preconditioner: str = 'FULL_ALL', algorithm: str = 'STRICT', rotation: bool = False, occupation_preconditioner: bool = False, energy_gap: float = -1, linesearch: str = '2PNT', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class OrbitalTransformation(minimizer: str = 'CG', preconditioner: str = 'FULL_ALL', algorithm: str = 'STRICT', rotation: bool = False, occupation_preconditioner: bool = False, energy_gap: float = -1, linesearch: str = '2PNT', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Turns on the Orbital Transformation scheme for diagonalizing the Hamiltonian. Often faster and with guaranteed convergence compared to normal diagonalization, but requires the system @@ -1924,7 +1924,7 @@

                                                                          Submodules
                                                                          -class PBE(parameterization: str = 'ORIG', scale_c: float = 1, scale_x: float = 1, keywords: dict | None = None, subsections: dict | None = None)[source]
                                                                          +class PBE(parameterization: str = 'ORIG', scale_c: float = 1, scale_x: float = 1, keywords: dict | None = None, subsections: dict | None = None)[source]

                                                                          Bases: Section

                                                                          Info about the PBE functional.

                                                                          @@ -1944,7 +1944,7 @@

                                                                          Submodules
                                                                          -class PDOS(nlumo: int = -1, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class PDOS(nlumo: int = -1, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls printing of projected density of states onto the different atom KINDS (elemental decomposed DOS).

                                                                          @@ -1962,12 +1962,12 @@

                                                                          Submodules
                                                                          -class PotentialFile(objects: Sequence | None = None)[source]
                                                                          +class PotentialFile(objects: Sequence | None = None)[source]

                                                                          Bases: DataFile

                                                                          Data file for potentials only.

                                                                          -classmethod from_str(string: str) → Self[source]
                                                                          +classmethod from_str(string: str) → Self[source]

                                                                          Initialize from a string representation.

                                                                          @@ -1975,12 +1975,12 @@

                                                                          Submodules
                                                                          -class PotentialInfo(electrons: int | None = None, potential_type: str | None = None, nlcc: bool | None = None, xc: str | None = None)[source]
                                                                          +class PotentialInfo(electrons: int | None = None, potential_type: str | None = None, nlcc: bool | None = None, xc: str | None = None)[source]

                                                                          Bases: MSONable

                                                                          Metadata for this potential.

                                                                          -electrons[source]
                                                                          +electrons[source]

                                                                          Total number of electrons

                                                                          Type:
                                                                          @@ -1991,7 +1991,7 @@

                                                                          Submodules
                                                                          -potential_type[source]
                                                                          +potential_type[source]

                                                                          Potential type (e.g. GTH)

                                                                          Type:
                                                                          @@ -2002,7 +2002,7 @@

                                                                          Submodules
                                                                          -nlcc[source]
                                                                          +nlcc[source]

                                                                          Nonlinear core corrected potential

                                                                          Type:
                                                                          @@ -2013,7 +2013,7 @@

                                                                          Submodules
                                                                          -xc[source]
                                                                          +xc[source]

                                                                          Exchange correlation functional used for creating this potential

                                                                          Type:
                                                                          @@ -2024,42 +2024,42 @@

                                                                          Submodules
                                                                          -electrons: int | None = None[source]
                                                                          +electrons: int | None = None[source]

                                                                          -classmethod from_str(string: str) → Self[source]
                                                                          +classmethod from_str(string: str) → Self[source]

                                                                          Get a cp2k formatted string representation.

                                                                          -nlcc: bool | None = None[source]
                                                                          +nlcc: bool | None = None[source]
                                                                          -potential_type: str | None = None[source]
                                                                          +potential_type: str | None = None[source]
                                                                          -softmatch(other)[source]
                                                                          +softmatch(other)[source]

                                                                          Soft matching to see if two potentials match.

                                                                          Will only match those attributes which are defined for this basis info object (one way checking)

                                                                          -xc: str | None = None[source]
                                                                          +xc: str | None = None[source]

                                                                          -class QS(method: str = 'GPW', eps_default: float = 1e-10, eps_pgf_orb: float | None = None, extrapolation: str = 'ASPC', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class QS(method: str = 'GPW', eps_default: float = 1e-10, eps_pgf_orb: float | None = None, extrapolation: str = 'ASPC', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls the quickstep settings (DFT driver).

                                                                          Initialize the QS Section.

                                                                          @@ -2086,7 +2086,7 @@

                                                                          Submodules
                                                                          -class Scf(max_scf: int = 50, eps_scf: float = 1e-06, scf_guess: str = 'RESTART', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class Scf(max_scf: int = 50, eps_scf: float = 1e-06, scf_guess: str = 'RESTART', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls the self consistent field loop.

                                                                          Initialize the Scf section.

                                                                          @@ -2120,7 +2120,7 @@

                                                                          Submodules
                                                                          -class Section(name: str, subsections: dict | None = None, repeats: bool = False, description: str | None = None, keywords: dict | None = None, section_parameters: list | tuple | None = None, location: str | None = None, verbose: bool | None = True, alias: str | None = None, **kwargs)[source]
                                                                          +class Section(name: str, subsections: dict | None = None, repeats: bool = False, description: str | None = None, keywords: dict | None = None, section_parameters: list | tuple | None = None, location: str | None = None, verbose: bool | None = True, alias: str | None = None, **kwargs)[source]

                                                                          Bases: MSONable

                                                                          Basic input representation of input to Cp2k. Activates functionality inside of the Cp2k executable.

                                                                          @@ -2162,13 +2162,13 @@

                                                                          Submodules
                                                                          -add(other)[source]
                                                                          +add(other)[source]

                                                                          Add another keyword to the current section.

                                                                          -by_path(path: str)[source]
                                                                          +by_path(path: str)[source]

                                                                          Access a sub-section using a path. Used by the file parser.

                                                                          Parameters:
                                                                          @@ -2179,7 +2179,7 @@

                                                                          Submodules
                                                                          -check(path: str)[source]
                                                                          +check(path: str)[source]

                                                                          Check if section exists within the current using a path. Can be useful for cross-checking whether or not required dependencies have been satisfied, which CP2K does not enforce.

                                                                          @@ -2191,7 +2191,7 @@

                                                                          Submodules
                                                                          -get(d, default=None)[source]
                                                                          +get(d, default=None)[source]

                                                                          Similar to get for dictionaries. This will attempt to retrieve the section or keyword matching d. Will not raise an error if d does not exist.

                                                                          @@ -2206,7 +2206,7 @@

                                                                          Submodules
                                                                          -get_keyword(d, default=None)[source]
                                                                          +get_keyword(d, default=None)[source]

                                                                          Get function, only for subsections.

                                                                          Parameters:
                                                                          @@ -2220,7 +2220,7 @@

                                                                          Submodules
                                                                          -get_section(d, default=None)[source]
                                                                          +get_section(d, default=None)[source]

                                                                          Get function, only for subsections.

                                                                          Parameters:
                                                                          @@ -2234,37 +2234,37 @@

                                                                          Submodules
                                                                          -get_str() → str[source]
                                                                          +get_str() → str[source]

                                                                          Get string representation of Section.

                                                                          -inc(dct: dict)[source]
                                                                          +inc(dct: dict)[source]

                                                                          Mongo style dict modification. Include.

                                                                          -insert(d)[source]
                                                                          +insert(d)[source]

                                                                          Insert a new section as a subsection of the current one.

                                                                          -safeset(dct: dict)[source]
                                                                          +safeset(dct: dict)[source]

                                                                          Alias for update with strict (no insertions). Used by custodian.

                                                                          -set(dct: dict)[source]
                                                                          +set(dct: dict)[source]

                                                                          Alias for update. Used by custodian.

                                                                          -setitem(key, value, strict=False)[source]
                                                                          +setitem(key, value, strict=False)[source]

                                                                          Helper function for setting items. Kept separate from the double-underscore function so that “strict” option can be made possible.

                                                                          strict will only set values for items that already have a key entry (no insertion).

                                                                          @@ -2272,19 +2272,19 @@

                                                                          Submodules
                                                                          -silence()[source]
                                                                          +silence()[source]

                                                                          Recursively delete all print sections so that only defaults are printed out.

                                                                          -unset(dct: dict)[source]
                                                                          +unset(dct: dict)[source]

                                                                          Dict based deletion. Used by custodian.

                                                                          -update(dct: dict, strict=False)[source]
                                                                          +update(dct: dict, strict=False)[source]

                                                                          Update the Section according to a dictionary argument. This is most useful for providing user-override settings to default parameters. As you pass a dictionary the class variables like “description”, “location”, or “repeats” @@ -2318,7 +2318,7 @@

                                                                          Submodules
                                                                          -verbosity(verbosity: bool) → None[source]
                                                                          +verbosity(verbosity: bool) → None[source]

                                                                          Change the section verbosity recursively by turning on/off the printing of descriptions. Turning off descriptions may reduce the appealing documentation of input files, but also helps de-clutter them.

                                                                          @@ -2328,7 +2328,7 @@

                                                                          Submodules
                                                                          -class SectionList(sections: Sequence[Section])[source]
                                                                          +class SectionList(sections: Sequence[Section])[source]

                                                                          Bases: MSONable

                                                                          Section list.

                                                                          Initialize a SectionList object using a sequence of sections.

                                                                          @@ -2339,32 +2339,32 @@

                                                                          Submodules
                                                                          -append(item) → None[source]
                                                                          +append(item) → None[source]

                                                                          Append the section list.

                                                                          -extend(lst: list) → None[source]
                                                                          +extend(lst: list) → None[source]

                                                                          Extend the section list.

                                                                          -get(d, index=-1)[source]
                                                                          +get(d, index=-1)[source]

                                                                          Get for section list. If index is specified, return the section at that index. Otherwise, return a get on the last section.

                                                                          -get_str() → str[source]
                                                                          +get_str() → str[source]

                                                                          Return string representation of section list.

                                                                          -verbosity(verbosity) → None[source]
                                                                          +verbosity(verbosity) → None[source]

                                                                          Silence all sections in section list.

                                                                          @@ -2372,7 +2372,7 @@

                                                                          Submodules
                                                                          -class Smear(elec_temp: float = 300, method: str = 'FERMI_DIRAC', fixed_magnetic_moment: float = -100.0, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class Smear(elec_temp: float = 300, method: str = 'FERMI_DIRAC', fixed_magnetic_moment: float = -100.0, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Control electron smearing.

                                                                          Basic object representing a CP2K Section. Sections activate different parts of the @@ -2415,7 +2415,7 @@

                                                                          Submodules
                                                                          -class Subsys(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class Subsys(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls the definition of the system to be simulated.

                                                                          Initialize the subsys section.

                                                                          @@ -2423,7 +2423,7 @@

                                                                          Submodules
                                                                          -class VHartreeCube(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class VHartreeCube(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Controls printing of the hartree potential as a cube file.

                                                                          Basic object representing a CP2K Section. Sections activate different parts of the @@ -2466,7 +2466,7 @@

                                                                          Submodules
                                                                          -class V_Hartree_Cube(*args, **kwargs)[source]
                                                                          +class V_Hartree_Cube(*args, **kwargs)[source]

                                                                          Bases: VHartreeCube

                                                                          Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate @@ -2508,7 +2508,7 @@

                                                                          Submodules
                                                                          -class XCFunctional(functionals: Iterable | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
                                                                          +class XCFunctional(functionals: Iterable | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]

                                                                          Bases: Section

                                                                          Info about which XC functional to use.

                                                                          Basic object representing a CP2K Section. Sections activate different parts of the @@ -2551,7 +2551,7 @@

                                                                          Submodules
                                                                          -class Xc_Functional(*args, **kwargs)[source]
                                                                          +class Xc_Functional(*args, **kwargs)[source]

                                                                          Bases: XCFunctional

                                                                          Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate @@ -2598,7 +2598,7 @@

                                                                          Submodules
                                                                          -class Cp2kOutput(filename, verbose=False, auto_load=False)[source]
                                                                          +class Cp2kOutput(filename, verbose=False, auto_load=False)[source]

                                                                          Bases: object

                                                                          Parse output file from CP2K. The CP2K output file is very flexible in the way that it is returned. This class will automatically parse parameters that should always be present, @@ -2617,93 +2617,93 @@

                                                                          Submodules
                                                                          -as_dict()[source]
                                                                          +as_dict()[source]

                                                                          Return dictionary representation of the output.

                                                                          -property band_structure: BandStructure | None[source]
                                                                          +property band_structure: BandStructure | None[source]

                                                                          Band structure object if it has been parsed.

                                                                          -property calculation_type[source]
                                                                          +property calculation_type[source]

                                                                          The calculation type (what io.vasp.outputs calls run_type).

                                                                          -property charge: float[source]
                                                                          +property charge: float[source]

                                                                          Charge from the input file.

                                                                          -property complete_dos: CompleteDos | None[source]
                                                                          +property complete_dos: CompleteDos | None[source]

                                                                          Complete dos object if it has been parsed.

                                                                          -property completed[source]
                                                                          +property completed[source]

                                                                          Did the calculation complete.

                                                                          -convergence()[source]
                                                                          +convergence()[source]

                                                                          Check whether or not the SCF and geometry optimization cycles converged.

                                                                          -property cp2k_version[source]
                                                                          +property cp2k_version[source]

                                                                          The cp2k version used in the calculation.

                                                                          -property is_hubbard: bool[source]
                                                                          +property is_hubbard: bool[source]

                                                                          True if hubbard +U correction was used.

                                                                          -property is_metal: bool[source]
                                                                          +property is_metal: bool[source]

                                                                          Was a band gap found? i.e. is it a metal.

                                                                          -property is_molecule: bool[source]
                                                                          +property is_molecule: bool[source]

                                                                          True if the cp2k output was generated for a molecule (i.e. no periodicity in the cell).

                                                                          -property multiplicity: int[source]
                                                                          +property multiplicity: int[source]

                                                                          The spin multiplicity from input file.

                                                                          -property num_warnings[source]
                                                                          +property num_warnings[source]

                                                                          How many warnings showed up during the run.

                                                                          -parse_atomic_kind_info()[source]
                                                                          +parse_atomic_kind_info()[source]

                                                                          Parse info on what atomic kinds are present and what basis/pseudopotential is describing each of them.

                                                                          -parse_bandstructure(bandstructure_filename=None) → None[source]
                                                                          +parse_bandstructure(bandstructure_filename=None) → None[source]

                                                                          Parse a CP2K bandstructure file.

                                                                          Parameters:
                                                                          @@ -2719,31 +2719,31 @@

                                                                          Submodules
                                                                          -parse_cell_params()[source]
                                                                          +parse_cell_params()[source]

                                                                          Parse the lattice parameters (initial) from the output file.

                                                                          -parse_chi_tensor(chi_filename=None)[source]
                                                                          +parse_chi_tensor(chi_filename=None)[source]

                                                                          Parse the magnetic susceptibility tensor.

                                                                          -parse_cp2k_params()[source]
                                                                          +parse_cp2k_params()[source]

                                                                          Parse the CP2K general parameters from CP2K output file into a dictionary.

                                                                          -parse_dft_params()[source]
                                                                          +parse_dft_params()[source]

                                                                          Parse the DFT parameters (as well as functional, HF, vdW params).

                                                                          -parse_dos(dos_file=None, pdos_files=None, ldos_files=None)[source]
                                                                          +parse_dos(dos_file=None, pdos_files=None, ldos_files=None)[source]

                                                                          Parse the dos files produced by cp2k calculation. CP2K produces different files based on the input file rather than assimilating them all into one file.

                                                                          One file type is the overall DOS file, which is used for k-point calculations. For @@ -2768,7 +2768,7 @@

                                                                          Submodules
                                                                          -parse_energies()[source]
                                                                          +parse_energies()[source]

                                                                          Get the total energy from a CP2K calculation. Presently, the energy reported in the trajectory (pos.xyz) file takes precedence over the energy reported in the main output file. This is because the trajectory file keeps track of energies in between restarts, @@ -2778,69 +2778,69 @@

                                                                          Submodules
                                                                          -parse_files()[source]
                                                                          +parse_files()[source]

                                                                          Identify files present in the directory with the cp2k output file. Looks for trajectories, dos, and cubes.

                                                                          -parse_forces()[source]
                                                                          +parse_forces()[source]

                                                                          Get the forces from the forces file, or from the main output file.

                                                                          -parse_global_params()[source]
                                                                          +parse_global_params()[source]

                                                                          Parse the GLOBAL section parameters from CP2K output file into a dictionary.

                                                                          -parse_gtensor(gtensor_filename=None)[source]
                                                                          +parse_gtensor(gtensor_filename=None)[source]

                                                                          Parse a file containing g tensor.

                                                                          -parse_hirshfeld()[source]
                                                                          +parse_hirshfeld()[source]

                                                                          Parse the hirshfeld population analysis for each step.

                                                                          -parse_homo_lumo()[source]
                                                                          +parse_homo_lumo()[source]

                                                                          Find the HOMO - LUMO gap in [eV]. Returns the last value. For gaps/eigenvalues decomposed by spin up/spin down channel and over many ionic steps, see parse_mo_eigenvalues().

                                                                          -parse_hyperfine(hyperfine_filename=None)[source]
                                                                          +parse_hyperfine(hyperfine_filename=None)[source]

                                                                          Parse a file containing hyperfine coupling tensors for each atomic site.

                                                                          -parse_initial_structure()[source]
                                                                          +parse_initial_structure()[source]

                                                                          Parse the initial structure from the main cp2k output file.

                                                                          -parse_input()[source]
                                                                          +parse_input()[source]

                                                                          Load in the input set from the input file (if it can be found).

                                                                          -parse_ionic_steps()[source]
                                                                          +parse_ionic_steps()[source]

                                                                          Parse the ionic step info. If already parsed, this will just assimilate.

                                                                          -parse_mo_eigenvalues()[source]
                                                                          +parse_mo_eigenvalues()[source]

                                                                          Parse the MO eigenvalues from the cp2k output file. Will get the eigenvalues (and band gap) at each ionic step (if more than one exist).

                                                                          Everything is decomposed by spin channel. If calculation was performed without spin @@ -2850,68 +2850,68 @@

                                                                          Submodules
                                                                          -parse_mulliken()[source]
                                                                          +parse_mulliken()[source]

                                                                          Parse the mulliken population analysis info for each step

                                                                          -parse_nmr_shift()[source]
                                                                          +parse_nmr_shift()[source]

                                                                          Parse NMR calculation.

                                                                          -parse_opt_steps()[source]
                                                                          +parse_opt_steps()[source]

                                                                          Parse the geometry optimization information.

                                                                          -parse_overlap_condition()[source]
                                                                          +parse_overlap_condition()[source]

                                                                          Retrieve the overlap condition number

                                                                          -parse_plus_u_params()[source]
                                                                          +parse_plus_u_params()[source]

                                                                          Parse the DFT+U params.

                                                                          -parse_qs_params()[source]
                                                                          +parse_qs_params()[source]

                                                                          Parse the DFT parameters (as well as functional, HF, vdW params).

                                                                          -parse_raman()[source]
                                                                          +parse_raman()[source]

                                                                          Parse raman calculation.

                                                                          -parse_scf_opt()[source]
                                                                          +parse_scf_opt()[source]

                                                                          Parse the SCF cycles (not usually important).

                                                                          -parse_scf_params()[source]
                                                                          +parse_scf_params()[source]

                                                                          Retrieve the most import SCF parameters: the max number of scf cycles (max_scf), the convergence cutoff for scf (eps_scf),.

                                                                          -parse_stresses()[source]
                                                                          +parse_stresses()[source]

                                                                          Get the stresses from stress file, or from the main output file.

                                                                          -parse_structures(trajectory_file=None, lattice_file=None)[source]
                                                                          +parse_structures(trajectory_file=None, lattice_file=None)[source]

                                                                          Parses the structures from a cp2k calculation. Static calculations simply use the initial structure. For calculations with ionic motion, the function will look for the appropriate trajectory and lattice files based on naming convention. If no file is given, and no file @@ -2922,31 +2922,31 @@

                                                                          Submodules
                                                                          -parse_tddfpt()[source]
                                                                          +parse_tddfpt()[source]

                                                                          Parse TDDFPT calculation.

                                                                          -parse_timing()[source]
                                                                          +parse_timing()[source]

                                                                          Parse the timing info (how long did the run take).

                                                                          -parse_total_numbers()[source]
                                                                          +parse_total_numbers()[source]

                                                                          Parse total numbers (not usually important).

                                                                          -property project_name: str[source]
                                                                          +property project_name: str[source]

                                                                          What project name was used for this calculation.

                                                                          -ran_successfully()[source]
                                                                          +ran_successfully()[source]

                                                                          Sanity checks that the program ran successfully. Looks at the bottom of the CP2K output file for the “PROGRAM ENDED” line, which is printed when successfully ran. Also grabs the number of warnings issued.

                                                                          @@ -2954,7 +2954,7 @@

                                                                          Submodules
                                                                          -read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]
                                                                          +read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]

                                                                          Originally from pymatgen.io.vasp.outputs.Outcar.

                                                                          General pattern reading. Uses monty’s regrep method. Takes the same arguments.

                                                                          @@ -2985,7 +2985,7 @@

                                                                          Submodules
                                                                          -read_table_pattern(header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=True, strip=None)[source]
                                                                          +read_table_pattern(header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=True, strip=None)[source]

                                                                          This function originated in pymatgen.io.vasp.outputs.Outcar.

                                                                          Parse table-like data. A table composes of three parts: header, main body, footer. All the data matches “row pattern” in the main body @@ -3030,13 +3030,13 @@

                                                                          Submodules
                                                                          -property run_type[source]
                                                                          +property run_type[source]

                                                                          What type of run (Energy, MD, etc.) was performed.

                                                                          -property spin_polarized: bool[source]
                                                                          +property spin_polarized: bool[source]

                                                                          Was the calculation spin polarized.

                                                                          @@ -3044,19 +3044,19 @@

                                                                          Submodules
                                                                          -parse_dos(dos_file=None)[source]
                                                                          +parse_dos(dos_file=None)[source]

                                                                          Parse a dos file. This format is different from the pdos files.

                                                                          -parse_energy_file(energy_file)[source]
                                                                          +parse_energy_file(energy_file)[source]

                                                                          Parse energy file for calculations with multiple ionic steps.

                                                                          -parse_pdos(dos_file=None, spin_channel=None, total=False)[source]
                                                                          +parse_pdos(dos_file=None, spin_channel=None, total=False)[source]

                                                                          Parse a single DOS file created by cp2k. Must contain one PDOS snapshot. i.e. you cannot use this cannot deal with multiple concatenated dos files.

                                                                          @@ -3112,7 +3112,7 @@

                                                                          Submodules
                                                                          -class CellOptSet(**kwargs)[source]
                                                                          +class CellOptSet(**kwargs)[source]

                                                                          Bases: DftSet

                                                                          Quick Constructor for cell optimization relaxation.

                                                                          @@ -3189,21 +3189,21 @@

                                                                          Submodules
                                                                          -exception Cp2kValidationError(message)[source]
                                                                          +exception Cp2kValidationError(message)[source]

                                                                          Bases: Exception

                                                                          Cp2k Validation Exception. Not exhausted. May raise validation errors for features which actually do work if using a newer version of cp2k.

                                                                          -CP2K_VERSION = 'v2022.1'[source]
                                                                          +CP2K_VERSION = 'v2022.1'[source]

                                                                          -class DftSet(structure: Structure | Molecule, project_name: str = 'CP2K', basis_and_potential: dict | None = None, xc_functionals: list | str | None = None, multiplicity: int = 0, ot: bool = True, energy_gap: float = -1, qs_method: str = 'GPW', eps_default: float = 1e-12, eps_scf: float = 1e-06, max_scf: int | None = None, minimizer: str = 'DIIS', preconditioner: str = 'FULL_SINGLE_INVERSE', algorithm: str = 'IRAC', linesearch: str = '2PNT', rotation: bool = True, occupation_preconditioner: bool = False, cutoff: float | None = None, rel_cutoff: int = 50, ngrids: int = 5, progression_factor: int = 3, override_default_params: dict | None = None, wfn_restart_file_name: str | None = None, kpoints: Kpoints | None = None, smearing: bool = False, **kwargs)[source]
                                                                          +class DftSet(structure: Structure | Molecule, project_name: str = 'CP2K', basis_and_potential: dict | None = None, xc_functionals: list | str | None = None, multiplicity: int = 0, ot: bool = True, energy_gap: float = -1, qs_method: str = 'GPW', eps_default: float = 1e-12, eps_scf: float = 1e-06, max_scf: int | None = None, minimizer: str = 'DIIS', preconditioner: str = 'FULL_SINGLE_INVERSE', algorithm: str = 'IRAC', linesearch: str = '2PNT', rotation: bool = True, occupation_preconditioner: bool = False, cutoff: float | None = None, rel_cutoff: int = 50, ngrids: int = 5, progression_factor: int = 3, override_default_params: dict | None = None, wfn_restart_file_name: str | None = None, kpoints: Kpoints | None = None, smearing: bool = False, **kwargs)[source]

                                                                          Bases: Cp2kInput

                                                                          Base for an input set using the Quickstep module (i.e. a DFT calculation). The DFT section is pretty vast in CP2K, so this set hopes to make the DFT setup fairly simple. The provided @@ -3280,19 +3280,19 @@

                                                                          Submodules
                                                                          -activate_epr(**kwargs) → None[source]
                                                                          +activate_epr(**kwargs) → None[source]

                                                                          Calculate g-tensor. Requires localize. Suggested with GAPW.

                                                                          -activate_fast_minimization(on) → None[source]
                                                                          +activate_fast_minimization(on) → None[source]

                                                                          Modify the set to use fast SCF minimization.

                                                                          -activate_hybrid(hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, max_memory: int = 2000, cutoff_radius: float = 8.0, potential_type: str | None = None, omega: float = 0.11, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, admm: bool = True, admm_method: str = 'BASIS_PROJECTION', admm_purification_method: str = 'NONE', admm_exch_correction_func: str = 'DEFAULT', eps_schwarz: float = 1e-07, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True) → None[source]
                                                                          +activate_hybrid(hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, max_memory: int = 2000, cutoff_radius: float = 8.0, potential_type: str | None = None, omega: float = 0.11, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, admm: bool = True, admm_method: str = 'BASIS_PROJECTION', admm_purification_method: str = 'NONE', admm_exch_correction_func: str = 'DEFAULT', eps_schwarz: float = 1e-07, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True) → None[source]

                                                                          Basic set for activating hybrid DFT calculation using Auxiliary Density Matrix Method.

                                                                          Note 1: When running ADMM with cp2k, memory is very important. If the memory requirements exceed what is available (see max_memory), then CP2K will have to calculate the 4-electron @@ -3360,13 +3360,13 @@

                                                                          Submodules
                                                                          -activate_hyperfine() → None[source]
                                                                          +activate_hyperfine() → None[source]

                                                                          Print the hyperfine coupling constants.

                                                                          -activate_localize(states='OCCUPIED', preconditioner='FULL_ALL', restart=False) → None[source]
                                                                          +activate_localize(states='OCCUPIED', preconditioner='FULL_ALL', restart=False) → None[source]

                                                                          Activate calculation of the maximally localized wannier functions.

                                                                          Parameters:
                                                                          @@ -3382,7 +3382,7 @@

                                                                          Submodules
                                                                          -activate_motion(max_drift: float = 0.003, rms_drift: float = 0.0015, max_force: float = 0.00045, rms_force: float = 0.0003, max_iter: int = 200, optimizer: str = 'BFGS', trust_radius: float = 0.25, line_search: str = '2PNT', ensemble: str = 'NVE', temperature: float = 300, timestep: float = 0.5, nsteps: int = 3, thermostat: str = 'NOSE', nproc_rep: int = 1) → None[source]
                                                                          +activate_motion(max_drift: float = 0.003, rms_drift: float = 0.0015, max_force: float = 0.00045, rms_force: float = 0.0003, max_iter: int = 200, optimizer: str = 'BFGS', trust_radius: float = 0.25, line_search: str = '2PNT', ensemble: str = 'NVE', temperature: float = 300, timestep: float = 0.5, nsteps: int = 3, thermostat: str = 'NOSE', nproc_rep: int = 1) → None[source]

                                                                          Turns on the motion section for GEO_OPT, CELL_OPT, etc. calculations. Will turn on the printing subsections and also bind any constraints to their respective atoms.

                                                                          @@ -3390,44 +3390,44 @@

                                                                          Submodules
                                                                          -activate_nmr(**kwargs) → None[source]
                                                                          +activate_nmr(**kwargs) → None[source]

                                                                          Calculate nmr shifts. Requires localize. Suggested with GAPW.

                                                                          -activate_nonperiodic(solver='ANALYTIC') → None[source]
                                                                          +activate_nonperiodic(solver='ANALYTIC') → None[source]

                                                                          Activates a calculation with non-periodic calculations by turning of PBC and changing the poisson solver. Still requires a CELL to put the atoms.

                                                                          -activate_polar(**kwargs) → None[source]
                                                                          +activate_polar(**kwargs) → None[source]

                                                                          Calculate polarizations (including raman).

                                                                          -activate_robust_minimization() → None[source]
                                                                          +activate_robust_minimization() → None[source]

                                                                          Modify the set to use more robust SCF minimization technique.

                                                                          -activate_spinspin(**kwargs) → None[source]
                                                                          +activate_spinspin(**kwargs) → None[source]

                                                                          Calculate spin-spin coupling tensor. Requires localize.

                                                                          -activate_tddfpt(**kwargs) → None[source]
                                                                          +activate_tddfpt(**kwargs) → None[source]

                                                                          Activate TDDFPT for calculating excited states. Only works with GPW. Supports hfx.

                                                                          -activate_vdw_potential(dispersion_functional: str, potential_type: str) → None[source]
                                                                          +activate_vdw_potential(dispersion_functional: str, potential_type: str) → None[source]

                                                                          Activate van der Waals dispersion corrections.

                                                                          Parameters:
                                                                          @@ -3443,19 +3443,19 @@

                                                                          Submodules
                                                                          -activate_very_strict_minimization() → None[source]
                                                                          +activate_very_strict_minimization() → None[source]

                                                                          Method to modify the set to use very strict SCF minimization scheme

                                                                          -create_subsys(structure: Structure | Molecule) → None[source]
                                                                          +create_subsys(structure: Structure | Molecule) → None[source]

                                                                          Create the structure for the input.

                                                                          -static get_basis_and_potential(structure, basis_and_potential)[source]
                                                                          +static get_basis_and_potential(structure, basis_and_potential)[source]

                                                                          Get a dictionary of basis and potential info for constructing the input file.

                                                                          data in basis_and_potential argument can be specified in several ways:

                                                                          @@ -3513,20 +3513,20 @@

                                                                          Submodules
                                                                          -static get_cutoff_from_basis(basis_sets, rel_cutoff) → float[source]
                                                                          +static get_cutoff_from_basis(basis_sets, rel_cutoff) → float[source]

                                                                          Given a basis and a relative cutoff. Determine the ideal cutoff variable.

                                                                          -static get_xc_functionals(xc_functionals: list | str | None = None) → list[source]
                                                                          +static get_xc_functionals(xc_functionals: list | str | None = None) → list[source]

                                                                          Get XC functionals. If simplified names are provided in kwargs, they will be expanded into their corresponding X and C names.

                                                                          -modify_dft_print_iters(iters, add_last='no')[source]
                                                                          +modify_dft_print_iters(iters, add_last='no')[source]

                                                                          Modify all DFT print iterations at once. Common use is to set iters to the max number of iterations + 1 and then set add_last to numeric. This would have the effect of printing only the first and last iteration, which might be useful for @@ -3547,7 +3547,7 @@

                                                                          Submodules
                                                                          -print_bandstructure(kpoints_line_density: int = 20) → None[source]
                                                                          +print_bandstructure(kpoints_line_density: int = 20) → None[source]

                                                                          Attaches a non-scf band structure calc the end of an SCF loop.

                                                                          This requires a kpoint calculation, which is not always default in cp2k.

                                                                          @@ -3559,7 +3559,7 @@

                                                                          Submodules
                                                                          -print_dos(ndigits=6) → None[source]
                                                                          +print_dos(ndigits=6) → None[source]

                                                                          Activate printing of the overall DOS file.

                                                                          Note: As of 2022.1, ndigits needs to be set to a sufficient value to ensure data is not lost. Note: As of 2022.1, can only be used with a k-point calculation.

                                                                          @@ -3567,25 +3567,25 @@

                                                                          Submodules
                                                                          -print_e_density(stride=(2, 2, 2)) → None[source]
                                                                          +print_e_density(stride=(2, 2, 2)) → None[source]

                                                                          Controls the printing of cube files with electronic density and, for UKS, the spin density.

                                                                          -print_forces() → None[source]
                                                                          +print_forces() → None[source]

                                                                          Print out the forces and stress during calculation.

                                                                          -print_hirshfeld(on=True) → None[source]
                                                                          +print_hirshfeld(on=True) → None[source]

                                                                          Activate or deactivate printing of Hirshfeld charges.

                                                                          -print_ldos(nlumo: int = -1) → None[source]
                                                                          +print_ldos(nlumo: int = -1) → None[source]

                                                                          Activate the printing of LDOS files, printing one for each atom kind by default.

                                                                          Parameters:
                                                                          @@ -3598,13 +3598,13 @@

                                                                          Submodules
                                                                          -print_mo() → None[source]
                                                                          +print_mo() → None[source]

                                                                          Print molecular orbitals when running non-OT diagonalization.

                                                                          -print_mo_cubes(write_cube: bool = False, nlumo: int = -1, nhomo: int = -1) → None[source]
                                                                          +print_mo_cubes(write_cube: bool = False, nlumo: int = -1, nhomo: int = -1) → None[source]

                                                                          Activate printing of molecular orbitals.

                                                                          Parameters:
                                                                          @@ -3619,13 +3619,13 @@

                                                                          Submodules
                                                                          -print_mulliken(on=False) → None[source]
                                                                          +print_mulliken(on=False) → None[source]

                                                                          Activate or deactivate printing of Mulliken charges.

                                                                          -print_pdos(nlumo: int = -1) → None[source]
                                                                          +print_pdos(nlumo: int = -1) → None[source]

                                                                          Activate creation of the PDOS file.

                                                                          Parameters:
                                                                          @@ -3638,7 +3638,7 @@

                                                                          Submodules
                                                                          -print_v_hartree(stride=(2, 2, 2)) → None[source]
                                                                          +print_v_hartree(stride=(2, 2, 2)) → None[source]
                                                                          Controls the printing of a cube file with eletrostatic potential generated by the

                                                                          total density (electrons+ions). It is valid only for QS with GPW formalism.

                                                                          @@ -3648,25 +3648,25 @@

                                                                          Submodules
                                                                          -set_charge(charge: int) → None[source]
                                                                          +set_charge(charge: int) → None[source]

                                                                          Set the overall charge of the simulation cell.

                                                                          -validate()[source]
                                                                          +validate()[source]

                                                                          Implements a few checks for a valid input set.

                                                                          -write_basis_set_file(basis_sets, fn='BASIS') → None[source]
                                                                          +write_basis_set_file(basis_sets, fn='BASIS') → None[source]

                                                                          Write the basis sets to a file.

                                                                          -write_potential_file(potentials, fn='POTENTIAL') → None[source]
                                                                          +write_potential_file(potentials, fn='POTENTIAL') → None[source]

                                                                          Write the potentials to a file.

                                                                          @@ -3674,7 +3674,7 @@

                                                                          Submodules
                                                                          -class HybridCellOptSet(**kwargs)[source]
                                                                          +class HybridCellOptSet(**kwargs)[source]

                                                                          Bases: DftSet

                                                                          Quick Constructor for hybrid cell optimization relaxation.

                                                                          @@ -3751,7 +3751,7 @@

                                                                          Submodules
                                                                          -class HybridRelaxSet(**kwargs)[source]
                                                                          +class HybridRelaxSet(**kwargs)[source]

                                                                          Bases: DftSet

                                                                          Quick Constructor for hybrid geometry relaxation.

                                                                          @@ -3828,7 +3828,7 @@

                                                                          Submodules
                                                                          -class HybridStaticSet(**kwargs)[source]
                                                                          +class HybridStaticSet(**kwargs)[source]

                                                                          Bases: DftSet

                                                                          Quick Constructor for static calculations.

                                                                          @@ -3905,7 +3905,7 @@

                                                                          Submodules
                                                                          -class RelaxSet(**kwargs)[source]
                                                                          +class RelaxSet(**kwargs)[source]

                                                                          Bases: DftSet

                                                                          Quick Constructor for geometry relaxation.

                                                                          @@ -3982,7 +3982,7 @@

                                                                          Submodules
                                                                          -class StaticSet(**kwargs)[source]
                                                                          +class StaticSet(**kwargs)[source]

                                                                          Bases: DftSet

                                                                          Quick Constructor for static calculations.

                                                                          @@ -4063,19 +4063,19 @@

                                                                          Submodules
                                                                          -chunk(string: str)[source]
                                                                          +chunk(string: str)[source]

                                                                          Chunk the string from a cp2k basis or potential file.

                                                                          -get_truncated_coulomb_cutoff(inp_struct: Structure)[source]
                                                                          +get_truncated_coulomb_cutoff(inp_struct: Structure)[source]

                                                                          Get the truncated Coulomb cutoff for a given structure.

                                                                          -get_unique_site_indices(struct: Structure | Molecule)[source]
                                                                          +get_unique_site_indices(struct: Structure | Molecule)[source]

                                                                          Get unique site indices for a structure according to site properties. Whatever site-property has the most unique values is used for indexing.

                                                                          For example, if you have magnetic CoO with half Co atoms having a positive moment, and the @@ -4089,7 +4089,7 @@

                                                                          Submodules
                                                                          -natural_keys(text: str)[source]
                                                                          +natural_keys(text: str)[source]

                                                                          Sort text by numbers coming after an underscore with natural number convention, Ex: [file_1, file_12, file_2] becomes [file_1, file_2, file_12].

                                                                          @@ -4097,7 +4097,7 @@

                                                                          Submodules
                                                                          -postprocessor(data: str) → str | float | bool | None[source]
                                                                          +postprocessor(data: str) → str | float | bool | None[source]

                                                                          Helper function to post process the results of the pattern matching functions in Cp2kOutput and turn them to Python types.

                                                                          @@ -4118,7 +4118,7 @@

                                                                          Submodules
                                                                          -preprocessor(data: str, dir: str = '.') → str[source]
                                                                          +preprocessor(data: str, dir: str = '.') → str[source]

                                                                          Cp2k contains internal preprocessor flags that are evaluated before execution. This helper function recognizes those preprocessor flags and replaces them with an equivalent cp2k input (this way everything is contained neatly in the cp2k input structure, even if the user preferred diff --git a/docs/pymatgen.io.exciting.html b/docs/pymatgen.io.exciting.html index db6d138be30..5abc445ad92 100644 --- a/docs/pymatgen.io.exciting.html +++ b/docs/pymatgen.io.exciting.html @@ -4,7 +4,7 @@ - pymatgen.io.exciting package — pymatgen 2024.6.4 documentation + pymatgen.io.exciting package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@

                                                                          - 2024.6.4 + 2024.6.10
                                                                          @@ -105,13 +105,13 @@

                                                                          Submodules
                                                                          -class ExcitingInput(structure: Structure, title=None, lockxyz=None)[source]
                                                                          +class ExcitingInput(structure: Structure, title=None, lockxyz=None)[source]

                                                                          Bases: MSONable

                                                                          Object for representing the data stored in the structure part of the exciting input.

                                                                          -structure[source]
                                                                          +structure[source]

                                                                          Associated Structure.

                                                                          Type:
                                                                          @@ -122,7 +122,7 @@

                                                                          Submodules
                                                                          -title[source]
                                                                          +title[source]

                                                                          Optional title string.

                                                                          Type:
                                                                          @@ -133,7 +133,7 @@

                                                                          Submodules
                                                                          -lockxyz[source]
                                                                          +lockxyz[source]

                                                                          Lockxyz attribute for each site if available. A Nx3 array of booleans.

                                                                          Type:
                                                                          @@ -155,12 +155,12 @@

                                                                          Submodules
                                                                          -bohr2ang = 0.5291692998219677[source]
                                                                          +bohr2ang = 0.5291692998219677[source]

                                                                          -classmethod from_file(filename: str | Path) → Self[source]
                                                                          +classmethod from_file(filename: str | Path) → Self[source]
                                                                          Parameters:

                                                                          filename – Filename

                                                                          @@ -173,19 +173,19 @@

                                                                          Submodules
                                                                          -classmethod from_str(data: str) → Self[source]
                                                                          +classmethod from_str(data: str) → Self[source]

                                                                          Reads the exciting input from a string.

                                                                          -property lockxyz[source]
                                                                          +property lockxyz[source]

                                                                          Selective dynamics site properties.

                                                                          -write_etree(celltype, cartesian=False, bandstr=False, symprec: float = 0.4, angle_tolerance=5, **kwargs)[source]
                                                                          +write_etree(celltype, cartesian=False, bandstr=False, symprec: float = 0.4, angle_tolerance=5, **kwargs)[source]

                                                                          Write the exciting input parameters to an XML object.

                                                                          Parameters:
                                                                          @@ -212,7 +212,7 @@

                                                                          Submodules
                                                                          -write_file(celltype, filename, cartesian=False, bandstr=False, symprec: float = 0.4, angle_tolerance=5, **kwargs)[source]
                                                                          +write_file(celltype, filename, cartesian=False, bandstr=False, symprec: float = 0.4, angle_tolerance=5, **kwargs)[source]

                                                                          Write exciting input file.

                                                                          Parameters:
                                                                          @@ -238,7 +238,7 @@

                                                                          Submodules
                                                                          -write_string(celltype, cartesian=False, bandstr=False, symprec: float = 0.4, angle_tolerance=5, **kwargs)[source]
                                                                          +write_string(celltype, cartesian=False, bandstr=False, symprec: float = 0.4, angle_tolerance=5, **kwargs)[source]

                                                                          Write exciting input.xml as a string.

                                                                          Parameters:
                                                                          diff --git a/docs/pymatgen.io.feff.html b/docs/pymatgen.io.feff.html index 6bd33b8742f..0013abca9e8 100644 --- a/docs/pymatgen.io.feff.html +++ b/docs/pymatgen.io.feff.html @@ -4,7 +4,7 @@ - pymatgen.io.feff package — pymatgen 2024.6.4 documentation + pymatgen.io.feff package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                          - 2024.6.4 + 2024.6.10
                                                                          @@ -207,7 +207,7 @@

                                                                          Submodules
                                                                          -class Atoms(struct, absorbing_atom, radius)[source]
                                                                          +class Atoms(struct, absorbing_atom, radius)[source]

                                                                          Bases: MSONable

                                                                          Atomic cluster centered around the absorbing atom.

                                                                          @@ -221,7 +221,7 @@

                                                                          Submodules
                                                                          -static atoms_string_from_file(filename)[source]
                                                                          +static atoms_string_from_file(filename)[source]

                                                                          Reads atomic shells from file such as feff.inp or ATOMS file The lines are arranged as follows:

                                                                          x y z ipot Atom Symbol Distance Number

                                                                          @@ -239,13 +239,13 @@

                                                                          Submodules
                                                                          -property cluster[source]
                                                                          +property cluster[source]

                                                                          The atomic cluster as a Molecule object.

                                                                          -static cluster_from_file(filename)[source]
                                                                          +static cluster_from_file(filename)[source]

                                                                          Parse the feff input file and return the atomic cluster as a Molecule object.

                                                                          @@ -267,7 +267,7 @@

                                                                          Submodules
                                                                          -get_lines() → list[list[str | int]][source]
                                                                          +get_lines() → list[list[str | int]][source]

                                                                          Get a list of string representations of the atomic configuration information(x, y, z, ipot, atom_symbol, distance, id).

                                                                          @@ -282,7 +282,7 @@

                                                                          Submodules
                                                                          -write_file(filename='ATOMS')[source]
                                                                          +write_file(filename='ATOMS')[source]

                                                                          Write Atoms list to file.

                                                                          Parameters:
                                                                          @@ -295,7 +295,7 @@

                                                                          Submodules
                                                                          -exception FeffParseError[source]
                                                                          +exception FeffParseError[source]

                                                                          Bases: ParseError

                                                                          Exception class for Structure. Raised when the structure has problems, e.g. atoms that are too close.

                                                                          @@ -303,7 +303,7 @@

                                                                          Submodules
                                                                          -class Header(struct: Structure | Molecule, source: str = '', comment: str = '', spacegroup_analyzer_settings=None)[source]
                                                                          +class Header(struct: Structure | Molecule, source: str = '', comment: str = '', spacegroup_analyzer_settings=None)[source]

                                                                          Bases: MSONable

                                                                          Create Header for the FEFF input file.

                                                                          Has the following format:

                                                                          @@ -340,13 +340,13 @@

                                                                          Submodules
                                                                          -property formula[source]
                                                                          +property formula[source]

                                                                          Formula of structure.

                                                                          -classmethod from_cif_file(cif_file: str, source: str = '', comment: str = '') → Self[source]
                                                                          +classmethod from_cif_file(cif_file: str, source: str = '', comment: str = '') → Self[source]

                                                                          Create Header object from cif_file.

                                                                          Parameters:
                                                                          @@ -365,13 +365,13 @@

                                                                          Submodules
                                                                          -classmethod from_file(filename: str) → Self[source]
                                                                          +classmethod from_file(filename: str) → Self[source]

                                                                          Get Header object from file.

                                                                          -classmethod from_str(header_str: str) → Self[source]
                                                                          +classmethod from_str(header_str: str) → Self[source]

                                                                          Reads Header string and returns Header object if header was generated by pymatgen. Note: Checks to see if generated by pymatgen, if not it is impossible

                                                                          @@ -391,7 +391,7 @@

                                                                          Submodules
                                                                          -static header_string_from_file(filename: str = 'feff.inp')[source]
                                                                          +static header_string_from_file(filename: str = 'feff.inp')[source]

                                                                          Reads Header string from either a HEADER file or feff.inp file Will also read a header from a non-pymatgen generated feff.inp file.

                                                                          @@ -406,13 +406,13 @@

                                                                          Submodules
                                                                          -property structure_symmetry: tuple[str, int][source]
                                                                          +property structure_symmetry: tuple[str, int][source]

                                                                          The space group symbol and space number of the structure.

                                                                          -write_file(filename='HEADER')[source]
                                                                          +write_file(filename='HEADER')[source]

                                                                          Write Header to file.

                                                                          Parameters:
                                                                          @@ -425,7 +425,7 @@

                                                                          Submodules
                                                                          -class Paths(atoms, paths, degeneracies=None)[source]
                                                                          +class Paths(atoms, paths, degeneracies=None)[source]

                                                                          Bases: MSONable

                                                                          Set FEFF scattering paths(‘paths.dat’ file used by the ‘genfmt’ module).

                                                                          @@ -441,7 +441,7 @@

                                                                          Submodules
                                                                          -write_file(filename='paths.dat')[source]
                                                                          +write_file(filename='paths.dat')[source]

                                                                          Write paths.dat.

                                                                          @@ -449,7 +449,7 @@

                                                                          Submodules
                                                                          -class Potential(struct, absorbing_atom)[source]
                                                                          +class Potential(struct, absorbing_atom)[source]

                                                                          Bases: MSONable

                                                                          FEFF atomic potential.

                                                                          @@ -462,7 +462,7 @@

                                                                          Submodules
                                                                          -static pot_dict_from_str(pot_data)[source]
                                                                          +static pot_dict_from_str(pot_data)[source]

                                                                          Creates atomic symbol/potential number dictionary forward and reverse.

                                                                          @@ -477,7 +477,7 @@

                                                                          Submodules
                                                                          -static pot_string_from_file(filename='feff.inp')[source]
                                                                          +static pot_string_from_file(filename='feff.inp')[source]

                                                                          Reads Potential parameters from a feff.inp or FEFFPOT file. The lines are arranged as follows:

                                                                          @@ -495,7 +495,7 @@

                                                                          Submodules
                                                                          -write_file(filename='POTENTIALS')[source]
                                                                          +write_file(filename='POTENTIALS')[source]

                                                                          Write to file.

                                                                          Parameters:
                                                                          @@ -508,7 +508,7 @@

                                                                          Submodules
                                                                          -class Tags(params=None)[source]
                                                                          +class Tags(params=None)[source]

                                                                          Bases: dict

                                                                          FEFF control parameters.

                                                                          @@ -518,7 +518,7 @@

                                                                          Submodules
                                                                          -as_dict()[source]
                                                                          +as_dict()[source]

                                                                          Dict representation.

                                                                          Returns:
                                                                          @@ -529,7 +529,7 @@

                                                                          Submodules
                                                                          -diff(other)[source]
                                                                          +diff(other)[source]

                                                                          Diff function. Compares two PARAMETER files and indicates which parameters are the same and which are not. Useful for checking whether two runs were done using the same parameters.

                                                                          @@ -553,7 +553,7 @@

                                                                          Submodules
                                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                                          +classmethod from_dict(dct: dict) → Self[source]

                                                                          Creates Tags object from a dictionary.

                                                                          Parameters:
                                                                          @@ -567,7 +567,7 @@

                                                                          Submodules
                                                                          -classmethod from_file(filename: str = 'feff.inp') → Self[source]
                                                                          +classmethod from_file(filename: str = 'feff.inp') → Self[source]

                                                                          Creates a Tags dictionary from a PARAMETER or feff.inp file.

                                                                          Parameters:
                                                                          @@ -581,7 +581,7 @@

                                                                          Submodules
                                                                          -get_str(sort_keys: bool = False, pretty: bool = False) → str[source]
                                                                          +get_str(sort_keys: bool = False, pretty: bool = False) → str[source]

                                                                          Get a string representation of the Tags. The reason why this method is different from the __str__ method is to provide options for pretty printing.

                                                                          @@ -604,7 +604,7 @@

                                                                          Submodules
                                                                          -static proc_val(key, val)[source]
                                                                          +static proc_val(key, val)[source]

                                                                          Static helper method to convert Feff parameters to proper types, e.g. integers, floats, lists, etc.

                                                                          @@ -619,7 +619,7 @@

                                                                          Submodules
                                                                          -write_file(filename='PARAMETERS')[source]
                                                                          +write_file(filename='PARAMETERS')[source]

                                                                          Write Tags to a Feff parameter tag file.

                                                                          Parameters:
                                                                          @@ -632,7 +632,7 @@

                                                                          Submodules
                                                                          -get_absorbing_atom_symbol_index(absorbing_atom, structure)[source]
                                                                          +get_absorbing_atom_symbol_index(absorbing_atom, structure)[source]

                                                                          Get the absorbing atom symbol and site index in the given structure.

                                                                          Parameters:
                                                                          @@ -652,7 +652,7 @@

                                                                          Submodules
                                                                          -get_atom_map(structure, absorbing_atom=None)[source]
                                                                          +get_atom_map(structure, absorbing_atom=None)[source]

                                                                          Get a dict that maps each atomic symbol to a unique integer starting from 1.

                                                                          Parameters:
                                                                          @@ -677,7 +677,7 @@

                                                                          Submodules
                                                                          -class Eels(data)[source]
                                                                          +class Eels(data)[source]

                                                                          Bases: MSONable

                                                                          Parse’eels.dat’ file.

                                                                          @@ -687,31 +687,31 @@

                                                                          Submodules
                                                                          -as_dict() → dict[source]
                                                                          +as_dict() → dict[source]

                                                                          Get dict representations of Xmu object.

                                                                          -property atomic_background: ndarray[source]
                                                                          +property atomic_background: ndarray[source]

                                                                          The atomic background of EELS.

                                                                          -property energies[source]
                                                                          +property energies[source]

                                                                          The energies in eV.

                                                                          -property fine_structure: ndarray[source]
                                                                          +property fine_structure: ndarray[source]

                                                                          The fine structure of EELS.

                                                                          -classmethod from_file(eels_dat_file: str = 'eels.dat') → Self[source]
                                                                          +classmethod from_file(eels_dat_file: str = 'eels.dat') → Self[source]

                                                                          Parse eels spectrum.

                                                                          Parameters:
                                                                          @@ -725,7 +725,7 @@

                                                                          Submodules
                                                                          -property total_spectrum[source]
                                                                          +property total_spectrum[source]

                                                                          The total eels spectrum.

                                                                          @@ -733,7 +733,7 @@

                                                                          Submodules
                                                                          -class LDos(complete_dos, charge_transfer)[source]
                                                                          +class LDos(complete_dos, charge_transfer)[source]

                                                                          Bases: MSONable

                                                                          Parser for ldos files ldos01, ldos02, …

                                                                          @@ -747,7 +747,7 @@

                                                                          Submodules
                                                                          -static charge_transfer_from_file(feff_inp_file, ldos_file)[source]
                                                                          +static charge_transfer_from_file(feff_inp_file, ldos_file)[source]

                                                                          Get charge transfer from file.

                                                                          Parameters:
                                                                          @@ -766,13 +766,13 @@

                                                                          Submodules
                                                                          -charge_transfer_to_str()[source]
                                                                          +charge_transfer_to_str()[source]

                                                                          Get charge transfer as string.

                                                                          -classmethod from_file(feff_inp_file: str = 'feff.inp', ldos_file: str = 'ldos') → Self[source]
                                                                          +classmethod from_file(feff_inp_file: str = 'feff.inp', ldos_file: str = 'ldos') → Self[source]

                                                                          Creates LDos object from raw Feff ldos files by by assuming they are numbered consecutively, i.e. ldos01.dat ldos02.dat…

                                                                          @@ -790,7 +790,7 @@

                                                                          Submodules
                                                                          -class Xmu(header, parameters, absorbing_atom, data)[source]
                                                                          +class Xmu(header, parameters, absorbing_atom, data)[source]

                                                                          Bases: MSONable

                                                                          Parser for data in ‘xmu.dat’ file. The file ‘xmu.dat’ contains XANES, EXAFS or NRIXS data depending on the @@ -823,43 +823,43 @@

                                                                          Submodules
                                                                          -as_dict()[source]
                                                                          +as_dict()[source]

                                                                          Get dict representations of Xmu object.

                                                                          -property calc[source]
                                                                          +property calc[source]

                                                                          Type of Feff calculation, XANES or EXAFS.

                                                                          -property chi[source]
                                                                          +property chi[source]

                                                                          The normalized fine structure.

                                                                          -property e_fermi[source]
                                                                          +property e_fermi[source]

                                                                          The Fermi level in eV.

                                                                          -property edge[source]
                                                                          +property edge[source]

                                                                          Excitation edge.

                                                                          -property energies[source]
                                                                          +property energies[source]

                                                                          The absolute energies in eV.

                                                                          -classmethod from_file(xmu_dat_file: str = 'xmu.dat', feff_inp_file: str = 'feff.inp') → Self[source]
                                                                          +classmethod from_file(xmu_dat_file: str = 'xmu.dat', feff_inp_file: str = 'feff.inp') → Self[source]

                                                                          Get Xmu from file.

                                                                          Parameters:
                                                                          @@ -876,37 +876,37 @@

                                                                          Submodules
                                                                          -property material_formula[source]
                                                                          +property material_formula[source]

                                                                          Chemical formula of material from feff.inp file.

                                                                          -property mu[source]
                                                                          +property mu[source]

                                                                          The total absorption cross-section.

                                                                          -property mu0[source]
                                                                          +property mu0[source]

                                                                          The embedded atomic background absorption.

                                                                          -property relative_energies[source]
                                                                          +property relative_energies[source]

                                                                          Energy with respect to the Fermi level E - E_f.

                                                                          -property source[source]
                                                                          +property source[source]

                                                                          Source identification from Header file.

                                                                          -property wavenumber[source]
                                                                          +property wavenumber[source]

                                                                          Get the wave number in units of AA^-1. k=sqrt(E - E_f) where E is the energy and E_f is the Fermi level computed from electron gas theory at the average interstitial charge density.

                                                                          @@ -924,7 +924,7 @@

                                                                          Submodules
                                                                          -class AbstractFeffInputSet[source]
                                                                          +class AbstractFeffInputSet[source]

                                                                          Bases: MSONable, ABC

                                                                          Abstract base class representing a set of Feff input parameters. The idea is that using a FeffInputSet, a complete set of input files @@ -932,13 +932,13 @@

                                                                          Submodules
                                                                          -all_input()[source]
                                                                          +all_input()[source]

                                                                          Get all input files as a dict of {filename: feffio object}.

                                                                          -abstract property atoms[source]
                                                                          +abstract property atoms[source]

                                                                          Get Atoms string from a structure that goes in feff.inp file.

                                                                          Returns:
                                                                          @@ -949,25 +949,25 @@

                                                                          Submodules
                                                                          -abstract header()[source]
                                                                          +abstract header()[source]

                                                                          Get header to be used in feff.inp file from a pymatgen structure.

                                                                          -abstract property potential[source]
                                                                          +abstract property potential[source]

                                                                          Get POTENTIAL section used in feff.inp from a structure.

                                                                          -abstract property tags[source]
                                                                          +abstract property tags[source]

                                                                          Get standard calculation parameters.

                                                                          -write_input(output_dir='.', make_dir_if_not_present=True)[source]
                                                                          +write_input(output_dir='.', make_dir_if_not_present=True)[source]

                                                                          Write a FEFF input set to a directory.

                                                                          Parameters:
                                                                          @@ -984,7 +984,7 @@

                                                                          Submodules
                                                                          -class FEFFDictSet(absorbing_atom: str | int, structure: Structure | Molecule, radius: float, config_dict: dict, edge: str = 'K', spectrum: str = 'EXAFS', nkpts=1000, user_tag_settings: dict | None = None, spacegroup_analyzer_settings: dict | None = None)[source]
                                                                          +class FEFFDictSet(absorbing_atom: str | int, structure: Structure | Molecule, radius: float, config_dict: dict, edge: str = 'K', spectrum: str = 'EXAFS', nkpts=1000, user_tag_settings: dict | None = None, spacegroup_analyzer_settings: dict | None = None)[source]

                                                                          Bases: AbstractFeffInputSet

                                                                          Standard implementation of FeffInputSet, which can be extended by specific implementations.

                                                                          @@ -1025,7 +1025,7 @@

                                                                          Submodules
                                                                          -property atoms: Atoms[source]
                                                                          +property atoms: Atoms[source]

                                                                          absorber + the rest.

                                                                          Returns:
                                                                          @@ -1036,14 +1036,14 @@

                                                                          Submodules
                                                                          -classmethod from_directory(input_dir: str) → Self[source]
                                                                          +classmethod from_directory(input_dir: str) → Self[source]

                                                                          Read in a set of FEFF input files from a directory, which is useful when existing FEFF input needs some adjustment.

                                                                          -header(source: str = '', comment: str = '')[source]
                                                                          +header(source: str = '', comment: str = '')[source]

                                                                          Creates header string from structure object.

                                                                          Parameters:
                                                                          @@ -1062,7 +1062,7 @@

                                                                          Submodules
                                                                          -property potential: Potential[source]
                                                                          +property potential: Potential[source]

                                                                          FEFF potential.

                                                                          Returns:
                                                                          @@ -1073,7 +1073,7 @@

                                                                          Submodules
                                                                          -property tags: Tags[source]
                                                                          +property tags: Tags[source]

                                                                          FEFF job parameters.

                                                                          Returns:
                                                                          @@ -1086,7 +1086,7 @@

                                                                          Submodules
                                                                          -class MPEELSDictSet(absorbing_atom, structure, edge, spectrum, radius, beam_energy, beam_direction, collection_angle, convergence_angle, config_dict, user_eels_settings=None, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]
                                                                          +class MPEELSDictSet(absorbing_atom, structure, edge, spectrum, radius, beam_energy, beam_direction, collection_angle, convergence_angle, config_dict, user_eels_settings=None, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

                                                                          Bases: FEFFDictSet

                                                                          FeffDictSet for ELNES spectroscopy.

                                                                          @@ -1115,7 +1115,7 @@

                                                                          Submodules
                                                                          -class MPELNESSet(absorbing_atom, structure, edge: str = 'K', radius: float = 10.0, beam_energy: float = 100, beam_direction=None, collection_angle: float = 1, convergence_angle: float = 1, user_eels_settings=None, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]
                                                                          +class MPELNESSet(absorbing_atom, structure, edge: str = 'K', radius: float = 10.0, beam_energy: float = 100, beam_direction=None, collection_angle: float = 1, convergence_angle: float = 1, user_eels_settings=None, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

                                                                          Bases: MPEELSDictSet

                                                                          FeffDictSet for ELNES spectroscopy.

                                                                          @@ -1141,14 +1141,14 @@

                                                                          Submodules
                                                                          -CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'ELNES': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': '4 0.04 0.1', 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-20.0 20.0 0.1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '6.0 0 30 0.2 1'}[source]
                                                                          +CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'ELNES': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': '4 0.04 0.1', 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-20.0 20.0 0.1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '6.0 0 30 0.2 1'}[source]

                                                                          -class MPEXAFSSet(absorbing_atom, structure, edge: str = 'K', radius: float = 10.0, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]
                                                                          +class MPEXAFSSet(absorbing_atom, structure, edge: str = 'K', radius: float = 10.0, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

                                                                          Bases: FEFFDictSet

                                                                          FeffDictSet for EXAFS spectroscopy.

                                                                          @@ -1167,14 +1167,14 @@

                                                                          Submodules
                                                                          -CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXAFS': 20, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '4.5 0 30 .2 1'}[source]
                                                                          +CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXAFS': 20, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '4.5 0 30 .2 1'}[source]

                                                                          -class MPEXELFSSet(absorbing_atom, structure, edge='K', radius: float = 10.0, beam_energy: float = 100, beam_direction=None, collection_angle: float = 1, convergence_angle: float = 1, user_eels_settings=None, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]
                                                                          +class MPEXELFSSet(absorbing_atom, structure, edge='K', radius: float = 10.0, beam_energy: float = 100, beam_direction=None, collection_angle: float = 1, convergence_angle: float = 1, user_eels_settings=None, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

                                                                          Bases: MPEELSDictSet

                                                                          FeffDictSet for EXELFS spectroscopy.

                                                                          @@ -1200,14 +1200,14 @@

                                                                          Submodules
                                                                          -CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'EXELFS': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': 20, 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '5.0 0 30 0.2 1'}[source]
                                                                          +CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'EXELFS': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': 20, 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '5.0 0 30 0.2 1'}[source]

                                                                          -class MPXANESSet(absorbing_atom, structure, edge: str = 'K', radius: float = 10.0, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]
                                                                          +class MPXANESSet(absorbing_atom, structure, edge: str = 'K', radius: float = 10.0, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

                                                                          Bases: FEFFDictSet

                                                                          FeffDictSet for XANES spectroscopy.

                                                                          @@ -1226,7 +1226,7 @@

                                                                          Submodules
                                                                          -CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-30. 15. .1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '4.5 0 30 .2 1', 'XANES': '3.7 .04 .1'}[source]
                                                                          +CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-30. 15. .1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '4.5 0 30 .2 1', 'XANES': '3.7 .04 .1'}[source]

                                                                          diff --git a/docs/pymatgen.io.html b/docs/pymatgen.io.html index 94c4ddfc639..9f077656268 100644 --- a/docs/pymatgen.io.html +++ b/docs/pymatgen.io.html @@ -4,7 +4,7 @@ - pymatgen.io namespace — pymatgen 2024.6.4 documentation + pymatgen.io namespace — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -36,7 +36,7 @@
                                                                          - 2024.6.4 + 2024.6.10
                                                                          @@ -3192,7 +3192,7 @@

                                                                          Submodules
                                                                          -class AdfInput(task)[source]
                                                                          +class AdfInput(task)[source]

                                                                          Bases: object

                                                                          A basic ADF input file writer.

                                                                          Initialization method.

                                                                          @@ -3203,7 +3203,7 @@

                                                                          Submodules
                                                                          -write_file(molecule, inp_file)[source]
                                                                          +write_file(molecule, inp_file)[source]

                                                                          Write an ADF input file.

                                                                          Parameters:
                                                                          @@ -3217,14 +3217,14 @@

                                                                          Submodules
                                                                          -exception AdfInputError[source]
                                                                          +exception AdfInputError[source]

                                                                          Bases: Exception

                                                                          The default error class for ADF.

                                                                          -class AdfKey(name, options=None, subkeys=None)[source]
                                                                          +class AdfKey(name, options=None, subkeys=None)[source]

                                                                          Bases: MSONable

                                                                          The basic input unit for ADF. A key is a string of characters that does not contain a delimiter (blank, comma or equal sign). A key may have multiple @@ -3246,7 +3246,7 @@

                                                                          Submodules
                                                                          -add_option(option)[source]
                                                                          +add_option(option)[source]

                                                                          Add a new option to this key.

                                                                          Parameters:
                                                                          @@ -3262,7 +3262,7 @@

                                                                          Submodules
                                                                          -add_subkey(subkey)[source]
                                                                          +add_subkey(subkey)[source]

                                                                          Add a new subkey to this key.

                                                                          Parameters:
                                                                          @@ -3275,18 +3275,18 @@

                                                                          Submodules
                                                                          -as_dict()[source]
                                                                          +as_dict()[source]

                                                                          A JSON-serializable dict representation of self.

                                                                          -block_keys = ('SCF', 'GEOMETRY', 'XC', 'UNITS', 'ATOMS', 'CHARGE', 'BASIS', 'SYMMETRY', 'RELATIVISTIC', 'OCCUPATIONS', 'SAVE', 'A1FIT', 'INTEGRATION', 'UNRESTRICTED', 'ZLMFIT', 'TITLE', 'EXACTDENSITY', 'TOTALENERGY', 'ANALYTICALFREQ')[source]
                                                                          +block_keys = ('SCF', 'GEOMETRY', 'XC', 'UNITS', 'ATOMS', 'CHARGE', 'BASIS', 'SYMMETRY', 'RELATIVISTIC', 'OCCUPATIONS', 'SAVE', 'A1FIT', 'INTEGRATION', 'UNRESTRICTED', 'ZLMFIT', 'TITLE', 'EXACTDENSITY', 'TOTALENERGY', 'ANALYTICALFREQ')[source]
                                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                                          +classmethod from_dict(dct: dict) → Self[source]

                                                                          Construct a MSONable AdfKey object from the JSON dict.

                                                                          Parameters:
                                                                          @@ -3303,7 +3303,7 @@

                                                                          Submodules
                                                                          -classmethod from_str(string: str) → Self[source]
                                                                          +classmethod from_str(string: str) → Self[source]

                                                                          Construct an AdfKey object from the string.

                                                                          Parameters:
                                                                          @@ -3323,7 +3323,7 @@

                                                                          Submodules
                                                                          -has_option(option: str) → bool[source]
                                                                          +has_option(option: str) → bool[source]
                                                                          Parameters:

                                                                          option (str) – The option.

                                                                          @@ -3339,7 +3339,7 @@

                                                                          Submodules
                                                                          -has_subkey(subkey: str | AdfKey) → bool[source]
                                                                          +has_subkey(subkey: str | AdfKey) → bool[source]
                                                                          Parameters:

                                                                          subkey (str | AdfKey) – A key name or AdfKey object.

                                                                          @@ -3355,19 +3355,19 @@

                                                                          Submodules
                                                                          -is_block_key() → bool[source]
                                                                          +is_block_key() → bool[source]

                                                                          Return True if this key is a block key.

                                                                          -property key: str[source]
                                                                          +property key: str[source]

                                                                          The name of this key. If this is a block key, the name will be converted to upper cases.

                                                                          -remove_option(option: str | int) → None[source]
                                                                          +remove_option(option: str | int) → None[source]

                                                                          Remove an option.

                                                                          Parameters:
                                                                          @@ -3381,7 +3381,7 @@

                                                                          Submodules
                                                                          -remove_subkey(subkey)[source]
                                                                          +remove_subkey(subkey)[source]

                                                                          Remove the given subkey, if existed, from this AdfKey.

                                                                          Parameters:
                                                                          @@ -3392,19 +3392,19 @@

                                                                          Submodules
                                                                          -sub_keys = ('AtomDepQuality',)[source]
                                                                          +sub_keys = ('AtomDepQuality',)[source]

                                                                          -class AdfOutput(filename)[source]
                                                                          +class AdfOutput(filename)[source]

                                                                          Bases: object

                                                                          A basic ADF output file parser.

                                                                          -is_failed[source]
                                                                          +is_failed[source]

                                                                          Whether the ADF job is failed.

                                                                          Type:
                                                                          @@ -3415,7 +3415,7 @@

                                                                          Submodules
                                                                          -is_internal_crash[source]
                                                                          +is_internal_crash[source]

                                                                          Whether the job crashed. Please read ‘TAPE13’ of the ADF manual for more detail.

                                                                          @@ -3427,7 +3427,7 @@

                                                                          Submodules
                                                                          -error[source]
                                                                          +error[source]

                                                                          The error description.

                                                                          Type:
                                                                          @@ -3438,7 +3438,7 @@

                                                                          Submodules
                                                                          -run_type[source]
                                                                          +run_type[source]

                                                                          The RunType of this ADF job. Possible options are: ‘SinglePoint’, ‘GeometryOptimization’, ‘AnalyticalFreq’ and ‘NUmericalFreq’.

                                                                          @@ -3450,7 +3450,7 @@

                                                                          Submodules
                                                                          -final_energy[source]
                                                                          +final_energy[source]

                                                                          The final molecule energy (a.u).

                                                                          Type:
                                                                          @@ -3461,7 +3461,7 @@

                                                                          Submodules
                                                                          -final_structure[source]
                                                                          +final_structure[source]

                                                                          The final structure of the molecule.

                                                                          Type:
                                                                          @@ -3472,7 +3472,7 @@

                                                                          Submodules
                                                                          -energies[source]
                                                                          +energies[source]

                                                                          The energy of each cycle.

                                                                          Type:
                                                                          @@ -3483,7 +3483,7 @@

                                                                          Submodules
                                                                          -structures[source]
                                                                          +structures[source]

                                                                          The structure of each cycle If geometry optimization is performed.

                                                                          Type:
                                                                          @@ -3494,7 +3494,7 @@

                                                                          Submodules
                                                                          -frequencies[source]
                                                                          +frequencies[source]

                                                                          The frequencies of the molecule.

                                                                          Type:
                                                                          @@ -3505,7 +3505,7 @@

                                                                          Submodules
                                                                          -normal_modes[source]
                                                                          +normal_modes[source]

                                                                          The normal modes of the molecule.

                                                                          Type:
                                                                          @@ -3516,7 +3516,7 @@

                                                                          Submodules
                                                                          -freq_type[source]
                                                                          +freq_type[source]

                                                                          Either ‘Analytical’ or ‘Numerical’.

                                                                          Type:
                                                                          @@ -3535,14 +3535,14 @@

                                                                          Submodules
                                                                          -exception AdfOutputError[source]
                                                                          +exception AdfOutputError[source]

                                                                          Bases: Exception

                                                                          The default error class for errors raised by AdfOutput.

                                                                          -class AdfTask(operation='energy', basis_set=None, xc=None, title='ADF_RUN', units=None, geo_subkeys=None, scf=None, other_directives=None)[source]
                                                                          +class AdfTask(operation='energy', basis_set=None, xc=None, title='ADF_RUN', units=None, geo_subkeys=None, scf=None, other_directives=None)[source]

                                                                          Bases: MSONable

                                                                          Basic task for ADF. All settings in this class are independent of molecules.

                                                                          Notes

                                                                          @@ -3565,13 +3565,13 @@

                                                                          Submodules
                                                                          -as_dict()[source]
                                                                          +as_dict()[source]

                                                                          A JSON-serializable dict representation of self.

                                                                          -classmethod from_dict(dct: dict) → Self[source]
                                                                          +classmethod from_dict(dct: dict) → Self[source]

                                                                          Construct a MSONable AdfTask object from the JSON dict.

                                                                          Parameters:
                                                                          @@ -3585,44 +3585,44 @@

                                                                          Submodules
                                                                          -static get_default_basis_set()[source]
                                                                          +static get_default_basis_set()[source]

                                                                          Get Default basis set.

                                                                          -static get_default_geo()[source]
                                                                          +static get_default_geo()[source]

                                                                          Get ADFKey using default geometry.

                                                                          -static get_default_scf()[source]
                                                                          +static get_default_scf()[source]

                                                                          Get ADF using default SCF.

                                                                          -static get_default_units()[source]
                                                                          +static get_default_units()[source]

                                                                          Get Default units.

                                                                          -static get_default_xc()[source]
                                                                          +static get_default_xc()[source]

                                                                          Get ADFKey using default XC.

                                                                          -operations: ClassVar[dict[str, str]] = {'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'numerical_frequencies': 'Compute molecular frequencies using numerical method.', 'optimize': 'Minimize the energy by varying the molecular structure.'}[source]
                                                                          +operations: ClassVar[dict[str, str]] = {'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'numerical_frequencies': 'Compute molecular frequencies using numerical method.', 'optimize': 'Minimize the energy by varying the molecular structure.'}[source]
                                                                          -is_numeric(string) → bool[source]
                                                                          +is_numeric(string) → bool[source]

                                                                          True if input string is numeric and can be converted to an int or a float.

                                                                          @@ -3633,12 +3633,12 @@

                                                                          Submodules
                                                                          -class AseAtomsAdaptor[source]
                                                                          +class AseAtomsAdaptor[source]

                                                                          Bases: object

                                                                          Adaptor serves as a bridge between ASE Atoms and pymatgen objects.

                                                                          -static get_atoms(structure: SiteCollection, msonable: bool = True, **kwargs) → MSONAtoms | Atoms[source]
                                                                          +static get_atoms(structure: SiteCollection, msonable: bool = True, **kwargs) → MSONAtoms | Atoms[source]

                                                                          Get ASE Atoms object from pymatgen structure or molecule.

                                                                          Parameters:
                                                                          @@ -3659,7 +3659,7 @@

                                                                          Submodules
                                                                          -static get_molecule(atoms: ~ase.atoms.Atoms, cls: type[~pymatgen.core.structure.Molecule] = <class 'pymatgen.core.structure.Molecule'>, **cls_kwargs) → Molecule[source]
                                                                          +static get_molecule(atoms: ~ase.atoms.Atoms, cls: type[~pymatgen.core.structure.Molecule] = <class 'pymatgen.core.structure.Molecule'>, **cls_kwargs) → Molecule[source]

                                                                          Get pymatgen molecule from ASE Atoms.

                                                                          Parameters:
                                                                          @@ -3680,7 +3680,7 @@

                                                                          Submodules
                                                                          -static get_structure(atoms: ~ase.atoms.Atoms, cls: type[~pymatgen.core.structure.Structure] = <class 'pymatgen.core.structure.Structure'>, **cls_kwargs) → Structure[source]
                                                                          +static get_structure(atoms: ~ase.atoms.Atoms, cls: type[~pymatgen.core.structure.Structure] = <class 'pymatgen.core.structure.Structure'>, **cls_kwargs) → Structure[source]

                                                                          Get pymatgen structure from ASE Atoms.

                                                                          Parameters:
                                                                          @@ -3703,18 +3703,18 @@

                                                                          Submodules
                                                                          -class MSONAtoms(symbols=None, positions=None, numbers=None, tags=None, momenta=None, masses=None, magmoms=None, charges=None, scaled_positions=None, cell=None, pbc=None, celldisp=None, constraint=None, calculator=None, info=None, velocities=None)[source]
                                                                          +class MSONAtoms(symbols=None, positions=None, numbers=None, tags=None, momenta=None, masses=None, magmoms=None, charges=None, scaled_positions=None, cell=None, pbc=None, celldisp=None, constraint=None, calculator=None, info=None, velocities=None)[source]

                                                                          Bases: Atoms, MSONable

                                                                          A custom subclass of ASE Atoms that is MSONable, including .as_dict() and .from_dict() methods.

                                                                          -as_dict() → dict[str, Any][source]
                                                                          +as_dict() → dict[str, Any][source]

                                                                          A JSON serializable dict representation of an object.

                                                                          -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                          +classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                          Parameters:

                                                                          d – Dict representation.

                                                                          @@ -3733,7 +3733,7 @@

                                                                          Submodules
                                                                          -class Mcsqs(structure: Structure)[source]
                                                                          +class Mcsqs(structure: Structure)[source]

                                                                          Bases: object

                                                                          Handle input/output for the crystal definition format used by mcsqs and other ATAT codes.

                                                                          @@ -3744,7 +3744,7 @@

                                                                          Submodules
                                                                          -static structure_from_str(data)[source]
                                                                          +static structure_from_str(data)[source]

                                                                          Parses a rndstr.in, lat.in or bestsqs.out file into pymatgen’s Structure format.

                                                                          @@ -3759,7 +3759,7 @@

                                                                          Submodules
                                                                          -to_str()[source]
                                                                          +to_str()[source]
                                                                          Returns:

                                                                          a structure in mcsqs rndstr.in format.

                                                                          @@ -3780,7 +3780,7 @@

                                                                          Submoduleshttps://openbabel.org.

                                                                          -class BabelMolAdaptor(mol: Molecule | openbabel.OBMol | pybel.Molecule)[source]
                                                                          +class BabelMolAdaptor(mol: Molecule | OBMol | Molecule)[source]

                                                                          Bases: object

                                                                          Adaptor serves as a bridge between OpenBabel’s Molecule and pymatgen’s Molecule.

                                                                          @@ -3792,13 +3792,13 @@

                                                                          Submodules
                                                                          -add_hydrogen() → None[source]
                                                                          +add_hydrogen() → None[source]

                                                                          Add hydrogens (make all hydrogen explicit).

                                                                          -confab_conformers(forcefield: str = 'mmff94', freeze_atoms: list[int] | None = None, rmsd_cutoff: float = 0.5, energy_cutoff: float = 50.0, conf_cutoff: int = 100000, verbose: bool = False) → list[Molecule][source]
                                                                          +confab_conformers(forcefield: str = 'mmff94', freeze_atoms: list[int] | None = None, rmsd_cutoff: float = 0.5, energy_cutoff: float = 50.0, conf_cutoff: int = 100000, verbose: bool = False) → list[Molecule][source]

                                                                          Conformer generation based on Confab to generate all diverse low-energy conformers for molecules. This is different from rotor_conformer or gen3d_conformer as it aims to not simply to find a low energy @@ -3829,7 +3829,7 @@

                                                                          Submodules
                                                                          -classmethod from_file(filename: str, file_format: str = 'xyz', return_all_molecules: bool = False) → Self | list[Self][source]
                                                                          +classmethod from_file(filename: str, file_format: str = 'xyz', return_all_molecules: bool = False) → Self | list[Self][source]

                                                                          Uses OpenBabel to read a molecule from a file in all supported formats.

                                                                          Parameters:
                                                                          @@ -3849,7 +3849,7 @@

                                                                          Submodules
                                                                          -classmethod from_molecule_graph(mol: MoleculeGraph) → Self[source]
                                                                          +classmethod from_molecule_graph(mol: MoleculeGraph) → Self[source]

                                                                          Read a molecule from a pymatgen MoleculeGraph object.

                                                                          Parameters:
                                                                          @@ -3863,7 +3863,7 @@

                                                                          Submodules
                                                                          -classmethod from_str(string_data: str, file_format: str = 'xyz') → Self[source]
                                                                          +classmethod from_str(string_data: str, file_format: str = 'xyz') → Self[source]

                                                                          Uses OpenBabel to read a molecule from a string in all supported formats.

                                                                          @@ -3881,7 +3881,7 @@

                                                                          Submodules
                                                                          -gen3d_conformer() → None[source]
                                                                          +gen3d_conformer() → None[source]

                                                                          A combined method to first generate 3D structures from 0D or 2D structures and then find the minimum energy conformer:

                                                                            @@ -3903,7 +3903,7 @@

                                                                            Submodules
                                                                            -localopt(forcefield: str = 'mmff94', steps: int = 500) → None[source]
                                                                            +localopt(forcefield: str = 'mmff94', steps: int = 500) → None[source]

                                                                            A wrapper to pybel’s localopt method to optimize a Molecule.

                                                                            Parameters:
                                                                            @@ -3918,7 +3918,7 @@

                                                                            Submodules
                                                                            -make3d(forcefield: str = 'mmff94', steps: int = 50) → None[source]
                                                                            +make3d(forcefield: str = 'mmff94', steps: int = 50) → None[source]

                                                                            A wrapper to pybel’s make3D method generate a 3D structure from a 2D or 0D structure. The 3D structure is made very quickly using a combination of rules @@ -3942,25 +3942,25 @@

                                                                            Submodules
                                                                            -property openbabel_mol[source]
                                                                            +property openbabel_mol[source]

                                                                            OpenBabel’s OBMol.

                                                                            -property pybel_mol: Molecule[source]
                                                                            +property pybel_mol: Molecule[source]

                                                                            Pybel’s Molecule object.

                                                                            -property pymatgen_mol: Molecule[source]
                                                                            +property pymatgen_mol: Molecule[source]

                                                                            Pymatgen Molecule object.

                                                                            -remove_bond(idx1: int, idx2: int) → None[source]
                                                                            +remove_bond(idx1: int, idx2: int) → None[source]

                                                                            Remove a bond from an openbabel molecule.

                                                                            Parameters:
                                                                            @@ -3974,7 +3974,7 @@

                                                                            Submodules
                                                                            -rotor_conformer(*rotor_args, algo: str = 'WeightedRotorSearch', forcefield: str = 'mmff94') → None[source]
                                                                            +rotor_conformer(*rotor_args, algo: str = 'WeightedRotorSearch', forcefield: str = 'mmff94') → None[source]

                                                                            Conformer search based on several Rotor Search algorithms of openbabel. If the input molecule is not 3D, make3d will be called (generate 3D structure, add hydrogen, a quick localopt). All hydrogen atoms need @@ -4001,7 +4001,7 @@

                                                                            Submodules
                                                                            -write_file(filename: str, file_format: str = 'xyz') → None[source]
                                                                            +write_file(filename: str, file_format: str = 'xyz') → None[source]

                                                                            Uses OpenBabel to output all supported formats.

                                                                            Parameters:
                                                                            @@ -4021,7 +4021,7 @@

                                                                            Submodules
                                                                            -class CifBlock(data: dict, loops: list[list[str]], header: str)[source]
                                                                            +class CifBlock(data: dict, loops: list[list[str]], header: str)[source]

                                                                            Bases: object

                                                                            Object for storing cif data. All data is stored in a single dictionary. Data inside loops are stored in lists in the data dictionary, and @@ -4039,7 +4039,7 @@

                                                                            Submodules
                                                                            -classmethod from_str(string: str) → Self[source]
                                                                            +classmethod from_str(string: str) → Self[source]

                                                                            Read CifBlock from string.

                                                                            Parameters:
                                                                            @@ -4053,14 +4053,14 @@

                                                                            Submodules
                                                                            -max_len = 70[source]
                                                                            +max_len = 70[source]

                                                                            -class CifFile(data: dict[str, CifBlock], orig_string: str | None = None, comment: str | None = None)[source]
                                                                            +class CifFile(data: dict[str, CifBlock], orig_string: str | None = None, comment: str | None = None)[source]

                                                                            Bases: object

                                                                            Read and parse CifBlocks from a .cif file or string.

                                                                            @@ -4074,7 +4074,7 @@

                                                                            Submodules
                                                                            -classmethod from_file(filename: PathLike) → Self[source]
                                                                            +classmethod from_file(filename: PathLike) → Self[source]

                                                                            Read CifFile from a filename.

                                                                            Parameters:
                                                                            @@ -4088,7 +4088,7 @@

                                                                            Submodules
                                                                            -classmethod from_str(string: str) → Self[source]
                                                                            +classmethod from_str(string: str) → Self[source]

                                                                            Read CifFile from a string.

                                                                            Parameters:
                                                                            @@ -4104,7 +4104,7 @@

                                                                            Submodules
                                                                            -class CifParser(filename: PathLike | StringIO, occupancy_tolerance: float = 1.0, site_tolerance: float = 0.0001, frac_tolerance: float = 0.0001, check_cif: bool = True, comp_tol: float = 0.01)[source]
                                                                            +class CifParser(filename: PathLike | StringIO, occupancy_tolerance: float = 1.0, site_tolerance: float = 0.0001, frac_tolerance: float = 0.0001, check_cif: bool = True, comp_tol: float = 0.01)[source]

                                                                            Bases: object

                                                                            CIF file parser. Attempt to fix CIFs that are out-of-spec, but will issue warnings if corrections applied. These are also stored in the CifParser’s warnings attribute. @@ -4132,13 +4132,13 @@

                                                                            Submodules
                                                                            -as_dict() → dict[source]
                                                                            +as_dict() → dict[source]

                                                                            MSONable dict

                                                                            -check(structure: Structure) → str | None[source]
                                                                            +check(structure: Structure) → str | None[source]

                                                                            Check whether a Structure created from CIF passes sanity checks.

                                                                            Checks:
                                                                              @@ -4178,7 +4178,7 @@

                                                                              Submodules
                                                                              -classmethod from_str(cif_string: str, **kwargs) → Self[source]
                                                                              +classmethod from_str(cif_string: str, **kwargs) → Self[source]

                                                                              Create a CifParser from a string.

                                                                              Parameters:
                                                                              @@ -4192,7 +4192,7 @@

                                                                              Submodules
                                                                              -get_bibtex_string() → str[source]
                                                                              +get_bibtex_string() → str[source]

                                                                              Get BibTeX reference from CIF file.

                                                                              Parameters:
                                                                              @@ -4206,7 +4206,7 @@

                                                                              Submodules
                                                                              -get_lattice(data: CifBlock, length_strings=('a', 'b', 'c'), angle_strings=('alpha', 'beta', 'gamma'), lattice_type=None) → Lattice | None[source]
                                                                              +get_lattice(data: CifBlock, length_strings=('a', 'b', 'c'), angle_strings=('alpha', 'beta', 'gamma'), lattice_type=None) → Lattice | None[source]

                                                                              Generate the lattice from the provided lattice parameters. In the absence of all six lattice parameters, the crystal system and necessary parameters are parsed.

                                                                              @@ -4214,7 +4214,7 @@

                                                                              Submodules
                                                                              -static get_lattice_no_exception(data: CifBlock, length_strings: tuple[str, str, str] = ('a', 'b', 'c'), angle_strings: tuple[str, str, str] = ('alpha', 'beta', 'gamma'), lattice_type: str | None = None) → Lattice[source]
                                                                              +static get_lattice_no_exception(data: CifBlock, length_strings: tuple[str, str, str] = ('a', 'b', 'c'), angle_strings: tuple[str, str, str] = ('alpha', 'beta', 'gamma'), lattice_type: str | None = None) → Lattice[source]

                                                                              Convert a CifBlock to a pymatgen Lattice.

                                                                              Parameters:
                                                                              @@ -4233,7 +4233,7 @@

                                                                              Submodules
                                                                              -get_magsymops(data: CifBlock) → list[MagSymmOp][source]
                                                                              +get_magsymops(data: CifBlock) → list[MagSymmOp][source]

                                                                              Equivalent to get_symops except for magnetic symmetry groups. Separate function since additional operation for time reversal symmetry (which changes magnetic moments on sites) needs to be returned.

                                                                              @@ -4241,12 +4241,12 @@

                                                                              Submodules
                                                                              -get_structures(**kwargs)[source]
                                                                              +get_structures(**kwargs)[source]

                                                                              -get_symops(data: CifBlock) → list[SymmOp][source]
                                                                              +get_symops(data: CifBlock) → list[SymmOp][source]

                                                                              Get the symmetry operations, in order to generate symmetry equivalent positions. If no symops are present, the space group symbol is parsed, and symops are generated.

                                                                              @@ -4254,13 +4254,13 @@

                                                                              Submodules
                                                                              -property has_errors: bool[source]
                                                                              +property has_errors: bool[source]

                                                                              Whether there are errors/warnings detected in CIF parsing.

                                                                              -parse_structures(primitive: bool | None = None, symmetrized: bool = False, check_occu: bool = True, on_error: Literal['ignore', 'warn', 'raise'] = 'warn') → list[Structure][source]
                                                                              +parse_structures(primitive: bool | None = None, symmetrized: bool = False, check_occu: bool = True, on_error: Literal['ignore', 'warn', 'raise'] = 'warn') → list[Structure][source]

                                                                              Return list of structures in CIF file.

                                                                              Parameters:
                                                                              @@ -4297,7 +4297,7 @@

                                                                              Submodules
                                                                              -class CifWriter(struct: Structure, symprec: float | None = None, write_magmoms: bool = False, significant_figures: int = 8, angle_tolerance: float = 5, refine_struct: bool = True, write_site_properties: bool = False)[source]
                                                                              +class CifWriter(struct: Structure, symprec: float | None = None, write_magmoms: bool = False, significant_figures: int = 8, angle_tolerance: float = 5, refine_struct: bool = True, write_site_properties: bool = False)[source]

                                                                              Bases: object

                                                                              A wrapper around CifFile to write CIF files from pymatgen Structure.

                                                                              @@ -4323,13 +4323,13 @@

                                                                              Submodules
                                                                              -property cif_file: CifFile[source]
                                                                              +property cif_file: CifFile[source]

                                                                              CifFile associated with the CifWriter.

                                                                              -write_file(filename: str | Path, mode: Literal['w', 'a', 'wt', 'at'] = 'w') → None[source]
                                                                              +write_file(filename: str | Path, mode: Literal['w', 'a', 'wt', 'at'] = 'w') → None[source]

                                                                              Write the CIF file.

                                                                              @@ -4337,7 +4337,7 @@

                                                                              Submodules
                                                                              -str2float(text: str) → float[source]
                                                                              +str2float(text: str) → float[source]

                                                                              Remove uncertainty brackets from strings and return the float.

                                                                              @@ -4347,13 +4347,13 @@

                                                                              Submodules
                                                                              -class VolumetricData(structure: Structure, data: dict[str, ndarray], distance_matrix: ndarray | None = None, data_aug: ndarray | None = None)[source]
                                                                              +class VolumetricData(structure: Structure, data: dict[str, ndarray], distance_matrix: ndarray | None = None, data_aug: ndarray | None = None)[source]

                                                                              Bases: MSONable

                                                                              Simple volumetric object. Used to read LOCPOT/CHGCAR files produced by vasp as well as cube files produced by other codes.

                                                                              -structure[source]
                                                                              +structure[source]

                                                                              Structure associated with the Volumetric Data object.

                                                                              Type:
                                                                              @@ -4364,7 +4364,7 @@

                                                                              Submodules
                                                                              -is_spin_polarized[source]
                                                                              +is_spin_polarized[source]

                                                                              True if run is spin polarized.

                                                                              Type:
                                                                              @@ -4375,7 +4375,7 @@

                                                                              Submodules
                                                                              -dim[source]
                                                                              +dim[source]

                                                                              Tuple of dimensions of volumetric grid in each direction (nx, ny, nz).

                                                                              Type:
                                                                              @@ -4386,7 +4386,7 @@

                                                                              Submodules
                                                                              -data[source]
                                                                              +data[source]

                                                                              Actual data as a dict of {string: np.array}. The string are “total” and “diff”, in accordance to the output format of Vasp LOCPOT and CHGCAR files where the total spin density is written first, followed @@ -4400,7 +4400,7 @@

                                                                              Submodules
                                                                              -ngridpts[source]
                                                                              +ngridpts[source]

                                                                              Total number of grid points in volumetric data.

                                                                              Type:
                                                                              @@ -4427,13 +4427,13 @@

                                                                              Submodules
                                                                              -copy() → Self[source]
                                                                              +copy() → Self[source]

                                                                              Make a copy of VolumetricData object

                                                                              -classmethod from_cube(filename: str | Path) → Self[source]
                                                                              +classmethod from_cube(filename: str | Path) → Self[source]

                                                                              Initialize the cube object and store the data as data.

                                                                              Parameters:
                                                                              @@ -4444,7 +4444,7 @@

                                                                              Submodules
                                                                              -classmethod from_hdf5(filename: str, **kwargs) → Self[source]
                                                                              +classmethod from_hdf5(filename: str, **kwargs) → Self[source]

                                                                              Reads VolumetricData from HDF5 file.

                                                                              Parameters:
                                                                              @@ -4458,7 +4458,7 @@

                                                                              Submodules
                                                                              -get_average_along_axis(ind)[source]
                                                                              +get_average_along_axis(ind)[source]

                                                                              Get the averaged total of the volumetric data a certain axis direction. For example, useful for visualizing Hartree Potentials from a LOCPOT file.

                                                                              @@ -4474,7 +4474,7 @@

                                                                              Submodules
                                                                              -get_axis_grid(ind)[source]
                                                                              +get_axis_grid(ind)[source]

                                                                              Get the grid for a particular axis.

                                                                              Parameters:
                                                                              @@ -4485,7 +4485,7 @@

                                                                              Submodules
                                                                              -get_integrated_diff(ind, radius, nbins=1)[source]
                                                                              +get_integrated_diff(ind, radius, nbins=1)[source]

                                                                              Get integrated difference of atom index ind up to radius. This can be an extremely computationally intensive process, depending on how many grid points are in the VolumetricData.

                                                                              @@ -4510,7 +4510,7 @@

                                                                              Submodules
                                                                              -linear_add(other, scale_factor=1.0)[source]
                                                                              +linear_add(other, scale_factor=1.0)[source]

                                                                              Method to do a linear sum of volumetric objects. Used by + and - operators as well. Returns a VolumetricData object containing the linear sum.

                                                                              @@ -4529,7 +4529,7 @@

                                                                              Submodules
                                                                              -linear_slice(p1, p2, n=100)[source]
                                                                              +linear_slice(p1, p2, n=100)[source]

                                                                              Get a linear slice of the volumetric data with n data points from point p1 to point p2, in the form of a list.

                                                                              @@ -4549,13 +4549,13 @@

                                                                              Submodules
                                                                              -scale(factor)[source]
                                                                              +scale(factor)[source]

                                                                              Scale the data in place by a factor.

                                                                              -property spin_data[source]
                                                                              +property spin_data[source]

                                                                              data}. Essentially, this provides the actual Spin.up and Spin.down data instead of the total and diff. Note that by definition, a @@ -4569,7 +4569,7 @@

                                                                              Submodules
                                                                              -to_cube(filename, comment: str = '')[source]
                                                                              +to_cube(filename, comment: str = '')[source]

                                                                              Write the total volumetric data to a cube file format, which consists of two comment lines, a header section defining the structure IN BOHR, and the data.

                                                                              @@ -4584,7 +4584,7 @@

                                                                              Submodules
                                                                              -to_hdf5(filename)[source]
                                                                              +to_hdf5(filename)[source]

                                                                              Write the VolumetricData to a HDF5 format, which is a highly optimized format for reading storing large data. The mapping of the VolumetricData to this file format is as follows:

                                                                              @@ -4608,7 +4608,7 @@

                                                                              Submodules
                                                                              -value_at(x, y, z)[source]
                                                                              +value_at(x, y, z)[source]

                                                                              Get a data value from self.data at a given point (x, y, z) in terms of fractional lattice parameters. Will be interpolated using a RegularGridInterpolator on self.data if (x, y, z) is not in the original @@ -4658,7 +4658,7 @@

                                                                              Submodules
                                                                              -class InputFile[source]
                                                                              +class InputFile[source]

                                                                              Bases: MSONable

                                                                              Abstract base class to represent a single input file. Note that use of this class is optional; it is possible create an InputSet that does not rely on underlying @@ -4669,7 +4669,7 @@

                                                                              Submodules
                                                                              -classmethod from_file(path: str | Path) → None[source]
                                                                              +classmethod from_file(path: str | Path) → None[source]

                                                                              Creates an InputFile object from a file.

                                                                              Parameters:
                                                                              @@ -4683,7 +4683,7 @@

                                                                              Submodules
                                                                              -abstract classmethod from_str(contents: str) → None[source]
                                                                              +abstract classmethod from_str(contents: str) → None[source]

                                                                              Create an InputFile object from a string.

                                                                              Parameters:
                                                                              @@ -4697,13 +4697,13 @@

                                                                              Submodules
                                                                              -abstract get_str() → str[source]
                                                                              +abstract get_str() → str[source]

                                                                              Return a string representation of an entire input file.

                                                                              -write_file(filename: str | PathLike) → None[source]
                                                                              +write_file(filename: str | PathLike) → None[source]

                                                                              Write the input file.

                                                                              Parameters:
                                                                              @@ -4716,14 +4716,14 @@

                                                                              Submodules
                                                                              -class InputGenerator[source]
                                                                              +class InputGenerator[source]

                                                                              Bases: MSONable

                                                                              InputGenerator classes serve as generators for Input objects. They contain settings or sets of instructions for how to create Input from a set of coordinates or a previous calculation directory.

                                                                              -abstract get_input_set(*args, **kwargs)[source]
                                                                              +abstract get_input_set(*args, **kwargs)[source]

                                                                              Generate an InputSet object. Typically the first argument to this method will be a Structure or other form of atomic coordinates.

                                                                              @@ -4732,7 +4732,7 @@

                                                                              Submodules
                                                                              -class InputSet(inputs: dict[str | Path, str | InputFile] | None = None, **kwargs)[source]
                                                                              +class InputSet(inputs: dict[str | Path, str | InputFile] | None = None, **kwargs)[source]

                                                                              Bases: MSONable, MutableMapping

                                                                              Abstract base class for all InputSet classes. InputSet are dict-like containers for all calculation input data.

                                                                              @@ -4759,7 +4759,7 @@

                                                                              Submodules
                                                                              -classmethod from_directory(directory: str | Path) → None[source]
                                                                              +classmethod from_directory(directory: str | Path) → None[source]

                                                                              Construct an InputSet from a directory of one or more files.

                                                                              Parameters:
                                                                              @@ -4770,7 +4770,7 @@

                                                                              Submodules
                                                                              -validate() → bool[source]
                                                                              +validate() → bool[source]

                                                                              A place to implement basic checks to verify the validity of an input set. Can be as simple or as complex as desired.

                                                                              Will raise a NotImplementedError unless overloaded by the inheriting class.

                                                                              @@ -4778,7 +4778,7 @@

                                                                              Submodules
                                                                              -write_input(directory: str | Path, make_dir: bool = True, overwrite: bool = True, zip_inputs: bool = False)[source]
                                                                              +write_input(directory: str | Path, make_dir: bool = True, overwrite: bool = True, zip_inputs: bool = False)[source]

                                                                              Write Inputs to one or more files.

                                                                              Parameters:
                                                                              @@ -4798,7 +4798,7 @@

                                                                              Submodules
                                                                              -exception ParseError[source]
                                                                              +exception ParseError[source]

                                                                              Bases: SyntaxError

                                                                              This exception indicates a problem was encountered during parsing due to unexpected formatting.

                                                                              @@ -4809,7 +4809,7 @@

                                                                              Submodules
                                                                              -class Cssr(structure: Structure)[source]
                                                                              +class Cssr(structure: Structure)[source]

                                                                              Bases: object

                                                                              Basic object for working with Cssr file. Right now, only conversion from a Structure to a Cssr file is supported.

                                                                              @@ -4820,7 +4820,7 @@

                                                                              Submodules
                                                                              -classmethod from_file(filename: str | Path) → Self[source]
                                                                              +classmethod from_file(filename: str | Path) → Self[source]

                                                                              Reads a CSSR file to a Cssr object.

                                                                              Parameters:
                                                                              @@ -4834,7 +4834,7 @@

                                                                              Submodules
                                                                              -classmethod from_str(string: str) → Self[source]
                                                                              +classmethod from_str(string: str) → Self[source]

                                                                              Reads a string representation to a Cssr object.

                                                                              Parameters:
                                                                              @@ -4848,7 +4848,7 @@

                                                                              Submodules
                                                                              -write_file(filename)[source]
                                                                              +write_file(filename)[source]

                                                                              Write out a CSSR file.

                                                                              Parameters:
                                                                              @@ -4870,7 +4870,7 @@

                                                                              Submodules
                                                                              -class BSEOutput(filename)[source]
                                                                              +class BSEOutput(filename)[source]

                                                                              Bases: object

                                                                              A bse output file parser. The start…

                                                                              All energies are in eV.

                                                                              @@ -4883,7 +4883,7 @@

                                                                              Submodules
                                                                              -class BasisSetReader(filename)[source]
                                                                              +class BasisSetReader(filename)[source]

                                                                              Bases: object

                                                                              A basis set reader. Basis set are stored in data as a dict: @@ -4896,12 +4896,12 @@

                                                                              Submodules
                                                                              -infos_on_basis_set()[source]
                                                                              +infos_on_basis_set()[source]

                                                                              -set_n_nlmo()[source]
                                                                              +set_n_nlmo()[source]

                                                                              the number of nlm orbitals for the basis set

                                                                              @@ -4909,7 +4909,7 @@

                                                                              Submodules
                                                                              -class FiestaInput(mol, correlation_grid: dict[str, str] | None = None, exc_dft_option: dict[str, str] | None = None, cohsex_options: dict[str, str] | None = None, gw_options: dict[str, str] | None = None, bse_tddft_options: dict[str, str] | None = None)[source]
                                                                              +class FiestaInput(mol, correlation_grid: dict[str, str] | None = None, exc_dft_option: dict[str, str] | None = None, cohsex_options: dict[str, str] | None = None, gw_options: dict[str, str] | None = None, bse_tddft_options: dict[str, str] | None = None)[source]

                                                                              Bases: MSONable

                                                                              Input File for Fiesta called “cell.in” by default (mandatory in Fiesta for now).

                                                                              @@ -4926,13 +4926,13 @@

                                                                              Submodules
                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              MSONable dict

                                                                              -dump_bse_data_in_gw_run(BSE_dump=True)[source]
                                                                              +dump_bse_data_in_gw_run(BSE_dump=True)[source]
                                                                              Parameters:

                                                                              BSE_dump – bool

                                                                              @@ -4945,7 +4945,7 @@

                                                                              Submodules
                                                                              -dump_tddft_data_in_gw_run(tddft_dump: bool = True)[source]
                                                                              +dump_tddft_data_in_gw_run(tddft_dump: bool = True)[source]
                                                                              Parameters:

                                                                              TDDFT_dump – bool

                                                                              @@ -4958,7 +4958,7 @@

                                                                              Submodules
                                                                              -classmethod from_dict(dct: dict) → Self[source]
                                                                              +classmethod from_dict(dct: dict) → Self[source]
                                                                              Parameters:

                                                                              dct (dict) – Dict representation

                                                                              @@ -4971,7 +4971,7 @@

                                                                              Submodules
                                                                              -classmethod from_file(filename: str | Path) → Self[source]
                                                                              +classmethod from_file(filename: str | Path) → Self[source]

                                                                              Read an Fiesta input from a file. Currently tested to work with files generated from this class itself.

                                                                              @@ -4986,7 +4986,7 @@

                                                                              Submodules
                                                                              -classmethod from_str(string_input: str) → Self[source]
                                                                              +classmethod from_str(string_input: str) → Self[source]

                                                                              Read an FiestaInput from a string. Currently tested to work with files generated from this class itself.

                                                                              @@ -5001,25 +5001,25 @@

                                                                              Submodules
                                                                              -property infos_on_system[source]
                                                                              +property infos_on_system[source]

                                                                              Infos on initial parameters as in the log file of Fiesta.

                                                                              -static make_full_bse_densities_folder(folder)[source]
                                                                              +static make_full_bse_densities_folder(folder)[source]

                                                                              Mkdir “FULL_BSE_Densities” folder (needed for bse run) in the desired folder.

                                                                              -property molecule[source]
                                                                              +property molecule[source]

                                                                              Molecule associated with this FiestaInput.

                                                                              -set_auxiliary_basis_set(folder, auxiliary_folder, auxiliary_basis_set_type='aug_cc_pvtz')[source]
                                                                              +set_auxiliary_basis_set(folder, auxiliary_folder, auxiliary_basis_set_type='aug_cc_pvtz')[source]

                                                                              copy in the desired folder the needed auxiliary basis set “X2.ion” where X is a specie.

                                                                              Parameters:
                                                                              @@ -5034,7 +5034,7 @@

                                                                              Submodules
                                                                              -set_bse_options(n_excitations=10, nit_bse=200)[source]
                                                                              +set_bse_options(n_excitations=10, nit_bse=200)[source]

                                                                              Set parameters in cell.in for a BSE computation

                                                                              Parameters:
                                                                              @@ -5050,7 +5050,7 @@

                                                                              Submodules
                                                                              -set_gw_options(nv_band=10, nc_band=10, n_iteration=5, n_grid=6, dE_grid=0.5)[source]
                                                                              +set_gw_options(nv_band=10, nc_band=10, n_iteration=5, n_grid=6, dE_grid=0.5)[source]

                                                                              Set parameters in cell.in for a GW computation

                                                                              Parameters:
                                                                              @@ -5066,7 +5066,7 @@

                                                                              Submodules
                                                                              -write_file(filename: str | Path) → None[source]
                                                                              +write_file(filename: str | Path) → None[source]

                                                                              Write FiestaInput to a file

                                                                              Parameters:
                                                                              @@ -5079,7 +5079,7 @@

                                                                              Submodules
                                                                              -class FiestaOutput(filename)[source]
                                                                              +class FiestaOutput(filename)[source]

                                                                              Bases: object

                                                                              A Fiesta output file parser.

                                                                              All energies are in eV.

                                                                              @@ -5092,7 +5092,7 @@

                                                                              Submodules
                                                                              -class FiestaRun(folder: str | None = None, grid: Tuple3Ints = (2, 2, 2), log_file: str = 'log')[source]
                                                                              +class FiestaRun(folder: str | None = None, grid: Tuple3Ints = (2, 2, 2), log_file: str = 'log')[source]

                                                                              Bases: MSONable

                                                                              To run FIESTA inside python:

                                                                              if grid is [x,x] then bse runs @@ -5111,19 +5111,19 @@

                                                                              Submodules
                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              MSONable dict

                                                                              -bse_run()[source]
                                                                              +bse_run()[source]

                                                                              Perform BSE run.

                                                                              -classmethod from_dict(dct: dict) → Self[source]
                                                                              +classmethod from_dict(dct: dict) → Self[source]
                                                                              Parameters:

                                                                              dct (dict) – Dict representation

                                                                              @@ -5136,7 +5136,7 @@

                                                                              Submodules
                                                                              -run()[source]
                                                                              +run()[source]

                                                                              Perform FIESTA (gw) run.

                                                                              @@ -5144,7 +5144,7 @@

                                                                              Submodules
                                                                              -class Nwchem2Fiesta(folder, filename='nwchem', log_file='log_n2f')[source]
                                                                              +class Nwchem2Fiesta(folder, filename='nwchem', log_file='log_n2f')[source]

                                                                              Bases: MSONable

                                                                              To run NWCHEM2FIESTA inside python:

                                                                              If nwchem.nw is the input, nwchem.out the output, and structure.movecs the @@ -5161,13 +5161,13 @@

                                                                              Submodules
                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              MSONable dict

                                                                              -classmethod from_dict(dct: dict) → Self[source]
                                                                              +classmethod from_dict(dct: dict) → Self[source]
                                                                              Parameters:

                                                                              dct (dict) – Dict representation.

                                                                              @@ -5180,7 +5180,7 @@

                                                                              Submodules
                                                                              -run()[source]
                                                                              +run()[source]

                                                                              Perform actual NWCHEM2FIESTA run.

                                                                              @@ -5192,7 +5192,7 @@

                                                                              Submodules
                                                                              -class GaussianInput(mol, charge=None, spin_multiplicity=None, title=None, functional='HF', basis_set='6-31G(d)', route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag='#P', gen_basis=None)[source]
                                                                              +class GaussianInput(mol, charge=None, spin_multiplicity=None, title=None, functional='HF', basis_set='6-31G(d)', route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag='#P', gen_basis=None)[source]

                                                                              Bases: object

                                                                              A Gaussian input file.

                                                                              @@ -5232,13 +5232,13 @@

                                                                              Submodules
                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              MSONable dict

                                                                              -classmethod from_dict(dct: dict) → Self[source]
                                                                              +classmethod from_dict(dct: dict) → Self[source]
                                                                              Parameters:

                                                                              dct – dict

                                                                              @@ -5251,7 +5251,7 @@

                                                                              Submodules
                                                                              -classmethod from_file(filename: str | Path) → Self[source]
                                                                              +classmethod from_file(filename: str | Path) → Self[source]

                                                                              Creates GaussianInput from a file.

                                                                              Parameters:
                                                                              @@ -5265,7 +5265,7 @@

                                                                              Submodules
                                                                              -classmethod from_str(contents: str) → Self[source]
                                                                              +classmethod from_str(contents: str) → Self[source]

                                                                              Creates GaussianInput from a string.

                                                                              Parameters:
                                                                              @@ -5279,25 +5279,25 @@

                                                                              Submodules
                                                                              -get_cart_coords() → str[source]
                                                                              +get_cart_coords() → str[source]

                                                                              Return the Cartesian coordinates of the molecule.

                                                                              -get_zmatrix()[source]
                                                                              +get_zmatrix()[source]

                                                                              Get a z-matrix representation of the molecule.

                                                                              -property molecule[source]
                                                                              +property molecule[source]

                                                                              Molecule associated with this GaussianInput.

                                                                              -to_str(cart_coords=False)[source]
                                                                              +to_str(cart_coords=False)[source]

                                                                              Return GaussianInput string.

                                                                              Parameters:
                                                                              @@ -5309,7 +5309,7 @@

                                                                              Submodules
                                                                              -write_file(filename, cart_coords=False)[source]
                                                                              +write_file(filename, cart_coords=False)[source]

                                                                              Write the input string into a file.

                                                                              Option: see __str__ method

                                                                              @@ -5318,13 +5318,13 @@

                                                                              Submodules
                                                                              -class GaussianOutput(filename)[source]
                                                                              +class GaussianOutput(filename)[source]

                                                                              Bases: object

                                                                              Parser for Gaussian output files.

                                                                              Note: Still in early beta.

                                                                              -structures[source]
                                                                              +structures[source]

                                                                              All structures from the calculation in the standard orientation. If the symmetry is not considered, the standard orientation is not printed out and the input orientation is used instead. Check the standard_orientation @@ -5338,7 +5338,7 @@

                                                                              Submodules
                                                                              -structures_input_orientation[source]
                                                                              +structures_input_orientation[source]

                                                                              All structures from the calculation in the input orientation or the Z-matrix orientation (if an opt=z-matrix was requested).

                                                                              @@ -5350,7 +5350,7 @@

                                                                              Submodules
                                                                              -opt_structures[source]
                                                                              +opt_structures[source]

                                                                              All optimized structures from the calculation in the standard orientation, if the attribute ‘standard_orientation’ is True, otherwise in the input or the Z-matrix orientation.

                                                                              @@ -5363,7 +5363,7 @@

                                                                              Submodules
                                                                              -energies[source]
                                                                              +energies[source]

                                                                              All energies from the calculation.

                                                                              Type:
                                                                              @@ -5374,7 +5374,7 @@

                                                                              Submodules
                                                                              -eigenvalues[source]
                                                                              +eigenvalues[source]

                                                                              List of eigenvalues for the last geometry.

                                                                              Type:
                                                                              @@ -5385,7 +5385,7 @@

                                                                              Submodules
                                                                              -MO_coefficients[source]
                                                                              +MO_coefficients[source]

                                                                              Matrix of MO coefficients for the last geometry.

                                                                              Type:
                                                                              @@ -5396,7 +5396,7 @@

                                                                              Submodules
                                                                              -cart_forces[source]
                                                                              +cart_forces[source]

                                                                              All Cartesian forces from the calculation.

                                                                              Type:
                                                                              @@ -5407,7 +5407,7 @@

                                                                              Submodules
                                                                              -frequencies[source]
                                                                              +frequencies[source]

                                                                              A list for each freq calculation and for each mode of a dict with {

                                                                              @@ -5431,7 +5431,7 @@

                                                                              Submodules
                                                                              -hessian[source]
                                                                              +hessian[source]

                                                                              Matrix of second derivatives of the energy with respect to cartesian coordinates in the input orientation frame. Need #P in the route section in order to be in the output.

                                                                              @@ -5444,7 +5444,7 @@

                                                                              Submodules
                                                                              -properly_terminated[source]
                                                                              +properly_terminated[source]

                                                                              True if run has properly terminated.

                                                                              Type:
                                                                              @@ -5455,7 +5455,7 @@

                                                                              Submodules
                                                                              -is_pcm[source]
                                                                              +is_pcm[source]

                                                                              True if run is a PCM run.

                                                                              Type:
                                                                              @@ -5466,7 +5466,7 @@

                                                                              Submodules
                                                                              -is_spin[source]
                                                                              +is_spin[source]

                                                                              True if it is an unrestricted run.

                                                                              Type:
                                                                              @@ -5477,7 +5477,7 @@

                                                                              Submodules
                                                                              -stationary_type[source]
                                                                              +stationary_type[source]

                                                                              If it is a relaxation run, indicates whether it is a minimum (Minimum) or a saddle point (“Saddle”).

                                                                              @@ -5489,7 +5489,7 @@

                                                                              Submodules
                                                                              -corrections[source]
                                                                              +corrections[source]

                                                                              Thermochemical corrections if this run is a Freq run as a dict. Keys are “Zero-point”, “Thermal”, “Enthalpy” and “Gibbs Free Energy”.

                                                                              @@ -5501,7 +5501,7 @@

                                                                              Submodules
                                                                              -functional[source]
                                                                              +functional[source]

                                                                              Functional used in the run.

                                                                              Type:
                                                                              @@ -5512,7 +5512,7 @@

                                                                              Submodules
                                                                              -basis_set[source]
                                                                              +basis_set[source]

                                                                              Basis set used in the run.

                                                                              Type:
                                                                              @@ -5523,7 +5523,7 @@

                                                                              Submodules
                                                                              -route[source]
                                                                              +route[source]

                                                                              Additional route parameters as a dict. For example, {‘SP’:””, “SCF”:”Tight”}.

                                                                              @@ -5535,7 +5535,7 @@

                                                                              Submodules
                                                                              -dieze_tag[source]
                                                                              +dieze_tag[source]

                                                                              # preceding the route line, e.g. “#P”.

                                                                              Type:
                                                                              @@ -5546,7 +5546,7 @@

                                                                              Submodules
                                                                              -link0[source]
                                                                              +link0[source]

                                                                              Link0 parameters as a dict. e.g. {“%mem”: “1000MW”}.

                                                                              Type:
                                                                              @@ -5557,7 +5557,7 @@

                                                                              Submodules
                                                                              -charge[source]
                                                                              +charge[source]

                                                                              Charge for structure.

                                                                              Type:
                                                                              @@ -5568,7 +5568,7 @@

                                                                              Submodules
                                                                              -spin_multiplicity[source]
                                                                              +spin_multiplicity[source]

                                                                              Spin multiplicity for structure.

                                                                              Type:
                                                                              @@ -5579,7 +5579,7 @@

                                                                              Submodules
                                                                              -num_basis_func[source]
                                                                              +num_basis_func[source]

                                                                              Number of basis functions in the run.

                                                                              Type:
                                                                              @@ -5590,7 +5590,7 @@

                                                                              Submodules
                                                                              -electrons[source]
                                                                              +electrons[source]

                                                                              Number of alpha and beta electrons as (N alpha, N beta).

                                                                              Type:
                                                                              @@ -5601,7 +5601,7 @@

                                                                              Submodules
                                                                              -pcm[source]
                                                                              +pcm[source]

                                                                              PCM parameters and output if available.

                                                                              Type:
                                                                              @@ -5612,7 +5612,7 @@

                                                                              Submodules
                                                                              -errors[source]
                                                                              +errors[source]

                                                                              Error if not properly terminated (list to be completed in error_defs).

                                                                              Type:
                                                                              @@ -5623,7 +5623,7 @@

                                                                              Submodules
                                                                              -Mulliken_charges[source]
                                                                              +Mulliken_charges[source]

                                                                              Mulliken atomic charges.

                                                                              Type:
                                                                              @@ -5634,7 +5634,7 @@

                                                                              Submodules
                                                                              -eigenvectors[source]
                                                                              +eigenvectors[source]

                                                                              Matrix of shape (num_basis_func, num_basis_func). Each column is an eigenvectors and contains AO coefficients of an MO. eigenvectors[Spin] = mat(num_basis_func, num_basis_func).

                                                                              @@ -5647,7 +5647,7 @@

                                                                              Submodules
                                                                              -molecular_orbital[source]
                                                                              +molecular_orbital[source]

                                                                              MO development coefficients on AO in a more convenient array dict for each atom and basis set label. mo[Spin][OM j][atom i] = {AO_k: coeff, AO_k: coeff … }.

                                                                              @@ -5660,7 +5660,7 @@

                                                                              Submodules
                                                                              -atom_basis_labels[source]
                                                                              +atom_basis_labels[source]

                                                                              Labels of AO for each atoms. These labels are those used in the output of molecular orbital coefficients (POP=Full) and in the molecular_orbital array dict. atom_basis_labels[iatom] = [AO_k, AO_k, …].

                                                                              @@ -5673,7 +5673,7 @@

                                                                              Submodules
                                                                              -resumes[source]
                                                                              +resumes[source]

                                                                              List of gaussian data resume given at the end of the output file before the quotation. The resumes are given as string.

                                                                              @@ -5685,7 +5685,7 @@

                                                                              Submodules
                                                                              -title[source]
                                                                              +title[source]

                                                                              Title of the gaussian run.

                                                                              Type:
                                                                              @@ -5696,7 +5696,7 @@

                                                                              Submodules
                                                                              -standard_orientation[source]
                                                                              +standard_orientation[source]

                                                                              If True, the geometries stored in the structures are in the standard orientation. Else, the geometries are in the input orientation.

                                                                              @@ -5708,7 +5708,7 @@

                                                                              Submodules
                                                                              -bond_orders[source]
                                                                              +bond_orders[source]

                                                                              Dict of bond order values read in the output file such as: {(0, 1): 0.8709, (1, 6): 1.234, …}. The keys are the atom indexes and the values are the Wiberg bond indexes that are @@ -5722,26 +5722,26 @@

                                                                              Submodules
                                                                              -to_input()[source]
                                                                              +to_input()[source]

                                                                              Return a GaussianInput object using the last geometry and the same calculation parameters.

                                                                              -read_scan()[source]
                                                                              +read_scan()[source]

                                                                              Read a potential energy surface from a gaussian scan calculation.

                                                                              -get_scan_plot()[source]
                                                                              +get_scan_plot()[source]

                                                                              Get a matplotlib plot of the potential energy surface

                                                                              -save_scan_plot()[source]
                                                                              +save_scan_plot()[source]

                                                                              Save a matplotlib plot of the potential energy surface to a file

                                                                              @@ -5752,25 +5752,25 @@

                                                                              Submodules
                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              JSON-serializable dict representation.

                                                                              -property final_energy[source]
                                                                              +property final_energy[source]

                                                                              Final energy in Gaussian output.

                                                                              -property final_structure[source]
                                                                              +property final_structure[source]

                                                                              Final structure in Gaussian output.

                                                                              -get_scan_plot(coords=None)[source]
                                                                              +get_scan_plot(coords=None)[source]

                                                                              Get a matplotlib plot of the potential energy surface.

                                                                              Parameters:
                                                                              @@ -5781,7 +5781,7 @@

                                                                              Submodules
                                                                              -get_spectre_plot(sigma=0.05, step=0.01)[source]
                                                                              +get_spectre_plot(sigma=0.05, step=0.01)[source]

                                                                              Get a matplotlib plot of the UV-visible xas. Transitions are plotted as vertical lines and as a sum of normal functions with sigma with. The broadening is applied in energy and the xas is plotted as a function @@ -5810,7 +5810,7 @@

                                                                              Submodules
                                                                              -read_excitation_energies()[source]
                                                                              +read_excitation_energies()[source]

                                                                              Read a excitation energies after a TD-DFT calculation.

                                                                              Returns:
                                                                              @@ -5828,7 +5828,7 @@

                                                                              Submodules
                                                                              -read_scan()[source]
                                                                              +read_scan()[source]

                                                                              Read a potential energy surface from a gaussian scan calculation.

                                                                              Returns:
                                                                              @@ -5846,7 +5846,7 @@

                                                                              Submodules
                                                                              -save_scan_plot(filename='scan.pdf', img_format='pdf', coords=None)[source]
                                                                              +save_scan_plot(filename='scan.pdf', img_format='pdf', coords=None)[source]

                                                                              Save matplotlib plot of the potential energy surface to a file.

                                                                              Parameters:
                                                                              @@ -5861,7 +5861,7 @@

                                                                              Submodules
                                                                              -save_spectre_plot(filename='spectre.pdf', img_format='pdf', sigma=0.05, step=0.01)[source]
                                                                              +save_spectre_plot(filename='spectre.pdf', img_format='pdf', sigma=0.05, step=0.01)[source]

                                                                              Save matplotlib plot of the spectre to a file.

                                                                              Parameters:
                                                                              @@ -5877,7 +5877,7 @@

                                                                              Submodules
                                                                              -to_input(mol=None, charge=None, spin_multiplicity=None, title=None, functional=None, basis_set=None, route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag=None, cart_coords=False)[source]
                                                                              +to_input(mol=None, charge=None, spin_multiplicity=None, title=None, functional=None, basis_set=None, route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag=None, cart_coords=False)[source]

                                                                              Create a new input object using by default the last geometry read in the output file and with the same calculation parameters. Arguments are the same as GaussianInput class.

                                                                              @@ -5895,7 +5895,7 @@

                                                                              Submodules
                                                                              -read_route_line(route)[source]
                                                                              +read_route_line(route)[source]

                                                                              read route line in gaussian input/output and return functional basis_set and a dictionary of other route parameters.

                                                                              @@ -5918,7 +5918,7 @@

                                                                              Submodules

                                                                              pymatgen.io.icet module

                                                                              -class IcetSQS(structure: Structure, scaling: int, instances: int | None, cluster_cutoffs: dict[int, float], sqs_method: str | None = None, sqs_kwargs: dict | None = None)[source]
                                                                              +class IcetSQS(structure: Structure, scaling: int, instances: int | None, cluster_cutoffs: dict[int, float], sqs_method: str | None = None, sqs_kwargs: dict | None = None)[source]

                                                                              Bases: object

                                                                              Interface to the Icet library of SQS structure generation tools.

                                                                              https://icet.materialsmodeling.org

                                                                              @@ -5951,7 +5951,7 @@

                                                                              Submodules
                                                                              -enumerate_sqs_structures(cluster_space: _ClusterSpace | None = None) → list[source]
                                                                              +enumerate_sqs_structures(cluster_space: _ClusterSpace | None = None) → list[source]

                                                                              Generate an SQS by enumeration of all possible arrangements.

                                                                              Adapted from icet.tools.structure_generation.generate_sqs_by_enumeration to accommodate multiprocessing.

                                                                              @@ -5978,7 +5978,7 @@

                                                                              Submodules
                                                                              -get_icet_sqs_obj(material: Atoms | Structure, cluster_space: _ClusterSpace | None = None) → float[source]
                                                                              +get_icet_sqs_obj(material: Atoms | Structure, cluster_space: _ClusterSpace | None = None) → float[source]

                                                                              Get the SQS objective function.

                                                                              Parameters:
                                                                              @@ -5998,13 +5998,13 @@

                                                                              Submodules
                                                                              -monte_carlo_sqs_structures() → list[source]
                                                                              +monte_carlo_sqs_structures() → list[source]

                                                                              Run self.instances Monte Carlo SQS search with Icet.

                                                                              -run() → Sqs[source]
                                                                              +run() → Sqs[source]

                                                                              Run the SQS search with icet.

                                                                              Returns:
                                                                              @@ -6015,12 +6015,12 @@

                                                                              Submodules
                                                                              -sqs_kwarg_names: ClassVar[dict[str, tuple[str, ...]]] = {'enumeration': ('include_smaller_cells', 'pbc', 'optimality_weight', 'tol'), 'monte_carlo': ('include_smaller_cells', 'pbc', 'T_start', 'T_stop', 'n_steps', 'optimality_weight', 'random_seed', 'tol')}[source]
                                                                              +sqs_kwarg_names: ClassVar[dict[str, tuple[str, ...]]] = {'enumeration': ('include_smaller_cells', 'pbc', 'optimality_weight', 'tol'), 'monte_carlo': ('include_smaller_cells', 'pbc', 'T_start', 'T_stop', 'n_steps', 'optimality_weight', 'random_seed', 'tol')}[source]

                                                                              -sqs_methods: tuple[str, ...] = ('enumeration', 'monte_carlo')[source]
                                                                              +sqs_methods: tuple[str, ...] = ('enumeration', 'monte_carlo')[source]
                                                                              @@ -6032,12 +6032,12 @@

                                                                              Submodules
                                                                              -class JarvisAtomsAdaptor[source]
                                                                              +class JarvisAtomsAdaptor[source]

                                                                              Bases: object

                                                                              Adaptor serves as a bridge between JARVIS Atoms and pymatgen objects.

                                                                              -static get_atoms(structure)[source]
                                                                              +static get_atoms(structure)[source]

                                                                              Get JARVIS Atoms object from pymatgen structure.

                                                                              Parameters:
                                                                              @@ -6051,7 +6051,7 @@

                                                                              Submodules
                                                                              -static get_structure(atoms)[source]
                                                                              +static get_structure(atoms)[source]

                                                                              Get pymatgen structure from JARVIS Atoms.

                                                                              Parameters:
                                                                              @@ -6073,12 +6073,12 @@

                                                                              Submodules
                                                                              -class LMTOCopl(filename='COPL', to_eV=False)[source]
                                                                              +class LMTOCopl(filename='COPL', to_eV=False)[source]

                                                                              Bases: object

                                                                              Read COPL files, which contain COHP data.

                                                                              -cohp_data[source]
                                                                              +cohp_data[source]

                                                                              Contains the COHP data of the form: {bond: {“COHP”: {Spin.up: cohps, Spin.down:cohps},

                                                                              @@ -6094,7 +6094,7 @@

                                                                              Submodules
                                                                              -efermi[source]
                                                                              +efermi[source]

                                                                              The Fermi energy in Ry or eV.

                                                                              Type:
                                                                              @@ -6105,7 +6105,7 @@

                                                                              Submodules
                                                                              -energies[source]
                                                                              +energies[source]

                                                                              Sequence of energies in Ry or eV.

                                                                              Type:
                                                                              @@ -6116,7 +6116,7 @@

                                                                              Submodules
                                                                              -is_spin_polarized[source]
                                                                              +is_spin_polarized[source]

                                                                              Boolean to indicate if the calculation is spin polarized.

                                                                              Type:
                                                                              @@ -6138,7 +6138,7 @@

                                                                              Submodules
                                                                              -class LMTOCtrl(structure: Structure, header: str | None = None, version: str = 'LMASA-47')[source]
                                                                              +class LMTOCtrl(structure: Structure, header: str | None = None, version: str = 'LMASA-47')[source]

                                                                              Bases: object

                                                                              Parse CTRL files from the Stuttgart LMTO-ASA code. Currently, only HEADER, VERS and the structure can be used.

                                                                              @@ -6154,7 +6154,7 @@

                                                                              Submodules
                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              Get the CTRL as a dictionary. “SITE” and “CLASS” are of the form {‘CATEGORY’: {‘TOKEN’: value}}, the rest is of the form ‘TOKEN’/’CATEGORY’: value. It gets the conventional standard @@ -6165,7 +6165,7 @@

                                                                              Submodules
                                                                              -classmethod from_dict(dct: dict) → Self[source]
                                                                              +classmethod from_dict(dct: dict) → Self[source]

                                                                              Creates a CTRL file object from a dictionary. The dictionary must contain the items “ALAT”, PLAT” and “SITE”.

                                                                              @@ -6190,7 +6190,7 @@

                                                                              Submodules
                                                                              -classmethod from_file(filename: str | Path = 'CTRL', **kwargs) → Self[source]
                                                                              +classmethod from_file(filename: str | Path = 'CTRL', **kwargs) → Self[source]

                                                                              Creates a CTRL file object from an existing file.

                                                                              Parameters:
                                                                              @@ -6204,7 +6204,7 @@

                                                                              Submodules
                                                                              -classmethod from_str(data: str, sigfigs: int = 8) → Self[source]
                                                                              +classmethod from_str(data: str, sigfigs: int = 8) → Self[source]

                                                                              Creates a CTRL file object from a string. This will mostly be used to read an LMTOCtrl object from a CTRL file. Empty spheres are ignored.

                                                                              @@ -6220,14 +6220,14 @@

                                                                              Submodules
                                                                              -get_str(sigfigs=8) → str[source]
                                                                              +get_str(sigfigs=8) → str[source]

                                                                              Generate the string representation of the CTRL file. This is the minimal CTRL file necessary to execute lmhart.run.

                                                                              -write_file(filename='CTRL', **kwargs)[source]
                                                                              +write_file(filename='CTRL', **kwargs)[source]

                                                                              Write a CTRL file with structure, HEADER, and VERS that can be used as input for lmhart.run.

                                                                              @@ -6262,7 +6262,7 @@

                                                                              Submodules
                                                                              -class NwInput(mol, tasks, directives=None, geometry_options=('units', 'angstroms'), symmetry_options=None, memory_options=None)[source]
                                                                              +class NwInput(mol, tasks, directives=None, geometry_options=('units', 'angstroms'), symmetry_options=None, memory_options=None)[source]

                                                                              Bases: MSONable

                                                                              An object representing a Nwchem input file, which is essentially a list of tasks on a particular molecule.

                                                                              @@ -6287,13 +6287,13 @@

                                                                              Submodules
                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              Get MSONable dict.

                                                                              -classmethod from_dict(dct: dict) → Self[source]
                                                                              +classmethod from_dict(dct: dict) → Self[source]
                                                                              Parameters:

                                                                              dct (dict) – Dict representation.

                                                                              @@ -6306,7 +6306,7 @@

                                                                              Submodules
                                                                              -classmethod from_file(filename: str | Path) → Self[source]
                                                                              +classmethod from_file(filename: str | Path) → Self[source]

                                                                              Read an NwInput from a file. Currently tested to work with files generated from this class itself.

                                                                              @@ -6321,7 +6321,7 @@

                                                                              Submodules
                                                                              -classmethod from_str(string_input: str) → Self[source]
                                                                              +classmethod from_str(string_input: str) → Self[source]

                                                                              Read an NwInput from a string. Currently tested to work with files generated from this class itself.

                                                                              @@ -6336,13 +6336,13 @@

                                                                              Submodules
                                                                              -property molecule[source]
                                                                              +property molecule[source]

                                                                              Molecule associated with this GaussianInput.

                                                                              -write_file(filename)[source]
                                                                              +write_file(filename)[source]
                                                                              Parameters:

                                                                              filename (str) – Filename.

                                                                              @@ -6354,14 +6354,14 @@

                                                                              Submodules
                                                                              -exception NwInputError[source]
                                                                              +exception NwInputError[source]

                                                                              Bases: Exception

                                                                              Error class for NwInput.

                                                                              -class NwOutput(filename)[source]
                                                                              +class NwOutput(filename)[source]

                                                                              Bases: object

                                                                              A Nwchem output file parser. Very basic for now - supports only dft and only parses energies and geometries. Please note that Nwchem typically @@ -6374,7 +6374,7 @@

                                                                              Submodules
                                                                              -get_excitation_spectrum(width=0.1, npoints=2000)[source]
                                                                              +get_excitation_spectrum(width=0.1, npoints=2000)[source]

                                                                              Generate an excitation spectra from the singlet roots of TDDFT calculations.

                                                                              Parameters:
                                                                              @@ -6395,7 +6395,7 @@

                                                                              Submodules
                                                                              -parse_tddft()[source]
                                                                              +parse_tddft()[source]

                                                                              Parses TDDFT roots. Adapted from nw_spectrum.py script.

                                                                              Returns:
                                                                              @@ -6415,7 +6415,7 @@

                                                                              Submodules
                                                                              -class NwTask(charge, spin_multiplicity, basis_set, basis_set_option='cartesian', title=None, theory='dft', operation='optimize', theory_directives=None, alternate_directives=None)[source]
                                                                              +class NwTask(charge, spin_multiplicity, basis_set, basis_set_option='cartesian', title=None, theory='dft', operation='optimize', theory_directives=None, alternate_directives=None)[source]

                                                                              Bases: MSONable

                                                                              Base task for Nwchem.

                                                                              Very flexible arguments to support many types of potential setups. @@ -6450,13 +6450,13 @@

                                                                              Submodules
                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              Get MSONable dict.

                                                                              -classmethod dft_task(mol, xc='b3lyp', **kwargs)[source]
                                                                              +classmethod dft_task(mol, xc='b3lyp', **kwargs)[source]

                                                                              A class method for quickly creating DFT tasks with optional cosmo parameter .

                                                                              @@ -6473,7 +6473,7 @@

                                                                              Submodules
                                                                              -classmethod esp_task(mol, **kwargs)[source]
                                                                              +classmethod esp_task(mol, **kwargs)[source]

                                                                              A class method for quickly creating ESP tasks with RESP charge fitting.

                                                                              @@ -6489,7 +6489,7 @@

                                                                              Submodules
                                                                              -classmethod from_dict(dct: dict) → Self[source]
                                                                              +classmethod from_dict(dct: dict) → Self[source]
                                                                              Parameters:

                                                                              dct (dict) – Dict representation.

                                                                              @@ -6502,7 +6502,7 @@

                                                                              Submodules
                                                                              -classmethod from_molecule(mol, theory, charge=None, spin_multiplicity=None, basis_set='6-31g', basis_set_option='cartesian', title=None, operation='optimize', theory_directives=None, alternate_directives=None) → Self[source]
                                                                              +classmethod from_molecule(mol, theory, charge=None, spin_multiplicity=None, basis_set='6-31g', basis_set_option='cartesian', title=None, operation='optimize', theory_directives=None, alternate_directives=None) → Self[source]

                                                                              Very flexible arguments to support many types of potential setups. Users should use more friendly static methods unless they need the flexibility.

                                                                              @@ -6539,12 +6539,12 @@

                                                                              Submodules
                                                                              -operations: ClassVar[dict[str, str]] = {'': 'dummy', 'dynamics': 'Perform classical molecular dynamics.', 'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'gradient': 'Evaluate the derivative of the energy with respect to nuclear coordinates.', 'hessian': 'Compute second derivatives.', 'optimize': 'Minimize the energy by varying the molecular structure.', 'property': 'Calculate the properties for the wave function.', 'saddle': 'Conduct a search for a transition state (or saddle point).', 'thermodynamics': 'Perform multi-configuration thermodynamic integration using classical MD.', 'vscf': 'Compute anharmonic contributions to the vibrational modes.'}[source]
                                                                              +operations: ClassVar[dict[str, str]] = {'': 'dummy', 'dynamics': 'Perform classical molecular dynamics.', 'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'gradient': 'Evaluate the derivative of the energy with respect to nuclear coordinates.', 'hessian': 'Compute second derivatives.', 'optimize': 'Minimize the energy by varying the molecular structure.', 'property': 'Calculate the properties for the wave function.', 'saddle': 'Conduct a search for a transition state (or saddle point).', 'thermodynamics': 'Perform multi-configuration thermodynamic integration using classical MD.', 'vscf': 'Compute anharmonic contributions to the vibrational modes.'}[source]

                                                                              -theories: ClassVar[dict[str, str]] = {'band': 'Pseudopotential plane-wave DFT for solids using NWPW', 'ccsd': 'Coupled-cluster single and double excitations', 'ccsd(t)': 'Coupled-cluster linearized triples approximation', 'ccsd+t(ccsd)': 'Fourth order triples contribution', 'dft': 'DFT', 'direct_mp2': 'MP2 using a full-direct algorithm', 'esp': 'ESP', 'g3gn': 'some description', 'mcscf': 'Multiconfiguration SCF', 'md': 'Classical molecular dynamics simulation', 'mp2': 'MP2 using a semi-direct algorithm', 'pspw': 'Pseudopotential plane-wave DFT for molecules and insulating solids using NWPW', 'rimp2': 'MP2 using the RI approximation', 'scf': 'Hartree-Fock', 'selci': 'Selected CI with perturbation correction', 'sodft': 'Spin-Orbit DFT', 'tce': 'Tensor Contraction Engine', 'tddft': 'Time Dependent DFT'}[source]
                                                                              +theories: ClassVar[dict[str, str]] = {'band': 'Pseudopotential plane-wave DFT for solids using NWPW', 'ccsd': 'Coupled-cluster single and double excitations', 'ccsd(t)': 'Coupled-cluster linearized triples approximation', 'ccsd+t(ccsd)': 'Fourth order triples contribution', 'dft': 'DFT', 'direct_mp2': 'MP2 using a full-direct algorithm', 'esp': 'ESP', 'g3gn': 'some description', 'mcscf': 'Multiconfiguration SCF', 'md': 'Classical molecular dynamics simulation', 'mp2': 'MP2 using a semi-direct algorithm', 'pspw': 'Pseudopotential plane-wave DFT for molecules and insulating solids using NWPW', 'rimp2': 'MP2 using the RI approximation', 'scf': 'Hartree-Fock', 'selci': 'Selected CI with perturbation correction', 'sodft': 'Spin-Orbit DFT', 'tce': 'Tensor Contraction Engine', 'tddft': 'Time Dependent DFT'}[source]

                                                                              @@ -6555,7 +6555,7 @@

                                                                              Submodules
                                                                              -add_conformer(openff_mol: tk.Molecule, geometry: pymatgen.core.Molecule | None) → tuple[tk.Molecule, dict[int, int]][source]
                                                                              +add_conformer(openff_mol: Molecule, geometry: Molecule | None) → tuple[Molecule, dict[int, int]][source]

                                                                              Add conformers to an OpenFF Molecule based on the provided geometry.

                                                                              If a geometry is provided, infers an OpenFF Molecule from it, finds an atom mapping between the inferred molecule and the @@ -6585,7 +6585,7 @@

                                                                              Submodules
                                                                              -assign_partial_charges(openff_mol: tk.Molecule, atom_map: dict[int, int], charge_method: str, partial_charges: None | list[float]) → tk.Molecule[source]
                                                                              +assign_partial_charges(openff_mol: Molecule, atom_map: dict[int, int], charge_method: str, partial_charges: None | list[float]) → Molecule[source]

                                                                              Assign partial charges to an OpenFF Molecule.

                                                                              If partial charges are provided, assigns them to the molecule based on the atom mapping. If the molecule has only one atom, @@ -6613,7 +6613,7 @@

                                                                              Submodules
                                                                              -create_openff_mol(smile: str, geometry: pymatgen.core.Molecule | str | Path | None = None, charge_scaling: float = 1, partial_charges: list[float] | None = None, backup_charge_method: str = 'am1bcc') → tk.Molecule[source]
                                                                              +create_openff_mol(smile: str, geometry: Molecule | str | Path | None = None, charge_scaling: float = 1, partial_charges: list[float] | None = None, backup_charge_method: str = 'am1bcc') → Molecule[source]

                                                                              Create an OpenFF Molecule from a SMILES string and optional geometry.

                                                                              Constructs an OpenFF Molecule from the provided SMILES string, adds conformers based on the provided geometry (if @@ -6645,7 +6645,7 @@

                                                                              Submodules
                                                                              -get_atom_map(inferred_mol: tk.Molecule, openff_mol: tk.Molecule) → tuple[bool, dict[int, int]][source]
                                                                              +get_atom_map(inferred_mol: Molecule, openff_mol: Molecule) → tuple[bool, dict[int, int]][source]

                                                                              Compute an atom mapping between two OpenFF Molecules.

                                                                              Attempts to find an isomorphism between the molecules, considering various matching criteria such as formal charges, stereochemistry, and bond orders. Returns the atom @@ -6672,7 +6672,7 @@

                                                                              Submodules
                                                                              -infer_openff_mol(mol_geometry: pymatgen.core.Molecule) → tk.Molecule[source]
                                                                              +infer_openff_mol(mol_geometry: Molecule) → Molecule[source]

                                                                              Infer an OpenFF Molecule from a Pymatgen Molecule.

                                                                              Constructs a MoleculeGraph from the Pymatgen Molecule using the OpenBabelNN local environment strategy and extends metal edges. Converts the resulting MoleculeGraph @@ -6692,7 +6692,7 @@

                                                                              Submodules
                                                                              -mol_graph_from_openff_mol(molecule: tk.Molecule) → MoleculeGraph[source]
                                                                              +mol_graph_from_openff_mol(molecule: Molecule) → MoleculeGraph[source]

                                                                              This is designed to closely mirror the graph structure generated by tk.Molecule.to_networkx

                                                                              Parameters:
                                                                              @@ -6709,7 +6709,7 @@

                                                                              Submodules
                                                                              -mol_graph_to_openff_mol(mol_graph: MoleculeGraph) → tk.Molecule[source]
                                                                              +mol_graph_to_openff_mol(mol_graph: MoleculeGraph) → Molecule[source]

                                                                              Convert a Pymatgen MoleculeGraph to an OpenFF Molecule.

                                                                              Parameters:
                                                                              @@ -6742,7 +6742,7 @@

                                                                              Submodules
                                                                              -class PackmolBoxGen(tolerance: float = 2.0, seed: int = 1, control_params: dict | None = None, inputfile: str | Path = 'packmol.inp', outputfile: str | Path = 'packmol_out.xyz', stdoutfile: str | Path = 'packmol.stdout')[source]
                                                                              +class PackmolBoxGen(tolerance: float = 2.0, seed: int = 1, control_params: dict | None = None, inputfile: str | Path = 'packmol.inp', outputfile: str | Path = 'packmol_out.xyz', stdoutfile: str | Path = 'packmol.stdout')[source]

                                                                              Bases: InputGenerator

                                                                              Generator for a Packmol InputSet that packs one or more molecules into a rectangular simulation box.

                                                                              @@ -6762,7 +6762,7 @@

                                                                              Submodules
                                                                              -get_input_set(molecules: list[dict], box: list[float] | None = None) → PackmolSet[source]
                                                                              +get_input_set(molecules: list[dict], box: list[float] | None = None) → PackmolSet[source]

                                                                              Generate a Packmol InputSet for a set of molecules.

                                                                              Parameters:
                                                                              @@ -6801,7 +6801,7 @@

                                                                              Submodules
                                                                              -class PackmolSet(inputs: dict[str | Path, str | InputFile] | None = None, **kwargs)[source]
                                                                              +class PackmolSet(inputs: dict[str | Path, str | InputFile] | None = None, **kwargs)[source]

                                                                              Bases: InputSet

                                                                              InputSet for the Packmol software. This class defines several attributes related to.

                                                                              Instantiate an InputSet.

                                                                              @@ -6821,7 +6821,7 @@

                                                                              Submodules
                                                                              -classmethod from_directory(directory: str | Path) → None[source]
                                                                              +classmethod from_directory(directory: str | Path) → None[source]

                                                                              Construct an InputSet from a directory of one or more files.

                                                                              Parameters:
                                                                              @@ -6832,7 +6832,7 @@

                                                                              Submodules
                                                                              -run(path: str | Path, timeout=30)[source]
                                                                              +run(path: str | Path, timeout=30)[source]

                                                                              Run packmol and write out the packed structure.

                                                                              Parameters:
                                                                              @@ -6858,7 +6858,7 @@

                                                                              Submoduleshttps://atztogo.github.io/phonopy/.

                                                                              -eigvec_to_eigdispl(eig_vec, q, frac_coords, mass)[source]
                                                                              +eigvec_to_eigdispl(eig_vec, q, frac_coords, mass)[source]

                                                                              Converts a single eigenvector to an eigendisplacement in the primitive cell according to the formula:

                                                                              @@ -6880,7 +6880,7 @@

                                                                              Submodules
                                                                              -get_complete_ph_dos(partial_dos_path, phonopy_yaml_path)[source]
                                                                              +get_complete_ph_dos(partial_dos_path, phonopy_yaml_path)[source]

                                                                              Create a pymatgen CompletePhononDos from a partial_dos.dat and phonopy.yaml files. The second is produced when generating a Dos and is needed to extract @@ -6897,7 +6897,7 @@

                                                                              Submodules
                                                                              -get_displaced_structures(pmg_structure, atom_disp=0.01, supercell_matrix=None, yaml_fname=None, **kwargs)[source]
                                                                              +get_displaced_structures(pmg_structure, atom_disp=0.01, supercell_matrix=None, yaml_fname=None, **kwargs)[source]

                                                                              Generate a set of symmetrically inequivalent displaced structures for phonon calculations.

                                                                              @@ -6920,7 +6920,7 @@

                                                                              Submodules
                                                                              -get_gruneisen_ph_bs_symm_line(gruneisen_path, structure=None, structure_path=None, labels_dict=None, fit=False)[source]
                                                                              +get_gruneisen_ph_bs_symm_line(gruneisen_path, structure=None, structure_path=None, labels_dict=None, fit=False)[source]

                                                                              Create a pymatgen GruneisenPhononBandStructure from a band.yaml file. The labels will be extracted from the dictionary, if present. If the ‘eigenvector’ key is found the eigendisplacements will be @@ -6949,7 +6949,7 @@

                                                                              Submodules
                                                                              -get_gruneisenparameter(gruneisen_path, structure=None, structure_path=None) → GruneisenParameter[source]
                                                                              +get_gruneisenparameter(gruneisen_path, structure=None, structure_path=None) → GruneisenParameter[source]

                                                                              Get Gruneisen object from gruneisen.yaml file, as obtained from phonopy (Frequencies in THz!). The order is structure > structure path > structure from gruneisen dict. Newer versions of phonopy include the structure in the YAML file, @@ -6970,7 +6970,7 @@

                                                                              Submodules
                                                                              -get_gs_ph_bs_symm_line_from_dict(gruneisen_dict, structure=None, structure_path=None, labels_dict=None, fit=False) → GruneisenPhononBandStructureSymmLine[source]
                                                                              +get_gs_ph_bs_symm_line_from_dict(gruneisen_dict, structure=None, structure_path=None, labels_dict=None, fit=False) → GruneisenPhononBandStructureSymmLine[source]

                                                                              Create a pymatgen GruneisenPhononBandStructure object from the dictionary extracted by the gruneisen.yaml file produced by phonopy. The labels will be extracted from the dictionary, if present. If the ‘eigenvector’ @@ -7002,7 +7002,7 @@

                                                                              Submodules
                                                                              -get_ph_bs_symm_line(bands_path, has_nac=False, labels_dict=None)[source]
                                                                              +get_ph_bs_symm_line(bands_path, has_nac=False, labels_dict=None)[source]

                                                                              Create a pymatgen PhononBandStructure from a band.yaml file. The labels will be extracted from the dictionary, if present. If the ‘eigenvector’ key is found the eigendisplacements will be @@ -7025,7 +7025,7 @@

                                                                              Submodules
                                                                              -get_ph_bs_symm_line_from_dict(bands_dict, has_nac=False, labels_dict=None) → PhononBandStructureSymmLine[source]
                                                                              +get_ph_bs_symm_line_from_dict(bands_dict, has_nac=False, labels_dict=None) → PhononBandStructureSymmLine[source]

                                                                              Create a pymatgen PhononBandStructure object from the dictionary extracted by the band.yaml file produced by phonopy. The labels will be extracted from the dictionary, if present. If the ‘eigenvector’ @@ -7056,7 +7056,7 @@

                                                                              Submodules
                                                                              -get_ph_dos(total_dos_path)[source]
                                                                              +get_ph_dos(total_dos_path)[source]

                                                                              Create a pymatgen PhononDos from a total_dos.dat file.

                                                                              Parameters:
                                                                              @@ -7067,7 +7067,7 @@

                                                                              Submodules
                                                                              -get_phonon_band_structure_from_fc(structure: Structure, supercell_matrix: ndarray, force_constants: ndarray, mesh_density: float = 100.0, **kwargs) → PhononBandStructure[source]
                                                                              +get_phonon_band_structure_from_fc(structure: Structure, supercell_matrix: ndarray, force_constants: ndarray, mesh_density: float = 100.0, **kwargs) → PhononBandStructure[source]

                                                                              Get a uniform phonon band structure from phonopy force constants.

                                                                              Parameters:
                                                                              @@ -7089,7 +7089,7 @@

                                                                              Submodules
                                                                              -get_phonon_band_structure_symm_line_from_fc(structure: Structure, supercell_matrix: ndarray, force_constants: ndarray, line_density: float = 20.0, symprec: float = 0.01, **kwargs) → PhononBandStructureSymmLine[source]
                                                                              +get_phonon_band_structure_symm_line_from_fc(structure: Structure, supercell_matrix: ndarray, force_constants: ndarray, line_density: float = 20.0, symprec: float = 0.01, **kwargs) → PhononBandStructureSymmLine[source]

                                                                              Get a phonon band structure along a high symmetry path from phonopy force constants.

                                                                              @@ -7113,7 +7113,7 @@

                                                                              Submodules
                                                                              -get_phonon_dos_from_fc(structure: Structure, supercell_matrix: ndarray, force_constants: ndarray, mesh_density: float = 100.0, num_dos_steps: int = 200, **kwargs) → CompletePhononDos[source]
                                                                              +get_phonon_dos_from_fc(structure: Structure, supercell_matrix: ndarray, force_constants: ndarray, mesh_density: float = 100.0, num_dos_steps: int = 200, **kwargs) → CompletePhononDos[source]

                                                                              Get a projected phonon density of states from phonopy force constants.

                                                                              Parameters:
                                                                              @@ -7136,7 +7136,7 @@

                                                                              Submodules
                                                                              -get_phonopy_structure(pmg_structure: Structure) → PhonopyAtoms[source]
                                                                              +get_phonopy_structure(pmg_structure: Structure) → PhonopyAtoms[source]

                                                                              Convert a pymatgen Structure object to a PhonopyAtoms object.

                                                                              Parameters:
                                                                              @@ -7147,7 +7147,7 @@

                                                                              Submodules
                                                                              -get_pmg_structure(phonopy_structure: PhonopyAtoms) → Structure[source]
                                                                              +get_pmg_structure(phonopy_structure: PhonopyAtoms) → Structure[source]

                                                                              Convert a PhonopyAtoms object to pymatgen Structure object.

                                                                              Parameters:
                                                                              @@ -7158,7 +7158,7 @@

                                                                              Submodules
                                                                              -get_structure_from_dict(dct) → Structure[source]
                                                                              +get_structure_from_dict(dct) → Structure[source]

                                                                              Extracts a structure from the dictionary extracted from the output files of phonopy like phonopy.yaml or band.yaml. Adds “phonopy_masses” in the site_properties of the structures. @@ -7167,7 +7167,7 @@

                                                                              Submodules
                                                                              -get_thermal_displacement_matrices(thermal_displacements_yaml='thermal_displacement_matrices.yaml', structure_path='POSCAR')[source]
                                                                              +get_thermal_displacement_matrices(thermal_displacements_yaml='thermal_displacement_matrices.yaml', structure_path='POSCAR')[source]

                                                                              Read “thermal_displacement_matrices.yaml” from phonopy and return a list of ThermalDisplacementMatrices objects

                                                                              @@ -7189,7 +7189,7 @@

                                                                              Submoduleshttp://prism-em.com) input files.

                                                                              -class Prismatic(structure: Structure, comment: str = 'Generated by pymatgen')[source]
                                                                              +class Prismatic(structure: Structure, comment: str = 'Generated by pymatgen')[source]

                                                                              Bases: object

                                                                              Write Prismatic (http://prism-em.com) input files. This is designed for STEM image simulation.

                                                                              @@ -7203,7 +7203,7 @@

                                                                              Submodules
                                                                              -to_str() → str[source]
                                                                              +to_str() → str[source]
                                                                              Returns:

                                                                              @@ -7226,7 +7226,7 @@

                                                                              Submodules
                                                                              -class PWInput(structure, pseudo=None, control=None, system=None, electrons=None, ions=None, cell=None, kpoints_mode='automatic', kpoints_grid=(1, 1, 1), kpoints_shift=(0, 0, 0))[source]
                                                                              +class PWInput(structure, pseudo=None, control=None, system=None, electrons=None, ions=None, cell=None, kpoints_mode='automatic', kpoints_grid=(1, 1, 1), kpoints_shift=(0, 0, 0))[source]

                                                                              Bases: object

                                                                              Base input file class. Right now, only supports no symmetry and is very basic.

                                                                              @@ -7258,7 +7258,7 @@

                                                                              Submodules
                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              Create a dictionary representation of a PWInput object.

                                                                              Returns:
                                                                              @@ -7269,7 +7269,7 @@

                                                                              Submodules
                                                                              -classmethod from_dict(dct: dict) → Self[source]
                                                                              +classmethod from_dict(dct: dict) → Self[source]

                                                                              Load a PWInput object from a dictionary.

                                                                              Parameters:
                                                                              @@ -7283,7 +7283,7 @@

                                                                              Submodules
                                                                              -classmethod from_file(filename: str | Path) → Self[source]
                                                                              +classmethod from_file(filename: str | Path) → Self[source]

                                                                              Reads an PWInput object from a file.

                                                                              Parameters:
                                                                              @@ -7297,7 +7297,7 @@

                                                                              Submodules
                                                                              -classmethod from_str(string: str) → Self[source]
                                                                              +classmethod from_str(string: str) → Self[source]

                                                                              Reads an PWInput object from a string.

                                                                              Parameters:
                                                                              @@ -7311,7 +7311,7 @@

                                                                              Submodules
                                                                              -static proc_val(key, val)[source]
                                                                              +static proc_val(key, val)[source]

                                                                              Static helper method to convert PWINPUT parameters to proper type, e.g. integers, floats, etc.

                                                                              @@ -7326,7 +7326,7 @@

                                                                              Submodules
                                                                              -write_file(filename)[source]
                                                                              +write_file(filename)[source]

                                                                              Write the PWSCF input file.

                                                                              Parameters:
                                                                              @@ -7339,14 +7339,14 @@

                                                                              Submodules
                                                                              -exception PWInputError[source]
                                                                              +exception PWInputError[source]

                                                                              Bases: BaseException

                                                                              Error for PWInput.

                                                                              -class PWOutput(filename)[source]
                                                                              +class PWOutput(filename)[source]

                                                                              Bases: object

                                                                              Parser for PWSCF output file.

                                                                              @@ -7356,13 +7356,13 @@

                                                                              Submodules
                                                                              -property final_energy: float[source]
                                                                              +property final_energy: float[source]

                                                                              The final energy from the PW output.

                                                                              -get_celldm(idx: int)[source]
                                                                              +get_celldm(idx: int)[source]
                                                                              Parameters:

                                                                              idx (int) – index.

                                                                              @@ -7375,18 +7375,18 @@

                                                                              Submodules
                                                                              -property lattice_type: int[source]
                                                                              +property lattice_type: int[source]

                                                                              The lattice type.

                                                                              -patterns: ClassVar[dict[str, str]] = {'celldm1': 'celldm\\(1\\)=\\s+([\\d\\.]+)\\s', 'celldm2': 'celldm\\(2\\)=\\s+([\\d\\.]+)\\s', 'celldm3': 'celldm\\(3\\)=\\s+([\\d\\.]+)\\s', 'celldm4': 'celldm\\(4\\)=\\s+([\\d\\.]+)\\s', 'celldm5': 'celldm\\(5\\)=\\s+([\\d\\.]+)\\s', 'celldm6': 'celldm\\(6\\)=\\s+([\\d\\.]+)\\s', 'ecut': 'kinetic\\-energy cutoff\\s+=\\s+([\\d\\.\\-]+)\\s+Ry', 'energies': 'total energy\\s+=\\s+([\\d\\.\\-]+)\\sRy', 'lattice_type': 'bravais\\-lattice index\\s+=\\s+(\\d+)', 'nkpts': 'number of k points=\\s+([\\d]+)'}[source]
                                                                              +patterns: ClassVar[dict[str, str]] = {'celldm1': 'celldm\\(1\\)=\\s+([\\d\\.]+)\\s', 'celldm2': 'celldm\\(2\\)=\\s+([\\d\\.]+)\\s', 'celldm3': 'celldm\\(3\\)=\\s+([\\d\\.]+)\\s', 'celldm4': 'celldm\\(4\\)=\\s+([\\d\\.]+)\\s', 'celldm5': 'celldm\\(5\\)=\\s+([\\d\\.]+)\\s', 'celldm6': 'celldm\\(6\\)=\\s+([\\d\\.]+)\\s', 'ecut': 'kinetic\\-energy cutoff\\s+=\\s+([\\d\\.\\-]+)\\s+Ry', 'energies': 'total energy\\s+=\\s+([\\d\\.\\-]+)\\sRy', 'lattice_type': 'bravais\\-lattice index\\s+=\\s+(\\d+)', 'nkpts': 'number of k points=\\s+([\\d]+)'}[source]
                                                                              -read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]
                                                                              +read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]

                                                                              General pattern reading. Uses monty’s regrep method. Takes the same arguments.

                                                                              @@ -7428,7 +7428,7 @@

                                                                              Submodules
                                                                              -class AirssProvider(res: Res, parse_rems: Literal['gentle', 'strict'] = 'gentle')[source]
                                                                              +class AirssProvider(res: Res, parse_rems: Literal['gentle', 'strict'] = 'gentle')[source]

                                                                              Bases: ResProvider

                                                                              Provides access to the res file as does ResProvider. This class additionally provides access to fields in the TITL entry and various other fields found in the REM entries @@ -7448,7 +7448,7 @@

                                                                              Submodulesfrom_str() and from_file() methods should be used instead of constructing this directly.

                                                                              -property appearances: int[source]
                                                                              +property appearances: int[source]

                                                                              This is sometimes the number of times a structure was found in an AIRSS search. Using the cryan tool that comes with AIRSS may be a better approach than relying on this property.

                                                                              @@ -7456,37 +7456,37 @@

                                                                              Submodules
                                                                              -as_dict(verbose: bool = True) → dict[str, Any][source]
                                                                              +as_dict(verbose: bool = True) → dict[str, Any][source]

                                                                              Get dict with title fields, structure and rems of this AirssProvider.

                                                                              -property energy: float[source]
                                                                              +property energy: float[source]

                                                                              Energy of the structure. With CASTEP, this is usually the enthalpy and is in eV.

                                                                              -property entry: ComputedStructureEntry[source]
                                                                              +property entry: ComputedStructureEntry[source]

                                                                              This res file as a ComputedStructureEntry.

                                                                              -classmethod from_file(filename: str | Path, parse_rems: Literal['gentle', 'strict'] = 'gentle') → Self[source]
                                                                              +classmethod from_file(filename: str | Path, parse_rems: Literal['gentle', 'strict'] = 'gentle') → Self[source]

                                                                              Construct a Provider from a file.

                                                                              -classmethod from_str(string: str, parse_rems: Literal['gentle', 'strict'] = 'gentle') → Self[source]
                                                                              +classmethod from_str(string: str, parse_rems: Literal['gentle', 'strict'] = 'gentle') → Self[source]

                                                                              Construct a Provider from a string.

                                                                              -get_airss_version() → tuple[str, date] | None[source]
                                                                              +get_airss_version() → tuple[str, date] | None[source]

                                                                              Retrieves the version of AIRSS that was used along with the build date (not compile date).

                                                                              Returns:
                                                                              @@ -7497,7 +7497,7 @@

                                                                              Submodules
                                                                              -get_castep_version() → str | None[source]
                                                                              +get_castep_version() → str | None[source]

                                                                              Retrieves the version of CASTEP that the res file was computed with from the REM entries.

                                                                              Returns:
                                                                              @@ -7508,7 +7508,7 @@

                                                                              Submodules
                                                                              -get_cut_grid_gmax_fsbc() → tuple[float, float, float, str] | None[source]
                                                                              +get_cut_grid_gmax_fsbc() → tuple[float, float, float, str] | None[source]

                                                                              Retrieves the cut-off energy, grid scale, Gmax, and finite basis set correction setting from the REM entries.

                                                                              @@ -7523,7 +7523,7 @@

                                                                              Submodules
                                                                              -get_func_rel_disp() → tuple[str, str, str] | None[source]
                                                                              +get_func_rel_disp() → tuple[str, str, str] | None[source]

                                                                              Retrieves the functional, relativity scheme, and dispersion correction from the REM entries.

                                                                              Returns:
                                                                              @@ -7537,7 +7537,7 @@

                                                                              Submodules
                                                                              -get_mpgrid_offset_nkpts_spacing() → tuple[Tuple3Ints, Vector3D, int, float] | None[source]
                                                                              +get_mpgrid_offset_nkpts_spacing() → tuple[Tuple3Ints, Vector3D, int, float] | None[source]

                                                                              Retrieves the MP grid, the grid offsets, number of kpoints, and maximum kpoint spacing.

                                                                              Returns:
                                                                              @@ -7551,7 +7551,7 @@

                                                                              Submodules
                                                                              -get_pspots() → dict[str, str][source]
                                                                              +get_pspots() → dict[str, str][source]

                                                                              Retrieves the OTFG pseudopotential string that can be used to generate the pseudopotentials used in the calculation.

                                                                              @@ -7563,7 +7563,7 @@

                                                                              Submodules
                                                                              -get_run_start_info() → tuple[date, str] | None[source]
                                                                              +get_run_start_info() → tuple[date, str] | None[source]

                                                                              Retrieves the run start date and the path it was started in from the REM entries.

                                                                              Returns:
                                                                              @@ -7577,38 +7577,38 @@

                                                                              Submodules
                                                                              -property integrated_absolute_spin_density: float[source]
                                                                              +property integrated_absolute_spin_density: float[source]

                                                                              Corresponds to the last Integrated |Spin Density| in the CASTEP file.

                                                                              -property integrated_spin_density: float[source]
                                                                              +property integrated_spin_density: float[source]

                                                                              Corresponds to the last Integrated Spin Density in the CASTEP file.

                                                                              -property pressure: float[source]
                                                                              +property pressure: float[source]

                                                                              Pressure for the run. This is in GPa if CASTEP was used.

                                                                              -property seed: str[source]
                                                                              +property seed: str[source]

                                                                              The seed name, typically also the name of the res file.

                                                                              -property spacegroup_label: str[source]
                                                                              +property spacegroup_label: str[source]

                                                                              The Hermann-Mauguin notation of the spacegroup with ascii characters. So no. 225 would be Fm-3m, and no. 194 would be P6_3/mmc.

                                                                              -property volume: float[source]
                                                                              +property volume: float[source]

                                                                              Volume of the structure. This is in cubic Angstroms if CASTEP was used.

                                                                              @@ -7616,152 +7616,152 @@

                                                                              Submodules
                                                                              -class AirssTITL(seed: 'str', pressure: 'float', volume: 'float', energy: 'float', integrated_spin_density: 'float', integrated_absolute_spin_density: 'float', spacegroup_label: 'str', appearances: 'int')[source]
                                                                              +class AirssTITL(seed: 'str', pressure: 'float', volume: 'float', energy: 'float', integrated_spin_density: 'float', integrated_absolute_spin_density: 'float', spacegroup_label: 'str', appearances: 'int')[source]

                                                                              Bases: object

                                                                              -appearances: int[source]
                                                                              +appearances: int[source]
                                                                              -energy: float[source]
                                                                              +energy: float[source]
                                                                              -integrated_absolute_spin_density: float[source]
                                                                              +integrated_absolute_spin_density: float[source]
                                                                              -integrated_spin_density: float[source]
                                                                              +integrated_spin_density: float[source]
                                                                              -pressure: float[source]
                                                                              +pressure: float[source]
                                                                              -seed: str[source]
                                                                              +seed: str[source]
                                                                              -spacegroup_label: str[source]
                                                                              +spacegroup_label: str[source]
                                                                              -volume: float[source]
                                                                              +volume: float[source]

                                                                              -class Ion(specie: 'str', specie_num: 'int', pos: 'Vector3D', occupancy: 'float', spin: 'float | None')[source]
                                                                              +class Ion(specie: 'str', specie_num: 'int', pos: 'Vector3D', occupancy: 'float', spin: 'float | None')[source]

                                                                              Bases: object

                                                                              -occupancy: float[source]
                                                                              +occupancy: float[source]
                                                                              -pos: Vector3D[source]
                                                                              +pos: Vector3D[source]
                                                                              -specie: str[source]
                                                                              +specie: str[source]
                                                                              -specie_num: int[source]
                                                                              +specie_num: int[source]
                                                                              -spin: float | None[source]
                                                                              +spin: float | None[source]
                                                                              -class Res(TITL: AirssTITL | None, REMS: list[str], CELL: ResCELL, SFAC: ResSFAC)[source]
                                                                              +class Res(TITL: AirssTITL | None, REMS: list[str], CELL: ResCELL, SFAC: ResSFAC)[source]

                                                                              Bases: object

                                                                              Representation for the data in a res file.

                                                                              -CELL: ResCELL[source]
                                                                              +CELL: ResCELL[source]
                                                                              -REMS: list[str][source]
                                                                              +REMS: list[str][source]
                                                                              -SFAC: ResSFAC[source]
                                                                              +SFAC: ResSFAC[source]
                                                                              -TITL: AirssTITL | None[source]
                                                                              +TITL: AirssTITL | None[source]
                                                                              -class ResCELL(unknown_field_1: 'float', a: 'float', b: 'float', c: 'float', alpha: 'float', beta: 'float', gamma: 'float')[source]
                                                                              +class ResCELL(unknown_field_1: 'float', a: 'float', b: 'float', c: 'float', alpha: 'float', beta: 'float', gamma: 'float')[source]

                                                                              Bases: object

                                                                              -a: float[source]
                                                                              +a: float[source]
                                                                              -alpha: float[source]
                                                                              +alpha: float[source]
                                                                              -b: float[source]
                                                                              +b: float[source]
                                                                              -beta: float[source]
                                                                              +beta: float[source]
                                                                              -c: float[source]
                                                                              +c: float[source]
                                                                              -gamma: float[source]
                                                                              +gamma: float[source]
                                                                              -unknown_field_1: float[source]
                                                                              +unknown_field_1: float[source]
                                                                              -exception ResError[source]
                                                                              +exception ResError[source]

                                                                              Bases: ValueError

                                                                              This exception indicates a problem was encountered while trying to retrieve a value or perform an action that a provider for the res file does not support.

                                                                              @@ -7769,7 +7769,7 @@

                                                                              Submodules
                                                                              -class ResIO[source]
                                                                              +class ResIO[source]

                                                                              Bases: object

                                                                              Convenience methods for converting a Structure or ComputedStructureEntry to/from a string or file in the res format as used by AIRSS.

                                                                              @@ -7782,49 +7782,49 @@

                                                                              Submodules
                                                                              -classmethod entry_from_file(filename: str) → ComputedStructureEntry[source]
                                                                              +classmethod entry_from_file(filename: str) → ComputedStructureEntry[source]

                                                                              Produce a pymatgen ComputedStructureEntry from a res file.

                                                                              -classmethod entry_from_str(string: str) → ComputedStructureEntry[source]
                                                                              +classmethod entry_from_str(string: str) → ComputedStructureEntry[source]

                                                                              Produce a pymatgen ComputedStructureEntry from contents of a res file.

                                                                              -classmethod entry_to_file(entry: ComputedStructureEntry, filename: str) → None[source]
                                                                              +classmethod entry_to_file(entry: ComputedStructureEntry, filename: str) → None[source]

                                                                              Write a pymatgen ComputedStructureEntry to a res file.

                                                                              -classmethod entry_to_str(entry: ComputedStructureEntry) → str[source]
                                                                              +classmethod entry_to_str(entry: ComputedStructureEntry) → str[source]

                                                                              Produce the contents of a res file from a pymatgen ComputedStructureEntry.

                                                                              -classmethod structure_from_file(filename: str) → Structure[source]
                                                                              +classmethod structure_from_file(filename: str) → Structure[source]

                                                                              Produces a pymatgen Structure from a res file.

                                                                              -classmethod structure_from_str(string: str) → Structure[source]
                                                                              +classmethod structure_from_str(string: str) → Structure[source]

                                                                              Produces a pymatgen Structure from contents of a res file.

                                                                              -classmethod structure_to_file(structure: Structure, filename: str) → None[source]
                                                                              +classmethod structure_to_file(structure: Structure, filename: str) → None[source]

                                                                              Write a pymatgen Structure to a res file.

                                                                              -classmethod structure_to_str(structure: Structure) → str[source]
                                                                              +classmethod structure_to_str(structure: Structure) → str[source]

                                                                              Produce the contents of a res file from a pymatgen Structure.

                                                                              @@ -7832,57 +7832,57 @@

                                                                              Submodules
                                                                              -exception ResParseError[source]
                                                                              +exception ResParseError[source]

                                                                              Bases: ParseError

                                                                              This exception indicates a problem was encountered during parsing due to unexpected formatting.

                                                                              -class ResParser[source]
                                                                              +class ResParser[source]

                                                                              Bases: object

                                                                              Parser for the ShelX res file.

                                                                              -class ResProvider(res: Res)[source]
                                                                              +class ResProvider(res: Res)[source]

                                                                              Bases: MSONable

                                                                              Access elements of the RES file as familiar pymatgen objects.

                                                                              The from_str() and from_file() methods should be used instead of constructing this directly.

                                                                              -classmethod from_file(filename: str | Path) → Self[source]
                                                                              +classmethod from_file(filename: str | Path) → Self[source]

                                                                              Construct a Provider from a file.

                                                                              -classmethod from_str(string: str) → Self[source]
                                                                              +classmethod from_str(string: str) → Self[source]

                                                                              Construct a Provider from a string.

                                                                              -property lattice: Lattice[source]
                                                                              +property lattice: Lattice[source]

                                                                              Construct a Lattice from the res file.

                                                                              -property rems: list[str][source]
                                                                              +property rems: list[str][source]

                                                                              The full list of REM entries contained within the res file.

                                                                              -property sites: list[PeriodicSite][source]
                                                                              +property sites: list[PeriodicSite][source]

                                                                              Construct a list of PeriodicSites from the res file.

                                                                              -property structure: Structure[source]
                                                                              +property structure: Structure[source]

                                                                              Construct a Structure from the res file.

                                                                              @@ -7890,35 +7890,35 @@

                                                                              Submodules
                                                                              -class ResSFAC(species: 'list[str]', ions: 'list[Ion]')[source]
                                                                              +class ResSFAC(species: 'list[str]', ions: 'list[Ion]')[source]

                                                                              Bases: object

                                                                              -ions: list[Ion][source]
                                                                              +ions: list[Ion][source]
                                                                              -species: list[str][source]
                                                                              +species: list[str][source]

                                                                              -class ResWriter(entry: Structure | ComputedStructureEntry)[source]
                                                                              +class ResWriter(entry: Structure | ComputedStructureEntry)[source]

                                                                              Bases: object

                                                                              This class provides a means to write a Structure or ComputedStructureEntry to a res file.

                                                                              This class can be constructed from either a pymatgen Structure or ComputedStructureEntry object.

                                                                              -property string: str[source]
                                                                              +property string: str[source]

                                                                              The contents of the res file.

                                                                              -write(filename: str) → None[source]
                                                                              +write(filename: str) → None[source]

                                                                              Write the res data to a file.

                                                                              @@ -7930,7 +7930,7 @@

                                                                              Submodules
                                                                              -class Control(ngrid: list[int] | None = None, temperature: float | dict[str, float] = 300, **kwargs)[source]
                                                                              +class Control(ngrid: list[int] | None = None, temperature: float | dict[str, float] = 300, **kwargs)[source]

                                                                              Bases: MSONable, dict

                                                                              Read, update, and write ShengBTE CONTROL files. See https://bitbucket.org/sousaw/shengbte/src/master/ for more @@ -7966,33 +7966,33 @@

                                                                              Submodules
                                                                              -allocations_keys = ('nelements', 'natoms', 'ngrid', 'norientations')[source]
                                                                              +allocations_keys = ('nelements', 'natoms', 'ngrid', 'norientations')[source]

                                                                              -as_dict()[source]
                                                                              +as_dict()[source]

                                                                              Get MSONable dict.

                                                                              -crystal_keys = ('lfactor', 'lattvec', 'types', 'elements', 'positions', 'masses', 'gfactors', 'epsilon', 'born', 'scell', 'orientations')[source]
                                                                              +crystal_keys = ('lfactor', 'lattvec', 'types', 'elements', 'positions', 'masses', 'gfactors', 'epsilon', 'born', 'scell', 'orientations')[source]
                                                                              -data_keys = ('nelements', 'natoms', 'ngrid', 'lattvec', 'types', 'elements', 'positions', 'scell')[source]
                                                                              +data_keys = ('nelements', 'natoms', 'ngrid', 'lattvec', 'types', 'elements', 'positions', 'scell')[source]
                                                                              -flags_keys = ('nonanalytic', 'convergence', 'isotopes', 'autoisotopes', 'nanowires', 'onlyharmonic', 'espresso')[source]
                                                                              +flags_keys = ('nonanalytic', 'convergence', 'isotopes', 'autoisotopes', 'nanowires', 'onlyharmonic', 'espresso')[source]
                                                                              -classmethod from_dict(control_dict: dict) → Self[source]
                                                                              +classmethod from_dict(control_dict: dict) → Self[source]

                                                                              Write a CONTROL file from a Python dictionary. Description and default parameters can be found at https://bitbucket.org/sousaw/shengbte/src/master/. @@ -8007,7 +8007,7 @@

                                                                              Submodules
                                                                              -classmethod from_file(filepath: str) → Self[source]
                                                                              +classmethod from_file(filepath: str) → Self[source]

                                                                              Read a CONTROL namelist file and output a ‘Control’ object.

                                                                              Parameters:
                                                                              @@ -8021,7 +8021,7 @@

                                                                              Submodules
                                                                              -classmethod from_structure(structure: Structure, reciprocal_density: int | None = 50000, **kwargs) → Self[source]
                                                                              +classmethod from_structure(structure: Structure, reciprocal_density: int | None = 50000, **kwargs) → Self[source]

                                                                              Get a ShengBTE control object from a structure.

                                                                              Parameters:
                                                                              @@ -8041,7 +8041,7 @@

                                                                              Submodules
                                                                              -get_structure() → Structure[source]
                                                                              +get_structure() → Structure[source]

                                                                              Get a pymatgen Structure from a ShengBTE control object.

                                                                              The control object must have the “lattvec”, “types”, “elements”, and “positions” settings otherwise an error will be thrown.

                                                                              @@ -8054,17 +8054,17 @@

                                                                              Submodules
                                                                              -params_keys = ('t', 't_min', 't_max', 't_step', 'omega_max', 'scalebroad', 'rmin', 'rmax', 'dr', 'maxiter', 'nticks', 'eps')[source]
                                                                              +params_keys = ('t', 't_min', 't_max', 't_step', 'omega_max', 'scalebroad', 'rmin', 'rmax', 'dr', 'maxiter', 'nticks', 'eps')[source]

                                                                              -required_params = ('nelements', 'natoms', 'ngrid', 'lattvec', 'types', 'elements', 'positions', 'scell')[source]
                                                                              +required_params = ('nelements', 'natoms', 'ngrid', 'lattvec', 'types', 'elements', 'positions', 'scell')[source]
                                                                              -to_file(filename: str = 'CONTROL') → None[source]
                                                                              +to_file(filename: str = 'CONTROL') → None[source]

                                                                              Write ShengBTE CONTROL file from ‘Control’ object.

                                                                              Parameters:
                                                                              @@ -8082,7 +8082,7 @@

                                                                              Submodules
                                                                              -class TemplateInputGen[source]
                                                                              +class TemplateInputGen[source]

                                                                              Bases: InputGenerator

                                                                              Concrete implementation of InputGenerator that is based on a single template input file with variables.

                                                                              @@ -8091,7 +8091,7 @@

                                                                              Submodules
                                                                              -get_input_set(template: str | Path, variables: dict | None = None, filename: str = 'input.txt')[source]
                                                                              +get_input_set(template: str | Path, variables: dict | None = None, filename: str = 'input.txt')[source]
                                                                              Parameters:
                                                                                @@ -8115,12 +8115,12 @@

                                                                                Submodules
                                                                                -class Unk(ik: int, data: ndarray)[source]
                                                                                +class Unk(ik: int, data: ndarray)[source]

                                                                                Bases: object

                                                                                Object representing the data in a UNK file.

                                                                                -ik[source]
                                                                                +ik[source]

                                                                                Index of kpoint for this file.

                                                                                Type:
                                                                                @@ -8131,7 +8131,7 @@

                                                                                Submodules
                                                                                -data[source]
                                                                                +data[source]

                                                                                Numpy array that contains the wavefunction data in the UNK file. The shape should be (nbnd, ngx, ngy, ngz) for regular calculations and (nbnd, 2, ngx, ngy, ngz) for noncollinear calculations.

                                                                                @@ -8144,7 +8144,7 @@

                                                                                Submodules
                                                                                -is_noncollinear[source]
                                                                                +is_noncollinear[source]

                                                                                Boolean that specifies if data is from a noncollinear calculation.

                                                                                Type:
                                                                                @@ -8155,7 +8155,7 @@

                                                                                Submodules
                                                                                -nbnd[source]
                                                                                +nbnd[source]

                                                                                Number of bands in data.

                                                                                Type:
                                                                                @@ -8166,7 +8166,7 @@

                                                                                Submodules
                                                                                -ng[source]
                                                                                +ng[source]

                                                                                Sequence of three integers that correspond to the grid size of the given data. The definition is ng = (ngx, ngy, ngz).

                                                                                @@ -8188,7 +8188,7 @@

                                                                                Submodules
                                                                                -property data: ndarray[source]
                                                                                +property data: ndarray[source]

                                                                                contains the wavefunction data in the UNK file. The shape should be (nbnd, ngx, ngy, ngz) for regular calculations and (nbnd, 2, ngx, ngy, ngz) for noncollinear calculations.

                                                                                @@ -8201,7 +8201,7 @@

                                                                                Submodules
                                                                                -classmethod from_file(filename: str) → Self[source]
                                                                                +classmethod from_file(filename: str) → Self[source]

                                                                                Reads the UNK data from file.

                                                                                Parameters:
                                                                                @@ -8215,27 +8215,27 @@

                                                                                Submodules
                                                                                -ik: int[source]
                                                                                +ik: int[source]

                                                                                -is_noncollinear: bool[source]
                                                                                +is_noncollinear: bool[source]
                                                                                -nbnd: int[source]
                                                                                +nbnd: int[source]
                                                                                -ng: Sequence[int][source]
                                                                                +ng: Sequence[int][source]
                                                                                -write_file(filename: str) → None[source]
                                                                                +write_file(filename: str) → None[source]

                                                                                Write the UNK file.

                                                                                Parameters:
                                                                                @@ -8254,7 +8254,7 @@

                                                                                Submodules
                                                                                -class XSF(structure: Structure)[source]
                                                                                +class XSF(structure: Structure)[source]

                                                                                Bases: object

                                                                                Parse XCrysden files.

                                                                                @@ -8264,7 +8264,7 @@

                                                                                Submodules
                                                                                -classmethod from_str(input_string: str, cls_=None) → Self[source]
                                                                                +classmethod from_str(input_string: str, cls_=None) → Self[source]

                                                                                Initialize a Structure object from a string with data in XSF format.

                                                                                Parameters:
                                                                                @@ -8298,7 +8298,7 @@

                                                                                Submodules
                                                                                -to_str(atom_symbol: bool = True) → str[source]
                                                                                +to_str(atom_symbol: bool = True) → str[source]

                                                                                Get a string with the structure in XSF format See http://www.xcrysden.org/doc/XSF.html.

                                                                                @@ -8321,7 +8321,7 @@

                                                                                Submodules
                                                                                -class Xr(structure: Structure)[source]
                                                                                +class Xr(structure: Structure)[source]

                                                                                Bases: object

                                                                                For working with XR files.

                                                                                @@ -8331,7 +8331,7 @@

                                                                                Submodules
                                                                                -classmethod from_file(filename: str | Path, use_cores: bool = True, thresh: float = 0.0001) → Self[source]
                                                                                +classmethod from_file(filename: str | Path, use_cores: bool = True, thresh: float = 0.0001) → Self[source]

                                                                                Reads an xr-formatted file to create an Xr object.

                                                                                Parameters:
                                                                                @@ -8360,7 +8360,7 @@

                                                                                Submodules
                                                                                -classmethod from_str(string: str, use_cores: bool = True, thresh: float = 0.0001) → Self[source]
                                                                                +classmethod from_str(string: str, use_cores: bool = True, thresh: float = 0.0001) → Self[source]

                                                                                Creates an Xr object from a string representation.

                                                                                Parameters:
                                                                                @@ -8389,7 +8389,7 @@

                                                                                Submodules
                                                                                -write_file(filename: str | Path) → None[source]
                                                                                +write_file(filename: str | Path) → None[source]

                                                                                Write out an xr file.

                                                                                Parameters:
                                                                                @@ -8406,7 +8406,7 @@

                                                                                Submodules
                                                                                -class XYZ(mol: Molecule | Structure | Sequence[Molecule | Structure], coord_precision: int = 6)[source]
                                                                                +class XYZ(mol: Molecule | Structure | Sequence[Molecule | Structure], coord_precision: int = 6)[source]

                                                                                Bases: object

                                                                                Basic class for importing and exporting Molecules or Structures in XYZ format.

                                                                                @@ -8427,13 +8427,13 @@

                                                                                Submodules
                                                                                -property all_molecules: list[Molecule][source]
                                                                                +property all_molecules: list[Molecule][source]

                                                                                All the frames of molecule associated with this XYZ.

                                                                                -as_dataframe()[source]
                                                                                +as_dataframe()[source]

                                                                                Generate a coordinates data frame with columns: atom, x, y, and z In case of multiple frame XYZ, returns the last frame.

                                                                                @@ -8445,7 +8445,7 @@

                                                                                Submodules
                                                                                -classmethod from_file(filename: str | Path) → Self[source]
                                                                                +classmethod from_file(filename: str | Path) → Self[source]

                                                                                Creates XYZ object from a file.

                                                                                Parameters:
                                                                                @@ -8459,7 +8459,7 @@

                                                                                Submodules
                                                                                -classmethod from_str(contents: str) → Self[source]
                                                                                +classmethod from_str(contents: str) → Self[source]

                                                                                Creates XYZ object from a string.

                                                                                Parameters:
                                                                                @@ -8473,14 +8473,14 @@

                                                                                Submodules
                                                                                -property molecule: Molecule[source]
                                                                                +property molecule: Molecule[source]

                                                                                Molecule associated with this XYZ. In case of multi-frame XYZ, returns the last frame.

                                                                                -write_file(filename: str) → None[source]
                                                                                +write_file(filename: str) → None[source]

                                                                                Write XYZ file.

                                                                                Parameters:
                                                                                @@ -8520,7 +8520,7 @@

                                                                                Zeo++ Post-Installation Checking:
                                                                                -class ZeoCssr(structure: Structure)[source]
                                                                                +class ZeoCssr(structure: Structure)[source]

                                                                                Bases: Cssr

                                                                                ZeoCssr adds extra fields to CSSR sites to conform with Zeo++ input CSSR format. The coordinate system is rotated from xyz to zyx. @@ -8533,7 +8533,7 @@

                                                                                Zeo++ Post-Installation Checking:
                                                                                -classmethod from_file(filename: str | Path) → Self[source]
                                                                                +classmethod from_file(filename: str | Path) → Self[source]

                                                                                Reads a CSSR file to a ZeoCssr object.

                                                                                Parameters:
                                                                                @@ -8547,7 +8547,7 @@

                                                                                Zeo++ Post-Installation Checking:
                                                                                -classmethod from_str(string: str) → Self[source]
                                                                                +classmethod from_str(string: str) → Self[source]

                                                                                Reads a string representation to a ZeoCssr object.

                                                                                Parameters:
                                                                                @@ -8563,7 +8563,7 @@

                                                                                Zeo++ Post-Installation Checking:
                                                                                -class ZeoVoronoiXYZ(mol)[source]
                                                                                +class ZeoVoronoiXYZ(mol)[source]

                                                                                Bases: XYZ

                                                                                Read Voronoi Nodes from XYZ file written by Zeo++. The sites have an additional column representing the voronoi node radius. @@ -8575,7 +8575,7 @@

                                                                                Zeo++ Post-Installation Checking:
                                                                                -classmethod from_file(filename: str | Path) → Self[source]
                                                                                +classmethod from_file(filename: str | Path) → Self[source]

                                                                                Creates XYZ object from a file.

                                                                                Parameters:
                                                                                @@ -8589,7 +8589,7 @@

                                                                                Zeo++ Post-Installation Checking:
                                                                                -classmethod from_str(contents: str) → Self[source]
                                                                                +classmethod from_str(contents: str) → Self[source]

                                                                                Creates Zeo++ Voronoi XYZ object from a string. from_string method of XYZ class is being redefined.

                                                                                @@ -8606,7 +8606,7 @@

                                                                                Zeo++ Post-Installation Checking:
                                                                                -get_free_sphere_params(structure, rad_dict=None, probe_rad=0.1)[source]
                                                                                +get_free_sphere_params(structure, rad_dict=None, probe_rad=0.1)[source]

                                                                                Analyze the void space in the input structure using voronoi decomposition Calls Zeo++ for Voronoi decomposition.

                                                                                @@ -8632,7 +8632,7 @@

                                                                                Zeo++ Post-Installation Checking:
                                                                                -get_high_accuracy_voronoi_nodes(structure, rad_dict, probe_rad=0.1)[source]
                                                                                +get_high_accuracy_voronoi_nodes(structure, rad_dict, probe_rad=0.1)[source]

                                                                                Analyze the void space in the input structure using high accuracy voronoi decomposition. Calls Zeo++ for Voronoi decomposition.

                                                                                @@ -8659,7 +8659,7 @@

                                                                                Zeo++ Post-Installation Checking:
                                                                                -get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1)[source]
                                                                                +get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1)[source]

                                                                                Analyze the void space in the input structure using voronoi decomposition Calls Zeo++ for Voronoi decomposition.

                                                                                diff --git a/docs/pymatgen.io.lammps.html b/docs/pymatgen.io.lammps.html index 4d7d613e13b..580dcc12f39 100644 --- a/docs/pymatgen.io.lammps.html +++ b/docs/pymatgen.io.lammps.html @@ -4,7 +4,7 @@ - pymatgen.io.lammps package — pymatgen 2024.6.4 documentation + pymatgen.io.lammps package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                - 2024.6.4 + 2024.6.10
                                                                                @@ -238,7 +238,7 @@

                                                                                Submodules
                                                                                -class CombinedData(list_of_molecules: list, list_of_names: list[str], list_of_numbers: list[int], coordinates: DataFrame, atom_style: str = 'full')[source]
                                                                                +class CombinedData(list_of_molecules: list, list_of_names: list[str], list_of_numbers: list[int], coordinates: DataFrame, atom_style: str = 'full')[source]

                                                                                Bases: LammpsData

                                                                                Object for a collective set of data for a series of LAMMPS data file. velocities not yet implemented.

                                                                                @@ -259,7 +259,7 @@

                                                                                Submodules
                                                                                -as_lammpsdata()[source]
                                                                                +as_lammpsdata()[source]

                                                                                Convert a CombinedData object to a LammpsData object. attributes are deep-copied.

                                                                                box (LammpsBox): Simulation box. force_fieldct (dict): Data for force field sections. Optional

                                                                                @@ -277,7 +277,7 @@

                                                                                Submodules
                                                                                -disassemble(atom_labels: Sequence[str] | None = None, guess_element: bool = True, ff_label: str = 'ff_map')[source]
                                                                                +disassemble(atom_labels: Sequence[str] | None = None, guess_element: bool = True, ff_label: str = 'ff_map')[source]

                                                                                Breaks down each LammpsData in CombinedData to building blocks (LammpsBox, ForceField and a series of Topology). RESTRICTIONS APPLIED: @@ -320,13 +320,13 @@

                                                                                Submodules
                                                                                -classmethod from_ff_and_topologies() → None[source]
                                                                                +classmethod from_ff_and_topologies() → None[source]

                                                                                Unsupported constructor for CombinedData objects.

                                                                                -classmethod from_files(coordinate_file: str, list_of_numbers: list[int], *filenames: str) → Self[source]
                                                                                +classmethod from_files(coordinate_file: str, list_of_numbers: list[int], *filenames: str) → Self[source]

                                                                                Constructor that parse a series of data file.

                                                                                Parameters:
                                                                                @@ -342,7 +342,7 @@

                                                                                Submodules
                                                                                -classmethod from_lammpsdata(mols: list, names: list, list_of_numbers: list, coordinates: pd.DataFrame, atom_style: str | None = None) → Self[source]
                                                                                +classmethod from_lammpsdata(mols: list, names: list, list_of_numbers: list, coordinates: pd.DataFrame, atom_style: str | None = None) → Self[source]

                                                                                Constructor that can infer atom_style. The input LammpsData objects are used non-destructively.

                                                                                @@ -362,13 +362,13 @@

                                                                                Submodules
                                                                                -classmethod from_structure() → None[source]
                                                                                +classmethod from_structure() → None[source]

                                                                                Unsupported constructor for CombinedData objects.

                                                                                -get_str(distance: int = 6, velocity: int = 8, charge: int = 4, hybrid: bool = True) → str[source]
                                                                                +get_str(distance: int = 6, velocity: int = 8, charge: int = 4, hybrid: bool = True) → str[source]

                                                                                Get the string representation of CombinedData, essentially the string to be written to a file. Combination info is included as a comment. For single molecule ID data, the info format is:

                                                                                @@ -407,7 +407,7 @@

                                                                                Submodules
                                                                                -classmethod parse_xyz(filename: str | Path) → DataFrame[source]
                                                                                +classmethod parse_xyz(filename: str | Path) → DataFrame[source]

                                                                                Load xyz file generated from packmol (for those who find it hard to install openbabel).

                                                                                Returns:
                                                                                @@ -418,7 +418,7 @@

                                                                                Submodules
                                                                                -property structure: Structure[source]
                                                                                +property structure: Structure[source]

                                                                                Exports a periodic structure object representing the simulation box.

                                                                                @@ -432,12 +432,12 @@

                                                                                Submodules
                                                                                -class ForceField(mass_info: list, nonbond_coeffs: list | None = None, topo_coeffs: dict | None = None)[source]
                                                                                +class ForceField(mass_info: list, nonbond_coeffs: list | None = None, topo_coeffs: dict | None = None)[source]

                                                                                Bases: MSONable

                                                                                Class carrying most data in masses and force field sections.

                                                                                -masses[source]
                                                                                +masses[source]

                                                                                DataFrame for masses section.

                                                                                Type:
                                                                                @@ -448,7 +448,7 @@

                                                                                Submodules
                                                                                -force_fieldct[source]
                                                                                +force_fieldct[source]

                                                                                Force field section keywords (keys) and data (values) as DataFrames.

                                                                                @@ -460,7 +460,7 @@

                                                                                Submodules
                                                                                -maps[source]
                                                                                +maps[source]

                                                                                Dict for labeling atoms and topologies.

                                                                                Type:
                                                                                @@ -527,7 +527,7 @@

                                                                                Submodules
                                                                                -classmethod from_dict(dct: dict) → Self[source]
                                                                                +classmethod from_dict(dct: dict) → Self[source]

                                                                                Constructor that reads in a dictionary.

                                                                                Parameters:
                                                                                @@ -538,7 +538,7 @@

                                                                                Submodules
                                                                                -classmethod from_file(filename: str) → Self[source]
                                                                                +classmethod from_file(filename: str) → Self[source]

                                                                                Constructor that reads in a file in YAML format.

                                                                                Parameters:
                                                                                @@ -549,7 +549,7 @@

                                                                                Submodules
                                                                                -to_file(filename: str) → None[source]
                                                                                +to_file(filename: str) → None[source]

                                                                                Save force field to a file in YAML format.

                                                                                Parameters:
                                                                                @@ -562,7 +562,7 @@

                                                                                Submodules
                                                                                -class LammpsBox(bounds: Sequence, tilt: Sequence | None = None)[source]
                                                                                +class LammpsBox(bounds: Sequence, tilt: Sequence | None = None)[source]

                                                                                Bases: MSONable

                                                                                Object for representing a simulation box in LAMMPS settings.

                                                                                @@ -578,7 +578,7 @@

                                                                                Submodules
                                                                                -get_box_shift(i: Sequence[int]) → np.ndarray[source]
                                                                                +get_box_shift(i: Sequence[int]) → np.ndarray[source]

                                                                                Calculates the coordinate shift due to PBC.

                                                                                Parameters:
                                                                                @@ -595,7 +595,7 @@

                                                                                Submodules
                                                                                -get_str(significant_figures: int = 6) → str[source]
                                                                                +get_str(significant_figures: int = 6) → str[source]

                                                                                Get the string representation of simulation box in LAMMPS data file format.

                                                                                Parameters:
                                                                                @@ -607,7 +607,7 @@

                                                                                Submodules
                                                                                -to_lattice() → Lattice[source]
                                                                                +to_lattice() → Lattice[source]

                                                                                Convert the simulation box to a more powerful Lattice backend. Note that Lattice is always periodic in 3D space while a simulation box is not necessarily periodic in all dimensions.

                                                                                @@ -620,7 +620,7 @@

                                                                                Submodules
                                                                                -property volume: float[source]
                                                                                +property volume: float[source]

                                                                                Volume of simulation box.

                                                                                @@ -628,7 +628,7 @@

                                                                                Submodules
                                                                                -class LammpsData(box: LammpsBox, masses: DataFrame, atoms: DataFrame, velocities: DataFrame = None, force_field: dict | None = None, topology: dict[str, DataFrame] | None = None, atom_style: str = 'full')[source]
                                                                                +class LammpsData(box: LammpsBox, masses: DataFrame, atoms: DataFrame, velocities: DataFrame = None, force_field: dict | None = None, topology: dict[str, DataFrame] | None = None, atom_style: str = 'full')[source]

                                                                                Bases: MSONable

                                                                                Object for representing the data in a LAMMPS data file.

                                                                                Low level constructor designed to work with parsed data or other bridging @@ -658,7 +658,7 @@

                                                                                Submodules
                                                                                -disassemble(atom_labels: Sequence[str] | None = None, guess_element: bool = True, ff_label: str = 'ff_map') → tuple[LammpsBox, ForceField, list[Topology]][source]
                                                                                +disassemble(atom_labels: Sequence[str] | None = None, guess_element: bool = True, ff_label: str = 'ff_map') → tuple[LammpsBox, ForceField, list[Topology]][source]

                                                                                Breaks down LammpsData to building blocks (LammpsBox, ForceField and a series of Topology). RESTRICTIONS APPLIED:

                                                                                @@ -702,7 +702,7 @@

                                                                                Submodules
                                                                                -classmethod from_ff_and_topologies(box: LammpsBox, ff: ForceField, topologies: Sequence[Topology], atom_style: str = 'full') → Self[source]
                                                                                +classmethod from_ff_and_topologies(box: LammpsBox, ff: ForceField, topologies: Sequence[Topology], atom_style: str = 'full') → Self[source]

                                                                                Constructor building LammpsData from a ForceField object and a list of Topology objects. Do not support intermolecular topologies since a Topology object includes data for ONE @@ -723,7 +723,7 @@

                                                                                Submodules
                                                                                -classmethod from_file(filename: str, atom_style: str = 'full', sort_id: bool = False) → Self[source]
                                                                                +classmethod from_file(filename: str, atom_style: str = 'full', sort_id: bool = False) → Self[source]

                                                                                Constructor that parses a file.

                                                                                Parameters:
                                                                                @@ -739,7 +739,7 @@

                                                                                Submodules
                                                                                -classmethod from_structure(structure: Structure, ff_elements: Sequence[str] | None = None, atom_style: Literal['atomic', 'charge'] = 'charge', is_sort: bool = False) → Self[source]
                                                                                +classmethod from_structure(structure: Structure, ff_elements: Sequence[str] | None = None, atom_style: Literal['atomic', 'charge'] = 'charge', is_sort: bool = False) → Self[source]

                                                                                Simple constructor building LammpsData from a structure without force field parameters and topologies.

                                                                                @@ -759,7 +759,7 @@

                                                                                Submodules
                                                                                -get_str(distance: int = 6, velocity: int = 8, charge: int = 4, hybrid: bool = True) → str[source]
                                                                                +get_str(distance: int = 6, velocity: int = 8, charge: int = 4, hybrid: bool = True) → str[source]

                                                                                Get the string representation of LammpsData, essentially the string to be written to a file. Supports hybrid style coeffs read and write.

                                                                                @@ -790,7 +790,7 @@

                                                                                Submodules
                                                                                -set_charge_atom(charges: dict[int, float]) → None[source]
                                                                                +set_charge_atom(charges: dict[int, float]) → None[source]

                                                                                Set the charges of specific atoms of the data.

                                                                                Parameters:
                                                                                @@ -803,7 +803,7 @@

                                                                                Submodules
                                                                                -set_charge_atom_type(charges: dict[str | int, float]) → None[source]
                                                                                +set_charge_atom_type(charges: dict[str | int, float]) → None[source]

                                                                                Add or modify charges of all atoms of a given type in the data.

                                                                                Parameters:
                                                                                @@ -821,7 +821,7 @@

                                                                                Submodules
                                                                                -property structure: Structure[source]
                                                                                +property structure: Structure[source]

                                                                                Exports a periodic structure object representing the simulation box.

                                                                                @@ -833,7 +833,7 @@

                                                                                Submodules
                                                                                -write_file(filename: str, distance: int = 6, velocity: int = 8, charge: int = 4) → None[source]
                                                                                +write_file(filename: str, distance: int = 6, velocity: int = 8, charge: int = 4) → None[source]

                                                                                Write LammpsData to file.

                                                                                Parameters:
                                                                                @@ -855,7 +855,7 @@

                                                                                Submodules
                                                                                -class Topology(sites: Sequence[Site] | SiteCollection, ff_label: str | None = None, charges: Sequence | None = None, velocities: Sequence[Sequence] | None = None, topologies: dict | None = None)[source]
                                                                                +class Topology(sites: Sequence[Site] | SiteCollection, ff_label: str | None = None, charges: Sequence | None = None, velocities: Sequence[Sequence] | None = None, topologies: dict | None = None)[source]

                                                                                Bases: MSONable

                                                                                Carry most data in Atoms, Velocities and Molecular Topology sections for ONE SINGLE Molecule or Structure object, or a plain list of Sites.

                                                                                @@ -892,7 +892,7 @@

                                                                                Submodules
                                                                                -classmethod from_bonding(molecule: Molecule, bond: bool = True, angle: bool = True, dihedral: bool = True, tol: float = 0.1, **kwargs) → Self[source]
                                                                                +classmethod from_bonding(molecule: Molecule, bond: bool = True, angle: bool = True, dihedral: bool = True, tol: float = 0.1, **kwargs) → Self[source]

                                                                                Another constructor that creates an instance from a molecule. Covalent bonds and other bond-based topologies (angles and dihedrals) can be automatically determined. Cannot be used for @@ -917,7 +917,7 @@

                                                                                Submodules
                                                                                -lattice_2_lmpbox(lattice: Lattice, origin: Sequence = (0, 0, 0)) → tuple[LammpsBox, SymmOp][source]
                                                                                +lattice_2_lmpbox(lattice: Lattice, origin: Sequence = (0, 0, 0)) → tuple[LammpsBox, SymmOp][source]

                                                                                Converts a lattice object to LammpsBox, and calculates the symmetry operation used.

                                                                                @@ -945,7 +945,7 @@

                                                                                Submoduleshttps://github.com/Matgenix/atomate2-lammps).

                                                                                -class BaseLammpsGenerator(inputfile: ~pymatgen.io.lammps.inputs.LammpsInputFile | None = None, template: str = <factory>, data: ~pymatgen.io.lammps.data.LammpsData | ~pymatgen.io.lammps.data.CombinedData | None = None, settings: dict = <factory>, calc_type: str = 'lammps', keep_stages: bool = True)[source]
                                                                                +class BaseLammpsGenerator(inputfile: ~pymatgen.io.lammps.inputs.LammpsInputFile | None = None, template: str = <factory>, data: ~pymatgen.io.lammps.data.LammpsData | ~pymatgen.io.lammps.data.CombinedData | None = None, settings: dict = <factory>, calc_type: str = 'lammps', keep_stages: bool = True)[source]

                                                                                Bases: InputGenerator

                                                                                Base class to generate LAMMPS input sets. Uses template files for the input. The variables that can be changed @@ -956,7 +956,7 @@

                                                                                Submodules
                                                                                -template[source]
                                                                                +template[source]

                                                                                Path (string) to the template file used to create the InputFile for LAMMPS.

                                                                                Type:
                                                                                @@ -967,7 +967,7 @@

                                                                                Submodules
                                                                                -calc_type[source]
                                                                                +calc_type[source]

                                                                                Human-readable string used to briefly describe the type of computations performed by LAMMPS.

                                                                                Type:
                                                                                @@ -978,7 +978,7 @@

                                                                                Submodules
                                                                                -settings[source]
                                                                                +settings[source]

                                                                                Dictionary containing the values of the parameters to replace in the template.

                                                                                Type:
                                                                                @@ -989,7 +989,7 @@

                                                                                Submodules
                                                                                -keep_stages[source]
                                                                                +keep_stages[source]

                                                                                If True, the string is formatted in a block structure with stage names

                                                                                Type:
                                                                                @@ -1015,45 +1015,45 @@

                                                                                Submoduleshttps://github.com/Matgenix/atomate2-lammps).

                                                                                -calc_type: str = 'lammps'[source]
                                                                                +calc_type: str = 'lammps'[source]
                                                                                -data: LammpsData | CombinedData | None = None[source]
                                                                                +data: LammpsData | CombinedData | None = None[source]
                                                                                -get_input_set(structure: Structure | LammpsData | CombinedData) → LammpsInputSet[source]
                                                                                +get_input_set(structure: Structure | LammpsData | CombinedData) → LammpsInputSet[source]

                                                                                Generate a LammpsInputSet from the structure/data, tailored to the template file.

                                                                                -inputfile: LammpsInputFile | None = None[source]
                                                                                +inputfile: LammpsInputFile | None = None[source]
                                                                                -keep_stages: bool = True[source]
                                                                                +keep_stages: bool = True[source]
                                                                                -settings: dict[source]
                                                                                +settings: dict[source]
                                                                                -template: str[source]
                                                                                +template: str[source]

                                                                                -class LammpsMinimization(template: str | None = None, units: str = 'metal', atom_style: str = 'full', dimension: int = 3, boundary: str = 'p p p', read_data: str = 'system.data', force_field: str = 'Unspecified force field!', keep_stages: bool = False)[source]
                                                                                +class LammpsMinimization(template: str | None = None, units: str = 'metal', atom_style: str = 'full', dimension: int = 3, boundary: str = 'p p p', read_data: str = 'system.data', force_field: str = 'Unspecified force field!', keep_stages: bool = False)[source]

                                                                                Bases: BaseLammpsGenerator

                                                                                Generator that yields a LammpsInputSet tailored for minimizing the energy of a system by iteratively adjusting atom coordinates. @@ -1095,37 +1095,37 @@

                                                                                Submodules
                                                                                -property atom_style: str[source]
                                                                                +property atom_style: str[source]

                                                                                The argument of the command ‘atom_style’ passed to the generator.

                                                                                -property boundary: str[source]
                                                                                +property boundary: str[source]

                                                                                The argument of the command ‘boundary’ passed to the generator.

                                                                                -property dimension: int[source]
                                                                                +property dimension: int[source]

                                                                                The argument of the command ‘dimension’ passed to the generator.

                                                                                -property force_field: str[source]
                                                                                +property force_field: str[source]

                                                                                The details of the force field commands passed to the generator.

                                                                                -property read_data: str[source]
                                                                                +property read_data: str[source]

                                                                                The argument of the command ‘read_data’ passed to the generator.

                                                                                -property units: str[source]
                                                                                +property units: str[source]

                                                                                The argument of the command ‘units’ passed to the generator.

                                                                                @@ -1140,7 +1140,7 @@

                                                                                Submoduleshttps://github.com/Matgenix/atomate2-lammps.

                                                                                -class LammpsInputFile(stages: list | None = None)[source]
                                                                                +class LammpsInputFile(stages: list | None = None)[source]

                                                                                Bases: InputFile

                                                                                LAMMPS input settings file such as in.lammps. Allows for LAMMPS input generation in line/stage wise manner. A stage @@ -1171,7 +1171,7 @@

                                                                                ]

                                                                                -add_commands(stage_name: str, commands: str | list[str] | dict) → None[source]
                                                                                +add_commands(stage_name: str, commands: str | list[str] | dict) → None[source]

                                                                                Method to add a LAMMPS commands and their arguments to a stage of the LammpsInputFile. The stage name should be provided: a default behavior is avoided here to avoid mistakes (e.g., the commands are added to the wrong stage).

                                                                                @@ -1220,7 +1220,7 @@

                                                                                )

                                                                                -add_stage(stage: dict | None = None, commands: str | list[str] | dict[str, str | float] | None = None, stage_name: str | None = None, after_stage: str | int | None = None) → None[source]
                                                                                +add_stage(stage: dict | None = None, commands: str | list[str] | dict[str, str | float] | None = None, stage_name: str | None = None, after_stage: str | int | None = None) → None[source]

                                                                                Adds a new stage to the LammpsInputFile, either from a whole stage (dict) or from a stage_name and commands. Both ways are mutually exclusive.

                                                                                Examples

                                                                                @@ -1310,7 +1310,7 @@

                                                                                ]

                                                                                -append(lmp_input_file: LammpsInputFile) → None[source]
                                                                                +append(lmp_input_file: LammpsInputFile) → None[source]

                                                                                Appends a LammpsInputFile to another. The stages are merged, and the numbering of stages/comments is either kept the same or updated.

                                                                                @@ -1322,7 +1322,7 @@

                                                                                ]

                                                                                -contains_command(command: str, stage_name: str | None = None) → bool[source]
                                                                                +contains_command(command: str, stage_name: str | None = None) → bool[source]

                                                                                Get whether a given command is present in the LammpsInputFile. A stage name can be given; in this case the search will happen only for this stage.

                                                                                @@ -1343,7 +1343,7 @@

                                                                                ]

                                                                                -classmethod from_file(path: str | Path, ignore_comments: bool = False, keep_stages: bool = False) → Self[source]
                                                                                +classmethod from_file(path: str | Path, ignore_comments: bool = False, keep_stages: bool = False) → Self[source]

                                                                                Creates an InputFile object from a file.

                                                                                Parameters:
                                                                                @@ -1362,7 +1362,7 @@

                                                                                ]

                                                                                -classmethod from_str(contents: str, ignore_comments: bool = False, keep_stages: bool = False) → Self[source]
                                                                                +classmethod from_str(contents: str, ignore_comments: bool = False, keep_stages: bool = False) → Self[source]

                                                                                Helper method to parse string representation of LammpsInputFile. If you created the input file by hand, there is no guarantee that the representation will be perfect as it is difficult to account for all the cosmetic changes you @@ -1387,7 +1387,7 @@

                                                                                ]

                                                                                -get_args(command: str, stage_name: str | None = None) → list | str[source]
                                                                                +get_args(command: str, stage_name: str | None = None) → list | str[source]

                                                                                Given a command, returns the corresponding arguments (or list of arguments) in the LammpsInputFile. A stage name can be given; in this case the search will happen only for this stage. If a stage name is not given, the command will be searched for through all of them. @@ -1408,7 +1408,7 @@

                                                                                ]

                                                                                -get_str(ignore_comments: bool = False, keep_stages: bool = True) → str[source]
                                                                                +get_str(ignore_comments: bool = False, keep_stages: bool = True) → str[source]

                                                                                Generate and ² the string representation of the LammpsInputFile. Stages are separated by empty lines. The headers of the stages will be put in comments preceding each stage. @@ -1433,7 +1433,7 @@

                                                                                ]

                                                                                -merge_stages(stage_names: list[str]) → None[source]
                                                                                +merge_stages(stage_names: list[str]) → None[source]

                                                                                Merges multiple stages of a LammpsInputFile together. The merged stage will be at the same index as the first of the stages to be merged. The others will appear in the same order as provided in the list. Other non-merged stages will follow.

                                                                                @@ -1446,20 +1446,20 @@

                                                                                ]

                                                                                -property ncomments: int[source]
                                                                                +property ncomments: int[source]

                                                                                The number of comments in the current LammpsInputFile. Includes the blocks of comments as well as inline comments (comment lines within blocks of LAMMPS commands).

                                                                                -property nstages: int[source]
                                                                                +property nstages: int[source]

                                                                                The number of stages in the current LammpsInputFile.

                                                                                -remove_command(command: str, stage_name: str | list[str] | None = None, remove_empty_stages: bool = True) → None[source]
                                                                                +remove_command(command: str, stage_name: str | list[str] | None = None, remove_empty_stages: bool = True) → None[source]

                                                                                Removes a given command from a given stage. If no stage is given, removes all occurrences of the command. In case removing a command completely empties a stage, the choice whether to keep this stage in the LammpsInputFile is given by remove_empty_stages.

                                                                                @@ -1476,7 +1476,7 @@

                                                                                ]

                                                                                -remove_stage(stage_name: str) → None[source]
                                                                                +remove_stage(stage_name: str) → None[source]

                                                                                Removes a whole stage from the LammpsInputFile.

                                                                                Parameters:
                                                                                @@ -1487,7 +1487,7 @@

                                                                                ]

                                                                                -rename_stage(stage_name: str, new_name: str) → None[source]
                                                                                +rename_stage(stage_name: str, new_name: str) → None[source]

                                                                                Renames a stage stage_name from LammpsInputFile into new_name. First checks that the stage to rename is present, and that the new name is not already a stage name.

                                                                                @@ -1503,7 +1503,7 @@

                                                                                ]

                                                                                -set_args(command: str, argument: str, stage_name: str | None = None, how: str | int | list[int] = 'all') → None[source]
                                                                                +set_args(command: str, argument: str, stage_name: str | None = None, how: str | int | list[int] = 'all') → None[source]

                                                                                Set the arguments for the given command to the given string. If the command is not found, nothing is done. Use LammpsInputFile.add_commands instead. If a stage name is specified, it will be replaced or set only for this stage. @@ -1526,13 +1526,13 @@

                                                                                ]

                                                                                -property stages_names: list[source]
                                                                                +property stages_names: list[source]

                                                                                List of names for all the stages present in stages.

                                                                                -write_file(filename: str | PathLike, ignore_comments: bool = False, keep_stages: bool = True) → None[source]
                                                                                +write_file(filename: str | PathLike, ignore_comments: bool = False, keep_stages: bool = True) → None[source]

                                                                                Write LAMMPS input file.

                                                                                Parameters:
                                                                                @@ -1551,7 +1551,7 @@

                                                                                ]

                                                                                -class LammpsRun(script_template: str, settings: dict, data: LammpsData | str, script_filename: str)[source]
                                                                                +class LammpsRun(script_template: str, settings: dict, data: LammpsData | str, script_filename: str)[source]

                                                                                Bases: MSONable

                                                                                Examples for various simple LAMMPS runs with given simulation box, force field and a few more settings. Experienced LAMMPS users should @@ -1576,7 +1576,7 @@

                                                                                ]

                                                                                -classmethod md(data: LammpsData | str, force_field: str, temperature: float, nsteps: int, other_settings: dict | None = None) → LammpsRun[source]
                                                                                +classmethod md(data: LammpsData | str, force_field: str, temperature: float, nsteps: int, other_settings: dict | None = None) → LammpsRun[source]

                                                                                Example for a simple MD run based on template md.template.

                                                                                Parameters:
                                                                                @@ -1596,7 +1596,7 @@

                                                                                ]

                                                                                -write_inputs(output_dir: str, **kwargs) → None[source]
                                                                                +write_inputs(output_dir: str, **kwargs) → None[source]

                                                                                Write all input files (input script, and data if needed). Other supporting files are not handled at this moment.

                                                                                @@ -1613,7 +1613,7 @@

                                                                                ]

                                                                                -class LammpsTemplateGen[source]
                                                                                +class LammpsTemplateGen[source]

                                                                                Bases: TemplateInputGen

                                                                                Create an InputSet object for a LAMMPS run based on a template file. The input script is constructed by substituting variables into placeholders @@ -1626,7 +1626,7 @@

                                                                                ]

                                                                                -get_input_set(script_template: str | Path, settings: dict | None = None, script_filename: str = 'in.lammps', data: LammpsData | CombinedData | None = None, data_filename: str = 'system.data') → InputSet[source]
                                                                                +get_input_set(script_template: str | Path, settings: dict | None = None, script_filename: str = 'in.lammps', data: LammpsData | CombinedData | None = None, data_filename: str = 'system.data') → InputSet[source]
                                                                                Parameters:
                                                                                  @@ -1655,7 +1655,7 @@

                                                                                  ]

                                                                                  -class LammpsDump(timestep: int, natoms: int, box: LammpsBox, data: DataFrame)[source]
                                                                                  +class LammpsDump(timestep: int, natoms: int, box: LammpsBox, data: DataFrame)[source]

                                                                                  Bases: MSONable

                                                                                  Object for representing dump data for a single snapshot.

                                                                                  Base constructor.

                                                                                  @@ -1671,13 +1671,13 @@

                                                                                  ]

                                                                                  -as_dict() → dict[str, Any][source]
                                                                                  +as_dict() → dict[str, Any][source]

                                                                                  Get MSONable dict.

                                                                                  -classmethod from_dict(dct: dict) → Self[source]
                                                                                  +classmethod from_dict(dct: dict) → Self[source]
                                                                                  Parameters:

                                                                                  dct (dict) – Dict representation.

                                                                                  @@ -1690,7 +1690,7 @@

                                                                                  ]

                                                                                  -classmethod from_str(string: str) → Self[source]
                                                                                  +classmethod from_str(string: str) → Self[source]

                                                                                  Constructor from string parsing.

                                                                                  Parameters:
                                                                                  @@ -1703,7 +1703,7 @@

                                                                                  ]

                                                                                  -parse_lammps_dumps(file_pattern)[source]
                                                                                  +parse_lammps_dumps(file_pattern)[source]

                                                                                  Generator that parses dump file(s).

                                                                                  Parameters:
                                                                                  @@ -1719,7 +1719,7 @@

                                                                                  ]

                                                                                  -parse_lammps_log(filename: str = 'log.lammps') → list[DataFrame][source]
                                                                                  +parse_lammps_log(filename: str = 'log.lammps') → list[DataFrame][source]

                                                                                  Parses log file with focus on thermo data. Both one and multi line formats are supported. Any incomplete runs (no “Loop time” marker) will not be parsed.

                                                                                  @@ -1748,7 +1748,7 @@

                                                                                  ]

                                                                                  https://github.com/Matgenix/atomate2-lammps).

                                                                                  -class LammpsInputSet(inputfile: LammpsInputFile | str, data: LammpsData | CombinedData, calc_type: str = '', template_file: str = '', keep_stages: bool = False)[source]
                                                                                  +class LammpsInputSet(inputfile: LammpsInputFile | str, data: LammpsData | CombinedData, calc_type: str = '', template_file: str = '', keep_stages: bool = False)[source]

                                                                                  Bases: InputSet

                                                                                  Container class for all LAMMPS inputs. This class is intended to provide general functionality that can be customized to many purposes. @@ -1774,7 +1774,7 @@

                                                                                  ]

                                                                                  -classmethod from_directory(directory: str | Path, keep_stages: bool = False) → Self[source]
                                                                                  +classmethod from_directory(directory: str | Path, keep_stages: bool = False) → Self[source]

                                                                                  Construct a LammpsInputSet from a directory of two or more files. TODO: accept directories with only the input file, that should include the structure as well.

                                                                                  @@ -1790,7 +1790,7 @@

                                                                                  ]

                                                                                  -validate() → bool[source]
                                                                                  +validate() → bool[source]

                                                                                  A place to implement basic checks to verify the validity of an input set. Can be as simple or as complex as desired. Will raise a NotImplementedError unless overloaded by the inheriting class.

                                                                                  @@ -1804,7 +1804,7 @@

                                                                                  ]

                                                                                  This module defines utility classes and functions.

                                                                                  -class LammpsRunner(input_filename: str = 'lammps.in', bin: str = 'lammps')[source]
                                                                                  +class LammpsRunner(input_filename: str = 'lammps.in', bin: str = 'lammps')[source]

                                                                                  Bases: object

                                                                                  LAMMPS wrapper.

                                                                                  @@ -1817,7 +1817,7 @@

                                                                                  ]

                                                                                  -run() → tuple[bytes, bytes][source]
                                                                                  +run() → tuple[bytes, bytes][source]

                                                                                  Write the input/data files and run LAMMPS.

                                                                                  @@ -1825,13 +1825,13 @@

                                                                                  ]

                                                                                  -class PackmolRunner(*args, **kwargs)[source]
                                                                                  +class PackmolRunner(*args, **kwargs)[source]

                                                                                  Bases: object

                                                                                  Wrapper for the Packmol software that can be used to pack various types of molecules into a one single unit.

                                                                                  -convert_obatoms_to_molecule(atoms: Sequence, residue_name: str | None = None, site_property: str = 'ff_map') → Molecule[source]
                                                                                  +convert_obatoms_to_molecule(atoms: Sequence, residue_name: str | None = None, site_property: str = 'ff_map') → Molecule[source]

                                                                                  Convert list of openbabel atoms to Molecule.

                                                                                  Parameters:
                                                                                  @@ -1850,7 +1850,7 @@

                                                                                  ]

                                                                                  -restore_site_properties(site_property: str = 'ff_map', filename: str | None = None) → Molecule[source]
                                                                                  +restore_site_properties(site_property: str = 'ff_map', filename: str | None = None) → Molecule[source]

                                                                                  Restore the site properties for the final packed molecule.

                                                                                  Parameters:
                                                                                  @@ -1867,7 +1867,7 @@

                                                                                  ]

                                                                                  -run(site_property: str | None = None) → Molecule[source]
                                                                                  +run(site_property: str | None = None) → Molecule[source]

                                                                                  Write the input file to the scratch directory, run packmol and return the packed molecule to the current working directory.

                                                                                  @@ -1883,7 +1883,7 @@

                                                                                  ]

                                                                                  -static write_pdb(mol: Molecule, filename: str, name: str | None = None, num=None) → None[source]
                                                                                  +static write_pdb(mol: Molecule, filename: str, name: str | None = None, num=None) → None[source]

                                                                                  Dump the molecule into pdb file with custom residue name and number.

                                                                                  @@ -1891,7 +1891,7 @@

                                                                                  ]

                                                                                  -class Polymer(start_monomer: Molecule, s_head: int, s_tail: int, monomer: Molecule, head: int, tail: int, end_monomer: Molecule, e_head: int, e_tail: int, n_units: int, link_distance: float = 1.0, linear_chain: bool = False)[source]
                                                                                  +class Polymer(start_monomer: Molecule, s_head: int, s_tail: int, monomer: Molecule, head: int, tail: int, end_monomer: Molecule, e_head: int, e_tail: int, n_units: int, link_distance: float = 1.0, linear_chain: bool = False)[source]

                                                                                  Bases: object

                                                                                  Generate polymer chain via Random walk. At each position there are a total of 5 possible moves(excluding the previous direction).

                                                                                  diff --git a/docs/pymatgen.io.lobster.html b/docs/pymatgen.io.lobster.html index 6b3b5b80d63..effe92234d7 100644 --- a/docs/pymatgen.io.lobster.html +++ b/docs/pymatgen.io.lobster.html @@ -4,7 +4,7 @@ - pymatgen.io.lobster package — pymatgen 2024.6.4 documentation + pymatgen.io.lobster package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                  - 2024.6.4 + 2024.6.10
                                                                                  @@ -314,7 +314,7 @@

                                                                                  Submodules
                                                                                  -class Lobsterin(settingsdict: dict)[source]
                                                                                  +class Lobsterin(settingsdict: dict)[source]

                                                                                  Bases: UserDict, MSONable

                                                                                  Handle and generate lobsterin files. Furthermore, it can also modify INCAR files for LOBSTER, generate KPOINTS files for fatband calculations in LOBSTER, @@ -328,38 +328,38 @@

                                                                                  Submodules
                                                                                  -AVAILABLE_KEYWORDS: ClassVar[dict[str, str]] = {'autorotate': 'autoRotate', 'bandwisespilling': 'bandwiseSpilling', 'basisfunctions': 'basisfunctions', 'basisrotation': 'basisRotation', 'basisset': 'basisSet', 'bwdf': 'BWDF', 'bwdfcohp': 'BWDFCOHP', 'cobibetween': 'cobiBetween', 'cohpbetween': 'cohpbetween', 'cohpendenergy': 'COHPendEnergy', 'cohpgenerator': 'cohpGenerator', 'cohpstartenergy': 'COHPstartEnergy', 'cohpsteps': 'COHPSteps', 'createfatband': 'createFatband', 'customstoforatom': 'customSTOforAtom', 'densityofenergy': 'DensityOfEnergy', 'donotignoreexcessivebands': 'doNotIgnoreExcessiveBands', 'donotorthogonalizebasis': 'doNotOrthogonalizeBasis', 'donotuseabsolutespilling': 'doNotUseAbsoluteSpilling', 'ewaldsum': 'EwaldSum', 'forceenergyrange': 'forceEnergyRange', 'forcev1hmatrix': 'forceV1HMatrix', 'gaussiansmearingwidth': 'gaussianSmearingWidth', 'kpointwisespilling': 'kpointwiseSpilling', 'kspacecohp': 'kSpaceCOHP', 'loadprojectionfromfile': 'loadProjectionFromFile', 'lsodos': 'LSODOS', 'nofftforvisualization': 'noFFTforVisualization', 'nomemorymappedfiles': 'noMemoryMappedFiles', 'onlyreadvasprun.xml': 'onlyReadVasprun.xml', 'printlcaorealspacewavefunction': 'printLCAORealSpaceWavefunction', 'printlmosonatoms': 'printLmosOnAtoms', 'printpawrealspacewavefunction': 'printPAWRealSpaceWavefunction', 'printtotalspilling': 'printTotalSpilling', 'realspacehamiltonian': 'realspaceHamiltonian', 'realspaceoverlap': 'realspaceOverlap', 'rmsp': 'RMSp', 'saveprojectiontofile': 'saveProjectionToFile', 'skipcobi': 'skipcobi', 'skipcohp': 'skipcohp', 'skipcoop': 'skipcoop', 'skipdos': 'skipdos', 'skipgrosspopulation': 'skipGrossPopulation', 'skipmadelungenergy': 'skipMadelungEnergy', 'skippaworthonormalitytest': 'skipPAWOrthonormalityTest', 'skippopulationanalysis': 'skipPopulationAnalysis', 'skipprojection': 'skipProjection', 'skipreorthonormalization': 'skipReOrthonormalization', 'usedecimalplaces': 'useDecimalPlaces', 'useoriginaltetrahedronmethod': 'useOriginalTetrahedronMethod', 'userecommendedbasisfunctions': 'userecommendedbasisfunctions', 'writebasisfunctions': 'writeBasisFunctions', 'writematricestofile': 'writeMatricesToFile'}[source]
                                                                                  +AVAILABLE_KEYWORDS: ClassVar[dict[str, str]] = {'autorotate': 'autoRotate', 'bandwisespilling': 'bandwiseSpilling', 'basisfunctions': 'basisfunctions', 'basisrotation': 'basisRotation', 'basisset': 'basisSet', 'bwdf': 'BWDF', 'bwdfcohp': 'BWDFCOHP', 'cobibetween': 'cobiBetween', 'cohpbetween': 'cohpbetween', 'cohpendenergy': 'COHPendEnergy', 'cohpgenerator': 'cohpGenerator', 'cohpstartenergy': 'COHPstartEnergy', 'cohpsteps': 'COHPSteps', 'createfatband': 'createFatband', 'customstoforatom': 'customSTOforAtom', 'densityofenergy': 'DensityOfEnergy', 'donotignoreexcessivebands': 'doNotIgnoreExcessiveBands', 'donotorthogonalizebasis': 'doNotOrthogonalizeBasis', 'donotuseabsolutespilling': 'doNotUseAbsoluteSpilling', 'ewaldsum': 'EwaldSum', 'forceenergyrange': 'forceEnergyRange', 'forcev1hmatrix': 'forceV1HMatrix', 'gaussiansmearingwidth': 'gaussianSmearingWidth', 'kpointwisespilling': 'kpointwiseSpilling', 'kspacecohp': 'kSpaceCOHP', 'loadprojectionfromfile': 'loadProjectionFromFile', 'lsodos': 'LSODOS', 'nofftforvisualization': 'noFFTforVisualization', 'nomemorymappedfiles': 'noMemoryMappedFiles', 'onlyreadvasprun.xml': 'onlyReadVasprun.xml', 'printlcaorealspacewavefunction': 'printLCAORealSpaceWavefunction', 'printlmosonatoms': 'printLmosOnAtoms', 'printpawrealspacewavefunction': 'printPAWRealSpaceWavefunction', 'printtotalspilling': 'printTotalSpilling', 'realspacehamiltonian': 'realspaceHamiltonian', 'realspaceoverlap': 'realspaceOverlap', 'rmsp': 'RMSp', 'saveprojectiontofile': 'saveProjectionToFile', 'skipcobi': 'skipcobi', 'skipcohp': 'skipcohp', 'skipcoop': 'skipcoop', 'skipdos': 'skipdos', 'skipgrosspopulation': 'skipGrossPopulation', 'skipmadelungenergy': 'skipMadelungEnergy', 'skippaworthonormalitytest': 'skipPAWOrthonormalityTest', 'skippopulationanalysis': 'skipPopulationAnalysis', 'skipprojection': 'skipProjection', 'skipreorthonormalization': 'skipReOrthonormalization', 'usedecimalplaces': 'useDecimalPlaces', 'useoriginaltetrahedronmethod': 'useOriginalTetrahedronMethod', 'userecommendedbasisfunctions': 'userecommendedbasisfunctions', 'writebasisfunctions': 'writeBasisFunctions', 'writematricestofile': 'writeMatricesToFile'}[source]

                                                                                  -BOOLEAN_KEYWORDS: ClassVar[dict[str, str]] = {'autorotate': 'autoRotate', 'bandwisespilling': 'bandwiseSpilling', 'bwdf': 'BWDF', 'bwdfcohp': 'BWDFCOHP', 'densityofenergy': 'DensityOfEnergy', 'donotignoreexcessivebands': 'doNotIgnoreExcessiveBands', 'donotorthogonalizebasis': 'doNotOrthogonalizeBasis', 'donotuseabsolutespilling': 'doNotUseAbsoluteSpilling', 'forceenergyrange': 'forceEnergyRange', 'forcev1hmatrix': 'forceV1HMatrix', 'kpointwisespilling': 'kpointwiseSpilling', 'loadprojectionfromfile': 'loadProjectionFromFile', 'lsodos': 'LSODOS', 'nofftforvisualization': 'noFFTforVisualization', 'nomemorymappedfiles': 'noMemoryMappedFiles', 'onlyreadvasprun.xml': 'onlyReadVasprun.xml', 'printlmosonatoms': 'printLmosOnAtoms', 'printtotalspilling': 'printTotalSpilling', 'rmsp': 'RMSp', 'saveprojectiontofile': 'saveProjectionToFile', 'skipcobi': 'skipcobi', 'skipcohp': 'skipcohp', 'skipcoop': 'skipcoop', 'skipdos': 'skipdos', 'skipgrosspopulation': 'skipGrossPopulation', 'skipmadelungenergy': 'skipMadelungEnergy', 'skippaworthonormalitytest': 'skipPAWOrthonormalityTest', 'skippopulationanalysis': 'skipPopulationAnalysis', 'skipprojection': 'skipProjection', 'skipreorthonormalization': 'skipReOrthonormalization', 'useoriginaltetrahedronmethod': 'useOriginalTetrahedronMethod', 'userecommendedbasisfunctions': 'userecommendedbasisfunctions', 'writebasisfunctions': 'writeBasisFunctions', 'writematricestofile': 'writeMatricesToFile'}[source]
                                                                                  +BOOLEAN_KEYWORDS: ClassVar[dict[str, str]] = {'autorotate': 'autoRotate', 'bandwisespilling': 'bandwiseSpilling', 'bwdf': 'BWDF', 'bwdfcohp': 'BWDFCOHP', 'densityofenergy': 'DensityOfEnergy', 'donotignoreexcessivebands': 'doNotIgnoreExcessiveBands', 'donotorthogonalizebasis': 'doNotOrthogonalizeBasis', 'donotuseabsolutespilling': 'doNotUseAbsoluteSpilling', 'forceenergyrange': 'forceEnergyRange', 'forcev1hmatrix': 'forceV1HMatrix', 'kpointwisespilling': 'kpointwiseSpilling', 'loadprojectionfromfile': 'loadProjectionFromFile', 'lsodos': 'LSODOS', 'nofftforvisualization': 'noFFTforVisualization', 'nomemorymappedfiles': 'noMemoryMappedFiles', 'onlyreadvasprun.xml': 'onlyReadVasprun.xml', 'printlmosonatoms': 'printLmosOnAtoms', 'printtotalspilling': 'printTotalSpilling', 'rmsp': 'RMSp', 'saveprojectiontofile': 'saveProjectionToFile', 'skipcobi': 'skipcobi', 'skipcohp': 'skipcohp', 'skipcoop': 'skipcoop', 'skipdos': 'skipdos', 'skipgrosspopulation': 'skipGrossPopulation', 'skipmadelungenergy': 'skipMadelungEnergy', 'skippaworthonormalitytest': 'skipPAWOrthonormalityTest', 'skippopulationanalysis': 'skipPopulationAnalysis', 'skipprojection': 'skipProjection', 'skipreorthonormalization': 'skipReOrthonormalization', 'useoriginaltetrahedronmethod': 'useOriginalTetrahedronMethod', 'userecommendedbasisfunctions': 'userecommendedbasisfunctions', 'writebasisfunctions': 'writeBasisFunctions', 'writematricestofile': 'writeMatricesToFile'}[source]
                                                                                  -FLOAT_KEYWORDS: ClassVar[dict[str, str]] = {'basisrotation': 'basisRotation', 'cohpendenergy': 'COHPendEnergy', 'cohpstartenergy': 'COHPstartEnergy', 'cohpsteps': 'COHPSteps', 'gaussiansmearingwidth': 'gaussianSmearingWidth', 'usedecimalplaces': 'useDecimalPlaces'}[source]
                                                                                  +FLOAT_KEYWORDS: ClassVar[dict[str, str]] = {'basisrotation': 'basisRotation', 'cohpendenergy': 'COHPendEnergy', 'cohpstartenergy': 'COHPstartEnergy', 'cohpsteps': 'COHPSteps', 'gaussiansmearingwidth': 'gaussianSmearingWidth', 'usedecimalplaces': 'useDecimalPlaces'}[source]
                                                                                  -LIST_KEYWORDS: ClassVar[dict[str, str]] = {'basisfunctions': 'basisfunctions', 'cobibetween': 'cobiBetween', 'cohpbetween': 'cohpbetween', 'createfatband': 'createFatband', 'customstoforatom': 'customSTOforAtom'}[source]
                                                                                  +LIST_KEYWORDS: ClassVar[dict[str, str]] = {'basisfunctions': 'basisfunctions', 'cobibetween': 'cobiBetween', 'cohpbetween': 'cohpbetween', 'createfatband': 'createFatband', 'customstoforatom': 'customSTOforAtom'}[source]
                                                                                  -STRING_KEYWORDS: ClassVar[dict[str, str]] = {'basisset': 'basisSet', 'cohpgenerator': 'cohpGenerator', 'ewaldsum': 'EwaldSum', 'kspacecohp': 'kSpaceCOHP', 'printlcaorealspacewavefunction': 'printLCAORealSpaceWavefunction', 'printpawrealspacewavefunction': 'printPAWRealSpaceWavefunction', 'realspacehamiltonian': 'realspaceHamiltonian', 'realspaceoverlap': 'realspaceOverlap'}[source]
                                                                                  +STRING_KEYWORDS: ClassVar[dict[str, str]] = {'basisset': 'basisSet', 'cohpgenerator': 'cohpGenerator', 'ewaldsum': 'EwaldSum', 'kspacecohp': 'kSpaceCOHP', 'printlcaorealspacewavefunction': 'printLCAORealSpaceWavefunction', 'printpawrealspacewavefunction': 'printPAWRealSpaceWavefunction', 'realspacehamiltonian': 'realspaceHamiltonian', 'realspaceoverlap': 'realspaceOverlap'}[source]
                                                                                  -as_dict() → dict[source]
                                                                                  +as_dict() → dict[source]

                                                                                  MSONable dict

                                                                                  -diff(other: Self) → dict[str, dict[str, Any]][source]
                                                                                  +diff(other: Self) → dict[str, dict[str, Any]][source]

                                                                                  Compare two Lobsterin and find which parameters are the same. Similar to the diff method of Incar.

                                                                                  @@ -377,7 +377,7 @@

                                                                                  Submodules
                                                                                  -classmethod from_dict(dct: dict) → Self[source]
                                                                                  +classmethod from_dict(dct: dict) → Self[source]
                                                                                  Parameters:

                                                                                  dct (dict) – Dict representation.

                                                                                  @@ -390,7 +390,7 @@

                                                                                  Submodules
                                                                                  -classmethod from_file(lobsterin: PathLike) → Self[source]
                                                                                  +classmethod from_file(lobsterin: PathLike) → Self[source]

                                                                                  Create Lobsterin from lobsterin file.

                                                                                  Parameters:
                                                                                  @@ -404,7 +404,7 @@

                                                                                  Submodules
                                                                                  -static get_all_possible_basis_functions(structure: Structure, potcar_symbols: list[str], address_basis_file_min: PathLike | None = None, address_basis_file_max: PathLike | None = None) → list[dict][source]
                                                                                  +static get_all_possible_basis_functions(structure: Structure, potcar_symbols: list[str], address_basis_file_min: PathLike | None = None, address_basis_file_max: PathLike | None = None) → list[dict][source]
                                                                                  Parameters:
                                                                                    @@ -429,7 +429,7 @@

                                                                                    Submodules
                                                                                    -static get_basis(structure: Structure, potcar_symbols: list[str], address_basis_file: PathLike | None = None) → list[str][source]
                                                                                    +static get_basis(structure: Structure, potcar_symbols: list[str], address_basis_file: PathLike | None = None) → list[str][source]

                                                                                    Get the basis functions from given potcar_symbols, e.g., [“Fe_pv”, “Si”].

                                                                                    Parameters:
                                                                                    @@ -447,7 +447,7 @@

                                                                                    Submodules
                                                                                    -classmethod standard_calculations_from_vasp_files(POSCAR_input: PathLike = 'POSCAR', INCAR_input: PathLike = 'INCAR', POTCAR_input: PathLike | None = None, Vasprun_output: PathLike = 'vasprun.xml', dict_for_basis: dict | None = None, option: str = 'standard') → Self[source]
                                                                                    +classmethod standard_calculations_from_vasp_files(POSCAR_input: PathLike = 'POSCAR', INCAR_input: PathLike = 'INCAR', POTCAR_input: PathLike | None = None, Vasprun_output: PathLike = 'vasprun.xml', dict_for_basis: dict | None = None, option: str = 'standard') → Self[source]

                                                                                    Generate lobsterin with standard settings.

                                                                                    Parameters:
                                                                                    @@ -479,7 +479,7 @@

                                                                                    Submodules
                                                                                    -write_INCAR(incar_input: PathLike = 'INCAR', incar_output: PathLike = 'INCAR.lobster', poscar_input: PathLike = 'POSCAR', isym: Literal[-1, 0] = 0, further_settings: dict | None = None) → None[source]
                                                                                    +write_INCAR(incar_input: PathLike = 'INCAR', incar_output: PathLike = 'INCAR.lobster', poscar_input: PathLike = 'POSCAR', isym: Literal[-1, 0] = 0, further_settings: dict | None = None) → None[source]

                                                                                    Write INCAR file. Will only make the run static, insert NBANDS, set ISYM=0, LWAVE=True and you have to check for the rest.

                                                                                    @@ -497,7 +497,7 @@

                                                                                    Submodules
                                                                                    -static write_KPOINTS(POSCAR_input: PathLike = 'POSCAR', KPOINTS_output: PathLike = 'KPOINTS.lobster', reciprocal_density: int = 100, isym: Literal[-1, 0] = 0, from_grid: bool = False, input_grid: Tuple3Ints = (5, 5, 5), line_mode: bool = True, kpoints_line_density: int = 20, symprec: float = 0.01) → None[source]
                                                                                    +static write_KPOINTS(POSCAR_input: PathLike = 'POSCAR', KPOINTS_output: PathLike = 'KPOINTS.lobster', reciprocal_density: int = 100, isym: Literal[-1, 0] = 0, from_grid: bool = False, input_grid: Tuple3Ints = (5, 5, 5), line_mode: bool = True, kpoints_line_density: int = 20, symprec: float = 0.01) → None[source]

                                                                                    Write a gamma-centered KPOINTS file for LOBSTER.

                                                                                    Parameters:
                                                                                    @@ -519,7 +519,7 @@

                                                                                    Submodules
                                                                                    -static write_POSCAR_with_standard_primitive(POSCAR_input: PathLike = 'POSCAR', POSCAR_output: PathLike = 'POSCAR.lobster', symprec: float = 0.01) → None[source]
                                                                                    +static write_POSCAR_with_standard_primitive(POSCAR_input: PathLike = 'POSCAR', POSCAR_output: PathLike = 'POSCAR.lobster', symprec: float = 0.01) → None[source]

                                                                                    Write a POSCAR with the standard primitive cell. This is needed to arrive at the correct kpath.

                                                                                    @@ -535,7 +535,7 @@

                                                                                    Submodules
                                                                                    -write_lobsterin(path: PathLike = 'lobsterin', overwritedict: dict | None = None) → None[source]
                                                                                    +write_lobsterin(path: PathLike = 'lobsterin', overwritedict: dict | None = None) → None[source]

                                                                                    Write a lobsterin file, and recover keys to Camel case.

                                                                                    Parameters:
                                                                                    @@ -551,7 +551,7 @@

                                                                                    Submodules
                                                                                    -get_all_possible_basis_combinations(min_basis: list, max_basis: list) → list[list[str]][source]
                                                                                    +get_all_possible_basis_combinations(min_basis: list, max_basis: list) → list[list[str]][source]

                                                                                    Get all possible basis combinations.

                                                                                    Parameters:
                                                                                    @@ -583,7 +583,7 @@

                                                                                    Submodules
                                                                                    -class ICOHPNeighborsInfo(total_icohp: float, list_icohps: list[float], n_bonds: int, labels: list[str], atoms: list[list[str]], central_isites: list[int] | None)[source]
                                                                                    +class ICOHPNeighborsInfo(total_icohp: float, list_icohps: list[float], n_bonds: int, labels: list[str], atoms: list[list[str]], central_isites: list[int] | None)[source]

                                                                                    Bases: NamedTuple

                                                                                    Tuple to represent information on relevant bonds :param total_icohp: sum of icohp values of neighbors to the selected sites [given by the id in structure] @@ -606,37 +606,37 @@

                                                                                    Submodules
                                                                                    -atoms: list[list[str]][source]
                                                                                    +atoms: list[list[str]][source]

                                                                                    Alias for field number 4

                                                                                    -central_isites: list[int] | None[source]
                                                                                    +central_isites: list[int] | None[source]

                                                                                    Alias for field number 5

                                                                                    -labels: list[str][source]
                                                                                    +labels: list[str][source]

                                                                                    Alias for field number 3

                                                                                    -list_icohps: list[float][source]
                                                                                    +list_icohps: list[float][source]

                                                                                    Alias for field number 1

                                                                                    -n_bonds: int[source]
                                                                                    +n_bonds: int[source]

                                                                                    Alias for field number 2

                                                                                    -total_icohp: float[source]
                                                                                    +total_icohp: float[source]

                                                                                    Alias for field number 0

                                                                                    @@ -644,7 +644,7 @@

                                                                                    Submodules
                                                                                    -class LobsterLightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)[source]
                                                                                    +class LobsterLightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)[source]

                                                                                    Bases: LightStructureEnvironments

                                                                                    Store LightStructureEnvironments based on Lobster outputs.

                                                                                    Constructor for the LightStructureEnvironments object.

                                                                                    @@ -664,7 +664,7 @@

                                                                                    Submodules
                                                                                    -as_dict()[source]
                                                                                    +as_dict()[source]

                                                                                    Bson-serializable dict representation of the LightStructureEnvironments object.

                                                                                    Returns:
                                                                                    @@ -675,7 +675,7 @@

                                                                                    Submodules
                                                                                    -classmethod from_Lobster(list_ce_symbol, list_csm, list_permutation, list_neighsite, list_neighisite, structure: Structure, valences=None) → Self[source]
                                                                                    +classmethod from_Lobster(list_ce_symbol, list_csm, list_permutation, list_neighsite, list_neighisite, structure: Structure, valences=None) → Self[source]

                                                                                    Will set up a LightStructureEnvironments from Lobster.

                                                                                    Parameters:
                                                                                    @@ -697,7 +697,7 @@

                                                                                    Submodules
                                                                                    -property uniquely_determines_coordination_environments[source]
                                                                                    +property uniquely_determines_coordination_environments[source]

                                                                                    True if the coordination environments are uniquely determined.

                                                                                    @@ -705,7 +705,7 @@

                                                                                    Submodules
                                                                                    -class LobsterNeighbors(structure: Structure, filename_icohp: str | None = 'ICOHPLIST.lobster', obj_icohp: Icohplist | None = None, are_coops: bool = False, are_cobis: bool = False, valences: list[float] | None = None, limits: tuple[float, float] | None = None, additional_condition: int = 0, only_bonds_to: list[str] | None = None, perc_strength_icohp: float = 0.15, noise_cutoff: float = 0.1, valences_from_charges: bool = False, filename_charge: str | None = None, obj_charge: Charge | None = None, which_charge: str = 'Mulliken', adapt_extremum_to_add_cond: bool = False, add_additional_data_sg: bool = False, filename_blist_sg1: str | None = None, filename_blist_sg2: str | None = None, id_blist_sg1: str = 'ICOOP', id_blist_sg2: str = 'ICOBI')[source]
                                                                                    +class LobsterNeighbors(structure: Structure, filename_icohp: str | None = 'ICOHPLIST.lobster', obj_icohp: Icohplist | None = None, are_coops: bool = False, are_cobis: bool = False, valences: list[float] | None = None, limits: tuple[float, float] | None = None, additional_condition: int = 0, only_bonds_to: list[str] | None = None, perc_strength_icohp: float = 0.15, noise_cutoff: float = 0.1, valences_from_charges: bool = False, filename_charge: str | None = None, obj_charge: Charge | None = None, which_charge: str = 'Mulliken', adapt_extremum_to_add_cond: bool = False, add_additional_data_sg: bool = False, filename_blist_sg1: str | None = None, filename_blist_sg2: str | None = None, id_blist_sg1: str = 'ICOOP', id_blist_sg2: str = 'ICOBI')[source]

                                                                                    Bases: NearNeighbors

                                                                                    This class combines capabilities from LocalEnv and ChemEnv to determine coordination environments based on bonding analysis.

                                                                                    @@ -752,7 +752,7 @@

                                                                                    Submodules
                                                                                    -property anion_types: set[Element][source]
                                                                                    +property anion_types: set[Element][source]

                                                                                    The types of anions present in crystal structure as a set.

                                                                                    Returns:
                                                                                    @@ -766,12 +766,12 @@

                                                                                    Submodules
                                                                                    -get_anion_types(**kwargs)[source]
                                                                                    +get_anion_types(**kwargs)[source]

                                                                                    -get_info_cohps_to_neighbors(path_to_cohpcar: str | None = 'COHPCAR.lobster', obj_cohpcar: CompleteCohp | None = None, isites: list[int] | None = None, only_bonds_to: list[str] | None = None, onlycation_isites: bool = True, per_bond: bool = True, summed_spin_channels: bool = False)[source]
                                                                                    +get_info_cohps_to_neighbors(path_to_cohpcar: str | None = 'COHPCAR.lobster', obj_cohpcar: CompleteCohp | None = None, isites: list[int] | None = None, only_bonds_to: list[str] | None = None, onlycation_isites: bool = True, per_bond: bool = True, summed_spin_channels: bool = False)[source]

                                                                                    Get info about the cohps (coops or cobis) as a summed cohp object and a label from all sites mentioned in isites with neighbors.

                                                                                    @@ -801,7 +801,7 @@

                                                                                    Submodules
                                                                                    -get_info_icohps_between_neighbors(isites=None, onlycation_isites=True)[source]
                                                                                    +get_info_icohps_between_neighbors(isites=None, onlycation_isites=True)[source]

                                                                                    Get infos about interactions between neighbors of a certain atom.

                                                                                    Parameters:
                                                                                    @@ -818,7 +818,7 @@

                                                                                    Submodules
                                                                                    -get_info_icohps_to_neighbors(isites=None, onlycation_isites=True)[source]
                                                                                    +get_info_icohps_to_neighbors(isites=None, onlycation_isites=True)[source]

                                                                                    Get information on the icohps of neighbors for certain sites as identified by their site id. This is useful for plotting the relevant cohps of a site in the structure. (could be ICOOPLIST.lobster or ICOHPLIST.lobster or ICOBILIST.lobster)

                                                                                    @@ -837,7 +837,7 @@

                                                                                    Submodules
                                                                                    -get_light_structure_environment(only_cation_environments=False, only_indices=None)[source]
                                                                                    +get_light_structure_environment(only_cation_environments=False, only_indices=None)[source]

                                                                                    Get a LobsterLightStructureEnvironments object if the structure only contains coordination environments smaller 13.

                                                                                    @@ -855,7 +855,7 @@

                                                                                    Submodules
                                                                                    -get_nn_info(structure: Structure, n: int, use_weights: bool = False) → dict[source]
                                                                                    +get_nn_info(structure: Structure, n: int, use_weights: bool = False) → dict[source]

                                                                                    Get coordination number, CN, of site with index n in structure.

                                                                                    Parameters:
                                                                                    @@ -884,13 +884,13 @@

                                                                                    Submodules
                                                                                    -property molecules_allowed: bool[source]
                                                                                    +property molecules_allowed: bool[source]

                                                                                    Whether this NearNeighbors class can be used with Molecule objects?

                                                                                    -plot_cohps_of_neighbors(path_to_cohpcar: str | None = 'COHPCAR.lobster', obj_cohpcar: CompleteCohp | None = None, isites: list[int] | None = None, onlycation_isites: bool = True, only_bonds_to: list[str] | None = None, per_bond: bool = False, summed_spin_channels: bool = False, xlim=None, ylim=(-10, 6), integrated: bool = False)[source]
                                                                                    +plot_cohps_of_neighbors(path_to_cohpcar: str | None = 'COHPCAR.lobster', obj_cohpcar: CompleteCohp | None = None, isites: list[int] | None = None, onlycation_isites: bool = True, only_bonds_to: list[str] | None = None, per_bond: bool = False, summed_spin_channels: bool = False, xlim=None, ylim=(-10, 6), integrated: bool = False)[source]

                                                                                    Will plot summed cohps or cobis or coops (please be careful in the spin polarized case (plots might overlap (exactly!)).

                                                                                    @@ -917,7 +917,7 @@

                                                                                    Submodules
                                                                                    -property structures_allowed: bool[source]
                                                                                    +property structures_allowed: bool[source]

                                                                                    Whether this NearNeighbors class can be used with Structure objects?

                                                                                    @@ -935,7 +935,7 @@

                                                                                    Submodules
                                                                                    -class Bandoverlaps(filename: str = 'bandOverlaps.lobster', band_overlaps_dict: dict[Any, dict] | None = None, max_deviation: list[float] | None = None)[source]
                                                                                    +class Bandoverlaps(filename: str = 'bandOverlaps.lobster', band_overlaps_dict: dict[Any, dict] | None = None, max_deviation: list[float] | None = None)[source]

                                                                                    Bases: MSONable

                                                                                    Read in bandOverlaps.lobster files. These files are not created during every Lobster run. .. attribute:: band_overlaps_dict

                                                                                    @@ -952,7 +952,7 @@

                                                                                    Submodules
                                                                                    -max_deviation[source]
                                                                                    +max_deviation[source]

                                                                                    A list of floats describing the maximal deviation for each problematic kpoint.

                                                                                    Type:
                                                                                    @@ -979,12 +979,12 @@

                                                                                    Submodules
                                                                                    -property bandoverlapsdict[source]
                                                                                    +property bandoverlapsdict[source]

                                                                                    -has_good_quality_check_occupied_bands(number_occ_bands_spin_up: int, number_occ_bands_spin_down: int | None = None, spin_polarized: bool = False, limit_deviation: float = 0.1) → bool[source]
                                                                                    +has_good_quality_check_occupied_bands(number_occ_bands_spin_up: int, number_occ_bands_spin_down: int | None = None, spin_polarized: bool = False, limit_deviation: float = 0.1) → bool[source]

                                                                                    Will check if the deviation from the ideal bandoverlap of all occupied bands is smaller or equal to limit_deviation.

                                                                                    @@ -1004,7 +1004,7 @@

                                                                                    Submodules
                                                                                    -has_good_quality_maxDeviation(limit_maxDeviation: float = 0.1) → bool[source]
                                                                                    +has_good_quality_maxDeviation(limit_maxDeviation: float = 0.1) → bool[source]

                                                                                    Will check if the maxDeviation from the ideal bandoverlap is smaller or equal to limit_maxDeviation

                                                                                    Parameters:
                                                                                    @@ -1020,12 +1020,12 @@

                                                                                    Submodules
                                                                                    -class Charge(filename: str = 'CHARGE.lobster', num_atoms: int | None = None, atomlist: list[str] | None = None, types: list[str] | None = None, mulliken: list[float] | None = None, loewdin: list[float] | None = None)[source]
                                                                                    +class Charge(filename: str = 'CHARGE.lobster', num_atoms: int | None = None, atomlist: list[str] | None = None, types: list[str] | None = None, mulliken: list[float] | None = None, loewdin: list[float] | None = None)[source]

                                                                                    Bases: MSONable

                                                                                    Read CHARGE files generated by LOBSTER.

                                                                                    -atomlist[source]
                                                                                    +atomlist[source]

                                                                                    List of atoms in CHARGE.lobster.

                                                                                    Type:
                                                                                    @@ -1036,7 +1036,7 @@

                                                                                    Submodules
                                                                                    -types[source]
                                                                                    +types[source]

                                                                                    List of types of atoms in CHARGE.lobster.

                                                                                    Type:
                                                                                    @@ -1047,7 +1047,7 @@

                                                                                    Submodules
                                                                                    -mulliken[source]
                                                                                    +mulliken[source]

                                                                                    List of Mulliken charges of atoms in CHARGE.lobster.

                                                                                    Type:
                                                                                    @@ -1058,7 +1058,7 @@

                                                                                    Submodules
                                                                                    -loewdin[source]
                                                                                    +loewdin[source]

                                                                                    List of Loewdin charges of atoms in CHARGE.Loewdin.

                                                                                    Type:
                                                                                    @@ -1069,7 +1069,7 @@

                                                                                    Submodules
                                                                                    -num_atoms[source]
                                                                                    +num_atoms[source]

                                                                                    Number of atoms in CHARGE.lobster.

                                                                                    Type:
                                                                                    @@ -1092,17 +1092,17 @@

                                                                                    Submodules
                                                                                    -property Loewdin[source]
                                                                                    +property Loewdin[source]

                                                                                    -property Mulliken[source]
                                                                                    +property Mulliken[source]
                                                                                    -get_structure_with_charges(structure_filename)[source]
                                                                                    +get_structure_with_charges(structure_filename)[source]

                                                                                    Get a Structure with Mulliken and Loewdin charges as site properties

                                                                                    Parameters:
                                                                                    @@ -1118,12 +1118,12 @@

                                                                                    Submodules
                                                                                    -class Cohpcar(are_coops: bool = False, are_cobis: bool = False, are_multi_center_cobis: bool = False, filename: str | None = None)[source]
                                                                                    +class Cohpcar(are_coops: bool = False, are_cobis: bool = False, are_multi_center_cobis: bool = False, filename: str | None = None)[source]

                                                                                    Bases: object

                                                                                    Read COHPCAR/COOPCAR/COBICAR files generated by LOBSTER.

                                                                                    -cohp_data[source]
                                                                                    +cohp_data[source]

                                                                                    A dictionary containing the COHP data of the form: {bond: {“COHP”: {Spin.up: cohps, Spin.down:cohps},

                                                                                    @@ -1141,7 +1141,7 @@

                                                                                    Submodules
                                                                                    -efermi[source]
                                                                                    +efermi[source]

                                                                                    The Fermi energy in eV.

                                                                                    Type:
                                                                                    @@ -1152,7 +1152,7 @@

                                                                                    Submodules
                                                                                    -energies[source]
                                                                                    +energies[source]

                                                                                    Sequence of energies in eV. Note that LOBSTER shifts the energies so that the Fermi energy is at zero.

                                                                                    @@ -1164,7 +1164,7 @@

                                                                                    Submodules
                                                                                    -is_spin_polarized[source]
                                                                                    +is_spin_polarized[source]

                                                                                    Boolean to indicate if the calculation is spin polarized.

                                                                                    Type:
                                                                                    @@ -1175,7 +1175,7 @@

                                                                                    Submodules
                                                                                    -orb_cohp[source]
                                                                                    +orb_cohp[source]

                                                                                    A dictionary containing the orbital-resolved COHPs of the form: orb_cohp[label] = {bond_data[“orb_label”]: {

                                                                                    @@ -1211,13 +1211,13 @@

                                                                                    Submodules
                                                                                    -class Doscar(doscar: str = 'DOSCAR.lobster', structure_file: str | None = 'POSCAR', structure: IStructure | Structure | None = None)[source]
                                                                                    +class Doscar(doscar: str = 'DOSCAR.lobster', structure_file: str | None = 'POSCAR', structure: IStructure | Structure | None = None)[source]

                                                                                    Bases: object

                                                                                    Deal with Lobster’s projected DOS and local projected DOS. The beforehand quantum-chemical calculation was performed with VASP.

                                                                                    -completedos[source]
                                                                                    +completedos[source]

                                                                                    LobsterCompleteDos Object.

                                                                                    Type:
                                                                                    @@ -1228,7 +1228,7 @@

                                                                                    Submodules
                                                                                    -pdos[source]
                                                                                    +pdos[source]

                                                                                    List of Dict including numpy arrays with pdos. Access as pdos[atomindex][‘orbitalstring’][‘Spin.up/Spin.down’].

                                                                                    @@ -1240,7 +1240,7 @@

                                                                                    Submodules
                                                                                    -tdos[source]
                                                                                    +tdos[source]

                                                                                    Dos Object of the total density of states.

                                                                                    Type:
                                                                                    @@ -1251,7 +1251,7 @@

                                                                                    Submodules
                                                                                    -energies[source]
                                                                                    +energies[source]

                                                                                    Numpy array of the energies at which the DOS was calculated (in eV, relative to Efermi).

                                                                                    @@ -1263,7 +1263,7 @@

                                                                                    Submodules
                                                                                    -tdensities[source]
                                                                                    +tdensities[source]

                                                                                    tdensities[Spin.up]: numpy array of the total density of states for the Spin.up contribution at each of the energies. tdensities[Spin.down]: numpy array of the total density of states for the Spin.down contribution at each of the energies. @@ -1277,7 +1277,7 @@

                                                                                    Submodules
                                                                                    -itdensities[source]
                                                                                    +itdensities[source]

                                                                                    itdensities[Spin.up]: numpy array of the total density of states for the Spin.up contribution at each of the energies. itdensities[Spin.down]: numpy array of the total density of states for the Spin.down contribution at each of the energies. @@ -1291,7 +1291,7 @@

                                                                                    Submodules
                                                                                    -is_spin_polarized[source]
                                                                                    +is_spin_polarized[source]

                                                                                    Boolean. Tells if the system is spin polarized.

                                                                                    Type:
                                                                                    @@ -1312,43 +1312,43 @@

                                                                                    Submodules
                                                                                    -property completedos: LobsterCompleteDos[source]
                                                                                    +property completedos: LobsterCompleteDos[source]

                                                                                    LobsterCompleteDos

                                                                                    -property energies: ndarray[source]
                                                                                    +property energies: ndarray[source]

                                                                                    Energies

                                                                                    -property is_spin_polarized: bool[source]
                                                                                    +property is_spin_polarized: bool[source]

                                                                                    Whether run is spin polarized.

                                                                                    -property itdensities: dict[Spin, ndarray][source]
                                                                                    +property itdensities: dict[Spin, ndarray][source]

                                                                                    integrated total densities as a np.ndarray

                                                                                    -property pdos: list[source]
                                                                                    +property pdos: list[source]

                                                                                    Projected DOS

                                                                                    -property tdensities: dict[Spin, ndarray][source]
                                                                                    +property tdensities: dict[Spin, ndarray][source]

                                                                                    total densities as a np.ndarray

                                                                                    -property tdos: Dos[source]
                                                                                    +property tdos: Dos[source]

                                                                                    Total DOS

                                                                                    @@ -1356,12 +1356,12 @@

                                                                                    Submodules
                                                                                    -class Fatband(filenames: str | list = '.', kpoints_file: str = 'KPOINTS', vasprun_file: str | None = 'vasprun.xml', structure: Structure | IStructure | None = None, efermi: float | None = None)[source]
                                                                                    +class Fatband(filenames: str | list = '.', kpoints_file: str = 'KPOINTS', vasprun_file: str | None = 'vasprun.xml', structure: Structure | IStructure | None = None, efermi: float | None = None)[source]

                                                                                    Bases: object

                                                                                    Read in FATBAND_x_y.lobster files.

                                                                                    -efermi[source]
                                                                                    +efermi[source]

                                                                                    Fermi energy read in from vasprun.xml.

                                                                                    Type:
                                                                                    @@ -1372,7 +1372,7 @@

                                                                                    Submodules
                                                                                    -eigenvals[source]
                                                                                    +eigenvals[source]

                                                                                    Eigenvalues as a dictionary of numpy arrays of shape (nbands, nkpoints). The first index of the array refers to the band and the second to the index of the kpoint. The kpoints are ordered according to the order of the kpoints_array attribute. @@ -1386,7 +1386,7 @@

                                                                                    Submodules
                                                                                    -is_spin_polarized[source]
                                                                                    +is_spin_polarized[source]

                                                                                    Boolean that tells you whether this was a spin-polarized calculation.

                                                                                    Type:
                                                                                    @@ -1397,7 +1397,7 @@

                                                                                    Submodules
                                                                                    -kpoints_array[source]
                                                                                    +kpoints_array[source]

                                                                                    List of kpoints as numpy arrays, in frac_coords of the given lattice by default.

                                                                                    @@ -1409,7 +1409,7 @@

                                                                                    Submodules
                                                                                    -label_dict[source]
                                                                                    +label_dict[source]

                                                                                    Dictionary that links a kpoint (in frac coords or Cartesian coordinates depending on the coords attribute) to a label.

                                                                                    @@ -1421,7 +1421,7 @@

                                                                                    Submodules
                                                                                    -lattice[source]
                                                                                    +lattice[source]

                                                                                    Lattice object of reciprocal lattice as read in from vasprun.xml.

                                                                                    Type:
                                                                                    @@ -1432,7 +1432,7 @@

                                                                                    Submodules
                                                                                    -nbands[source]
                                                                                    +nbands[source]

                                                                                    Number of bands used in the calculation.

                                                                                    Type:
                                                                                    @@ -1443,7 +1443,7 @@

                                                                                    Submodules
                                                                                    -p_eigenvals[source]
                                                                                    +p_eigenvals[source]

                                                                                    Dictionary of orbital projections as {spin: array of dict}. The indices of the array are [band_index, kpoint_index]. The dict is then built the following way: {“string of element”: “string of orbital as read in @@ -1457,7 +1457,7 @@

                                                                                    Submodules
                                                                                    -structure[source]
                                                                                    +structure[source]

                                                                                    Structure read in from Structure object.

                                                                                    Type:
                                                                                    @@ -1482,7 +1482,7 @@

                                                                                    Submodules
                                                                                    -get_bandstructure()[source]
                                                                                    +get_bandstructure()[source]

                                                                                    Get a LobsterBandStructureSymmLine object which can be plotted with a normal BSPlotter.

                                                                                    @@ -1490,12 +1490,12 @@

                                                                                    Submodules
                                                                                    -class Grosspop(filename: str = 'GROSSPOP.lobster', list_dict_grosspop: list[dict] | None = None)[source]
                                                                                    +class Grosspop(filename: str = 'GROSSPOP.lobster', list_dict_grosspop: list[dict] | None = None)[source]

                                                                                    Bases: MSONable

                                                                                    Read in GROSSPOP.lobster files.

                                                                                    -list_dict_grosspop[source]
                                                                                    +list_dict_grosspop[source]

                                                                                    List of dictionaries including all information about the grosspopulations. Each dictionary contains the following keys: - ‘element’: The element symbol of the atom. @@ -1528,7 +1528,7 @@

                                                                                    Submodules
                                                                                    -get_structure_with_total_grosspop(structure_filename: str) → Structure[source]
                                                                                    +get_structure_with_total_grosspop(structure_filename: str) → Structure[source]

                                                                                    Get a Structure with Mulliken and Loewdin total grosspopulations as site properties

                                                                                    Parameters:
                                                                                    @@ -1544,12 +1544,12 @@

                                                                                    Submodules
                                                                                    -class Icohplist(are_coops: bool = False, are_cobis: bool = False, filename: str | None = None, is_spin_polarized: bool = False, orbitalwise: bool = False, icohpcollection=None)[source]
                                                                                    +class Icohplist(are_coops: bool = False, are_cobis: bool = False, filename: str | None = None, is_spin_polarized: bool = False, orbitalwise: bool = False, icohpcollection=None)[source]

                                                                                    Bases: MSONable

                                                                                    Read ICOHPLIST/ICOOPLIST files generated by LOBSTER.

                                                                                    -are_coops[source]
                                                                                    +are_coops[source]

                                                                                    Indicates whether the object is consisting of COOPs.

                                                                                    Type:
                                                                                    @@ -1560,7 +1560,7 @@

                                                                                    Submodules
                                                                                    -is_spin_polarized[source]
                                                                                    +is_spin_polarized[source]

                                                                                    Boolean to indicate if the calculation is spin polarized.

                                                                                    Type:
                                                                                    @@ -1571,7 +1571,7 @@

                                                                                    Submodules
                                                                                    -Icohplist[source]
                                                                                    +Icohplist[source]

                                                                                    Dict containing the listfile data of the form: {

                                                                                    @@ -1589,7 +1589,7 @@

                                                                                    Submodules
                                                                                    -IcohpCollection[source]
                                                                                    +IcohpCollection[source]

                                                                                    IcohpCollection Object.

                                                                                    Type:
                                                                                    @@ -1614,13 +1614,13 @@

                                                                                    Submodules
                                                                                    -property icohpcollection[source]
                                                                                    +property icohpcollection[source]

                                                                                    The IcohpCollection object.

                                                                                    -property icohplist: dict[Any, dict[str, Any]][source]
                                                                                    +property icohplist: dict[Any, dict[str, Any]][source]

                                                                                    The ICOHP list compatible with older version of this class.

                                                                                    @@ -1628,7 +1628,7 @@

                                                                                    Submodules
                                                                                    -class LobsterMatrices(e_fermi=None, filename: str = 'hamiltonMatrices.lobster')[source]
                                                                                    +class LobsterMatrices(e_fermi=None, filename: str = 'hamiltonMatrices.lobster')[source]

                                                                                    Bases: object

                                                                                    Read Matrices file generated by LOBSTER (e.g. hamiltonMatrices.lobster).

                                                                                    @@ -1638,7 +1638,7 @@

                                                                                    Submodules
                                                                                    -onsite_energies[source]
                                                                                    +onsite_energies[source]

                                                                                    List real part of onsite energies from the matrices each k-point.

                                                                                    Type:
                                                                                    @@ -1649,7 +1649,7 @@

                                                                                    Submodules
                                                                                    -average_onsite_energies[source]
                                                                                    +average_onsite_energies[source]

                                                                                    dict with average onsite elements energies for all k-points with keys as basis used in the LOBSTER computation (uses only real part of matrix).

                                                                                    @@ -1661,7 +1661,7 @@

                                                                                    Submodules
                                                                                    -hamilton_matrices[source]
                                                                                    +hamilton_matrices[source]

                                                                                    dict with the complex hamilton matrix at each k-point with k-point and spin as keys

                                                                                    @@ -1678,7 +1678,7 @@

                                                                                    Submodules
                                                                                    -onsite_coefficients[source]
                                                                                    +onsite_coefficients[source]

                                                                                    List real part of onsite coefficients from the matrices each k-point.

                                                                                    Type:
                                                                                    @@ -1689,7 +1689,7 @@

                                                                                    Submodules
                                                                                    -average_onsite_coefficient[source]
                                                                                    +average_onsite_coefficient[source]

                                                                                    dict with average onsite elements coefficients for all k-points with keys as basis used in the LOBSTER computation (uses only real part of matrix).

                                                                                    @@ -1701,7 +1701,7 @@

                                                                                    Submodules
                                                                                    -coefficient_matrices[source]
                                                                                    +coefficient_matrices[source]

                                                                                    dict with the coefficients matrix at each k-point with k-point and spin as keys

                                                                                    @@ -1718,7 +1718,7 @@

                                                                                    Submodules
                                                                                    -onsite_transfer[source]
                                                                                    +onsite_transfer[source]

                                                                                    List real part of onsite transfer coefficients from the matrices at each k-point.

                                                                                    @@ -1730,7 +1730,7 @@

                                                                                    Submodules
                                                                                    -average_onsite_transfer[source]
                                                                                    +average_onsite_transfer[source]

                                                                                    dict with average onsite elements transfer coefficients for all k-points with keys as basis used in the LOBSTER computation (uses only real part of matrix).

                                                                                    @@ -1742,7 +1742,7 @@

                                                                                    Submodules
                                                                                    -transfer_matrices[source]
                                                                                    +transfer_matrices[source]

                                                                                    dict with the coefficients matrix at each k-point with k-point and spin as keys

                                                                                    @@ -1759,7 +1759,7 @@

                                                                                    Submodules
                                                                                    -onsite_overlaps[source]
                                                                                    +onsite_overlaps[source]

                                                                                    List real part of onsite overlaps from the matrices each k-point.

                                                                                    Type:
                                                                                    @@ -1770,7 +1770,7 @@

                                                                                    Submodules
                                                                                    -average_onsite_overlaps[source]
                                                                                    +average_onsite_overlaps[source]

                                                                                    dict with average onsite elements overlaps for all k-points with keys as basis used in the LOBSTER computation (uses only real part of matrix).

                                                                                    @@ -1782,7 +1782,7 @@

                                                                                    Submodules
                                                                                    -overlap_matrices[source]
                                                                                    +overlap_matrices[source]

                                                                                    dict with the overlap matrix at each k-point with k-point as keys

                                                                                    @@ -1805,12 +1805,12 @@

                                                                                    Submodules
                                                                                    -class Lobsterout(filename: str | None, **kwargs)[source]
                                                                                    +class Lobsterout(filename: str | None, **kwargs)[source]

                                                                                    Bases: MSONable

                                                                                    Read in the lobsterout and evaluate the spilling, save the basis, save warnings, save infos.

                                                                                    -basis_functions[source]
                                                                                    +basis_functions[source]

                                                                                    List of basis functions that were used in lobster run as strings.

                                                                                    Type:
                                                                                    @@ -1821,7 +1821,7 @@

                                                                                    Submodules
                                                                                    -basis_type[source]
                                                                                    +basis_type[source]

                                                                                    List of basis type that were used in lobster run as strings.

                                                                                    Type:
                                                                                    @@ -1832,7 +1832,7 @@

                                                                                    Submodules
                                                                                    -charge_spilling[source]
                                                                                    +charge_spilling[source]

                                                                                    List of charge spilling (first entry: result for spin 1, second entry: result for spin 2 or not present).

                                                                                    @@ -1844,7 +1844,7 @@

                                                                                    Submodules
                                                                                    -dft_program[source]
                                                                                    +dft_program[source]

                                                                                    String representing the DFT program used for the calculation of the wave function.

                                                                                    Type:
                                                                                    @@ -1855,7 +1855,7 @@

                                                                                    Submodules
                                                                                    -elements[source]
                                                                                    +elements[source]

                                                                                    List of strings of elements that were present in lobster calculation.

                                                                                    Type:
                                                                                    @@ -1866,7 +1866,7 @@

                                                                                    Submodules
                                                                                    -has_charge[source]
                                                                                    +has_charge[source]

                                                                                    Whether CHARGE.lobster is present.

                                                                                    Type:
                                                                                    @@ -1877,7 +1877,7 @@

                                                                                    Submodules
                                                                                    -has_cohpcar[source]
                                                                                    +has_cohpcar[source]

                                                                                    Whether COHPCAR.lobster and ICOHPLIST.lobster are present.

                                                                                    Type:
                                                                                    @@ -1888,7 +1888,7 @@

                                                                                    Submodules
                                                                                    -has_madelung[source]
                                                                                    +has_madelung[source]

                                                                                    Whether SitePotentials.lobster and MadelungEnergies.lobster are present.

                                                                                    Type:
                                                                                    @@ -1899,7 +1899,7 @@

                                                                                    Submodules
                                                                                    -has_coopcar[source]
                                                                                    +has_coopcar[source]

                                                                                    Whether COOPCAR.lobster and ICOOPLIST.lobster are present.

                                                                                    Type:
                                                                                    @@ -1910,7 +1910,7 @@

                                                                                    Submodules
                                                                                    -has_cobicar[source]
                                                                                    +has_cobicar[source]

                                                                                    Whether COBICAR.lobster and ICOBILIST.lobster are present.

                                                                                    Type:
                                                                                    @@ -1921,7 +1921,7 @@

                                                                                    Submodules
                                                                                    -has_doscar[source]
                                                                                    +has_doscar[source]

                                                                                    Whether DOSCAR.lobster is present.

                                                                                    Type:
                                                                                    @@ -1932,7 +1932,7 @@

                                                                                    Submodules
                                                                                    -has_doscar_lso[source]
                                                                                    +has_doscar_lso[source]

                                                                                    Whether DOSCAR.LSO.lobster is present.

                                                                                    Type:
                                                                                    @@ -1943,7 +1943,7 @@

                                                                                    Submodules
                                                                                    -has_projection[source]
                                                                                    +has_projection[source]

                                                                                    Whether projectionData.lobster is present.

                                                                                    Type:
                                                                                    @@ -1954,7 +1954,7 @@

                                                                                    Submodules
                                                                                    -has_bandoverlaps[source]
                                                                                    +has_bandoverlaps[source]

                                                                                    Whether bandOverlaps.lobster is present.

                                                                                    Type:
                                                                                    @@ -1965,7 +1965,7 @@

                                                                                    Submodules
                                                                                    -has_density_of_energies[source]
                                                                                    +has_density_of_energies[source]

                                                                                    Whether DensityOfEnergy.lobster is present.

                                                                                    Type:
                                                                                    @@ -1976,7 +1976,7 @@

                                                                                    Submodules
                                                                                    -has_fatbands[source]
                                                                                    +has_fatbands[source]

                                                                                    Whether fatband calculation was performed.

                                                                                    Type:
                                                                                    @@ -1987,7 +1987,7 @@

                                                                                    Submodules
                                                                                    -has_grosspopulation[source]
                                                                                    +has_grosspopulation[source]

                                                                                    Whether GROSSPOP.lobster is present.

                                                                                    Type:
                                                                                    @@ -1998,7 +1998,7 @@

                                                                                    Submodules
                                                                                    -info_lines[source]
                                                                                    +info_lines[source]

                                                                                    String with additional infos on the run.

                                                                                    Type:
                                                                                    @@ -2009,7 +2009,7 @@

                                                                                    Submodules
                                                                                    -info_orthonormalization[source]
                                                                                    +info_orthonormalization[source]

                                                                                    String with infos on orthonormalization.

                                                                                    Type:
                                                                                    @@ -2020,7 +2020,7 @@

                                                                                    Submodules
                                                                                    -is_restart_from_projection[source]
                                                                                    +is_restart_from_projection[source]

                                                                                    Boolean that indicates that calculation was restarted from existing projection file.

                                                                                    @@ -2032,7 +2032,7 @@

                                                                                    Submodules
                                                                                    -lobster_version[source]
                                                                                    +lobster_version[source]

                                                                                    String that indicates Lobster version.

                                                                                    Type:
                                                                                    @@ -2043,7 +2043,7 @@

                                                                                    Submodules
                                                                                    -number_of_spins[source]
                                                                                    +number_of_spins[source]

                                                                                    Integer indicating the number of spins.

                                                                                    Type:
                                                                                    @@ -2054,7 +2054,7 @@

                                                                                    Submodules
                                                                                    -number_of_threads[source]
                                                                                    +number_of_threads[source]

                                                                                    Integer that indicates how many threads were used.

                                                                                    Type:
                                                                                    @@ -2065,7 +2065,7 @@

                                                                                    Submodules
                                                                                    -timing[source]
                                                                                    +timing[source]

                                                                                    Dictionary with infos on timing.

                                                                                    Type:
                                                                                    @@ -2076,7 +2076,7 @@

                                                                                    Submodules
                                                                                    -total_spilling[source]
                                                                                    +total_spilling[source]

                                                                                    List of values indicating the total spilling for spin channel 1 (and spin channel 2).

                                                                                    @@ -2088,7 +2088,7 @@

                                                                                    Submodules
                                                                                    -warning_lines[source]
                                                                                    +warning_lines[source]

                                                                                    String with all warnings.

                                                                                    Type:
                                                                                    @@ -2107,13 +2107,13 @@

                                                                                    Submodules
                                                                                    -as_dict()[source]
                                                                                    +as_dict()[source]

                                                                                    MSONable dict

                                                                                    -get_doc() → dict[str, Any][source]
                                                                                    +get_doc() → dict[str, Any][source]

                                                                                    Get the LobsterDict with all the information stored in lobsterout.

                                                                                    @@ -2121,12 +2121,12 @@

                                                                                    Submodules
                                                                                    -class MadelungEnergies(filename: str = 'MadelungEnergies.lobster', ewald_splitting: float | None = None, madelungenergies_mulliken: float | None = None, madelungenergies_loewdin: float | None = None)[source]
                                                                                    +class MadelungEnergies(filename: str = 'MadelungEnergies.lobster', ewald_splitting: float | None = None, madelungenergies_mulliken: float | None = None, madelungenergies_loewdin: float | None = None)[source]

                                                                                    Bases: MSONable

                                                                                    Read MadelungEnergies.lobster files generated by LOBSTER.

                                                                                    -madelungenergies_mulliken[source]
                                                                                    +madelungenergies_mulliken[source]

                                                                                    Float that gives the Madelung energy based on the Mulliken approach.

                                                                                    Type:
                                                                                    @@ -2137,7 +2137,7 @@

                                                                                    Submodules
                                                                                    -madelungenergies_loewdin[source]
                                                                                    +madelungenergies_loewdin[source]

                                                                                    Float that gives the Madelung energy based on the Loewdin approach.

                                                                                    Type:
                                                                                    @@ -2148,7 +2148,7 @@

                                                                                    Submodules
                                                                                    -ewald_splitting[source]
                                                                                    +ewald_splitting[source]

                                                                                    Ewald splitting parameter to compute SitePotentials.

                                                                                    Type:
                                                                                    @@ -2164,24 +2164,24 @@

                                                                                    Submodules
                                                                                    -property madelungenergies_Loewdin[source]
                                                                                    +property madelungenergies_Loewdin[source]

                                                                                    -property madelungenergies_Mulliken[source]
                                                                                    +property madelungenergies_Mulliken[source]

                                                                                    -class NciCobiList(filename: str | None = 'NcICOBILIST.lobster')[source]
                                                                                    +class NciCobiList(filename: str | None = 'NcICOBILIST.lobster')[source]

                                                                                    Bases: object

                                                                                    Read NcICOBILIST (multi-center ICOBI) files generated by LOBSTER.

                                                                                    -is_spin_polarized[source]
                                                                                    +is_spin_polarized[source]

                                                                                    Boolean to indicate if the calculation is spin polarized.

                                                                                    Type:
                                                                                    @@ -2192,7 +2192,7 @@

                                                                                    Submodules
                                                                                    -NciCobiList[source]
                                                                                    +NciCobiList[source]

                                                                                    Dict containing the listfile data of the form:

                                                                                    Type:
                                                                                    @@ -2216,7 +2216,7 @@

                                                                                    Submodules
                                                                                    -property ncicobi_list: dict[Any, dict[str, Any]][source]
                                                                                    +property ncicobi_list: dict[Any, dict[str, Any]][source]

                                                                                    ncicobilist.

                                                                                    Type:
                                                                                    @@ -2229,12 +2229,12 @@

                                                                                    Submodules
                                                                                    -class SitePotential(filename: str = 'SitePotentials.lobster', ewald_splitting: float | None = None, num_atoms: int | None = None, atomlist: list[str] | None = None, types: list[str] | None = None, sitepotentials_loewdin: list[float] | None = None, sitepotentials_mulliken: list[float] | None = None, madelungenergies_mulliken: float | None = None, madelungenergies_loewdin: float | None = None)[source]
                                                                                    +class SitePotential(filename: str = 'SitePotentials.lobster', ewald_splitting: float | None = None, num_atoms: int | None = None, atomlist: list[str] | None = None, types: list[str] | None = None, sitepotentials_loewdin: list[float] | None = None, sitepotentials_mulliken: list[float] | None = None, madelungenergies_mulliken: float | None = None, madelungenergies_loewdin: float | None = None)[source]

                                                                                    Bases: MSONable

                                                                                    Read SitePotentials.lobster files generated by LOBSTER.

                                                                                    -atomlist[source]
                                                                                    +atomlist[source]

                                                                                    List of atoms in SitePotentials.lobster.

                                                                                    Type:
                                                                                    @@ -2245,7 +2245,7 @@

                                                                                    Submodules
                                                                                    -types[source]
                                                                                    +types[source]

                                                                                    List of types of atoms in SitePotentials.lobster.

                                                                                    Type:
                                                                                    @@ -2256,7 +2256,7 @@

                                                                                    Submodules
                                                                                    -num_atoms[source]
                                                                                    +num_atoms[source]

                                                                                    Number of atoms in SitePotentials.lobster.

                                                                                    Type:
                                                                                    @@ -2267,7 +2267,7 @@

                                                                                    Submodules
                                                                                    -sitepotentials_mulliken[source]
                                                                                    +sitepotentials_mulliken[source]

                                                                                    List of Mulliken potentials of sites in SitePotentials.lobster.

                                                                                    Type:
                                                                                    @@ -2278,7 +2278,7 @@

                                                                                    Submodules
                                                                                    -sitepotentials_loewdin[source]
                                                                                    +sitepotentials_loewdin[source]

                                                                                    List of Loewdin potentials of sites in SitePotentials.lobster.

                                                                                    Type:
                                                                                    @@ -2289,7 +2289,7 @@

                                                                                    Submodules
                                                                                    -madelungenergies_mulliken[source]
                                                                                    +madelungenergies_mulliken[source]

                                                                                    Float that gives the Madelung energy based on the Mulliken approach.

                                                                                    Type:
                                                                                    @@ -2300,7 +2300,7 @@

                                                                                    Submodules
                                                                                    -madelungenergies_loewdin[source]
                                                                                    +madelungenergies_loewdin[source]

                                                                                    Float that gives the Madelung energy based on the Loewdin approach.

                                                                                    Type:
                                                                                    @@ -2311,7 +2311,7 @@

                                                                                    Submodules
                                                                                    -ewald_splitting[source]
                                                                                    +ewald_splitting[source]

                                                                                    Ewald Splitting parameter to compute SitePotentials.

                                                                                    Type:
                                                                                    @@ -2337,7 +2337,7 @@

                                                                                    Submodules
                                                                                    -get_structure_with_site_potentials(structure_filename)[source]
                                                                                    +get_structure_with_site_potentials(structure_filename)[source]

                                                                                    Get a Structure with Mulliken and Loewdin charges as site properties

                                                                                    Parameters:
                                                                                    @@ -2351,34 +2351,34 @@

                                                                                    Submodules
                                                                                    -property madelungenergies_Loewdin[source]
                                                                                    +property madelungenergies_Loewdin[source]

                                                                                    -property madelungenergies_Mulliken[source]
                                                                                    +property madelungenergies_Mulliken[source]
                                                                                    -property sitepotentials_Loewdin[source]
                                                                                    +property sitepotentials_Loewdin[source]
                                                                                    -property sitepotentials_Mulliken[source]
                                                                                    +property sitepotentials_Mulliken[source]

                                                                                    -class Wavefunction(filename, structure)[source]
                                                                                    +class Wavefunction(filename, structure)[source]

                                                                                    Bases: object

                                                                                    Read in wave function files from Lobster and transfer them into an object of the type VolumetricData.

                                                                                    -grid[source]
                                                                                    +grid[source]

                                                                                    Grid for the wave function [Nx+1,Ny+1,Nz+1].

                                                                                    Type:
                                                                                    @@ -2389,7 +2389,7 @@

                                                                                    Submodules
                                                                                    -points[source]
                                                                                    +points[source]

                                                                                    List of points.

                                                                                    Type:
                                                                                    @@ -2400,7 +2400,7 @@

                                                                                    Submodules
                                                                                    -real[source]
                                                                                    +real[source]

                                                                                    List of real part of wave function.

                                                                                    Type:
                                                                                    @@ -2411,7 +2411,7 @@

                                                                                    Submodules
                                                                                    -imaginary[source]
                                                                                    +imaginary[source]

                                                                                    List of imaginary part of wave function.

                                                                                    Type:
                                                                                    @@ -2422,7 +2422,7 @@

                                                                                    Submodules
                                                                                    -distance[source]
                                                                                    +distance[source]

                                                                                    List of distance to first point in wave function file.

                                                                                    Type:
                                                                                    @@ -2441,7 +2441,7 @@

                                                                                    Submodules
                                                                                    -get_volumetricdata_density()[source]
                                                                                    +get_volumetricdata_density()[source]

                                                                                    Will return a VolumetricData object including the imaginary part of the wave function.

                                                                                    Returns:
                                                                                    @@ -2452,7 +2452,7 @@

                                                                                    Submodules
                                                                                    -get_volumetricdata_imaginary()[source]
                                                                                    +get_volumetricdata_imaginary()[source]

                                                                                    Will return a VolumetricData object including the imaginary part of the wave function.

                                                                                    Returns:
                                                                                    @@ -2463,7 +2463,7 @@

                                                                                    Submodules
                                                                                    -get_volumetricdata_real()[source]
                                                                                    +get_volumetricdata_real()[source]

                                                                                    Will return a VolumetricData object including the real part of the wave function.

                                                                                    Returns:
                                                                                    @@ -2474,7 +2474,7 @@

                                                                                    Submodules
                                                                                    -set_volumetric_data(grid, structure)[source]
                                                                                    +set_volumetric_data(grid, structure)[source]

                                                                                    Will create the VolumetricData Objects.

                                                                                    Parameters:
                                                                                    @@ -2488,7 +2488,7 @@

                                                                                    Submodules
                                                                                    -write_file(filename='WAVECAR.vasp', part='real')[source]
                                                                                    +write_file(filename='WAVECAR.vasp', part='real')[source]

                                                                                    Will save the wavefunction in a file format that can be read by VESTA This will only work if the wavefunction from lobster was constructed with: “printLCAORealSpaceWavefunction kpoint 1 coordinates 0.0 0.0 0.0 coordinates 1.0 1.0 1.0 box bandlist 1 2 3 4 @@ -2508,7 +2508,7 @@

                                                                                    Submodules
                                                                                    -get_orb_from_str(orbs)[source]
                                                                                    +get_orb_from_str(orbs)[source]
                                                                                    Parameters:

                                                                                    orbs – list of two or more str, e.g. [“2p_x”, “3s”].

                                                                                    diff --git a/docs/pymatgen.io.pwmat.html b/docs/pymatgen.io.pwmat.html index c9b7c784dd3..56873ac14e5 100644 --- a/docs/pymatgen.io.pwmat.html +++ b/docs/pymatgen.io.pwmat.html @@ -4,7 +4,7 @@ - pymatgen.io.pwmat package — pymatgen 2024.6.4 documentation + pymatgen.io.pwmat package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                    - 2024.6.4 + 2024.6.10
                                                                                    @@ -178,7 +178,7 @@

                                                                                    Submodules

                                                                                    pymatgen.io.pwmat.inputs module

                                                                                    -class ACExtractor(file_path: PathLike)[source]
                                                                                    +class ACExtractor(file_path: PathLike)[source]

                                                                                    Bases: ACExtractorBase

                                                                                    Extract information contained in atom.config : number of atoms, lattice, types, frac_coords, magmoms

                                                                                    Initialization function

                                                                                    @@ -188,7 +188,7 @@

                                                                                    Submodules
                                                                                    -get_coords() → ndarray[source]
                                                                                    +get_coords() → ndarray[source]

                                                                                    Return the fractional coordinates in structure.

                                                                                    Returns:
                                                                                    @@ -202,7 +202,7 @@

                                                                                    Submodules
                                                                                    -get_lattice() → ndarray[source]
                                                                                    +get_lattice() → ndarray[source]

                                                                                    Return the lattice of structure.

                                                                                    Returns:
                                                                                    @@ -216,7 +216,7 @@

                                                                                    Submodules
                                                                                    -get_magmoms() → ndarray[source]
                                                                                    +get_magmoms() → ndarray[source]

                                                                                    Return the magenetic moments of atoms in structure.

                                                                                    Returns:
                                                                                    @@ -230,13 +230,13 @@

                                                                                    Submodules
                                                                                    -get_n_atoms() → int[source]
                                                                                    +get_n_atoms() → int[source]

                                                                                    Return the number of atoms in the structure.

                                                                                    -get_types() → ndarray[source]
                                                                                    +get_types() → ndarray[source]

                                                                                    Return the atomic number of atoms in structure.

                                                                                    Returns:
                                                                                    @@ -252,36 +252,36 @@

                                                                                    Submodules
                                                                                    -class ACExtractorBase[source]
                                                                                    +class ACExtractorBase[source]

                                                                                    Bases: ABC

                                                                                    A parent class of ACExtractor and ACstrExtractor, ensuring that they are as consistent as possible

                                                                                    -abstract get_coords() → ndarray[source]
                                                                                    +abstract get_coords() → ndarray[source]

                                                                                    Get fractional coordinates of atoms in structure defined by atom.config file

                                                                                    -abstract get_lattice() → ndarray[source]
                                                                                    +abstract get_lattice() → ndarray[source]

                                                                                    Get the lattice of structure defined by atom.config file

                                                                                    -abstract get_magmoms() → ndarray[source]
                                                                                    +abstract get_magmoms() → ndarray[source]

                                                                                    Get atomic magmoms of atoms in structure defined by atom.config file

                                                                                    -abstract get_n_atoms() → int[source]
                                                                                    +abstract get_n_atoms() → int[source]

                                                                                    Get the number of atoms in structure defined by atom.config file.

                                                                                    -abstract get_types() → ndarray[source]
                                                                                    +abstract get_types() → ndarray[source]

                                                                                    Get atomic number of atoms in structure defined by atom.config file

                                                                                    @@ -289,7 +289,7 @@

                                                                                    Submodules
                                                                                    -class ACstrExtractor(atom_config_str: str)[source]
                                                                                    +class ACstrExtractor(atom_config_str: str)[source]

                                                                                    Bases: ACExtractorBase

                                                                                    Extract information from atom.config file. You can get str by slicing the MOVEMENT.

                                                                                    Initialization function.

                                                                                    @@ -300,7 +300,7 @@

                                                                                    Submodules
                                                                                    -get_atom_energies() → ndarray | None[source]
                                                                                    +get_atom_energies() → ndarray | None[source]

                                                                                    Return the energies of individual atoms in material system.

                                                                                    When turning on ENERGY DEPOSITION, PWmat will output energy per atom.

                                                                                    @@ -315,7 +315,7 @@

                                                                                    Submodules
                                                                                    -get_atom_forces() → ndarray[source]
                                                                                    +get_atom_forces() → ndarray[source]

                                                                                    Return the force on atoms in material system.

                                                                                    Returns:
                                                                                    @@ -329,7 +329,7 @@

                                                                                    Submodules
                                                                                    -get_coords() → ndarray[source]
                                                                                    +get_coords() → ndarray[source]

                                                                                    Return the fractional coordinate of atoms in structure.

                                                                                    Returns:
                                                                                    @@ -343,7 +343,7 @@

                                                                                    Submodules
                                                                                    -get_e_tot() → ndarray[source]
                                                                                    +get_e_tot() → ndarray[source]

                                                                                    Return the total energy of structure.

                                                                                    Returns:
                                                                                    @@ -357,7 +357,7 @@

                                                                                    Submodules
                                                                                    -get_lattice() → ndarray[source]
                                                                                    +get_lattice() → ndarray[source]

                                                                                    Return the lattice of structure.

                                                                                    Returns:
                                                                                    @@ -371,7 +371,7 @@

                                                                                    Submodules
                                                                                    -get_magmoms() → ndarray[source]
                                                                                    +get_magmoms() → ndarray[source]

                                                                                    Return the magnetic moments of atoms in structure.

                                                                                    Returns:
                                                                                    @@ -385,7 +385,7 @@

                                                                                    Submodules
                                                                                    -get_n_atoms() → int[source]
                                                                                    +get_n_atoms() → int[source]

                                                                                    Return the number of atoms in structure.

                                                                                    Returns:
                                                                                    @@ -399,7 +399,7 @@

                                                                                    Submodules
                                                                                    -get_types() → ndarray[source]
                                                                                    +get_types() → ndarray[source]

                                                                                    Return the atomic number of atoms in structure.

                                                                                    Returns:
                                                                                    @@ -413,7 +413,7 @@

                                                                                    Submodules
                                                                                    -get_virial() → ndarray | None[source]
                                                                                    +get_virial() → ndarray | None[source]

                                                                                    Return the virial tensor of material system.

                                                                                    Returns:
                                                                                    @@ -429,7 +429,7 @@

                                                                                    Submodules
                                                                                    -class AtomConfig(structure: Structure, sort_structure: bool = False)[source]
                                                                                    +class AtomConfig(structure: Structure, sort_structure: bool = False)[source]

                                                                                    Bases: MSONable

                                                                                    Object for representing the data in a atom.config or final.config file.

                                                                                    Initialization function.

                                                                                    @@ -444,7 +444,7 @@

                                                                                    Submodules
                                                                                    -as_dict()[source]
                                                                                    +as_dict()[source]
                                                                                    Returns:

                                                                                    dict

                                                                                    @@ -454,7 +454,7 @@

                                                                                    Submodules
                                                                                    -classmethod from_dict(dct: dict) → Self[source]
                                                                                    +classmethod from_dict(dct: dict) → Self[source]

                                                                                    Get a AtomConfig object from a dictionary.

                                                                                    Parameters:
                                                                                    @@ -468,7 +468,7 @@

                                                                                    Submodules
                                                                                    -classmethod from_file(filename: PathLike, mag: bool = False) → Self[source]
                                                                                    +classmethod from_file(filename: PathLike, mag: bool = False) → Self[source]

                                                                                    Get a AtomConfig from a file

                                                                                    Parameters:
                                                                                    @@ -485,7 +485,7 @@

                                                                                    Submodules
                                                                                    -classmethod from_str(data: str, mag: bool = False) → Self[source]
                                                                                    +classmethod from_str(data: str, mag: bool = False) → Self[source]

                                                                                    Reads a atom.config from a string.

                                                                                    Parameters:
                                                                                    @@ -502,7 +502,7 @@

                                                                                    Submodules
                                                                                    -get_str() → str[source]
                                                                                    +get_str() → str[source]

                                                                                    Return a string describing the structure in atom.config format.

                                                                                    Returns:
                                                                                    @@ -516,7 +516,7 @@

                                                                                    Submodules
                                                                                    -write_file(filename: PathLike, **kwargs)[source]
                                                                                    +write_file(filename: PathLike, **kwargs)[source]

                                                                                    Write AtomConfig to a file.

                                                                                    @@ -524,7 +524,7 @@

                                                                                    Submodules
                                                                                    -class GenKpt(reciprocal_lattice: ndarray, kpoints: dict[str, ndarray], path: list[list[str]], density: float = 0.01)[source]
                                                                                    +class GenKpt(reciprocal_lattice: ndarray, kpoints: dict[str, ndarray], path: list[list[str]], density: float = 0.01)[source]

                                                                                    Bases: MSONable

                                                                                    Read and write gen.kpt. This file just generates line-mode kpoints.

                                                                                    Initialization function.

                                                                                    @@ -540,7 +540,7 @@

                                                                                    Submodules
                                                                                    -classmethod from_structure(structure: Structure, dim: int, density: float = 0.01) → Self[source]
                                                                                    +classmethod from_structure(structure: Structure, dim: int, density: float = 0.01) → Self[source]

                                                                                    Obtain a AtomConfig object from Structure object.

                                                                                    Parameters:
                                                                                    @@ -556,13 +556,13 @@

                                                                                    Submodules
                                                                                    -get_str()[source]
                                                                                    +get_str()[source]

                                                                                    Get a string to be written as a gen.kpt file.

                                                                                    -write_file(filename: PathLike)[source]
                                                                                    +write_file(filename: PathLike)[source]

                                                                                    Write gen.kpt to a file.

                                                                                    Parameters:
                                                                                    @@ -575,7 +575,7 @@

                                                                                    Submodules
                                                                                    -class HighSymmetryPoint(reciprocal_lattice: ndarray, kpts: dict[str, list], path: list[list[str]], density: float)[source]
                                                                                    +class HighSymmetryPoint(reciprocal_lattice: ndarray, kpts: dict[str, list], path: list[list[str]], density: float)[source]

                                                                                    Bases: MSONable

                                                                                    Read and write HIGH_SYMMETRY_POINTS file which generate line-mode kpoints.

                                                                                    Initialization function.

                                                                                    @@ -591,7 +591,7 @@

                                                                                    Submodules
                                                                                    -classmethod from_structure(structure: Structure, dim: int, density: float = 0.01) → Self[source]
                                                                                    +classmethod from_structure(structure: Structure, dim: int, density: float = 0.01) → Self[source]

                                                                                    Obtain HighSymmetry object from Structure object.

                                                                                    Parameters:
                                                                                    @@ -607,13 +607,13 @@

                                                                                    Submodules
                                                                                    -get_str() → str[source]
                                                                                    +get_str() → str[source]

                                                                                    Get a string describing high symmetry points in HIGH_SYMMETRY_POINTS format.

                                                                                    -write_file(filename: PathLike)[source]
                                                                                    +write_file(filename: PathLike)[source]

                                                                                    Write HighSymmetryPoint to a file.

                                                                                    @@ -621,12 +621,12 @@

                                                                                    Submodules
                                                                                    -class LineLocator[source]
                                                                                    +class LineLocator[source]

                                                                                    Bases: MSONable

                                                                                    Find the line indices (starts from 1) of a certain paragraph of text from the file.

                                                                                    -static locate_all_lines(file_path: PathLike, content: str, exclusion: str = '') → list[int][source]
                                                                                    +static locate_all_lines(file_path: PathLike, content: str, exclusion: str = '') → list[int][source]

                                                                                    Locate the line in file where a certain paragraph of text is located (return all indices)

                                                                                    Parameters:
                                                                                    @@ -643,12 +643,12 @@

                                                                                    Submodules
                                                                                    -class ListLocator[source]
                                                                                    +class ListLocator[source]

                                                                                    Bases: MSONable

                                                                                    Find the element indices (starts from 0) of a certain paragraph of text from the list.

                                                                                    -static locate_all_lines(strs_lst: list[str], content: str, exclusion: str = '') → list[int][source]
                                                                                    +static locate_all_lines(strs_lst: list[str], content: str, exclusion: str = '') → list[int][source]

                                                                                    Locate the elements in list where a certain paragraph of text is located (return all indices)

                                                                                    Parameters:
                                                                                    @@ -668,7 +668,7 @@

                                                                                    Submodules

                                                                                    pymatgen.io.pwmat.outputs module

                                                                                    -class DosSpin(filename: PathLike)[source]
                                                                                    +class DosSpin(filename: PathLike)[source]

                                                                                    Bases: MSONable

                                                                                    Extract information of DOS from DOS_SPIN file: - DOS.totalspin, DOS.totalspin_projected @@ -676,13 +676,13 @@

                                                                                    Submodules
                                                                                    -property dos: ndarray[source]
                                                                                    +property dos: ndarray[source]

                                                                                    Value of density of state.

                                                                                    -get_partial_dos(part: str) → ndarray[source]
                                                                                    +get_partial_dos(part: str) → ndarray[source]

                                                                                    Get partial dos for give element or orbital.

                                                                                    Parameters:
                                                                                    @@ -707,7 +707,7 @@

                                                                                    Submodules
                                                                                    -property labels: list[str][source]
                                                                                    +property labels: list[str][source]

                                                                                    The name of the partial density of states

                                                                                    @@ -715,7 +715,7 @@

                                                                                    Submodules
                                                                                    -class Movement(filename: PathLike, ionic_step_skip: int | None = None, ionic_step_offset: int | None = None)[source]
                                                                                    +class Movement(filename: PathLike, ionic_step_skip: int | None = None, ionic_step_offset: int | None = None)[source]

                                                                                    Bases: MSONable

                                                                                    Parser for data in MOVEMENT which records trajectory during MD.

                                                                                    Initialization function.

                                                                                    @@ -735,7 +735,7 @@

                                                                                    Submodules
                                                                                    -property atom_configs: list[Structure][source]
                                                                                    +property atom_configs: list[Structure][source]

                                                                                    AtomConfig for structures contained in MOVEMENT file.

                                                                                    Returns:
                                                                                    @@ -749,7 +749,7 @@

                                                                                    Submodules
                                                                                    -property atom_forces: ndarray[source]
                                                                                    +property atom_forces: ndarray[source]

                                                                                    Forces on atoms in each structures contained in MOVEMENT.

                                                                                    Returns:
                                                                                    @@ -767,7 +767,7 @@

                                                                                    Submodules
                                                                                    -property e_atoms: ndarray[source]
                                                                                    +property e_atoms: ndarray[source]

                                                                                    Individual energies of atoms in each ionic step structures contained in MOVEMENT.

                                                                                    @@ -786,7 +786,7 @@

                                                                                    Submodules
                                                                                    -property e_tots: ndarray[source]
                                                                                    +property e_tots: ndarray[source]

                                                                                    Total energies of each ionic step structures contained in MOVEMENT.

                                                                                    Returns:
                                                                                    @@ -804,7 +804,7 @@

                                                                                    Submodules
                                                                                    -property virials: ndarray[source]
                                                                                    +property virials: ndarray[source]

                                                                                    Virial tensor of each ionic step structure contained in MOVEMENT.

                                                                                    Returns:
                                                                                    @@ -824,7 +824,7 @@

                                                                                    Submodules
                                                                                    -class OutFermi(filename: PathLike)[source]
                                                                                    +class OutFermi(filename: PathLike)[source]

                                                                                    Bases: MSONable

                                                                                    Extract fermi energy (eV) from OUT.FERMI

                                                                                    Initialization function

                                                                                    @@ -835,7 +835,7 @@

                                                                                    Submodules
                                                                                    -property e_fermi: float[source]
                                                                                    +property e_fermi: float[source]

                                                                                    The fermi energy level.

                                                                                    Returns:
                                                                                    @@ -851,7 +851,7 @@

                                                                                    Submodules
                                                                                    -class Report(filename: PathLike)[source]
                                                                                    +class Report(filename: PathLike)[source]

                                                                                    Bases: MSONable

                                                                                    Extract information of spin, kpoints, bands, eigenvalues from REPORT file.

                                                                                    Initialization function.

                                                                                    @@ -862,7 +862,7 @@

                                                                                    Submodules
                                                                                    -property eigenvalues: ndarray[source]
                                                                                    +property eigenvalues: ndarray[source]

                                                                                    The eigenvalues.

                                                                                    Returns:
                                                                                    @@ -880,38 +880,38 @@

                                                                                    Submodules
                                                                                    -property hsps: dict[str, ndarray][source]
                                                                                    +property hsps: dict[str, ndarray][source]

                                                                                    The labels and fractional coordinates of high symmetry points as dict[str, np.ndarray]. Empty dict when task is not line-mode kpath.

                                                                                    -property kpoints: ndarray[source]
                                                                                    +property kpoints: ndarray[source]

                                                                                    The fractional coordinates of kpoints.

                                                                                    -property kpoints_weight: ndarray[source]
                                                                                    +property kpoints_weight: ndarray[source]

                                                                                    The weight of kpoints.

                                                                                    -property n_bands: int[source]
                                                                                    +property n_bands: int[source]

                                                                                    The number of bands.

                                                                                    -property n_kpoints: int[source]
                                                                                    +property n_kpoints: int[source]

                                                                                    The number of k-points.

                                                                                    -property spin: int[source]
                                                                                    +property spin: int[source]

                                                                                    The spin switches.

                                                                                    Returns:
                                                                                    diff --git a/docs/pymatgen.io.qchem.html b/docs/pymatgen.io.qchem.html index 129a5b518a7..b9f425cb18f 100644 --- a/docs/pymatgen.io.qchem.html +++ b/docs/pymatgen.io.qchem.html @@ -4,7 +4,7 @@ - pymatgen.io.qchem package — pymatgen 2024.6.4 documentation + pymatgen.io.qchem package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                    - 2024.6.4 + 2024.6.10
                                                                                    @@ -174,7 +174,7 @@

                                                                                    Submodules
                                                                                    -class QCInput(molecule: Molecule | list[Molecule] | Literal['read'], rem: dict, opt: dict[str, list] | None = None, pcm: dict | None = None, solvent: dict | None = None, smx: dict | None = None, scan: dict[str, list] | None = None, van_der_waals: dict[str, float] | None = None, vdw_mode: str = 'atomic', plots: dict | None = None, nbo: dict | None = None, geom_opt: dict | None = None, cdft: list[list[dict]] | None = None, almo_coupling: list[list[tuple[int, int]]] | None = None, svp: dict | None = None, pcm_nonels: dict | None = None)[source]
                                                                                    +class QCInput(molecule: Molecule | list[Molecule] | Literal['read'], rem: dict, opt: dict[str, list] | None = None, pcm: dict | None = None, solvent: dict | None = None, smx: dict | None = None, scan: dict[str, list] | None = None, van_der_waals: dict[str, float] | None = None, vdw_mode: str = 'atomic', plots: dict | None = None, nbo: dict | None = None, geom_opt: dict | None = None, cdft: list[list[dict]] | None = None, almo_coupling: list[list[tuple[int, int]]] | None = None, svp: dict | None = None, pcm_nonels: dict | None = None)[source]

                                                                                    Bases: InputFile

                                                                                    An object representing a QChem input file. QCInput attributes represent different sections of a QChem input file. To add a new section one needs to modify __init__, __str__, from_sting and add static methods @@ -331,7 +331,7 @@

                                                                                    Submodules
                                                                                    -static almo_template(almo_coupling: list[list[tuple[int, int]]]) → str[source]
                                                                                    +static almo_template(almo_coupling: list[list[tuple[int, int]]]) → str[source]
                                                                                    Parameters:

                                                                                    almo – list of lists of int 2-tuples.

                                                                                    @@ -347,7 +347,7 @@

                                                                                    Submodules
                                                                                    -static cdft_template(cdft: list[list[dict]]) → str[source]
                                                                                    +static cdft_template(cdft: list[list[dict]]) → str[source]
                                                                                    Parameters:

                                                                                    cdft – list of lists of dicts.

                                                                                    @@ -363,7 +363,7 @@

                                                                                    Submodules
                                                                                    -static find_sections(string: str) → list[source]
                                                                                    +static find_sections(string: str) → list[source]

                                                                                    Find sections in the string.

                                                                                    Parameters:
                                                                                    @@ -377,7 +377,7 @@

                                                                                    Submodules
                                                                                    -classmethod from_file(filename: str | Path) → Self[source]
                                                                                    +classmethod from_file(filename: str | Path) → Self[source]

                                                                                    Create QcInput from file.

                                                                                    Parameters:
                                                                                    @@ -391,7 +391,7 @@

                                                                                    Submodules
                                                                                    -classmethod from_multi_jobs_file(filename: str) → list[Self][source]
                                                                                    +classmethod from_multi_jobs_file(filename: str) → list[Self][source]

                                                                                    Create list of QcInput from a file.

                                                                                    Parameters:
                                                                                    @@ -405,7 +405,7 @@

                                                                                    Submodules
                                                                                    -classmethod from_str(string: str) → Self[source]
                                                                                    +classmethod from_str(string: str) → Self[source]

                                                                                    Read QcInput from string.

                                                                                    Parameters:
                                                                                    @@ -419,7 +419,7 @@

                                                                                    Submodules
                                                                                    -static geom_opt_template(geom_opt: dict) → str[source]
                                                                                    +static geom_opt_template(geom_opt: dict) → str[source]
                                                                                    Parameters:

                                                                                    () (geom_opt)

                                                                                    @@ -435,13 +435,13 @@

                                                                                    Submodules
                                                                                    -get_str() → str[source]
                                                                                    +get_str() → str[source]

                                                                                    Return a string representation of an entire input file.

                                                                                    -static molecule_template(molecule: Molecule | list[Molecule] | Literal['read']) → str[source]
                                                                                    +static molecule_template(molecule: Molecule | list[Molecule] | Literal['read']) → str[source]
                                                                                    Parameters:

                                                                                    molecule (Molecule, list of Molecules, or "read")

                                                                                    @@ -457,7 +457,7 @@

                                                                                    Submodules
                                                                                    -static multi_job_string(job_list: list[QCInput]) → str[source]
                                                                                    +static multi_job_string(job_list: list[QCInput]) → str[source]
                                                                                    Parameters:

                                                                                    () (job_list) – List of jobs.

                                                                                    @@ -473,7 +473,7 @@

                                                                                    Submodules
                                                                                    -static nbo_template(nbo: dict) → str[source]
                                                                                    +static nbo_template(nbo: dict) → str[source]
                                                                                    Parameters:

                                                                                    () (nbo)

                                                                                    @@ -489,7 +489,7 @@

                                                                                    Submodules
                                                                                    -static opt_template(opt: dict[str, list]) → str[source]
                                                                                    +static opt_template(opt: dict[str, list]) → str[source]

                                                                                    Optimization template.

                                                                                    Parameters:
                                                                                    @@ -506,7 +506,7 @@

                                                                                    Submodules
                                                                                    -static pcm_nonels_template(pcm_nonels: dict) → str[source]
                                                                                    +static pcm_nonels_template(pcm_nonels: dict) → str[source]

                                                                                    Template for the $pcm_nonels section.

                                                                                    Arg

                                                                                    pcm_nonels: dict of CMIRS parameters, e.g. @@ -542,7 +542,7 @@

                                                                                    Submodules
                                                                                    -static pcm_template(pcm: dict) → str[source]
                                                                                    +static pcm_template(pcm: dict) → str[source]

                                                                                    PCM run template.

                                                                                    Parameters:
                                                                                    @@ -559,7 +559,7 @@

                                                                                    Submodules
                                                                                    -static plots_template(plots: dict) → str[source]
                                                                                    +static plots_template(plots: dict) → str[source]
                                                                                    Parameters:

                                                                                    () (plots)

                                                                                    @@ -575,7 +575,7 @@

                                                                                    Submodules
                                                                                    -static read_almo(string: str) → list[list[tuple[int, int]]][source]
                                                                                    +static read_almo(string: str) → list[list[tuple[int, int]]][source]

                                                                                    Read ALMO coupling parameters from string.

                                                                                    Parameters:
                                                                                    @@ -592,7 +592,7 @@

                                                                                    Submodules
                                                                                    -static read_cdft(string: str) → list[list[dict]][source]
                                                                                    +static read_cdft(string: str) → list[list[dict]][source]

                                                                                    Read cdft parameters from string.

                                                                                    Parameters:
                                                                                    @@ -609,7 +609,7 @@

                                                                                    Submodules
                                                                                    -static read_geom_opt(string: str) → dict[source]
                                                                                    +static read_geom_opt(string: str) → dict[source]

                                                                                    Read geom_opt parameters from string.

                                                                                    Parameters:
                                                                                    @@ -626,7 +626,7 @@

                                                                                    Submodules
                                                                                    -static read_molecule(string: str) → Molecule | list[Molecule] | Literal['read'][source]
                                                                                    +static read_molecule(string: str) → Molecule | list[Molecule] | Literal['read'][source]

                                                                                    Read molecule from string.

                                                                                    Parameters:
                                                                                    @@ -640,7 +640,7 @@

                                                                                    Submodules
                                                                                    -static read_nbo(string: str) → dict[source]
                                                                                    +static read_nbo(string: str) → dict[source]

                                                                                    Read nbo parameters from string.

                                                                                    Parameters:
                                                                                    @@ -657,7 +657,7 @@

                                                                                    Submodules
                                                                                    -static read_opt(string: str) → dict[str, list][source]
                                                                                    +static read_opt(string: str) → dict[str, list][source]

                                                                                    Read opt section from string.

                                                                                    Parameters:
                                                                                    @@ -674,7 +674,7 @@

                                                                                    Submodules
                                                                                    -static read_pcm(string: str) → dict[source]
                                                                                    +static read_pcm(string: str) → dict[source]

                                                                                    Read pcm parameters from string.

                                                                                    Parameters:
                                                                                    @@ -691,7 +691,7 @@

                                                                                    Submodules
                                                                                    -static read_pcm_nonels(string: str) → dict[source]
                                                                                    +static read_pcm_nonels(string: str) → dict[source]

                                                                                    Read pcm_nonels parameters from string.

                                                                                    Parameters:
                                                                                    @@ -708,7 +708,7 @@

                                                                                    Submodules
                                                                                    -static read_plots(string: str) → dict[source]
                                                                                    +static read_plots(string: str) → dict[source]

                                                                                    Read plots parameters from string.

                                                                                    Parameters:
                                                                                    @@ -725,7 +725,7 @@

                                                                                    Submodules
                                                                                    -static read_rem(string: str) → dict[source]
                                                                                    +static read_rem(string: str) → dict[source]

                                                                                    Parse rem from string.

                                                                                    Parameters:
                                                                                    @@ -742,7 +742,7 @@

                                                                                    Submodules
                                                                                    -static read_scan(string: str) → dict[str, list][source]
                                                                                    +static read_scan(string: str) → dict[str, list][source]

                                                                                    Read scan section from a string.

                                                                                    Parameters:
                                                                                    @@ -756,7 +756,7 @@

                                                                                    Submodules
                                                                                    -static read_smx(string: str) → dict[source]
                                                                                    +static read_smx(string: str) → dict[source]

                                                                                    Read smx parameters from string.

                                                                                    Parameters:
                                                                                    @@ -770,7 +770,7 @@

                                                                                    Submodules
                                                                                    -static read_solvent(string: str) → dict[source]
                                                                                    +static read_solvent(string: str) → dict[source]

                                                                                    Read solvent parameters from string.

                                                                                    Parameters:
                                                                                    @@ -787,13 +787,13 @@

                                                                                    Submodules
                                                                                    -static read_svp(string: str) → dict[source]
                                                                                    +static read_svp(string: str) → dict[source]

                                                                                    Read svp parameters from string.

                                                                                    -static read_vdw(string: str) → tuple[str, dict][source]
                                                                                    +static read_vdw(string: str) → tuple[str, dict][source]

                                                                                    Read van der Waals parameters from string.

                                                                                    Parameters:
                                                                                    @@ -810,7 +810,7 @@

                                                                                    Submodules
                                                                                    -static rem_template(rem: dict) → str[source]
                                                                                    +static rem_template(rem: dict) → str[source]
                                                                                    Parameters:

                                                                                    () (rem)

                                                                                    @@ -826,7 +826,7 @@

                                                                                    Submodules
                                                                                    -static scan_template(scan: dict[str, list]) → str[source]
                                                                                    +static scan_template(scan: dict[str, list]) → str[source]

                                                                                    Get string representing Q-Chem input format for scan section.

                                                                                    Parameters:
                                                                                    @@ -838,7 +838,7 @@

                                                                                    Submodules
                                                                                    -static smx_template(smx: dict) → str[source]
                                                                                    +static smx_template(smx: dict) → str[source]
                                                                                    Parameters:

                                                                                    () (smx)

                                                                                    @@ -854,7 +854,7 @@

                                                                                    Submodules
                                                                                    -static solvent_template(solvent: dict) → str[source]
                                                                                    +static solvent_template(solvent: dict) → str[source]

                                                                                    Solvent template.

                                                                                    Parameters:
                                                                                    @@ -871,7 +871,7 @@

                                                                                    Submodules
                                                                                    -static svp_template(svp: dict) → str[source]
                                                                                    +static svp_template(svp: dict) → str[source]

                                                                                    Template for the $svp section.

                                                                                    Parameters:
                                                                                    @@ -896,7 +896,7 @@

                                                                                    Submodules
                                                                                    -static van_der_waals_template(radii: dict[str, float], mode: str = 'atomic') → str[source]
                                                                                    +static van_der_waals_template(radii: dict[str, float], mode: str = 'atomic') → str[source]
                                                                                    Parameters:
                                                                                      @@ -922,7 +922,7 @@

                                                                                      Submodules
                                                                                      -static write_multi_job_file(job_list: list[QCInput], filename: str)[source]
                                                                                      +static write_multi_job_file(job_list: list[QCInput], filename: str)[source]

                                                                                      Write a multijob file.

                                                                                      Parameters:
                                                                                      @@ -942,7 +942,7 @@

                                                                                      Submodules
                                                                                      -class QCOutput(filename: str)[source]
                                                                                      +class QCOutput(filename: str)[source]

                                                                                      Bases: MSONable

                                                                                      Parse QChem output files.

                                                                                      @@ -952,13 +952,13 @@

                                                                                      Submodules
                                                                                      -as_dict()[source]
                                                                                      +as_dict()[source]

                                                                                      Get MSONable dict representation of QCOutput.

                                                                                      -static multiple_outputs_from_file(filename, keep_sub_files=True)[source]
                                                                                      +static multiple_outputs_from_file(filename, keep_sub_files=True)[source]

                                                                                      Parses a QChem output file with multiple calculations # 1.) Separates the output into sub-files

                                                                                      @@ -973,7 +973,7 @@

                                                                                      Submodules
                                                                                      -check_for_structure_changes(mol1: Molecule, mol2: Molecule) → str[source]
                                                                                      +check_for_structure_changes(mol1: Molecule, mol2: Molecule) → str[source]

                                                                                      Compares connectivity of two molecules (using MoleculeGraph w/ OpenBabelNN). This function will work with two molecules with different atom orderings,

                                                                                      @@ -1008,7 +1008,7 @@

                                                                                      Submodules
                                                                                      -get_percentage(line: str, orbital: str) → str[source]
                                                                                      +get_percentage(line: str, orbital: str) → str[source]

                                                                                      Retrieve the percent character of an orbital.

                                                                                      Parameters:
                                                                                      @@ -1028,7 +1028,7 @@

                                                                                      Submodules
                                                                                      -gradient_parser(filename: str = '131.0') → NDArray[source]
                                                                                      +gradient_parser(filename: str = '131.0') → NDArray[source]

                                                                                      Parse the gradient data from a gradient scratch file.

                                                                                      Parameters:
                                                                                      @@ -1045,7 +1045,7 @@

                                                                                      Submodules
                                                                                      -hessian_parser(filename: str = '132.0', n_atoms: int | None = None) → NDArray[source]
                                                                                      +hessian_parser(filename: str = '132.0', n_atoms: int | None = None) → NDArray[source]

                                                                                      Parse the Hessian data from a Hessian scratch file.

                                                                                      Parameters:
                                                                                      @@ -1065,7 +1065,7 @@

                                                                                      Submodules
                                                                                      -jump_to_header(lines: list[str], header: str) → list[str][source]
                                                                                      +jump_to_header(lines: list[str], header: str) → list[str][source]

                                                                                      Given a list of lines, truncate the start of the list so that the first line of the new list contains the header.

                                                                                      @@ -1086,7 +1086,7 @@

                                                                                      Submodules
                                                                                      -nbo_parser(filename: str) → dict[str, list[DataFrame]][source]
                                                                                      +nbo_parser(filename: str) → dict[str, list[DataFrame]][source]

                                                                                      Parse all the important sections of NBO output.

                                                                                      Parameters:
                                                                                      @@ -1103,7 +1103,7 @@

                                                                                      Submodules
                                                                                      -orbital_coeffs_parser(filename: str = '53.0') → NDArray[source]
                                                                                      +orbital_coeffs_parser(filename: str = '53.0') → NDArray[source]

                                                                                      Parse the orbital coefficients from a scratch file.

                                                                                      Parameters:
                                                                                      @@ -1120,7 +1120,7 @@

                                                                                      Submodules
                                                                                      -parse_hybridization_character(lines: list[str]) → list[DataFrame][source]
                                                                                      +parse_hybridization_character(lines: list[str]) → list[DataFrame][source]

                                                                                      Parse the hybridization character section of NBO output.

                                                                                      Parameters:
                                                                                      @@ -1137,7 +1137,7 @@

                                                                                      Submodules
                                                                                      -parse_hyperbonds(lines: list[str]) → list[DataFrame][source]
                                                                                      +parse_hyperbonds(lines: list[str]) → list[DataFrame][source]

                                                                                      Parse the natural populations section of NBO output.

                                                                                      Parameters:
                                                                                      @@ -1154,7 +1154,7 @@

                                                                                      Submodules
                                                                                      -parse_natural_populations(lines: list[str]) → list[DataFrame][source]
                                                                                      +parse_natural_populations(lines: list[str]) → list[DataFrame][source]

                                                                                      Parse the natural populations section of NBO output.

                                                                                      Parameters:
                                                                                      @@ -1171,7 +1171,7 @@

                                                                                      Submodules
                                                                                      -parse_perturbation_energy(lines: list[str]) → list[DataFrame][source]
                                                                                      +parse_perturbation_energy(lines: list[str]) → list[DataFrame][source]

                                                                                      Parse the perturbation energy section of NBO output.

                                                                                      Parameters:
                                                                                      @@ -1188,7 +1188,7 @@

                                                                                      Submodules
                                                                                      -z_int(string: str) → int[source]
                                                                                      +z_int(string: str) → int[source]

                                                                                      Convert string to integer. If string empty, return -1.

                                                                                      @@ -1210,7 +1210,7 @@

                                                                                      Submodules
                                                                                      -class ForceSet(molecule: Molecule, basis_set: str = 'def2-tzvpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', cdft_constraints: list[list[dict]] | None = None, overwrite_inputs: dict | None = None)[source]
                                                                                      +class ForceSet(molecule: Molecule, basis_set: str = 'def2-tzvpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', cdft_constraints: list[list[dict]] | None = None, overwrite_inputs: dict | None = None)[source]

                                                                                      Bases: QChemDictSet

                                                                                      QChemDictSet for a force (gradient) calculation.

                                                                                      @@ -1378,7 +1378,7 @@

                                                                                      Submodules
                                                                                      -class FreqSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', cdft_constraints: list[list[dict]] | None = None, overwrite_inputs: dict | None = None)[source]
                                                                                      +class FreqSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', cdft_constraints: list[list[dict]] | None = None, overwrite_inputs: dict | None = None)[source]

                                                                                      Bases: QChemDictSet

                                                                                      QChemDictSet for a frequency calculation.

                                                                                      @@ -1546,7 +1546,7 @@

                                                                                      Submodules
                                                                                      -class OptSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, geom_opt: dict | None = None, cdft_constraints: list[list[dict]] | None = None, overwrite_inputs: dict | None = None)[source]
                                                                                      +class OptSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, geom_opt: dict | None = None, cdft_constraints: list[list[dict]] | None = None, overwrite_inputs: dict | None = None)[source]

                                                                                      Bases: QChemDictSet

                                                                                      QChemDictSet for a geometry optimization.

                                                                                      @@ -1729,7 +1729,7 @@

                                                                                      Submodules
                                                                                      -class PESScanSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
                                                                                      +class PESScanSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]

                                                                                      Bases: QChemDictSet

                                                                                      QChemDictSet for a potential energy surface scan (PES_SCAN) calculation, used primarily to identify possible transition states or to sample different @@ -1829,7 +1829,7 @@

                                                                                      Submodules
                                                                                      -class QChemDictSet(molecule: Molecule, job_type: str, basis_set: str, scf_algorithm: str, qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, max_scf_cycles: int = 100, geom_opt_max_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, geom_opt: dict | None = None, cdft_constraints: list[list[dict]] | None = None, almo_coupling_states: list[list[tuple[int, int]]] | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', extra_scf_print: bool = False)[source]
                                                                                      +class QChemDictSet(molecule: Molecule, job_type: str, basis_set: str, scf_algorithm: str, qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, max_scf_cycles: int = 100, geom_opt_max_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, geom_opt: dict | None = None, cdft_constraints: list[list[dict]] | None = None, almo_coupling_states: list[list[tuple[int, int]]] | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', extra_scf_print: bool = False)[source]

                                                                                      Bases: QCInput

                                                                                      Build a QCInput given all the various input parameters. Can be extended by standard implementations below.

                                                                                      @@ -2056,7 +2056,7 @@

                                                                                      Submodules
                                                                                      -write(input_file: str)[source]
                                                                                      +write(input_file: str)[source]
                                                                                      Parameters:

                                                                                      input_file (str) – Filename.

                                                                                      @@ -2068,7 +2068,7 @@

                                                                                      Submodules
                                                                                      -class SinglePointSet(molecule: Molecule, basis_set: str = 'def2-tzvpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', cdft_constraints: list[list[dict]] | None = None, almo_coupling_states: list[list[tuple[int, int]]] | None = None, extra_scf_print: bool = False, overwrite_inputs: dict | None = None)[source]
                                                                                      +class SinglePointSet(molecule: Molecule, basis_set: str = 'def2-tzvpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', cdft_constraints: list[list[dict]] | None = None, almo_coupling_states: list[list[tuple[int, int]]] | None = None, extra_scf_print: bool = False, overwrite_inputs: dict | None = None)[source]

                                                                                      Bases: QChemDictSet

                                                                                      QChemDictSet for a single point calculation.

                                                                                      @@ -2275,7 +2275,7 @@

                                                                                      Submodules
                                                                                      -class TransitionStateSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, geom_opt: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode='atomic')[source]
                                                                                      +class TransitionStateSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, geom_opt: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode='atomic')[source]

                                                                                      Bases: QChemDictSet

                                                                                      QChemDictSet for a transition-state search.

                                                                                      @@ -2368,7 +2368,7 @@

                                                                                      Submodules
                                                                                      -lower_and_check_unique(dict_to_check)[source]
                                                                                      +lower_and_check_unique(dict_to_check)[source]

                                                                                      Takes a dictionary and makes all the keys lower case. Also converts all numeric values (floats, ints) to str and replaces “jobtype” with “job_type” just so that key specifically can be called elsewhere without ambiguity. Finally, ensures that @@ -2393,14 +2393,14 @@

                                                                                      Submodules
                                                                                      -process_parsed_coords(coords)[source]
                                                                                      +process_parsed_coords(coords)[source]

                                                                                      Takes a set of parsed coordinates, which come as an array of strings, and returns a numpy array of floats.

                                                                                      -process_parsed_fock_matrix(fock_matrix)[source]
                                                                                      +process_parsed_fock_matrix(fock_matrix)[source]

                                                                                      The Fock matrix is parsed as a list, while it should actually be a square matrix, this function takes the list of finds the right dimensions in order to reshape the matrix.

                                                                                      @@ -2408,7 +2408,7 @@

                                                                                      Submodules
                                                                                      -process_parsed_hess(hess_data)[source]
                                                                                      +process_parsed_hess(hess_data)[source]

                                                                                      Takes the information contained in a HESS file and converts it into the format of the machine-readable 132.0 file which can be printed out to be read into subsequent optimizations.

                                                                                      @@ -2416,13 +2416,13 @@

                                                                                      Submodules
                                                                                      -read_matrix_pattern(header_pattern, footer_pattern, elements_pattern, text, postprocess=<class 'str'>)[source]
                                                                                      +read_matrix_pattern(header_pattern, footer_pattern, elements_pattern, text, postprocess=<class 'str'>)[source]

                                                                                      Parse a matrix to get the quantities in a numpy array.

                                                                                      -read_pattern(text_str, patterns, terminate_on_match=False, postprocess=<class 'str'>)[source]
                                                                                      +read_pattern(text_str, patterns, terminate_on_match=False, postprocess=<class 'str'>)[source]

                                                                                      General pattern reading on an input string.

                                                                                      Parameters:
                                                                                      @@ -2449,7 +2449,7 @@

                                                                                      Submodules
                                                                                      -read_table_pattern(text_str, header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=False)[source]
                                                                                      +read_table_pattern(text_str, header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=False)[source]

                                                                                      Parse table-like data. A table composes of three parts: header, main body, footer. All the data matches “row pattern” in the main body will be returned.

                                                                                      diff --git a/docs/pymatgen.io.vasp.html b/docs/pymatgen.io.vasp.html index f4a37f0e275..beeefc1f65a 100644 --- a/docs/pymatgen.io.vasp.html +++ b/docs/pymatgen.io.vasp.html @@ -4,7 +4,7 @@ - pymatgen.io.vasp package — pymatgen 2024.6.4 documentation + pymatgen.io.vasp package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                      - 2024.6.4 + 2024.6.10
                                                                                      @@ -818,13 +818,13 @@

                                                                                      Submodules
                                                                                      -class VaspDoc[source]
                                                                                      +class VaspDoc[source]

                                                                                      Bases: object

                                                                                      A VASP documentation helper.

                                                                                      Init for VaspDoc.

                                                                                      -classmethod get_help(tag: str, fmt: str = 'text') → str[source]
                                                                                      +classmethod get_help(tag: str, fmt: str = 'text') → str[source]

                                                                                      Get help on a VASP tag.

                                                                                      Parameters:
                                                                                      @@ -838,13 +838,13 @@

                                                                                      Submodules
                                                                                      -classmethod get_incar_tags() → list[str][source]
                                                                                      +classmethod get_incar_tags() → list[str][source]

                                                                                      Get a list of all INCAR tags from the VASP wiki.

                                                                                      -print_help(tag: str) → None[source]
                                                                                      +print_help(tag: str) → None[source]

                                                                                      Print the help for a TAG.

                                                                                      Parameters:
                                                                                      @@ -855,7 +855,7 @@

                                                                                      Submodules
                                                                                      -print_jupyter_help(tag: str) → None[source]
                                                                                      +print_jupyter_help(tag: str) → None[source]

                                                                                      Display HTML help in ipython notebook.

                                                                                      Parameters:
                                                                                      @@ -873,21 +873,21 @@

                                                                                      Submodules
                                                                                      -exception BadIncarWarning[source]
                                                                                      +exception BadIncarWarning[source]

                                                                                      Bases: UserWarning

                                                                                      Warning class for bad INCAR parameters.

                                                                                      -exception BadPoscarWarning[source]
                                                                                      +exception BadPoscarWarning[source]

                                                                                      Bases: UserWarning

                                                                                      Warning class for bad POSCAR entries.

                                                                                      -class Incar(params: dict[str, Any] | None = None)[source]
                                                                                      +class Incar(params: dict[str, Any] | None = None)[source]

                                                                                      Bases: dict, MSONable

                                                                                      INCAR object for reading and writing INCAR files. Essentially a dictionary with some helper functions.

                                                                                      @@ -899,13 +899,13 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      MSONable dict.

                                                                                      -check_params() → None[source]
                                                                                      +check_params() → None[source]

                                                                                      Check INCAR for invalid tags or values. If a tag doesn’t exist, calculation will still run, however VASP will ignore the tag and set it as default without letting you know.

                                                                                      @@ -913,12 +913,12 @@

                                                                                      Submodules
                                                                                      -copy() → a shallow copy of D[source]
                                                                                      +copy() → a shallow copy of D[source]

                                                                                      -diff(other: Self) → dict[str, dict[str, Any]][source]
                                                                                      +diff(other: Self) → dict[str, dict[str, Any]][source]

                                                                                      Diff function for Incar. Compare two Incars and indicate which parameters are the same and which are not. Useful for checking whether two runs were done using the same parameters.

                                                                                      @@ -942,7 +942,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                                      +classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Serialized Incar

                                                                                      @@ -955,7 +955,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_file(filename: PathLike) → Self[source]
                                                                                      +classmethod from_file(filename: PathLike) → Self[source]

                                                                                      Read an Incar object from a file.

                                                                                      Parameters:
                                                                                      @@ -969,7 +969,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_str(string: str) → Self[source]
                                                                                      +classmethod from_str(string: str) → Self[source]

                                                                                      Read an Incar object from a string.

                                                                                      Parameters:
                                                                                      @@ -983,7 +983,7 @@

                                                                                      Submodules
                                                                                      -get_str(sort_keys: bool = False, pretty: bool = False) → str[source]
                                                                                      +get_str(sort_keys: bool = False, pretty: bool = False) → str[source]

                                                                                      Get a string representation of the INCAR. Differ from the __str__ method to provide options for pretty printing.

                                                                                      @@ -1000,7 +1000,7 @@

                                                                                      Submodules
                                                                                      -static proc_val(key: str, val: Any) → list | bool | float | int | str[source]
                                                                                      +static proc_val(key: str, val: Any) → list | bool | float | int | str[source]

                                                                                      Helper method to convert INCAR parameters to proper types like ints, floats, lists, etc.

                                                                                      @@ -1015,7 +1015,7 @@

                                                                                      Submodules
                                                                                      -write_file(filename: PathLike) → None[source]
                                                                                      +write_file(filename: PathLike) → None[source]

                                                                                      Write Incar to a file.

                                                                                      Parameters:
                                                                                      @@ -1028,7 +1028,7 @@

                                                                                      Submodules
                                                                                      -class Kpoints(comment: str = 'Default gamma', num_kpts: int = 0, style: KpointsSupportedModes = KpointsSupportedModes.Gamma, kpts: Sequence[Kpoint] = ((1, 1, 1),), kpts_shift: Vector3D = (0, 0, 0), kpts_weights: list[float] | None = None, coord_type: Literal['Reciprocal', 'Cartesian'] | None = None, labels: list[str] | None = None, tet_number: int = 0, tet_weight: float = 0, tet_connections: list[tuple] | None = None)[source]
                                                                                      +class Kpoints(comment: str = 'Default gamma', num_kpts: int = 0, style: KpointsSupportedModes = KpointsSupportedModes.Gamma, kpts: Sequence[Kpoint] = ((1, 1, 1),), kpts_shift: Vector3D = (0, 0, 0), kpts_weights: list[float] | None = None, coord_type: Literal['Reciprocal', 'Cartesian'] | None = None, labels: list[str] | None = None, tet_number: int = 0, tet_weight: float = 0, tet_connections: list[tuple] | None = None)[source]

                                                                                      Bases: MSONable

                                                                                      KPOINTS reader/writer.

                                                                                      Highly flexible constructor for Kpoints object. The flexibility comes @@ -1073,13 +1073,13 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      MSONable dict.

                                                                                      -classmethod automatic(subdivisions: int) → Self[source]
                                                                                      +classmethod automatic(subdivisions: int) → Self[source]

                                                                                      Constructor for a fully automatic Kpoint grid, with gamma centered Monkhorst-Pack grids and the number of subdivisions along each reciprocal lattice vector determined by the scheme in the @@ -1097,7 +1097,7 @@

                                                                                      Submodules
                                                                                      -classmethod automatic_density(structure: Structure, kppa: float, force_gamma: bool = False) → Self[source]
                                                                                      +classmethod automatic_density(structure: Structure, kppa: float, force_gamma: bool = False) → Self[source]

                                                                                      Get an automatic Kpoint object based on a structure and a kpoint density. Uses Gamma centered meshes for hexagonal cells and face-centered cells, Monkhorst-Pack grids otherwise.

                                                                                      @@ -1123,7 +1123,7 @@

                                                                                      Submodules
                                                                                      -classmethod automatic_density_by_lengths(structure: Structure, length_densities: Sequence[float], force_gamma: bool = False) → Self[source]
                                                                                      +classmethod automatic_density_by_lengths(structure: Structure, length_densities: Sequence[float], force_gamma: bool = False) → Self[source]

                                                                                      Get an automatic Kpoint object based on a structure and a k-point density normalized by lattice constants.

                                                                                      @@ -1152,7 +1152,7 @@

                                                                                      Submodules
                                                                                      -classmethod automatic_density_by_vol(structure: Structure, kppvol: int, force_gamma: bool = False) → Self[source]
                                                                                      +classmethod automatic_density_by_vol(structure: Structure, kppvol: int, force_gamma: bool = False) → Self[source]

                                                                                      Get an automatic Kpoint object based on a structure and a kpoint density per inverse Angstrom^3 of reciprocal cell.

                                                                                      @@ -1175,7 +1175,7 @@

                                                                                      Submodules
                                                                                      -classmethod automatic_gamma_density(structure: Structure, kppa: float) → Self[source]
                                                                                      +classmethod automatic_gamma_density(structure: Structure, kppa: float) → Self[source]

                                                                                      Get an automatic Kpoint object based on a structure and a kpoint density. Uses Gamma centered meshes always. For GW.

                                                                                      @@ -1195,7 +1195,7 @@

                                                                                      Submodules
                                                                                      -classmethod automatic_linemode(divisions: int, ibz: HighSymmKpath) → Self[source]
                                                                                      +classmethod automatic_linemode(divisions: int, ibz: HighSymmKpath) → Self[source]

                                                                                      Convenient static constructor for a KPOINTS in mode line_mode. gamma centered Monkhorst-Pack grids and the number of subdivisions along each reciprocal lattice vector determined by the scheme in the @@ -1215,13 +1215,13 @@

                                                                                      Submodules
                                                                                      -copy() → Self[source]
                                                                                      +copy() → Self[source]

                                                                                      Make a copy of the Kpoints object.

                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -1234,7 +1234,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_file(filename: str | Path) → Self[source]
                                                                                      +classmethod from_file(filename: str | Path) → Self[source]

                                                                                      Reads a Kpoints object from a KPOINTS file.

                                                                                      Parameters:
                                                                                      @@ -1248,7 +1248,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_str(string: str) → Self[source]
                                                                                      +classmethod from_str(string: str) → Self[source]

                                                                                      Reads a Kpoints object from a KPOINTS string.

                                                                                      Parameters:
                                                                                      @@ -1262,7 +1262,7 @@

                                                                                      Submodules
                                                                                      -classmethod gamma_automatic(kpts: Kpoint = (1, 1, 1), shift: Vector3D = (0, 0, 0)) → Self[source]
                                                                                      +classmethod gamma_automatic(kpts: Kpoint = (1, 1, 1), shift: Vector3D = (0, 0, 0)) → Self[source]

                                                                                      Constructor for an automatic Gamma centered Kpoint grid.

                                                                                      Parameters:
                                                                                      @@ -1280,13 +1280,13 @@

                                                                                      Submodules
                                                                                      -property kpts: Sequence[tuple[float, float, float] | tuple[int]][source]
                                                                                      +property kpts: Sequence[tuple[float, float, float] | tuple[int]][source]

                                                                                      A sequence of Kpoints, where each Kpoint is a tuple of 3 or 1.

                                                                                      -classmethod monkhorst_automatic(kpts: Kpoint = (2, 2, 2), shift: Vector3D = (0, 0, 0)) → Self[source]
                                                                                      +classmethod monkhorst_automatic(kpts: Kpoint = (2, 2, 2), shift: Vector3D = (0, 0, 0)) → Self[source]

                                                                                      Convenient static constructor for an automatic Monkhorst pack Kpoint grid.

                                                                                      @@ -1305,19 +1305,19 @@

                                                                                      Submodules
                                                                                      -property style: KpointsSupportedModes[source]
                                                                                      +property style: KpointsSupportedModes[source]

                                                                                      Style for kpoint generation. One of Kpoints_supported_modes enum.

                                                                                      -supported_modes[source]
                                                                                      +supported_modes[source]

                                                                                      alias of KpointsSupportedModes

                                                                                      -write_file(filename: PathLike) → None[source]
                                                                                      +write_file(filename: PathLike) → None[source]

                                                                                      Write Kpoints to a file.

                                                                                      Parameters:
                                                                                      @@ -1330,42 +1330,42 @@

                                                                                      Submodules
                                                                                      -class KpointsSupportedModes(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
                                                                                      +class KpointsSupportedModes(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

                                                                                      Bases: Enum

                                                                                      Enum type of all supported modes for Kpoint generation.

                                                                                      -Automatic = 0[source]
                                                                                      +Automatic = 0[source]
                                                                                      -Cartesian = 4[source]
                                                                                      +Cartesian = 4[source]
                                                                                      -Gamma = 1[source]
                                                                                      +Gamma = 1[source]
                                                                                      -Line_mode = 3[source]
                                                                                      +Line_mode = 3[source]
                                                                                      -Monkhorst = 2[source]
                                                                                      +Monkhorst = 2[source]
                                                                                      -Reciprocal = 5[source]
                                                                                      +Reciprocal = 5[source]
                                                                                      -classmethod from_str(mode: str) → Self[source]
                                                                                      +classmethod from_str(mode: str) → Self[source]
                                                                                      Parameters:

                                                                                      mode – String

                                                                                      @@ -1380,36 +1380,36 @@

                                                                                      Submodules
                                                                                      -class Orbital(n, l, j, E, occ)[source]
                                                                                      +class Orbital(n, l, j, E, occ)[source]

                                                                                      Bases: NamedTuple

                                                                                      Create new instance of Orbital(n, l, j, E, occ)

                                                                                      -E: float[source]
                                                                                      +E: float[source]

                                                                                      Alias for field number 3

                                                                                      -j: float[source]
                                                                                      +j: float[source]

                                                                                      Alias for field number 2

                                                                                      -l: int[source]
                                                                                      +l: int[source]

                                                                                      Alias for field number 1

                                                                                      -n: int[source]
                                                                                      +n: int[source]

                                                                                      Alias for field number 0

                                                                                      -occ: float[source]
                                                                                      +occ: float[source]

                                                                                      Alias for field number 4

                                                                                      @@ -1417,42 +1417,42 @@

                                                                                      Submodules
                                                                                      -class OrbitalDescription(l, E, Type, Rcut, Type2, Rcut2)[source]
                                                                                      +class OrbitalDescription(l, E, Type, Rcut, Type2, Rcut2)[source]

                                                                                      Bases: NamedTuple

                                                                                      Create new instance of OrbitalDescription(l, E, Type, Rcut, Type2, Rcut2)

                                                                                      -E: float[source]
                                                                                      +E: float[source]

                                                                                      Alias for field number 1

                                                                                      -Rcut: float[source]
                                                                                      +Rcut: float[source]

                                                                                      Alias for field number 3

                                                                                      -Rcut2: float | None[source]
                                                                                      +Rcut2: float | None[source]

                                                                                      Alias for field number 5

                                                                                      -Type: int[source]
                                                                                      +Type: int[source]

                                                                                      Alias for field number 2

                                                                                      -Type2: int | None[source]
                                                                                      +Type2: int | None[source]

                                                                                      Alias for field number 4

                                                                                      -l: int[source]
                                                                                      +l: int[source]

                                                                                      Alias for field number 0

                                                                                      @@ -1460,66 +1460,66 @@

                                                                                      Submodules
                                                                                      -class Poscar(structure: Structure, comment: str | None = None, selective_dynamics: ArrayLike | None = None, true_names: bool = True, velocities: ArrayLike | None = None, predictor_corrector: ArrayLike | None = None, predictor_corrector_preamble: str | None = None, lattice_velocities: ArrayLike | None = None, sort_structure: bool = False)[source]
                                                                                      +class Poscar(structure: Structure, comment: str | None = None, selective_dynamics: ArrayLike | None = None, true_names: bool = True, velocities: ArrayLike | None = None, predictor_corrector: ArrayLike | None = None, predictor_corrector_preamble: str | None = None, lattice_velocities: ArrayLike | None = None, sort_structure: bool = False)[source]

                                                                                      Bases: MSONable

                                                                                      Object for representing the data in a POSCAR or CONTCAR file.

                                                                                      -structure[source]
                                                                                      +structure[source]

                                                                                      Associated Structure.

                                                                                      -comment[source]
                                                                                      +comment[source]

                                                                                      Optional comment string.

                                                                                      -true_names[source]
                                                                                      +true_names[source]

                                                                                      Boolean indication whether Poscar contains actual real names parsed from either a POTCAR or the POSCAR itself.

                                                                                      -selective_dynamics[source]
                                                                                      +selective_dynamics[source]

                                                                                      Selective dynamics attribute for each site if available. A Nx3 array of booleans.

                                                                                      -velocities[source]
                                                                                      +velocities[source]

                                                                                      Velocities for each site (typically read in from a CONTCAR). A Nx3 array of floats.

                                                                                      -predictor_corrector[source]
                                                                                      +predictor_corrector[source]

                                                                                      Predictor corrector coordinates and derivatives for each site; i.e. a list of three 1x3 arrays for each site (typically read in from an MD CONTCAR).

                                                                                      -predictor_corrector_preamble[source]
                                                                                      +predictor_corrector_preamble[source]

                                                                                      Predictor corrector preamble contains the predictor-corrector key, POTIM, and thermostat parameters that precede the site-specific predictor corrector data in MD CONTCAR.

                                                                                      -lattice_velocities[source]
                                                                                      +lattice_velocities[source]

                                                                                      Lattice velocities and current lattice (typically read in from an MD CONTCAR). A 6x3 array of floats.

                                                                                      -temperature[source]
                                                                                      +temperature[source]

                                                                                      Temperature of velocity Maxwell-Boltzmann initialization. Initialized to -1 (MB hasn’t been performed).

                                                                                      @@ -1551,13 +1551,13 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      MSONable dict.

                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -1570,7 +1570,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_file(filename: PathLike, check_for_potcar: bool = True, read_velocities: bool = True, **kwargs: dict[str, Any]) → Self[source]
                                                                                      +classmethod from_file(filename: PathLike, check_for_potcar: bool = True, read_velocities: bool = True, **kwargs: dict[str, Any]) → Self[source]

                                                                                      Read POSCAR from a file.

                                                                                      The code will try its best to determine the elements in the POSCAR in the following order:

                                                                                      @@ -1605,7 +1605,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_str(data: str, default_names: list[str] | None = None, read_velocities: bool = True) → Self[source]
                                                                                      +classmethod from_str(data: str, default_names: list[str] | None = None, read_velocities: bool = True) → Self[source]

                                                                                      Read POSCAR from a string.

                                                                                      The code will try its best to determine the elements in the POSCAR in the following order:

                                                                                      @@ -1639,7 +1639,7 @@

                                                                                      Submodules
                                                                                      -get_str(direct: bool = True, vasp4_compatible: bool = False, significant_figures: int = 16) → str[source]
                                                                                      +get_str(direct: bool = True, vasp4_compatible: bool = False, significant_figures: int = 16) → str[source]

                                                                                      Return a string to be written as a POSCAR file. By default, site symbols are written, which is compatible for vasp >= 5.

                                                                                      @@ -1667,7 +1667,7 @@

                                                                                      Submodules
                                                                                      -get_string(direct: bool = True, vasp4_compatible: bool = False, significant_figures: int = 16) → str[source]
                                                                                      +get_string(direct: bool = True, vasp4_compatible: bool = False, significant_figures: int = 16) → str[source]

                                                                                      Return a string to be written as a POSCAR file. By default, site symbols are written, which is compatible for vasp >= 5.

                                                                                      @@ -1695,38 +1695,38 @@

                                                                                      Submodules
                                                                                      -property lattice_velocities: ArrayLike | None[source]
                                                                                      +property lattice_velocities: ArrayLike | None[source]

                                                                                      Lattice velocities in Poscar (including the current lattice vectors).

                                                                                      -property natoms: list[int][source]
                                                                                      +property natoms: list[int][source]

                                                                                      Sequence of number of sites of each type associated with the Poscar. Similar to 7th line in vasp 5+ POSCAR or the 6th line in vasp 4 POSCAR.

                                                                                      -property predictor_corrector: ArrayLike | None[source]
                                                                                      +property predictor_corrector: ArrayLike | None[source]

                                                                                      Predictor corrector in Poscar.

                                                                                      -property predictor_corrector_preamble: str | None[source]
                                                                                      +property predictor_corrector_preamble: str | None[source]

                                                                                      Predictor corrector preamble in Poscar.

                                                                                      -property selective_dynamics: ArrayLike | None[source]
                                                                                      +property selective_dynamics: ArrayLike | None[source]

                                                                                      Selective dynamics in Poscar.

                                                                                      -set_temperature(temperature: float) → None[source]
                                                                                      +set_temperature(temperature: float) → None[source]

                                                                                      Initialize the velocities based on Maxwell-Boltzmann distribution. Removes linear, but not angular drift (same as VASP).

                                                                                      Scale the energies to the exact temperature (microcanonical ensemble) @@ -1743,19 +1743,19 @@

                                                                                      Submodules
                                                                                      -property site_symbols: list[str][source]
                                                                                      +property site_symbols: list[str][source]

                                                                                      Sequence of symbols associated with the Poscar. Similar to 6th line in VASP 5+ POSCAR.

                                                                                      -property velocities: ArrayLike | None[source]
                                                                                      +property velocities: ArrayLike | None[source]

                                                                                      Velocities in Poscar.

                                                                                      -write_file(filename: PathLike, **kwargs) → None[source]
                                                                                      +write_file(filename: PathLike, **kwargs) → None[source]

                                                                                      Write POSCAR to a file. The supported kwargs are the same as those for the Poscar.get_str method and are passed through directly.

                                                                                      @@ -1764,7 +1764,7 @@

                                                                                      Submodules
                                                                                      -class Potcar(symbols: Sequence[str] | None = None, functional: str | None = None, sym_potcar_map: dict[str, str] | None = None)[source]
                                                                                      +class Potcar(symbols: Sequence[str] | None = None, functional: str | None = None, sym_potcar_map: dict[str, str] | None = None)[source]

                                                                                      Bases: list, MSONable

                                                                                      Read and write POTCAR files for calculations. Consists of a list of PotcarSingle.

                                                                                      @@ -1787,18 +1787,18 @@

                                                                                      Submodules
                                                                                      -FUNCTIONAL_CHOICES = ('PBE', 'PBE_52', 'PBE_52_W_HASH', 'PBE_54', 'PBE_54_W_HASH', 'PBE_64', 'LDA', 'LDA_52', 'LDA_52_W_HASH', 'LDA_54', 'LDA_54_W_HASH', 'LDA_64', 'PW91', 'LDA_US', 'PW91_US', 'Perdew_Zunger81')[source]
                                                                                      +FUNCTIONAL_CHOICES = ('PBE', 'PBE_52', 'PBE_52_W_HASH', 'PBE_54', 'PBE_54_W_HASH', 'PBE_64', 'LDA', 'LDA_52', 'LDA_52_W_HASH', 'LDA_54', 'LDA_54_W_HASH', 'LDA_64', 'PW91', 'LDA_US', 'PW91_US', 'Perdew_Zunger81')[source]

                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      MSONable dict representation.

                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -1811,7 +1811,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_file(filename: PathLike) → Self[source]
                                                                                      +classmethod from_file(filename: PathLike) → Self[source]

                                                                                      Reads Potcar from file.

                                                                                      Parameters:
                                                                                      @@ -1825,7 +1825,7 @@

                                                                                      Submodules
                                                                                      -set_symbols(symbols: Sequence[str], functional: str | None = None, sym_potcar_map: dict[str, str] | None = None) → None[source]
                                                                                      +set_symbols(symbols: Sequence[str], functional: str | None = None, sym_potcar_map: dict[str, str] | None = None) → None[source]

                                                                                      Initialize the POTCAR from a set of symbols. Currently, the POTCARs can be fetched from a location specified in .pmgrc.yaml. Use pmg config to add this setting.

                                                                                      @@ -1846,19 +1846,19 @@

                                                                                      Submodules
                                                                                      -property spec: list[dict][source]
                                                                                      +property spec: list[dict][source]

                                                                                      The atomic symbols and hash of all the atoms in the POTCAR file.

                                                                                      -property symbols: list[str][source]
                                                                                      +property symbols: list[str][source]

                                                                                      The atomic symbols of all the atoms in the POTCAR file.

                                                                                      -write_file(filename: PathLike) → None[source]
                                                                                      +write_file(filename: PathLike) → None[source]

                                                                                      Write Potcar to a file.

                                                                                      Parameters:
                                                                                      @@ -1871,13 +1871,13 @@

                                                                                      Submodules
                                                                                      -class PotcarSingle(data: str, symbol: str | None = None)[source]
                                                                                      +class PotcarSingle(data: str, symbol: str | None = None)[source]

                                                                                      Bases: object

                                                                                      Object for a single POTCAR. The builder assumes the POTCAR contains the complete untouched string “data” and a dict of keywords.

                                                                                      -data[source]
                                                                                      +data[source]

                                                                                      POTCAR data as a string.

                                                                                      Type:
                                                                                      @@ -1888,7 +1888,7 @@

                                                                                      Submodules
                                                                                      -keywords[source]
                                                                                      +keywords[source]

                                                                                      Keywords parsed from the POTCAR as a dict. All keywords are also accessible as attributes in themselves. e.g. potcar.enmax, potcar.encut, etc.

                                                                                      @@ -1914,13 +1914,13 @@

                                                                                      Submodules
                                                                                      -property atomic_no: int[source]
                                                                                      +property atomic_no: int[source]

                                                                                      Attempt to return the atomic number based on the VRHFIN keyword.

                                                                                      -copy() → Self[source]
                                                                                      +copy() → Self[source]

                                                                                      Return a copy of the PotcarSingle.

                                                                                      Returns:
                                                                                      @@ -1931,19 +1931,19 @@

                                                                                      Submodules
                                                                                      -property electron_configuration: list[tuple[int, str, int]] | None[source]
                                                                                      +property electron_configuration: list[tuple[int, str, int]] | None[source]

                                                                                      Electronic configuration of the PotcarSingle.

                                                                                      -property element: str[source]
                                                                                      +property element: str[source]

                                                                                      Attempt to return the atomic symbol based on the VRHFIN keyword.

                                                                                      -classmethod from_file(filename: PathLike) → Self[source]
                                                                                      +classmethod from_file(filename: PathLike) → Self[source]

                                                                                      Read PotcarSingle from file.

                                                                                      Parameters:
                                                                                      @@ -1957,7 +1957,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_symbol_and_functional(symbol: str, functional: str | None = None) → Self[source]
                                                                                      +classmethod from_symbol_and_functional(symbol: str, functional: str | None = None) → Self[source]

                                                                                      Make a PotcarSingle from a symbol and functional.

                                                                                      Parameters:
                                                                                      @@ -1974,35 +1974,35 @@

                                                                                      Submodules
                                                                                      -property functional: str | None[source]
                                                                                      +property functional: str | None[source]

                                                                                      Functional associated with PotcarSingle.

                                                                                      -property functional_class: str | None[source]
                                                                                      +property functional_class: str | None[source]

                                                                                      Functional class associated with PotcarSingle.

                                                                                      -functional_dir: ClassVar[dict[str, str]] = {'LDA': 'POT_LDA_PAW', 'LDA_52': 'POT_LDA_PAW_52', 'LDA_52_W_HASH': 'POTPAW_LDA_52', 'LDA_54': 'POT_LDA_PAW_54', 'LDA_54_W_HASH': 'POTPAW_LDA_54', 'LDA_64': 'POT_LDA_PAW_64', 'LDA_US': 'POT_LDA_US', 'PBE': 'POT_GGA_PAW_PBE', 'PBE_52': 'POT_GGA_PAW_PBE_52', 'PBE_52_W_HASH': 'POTPAW_PBE_52', 'PBE_54': 'POT_GGA_PAW_PBE_54', 'PBE_54_W_HASH': 'POTPAW_PBE_54', 'PBE_64': 'POT_PAW_PBE_64', 'PW91': 'POT_GGA_PAW_PW91', 'PW91_US': 'POT_GGA_US_PW91', 'Perdew_Zunger81': 'POT_LDA_PAW'}[source]
                                                                                      +functional_dir: ClassVar[dict[str, str]] = {'LDA': 'POT_LDA_PAW', 'LDA_52': 'POT_LDA_PAW_52', 'LDA_52_W_HASH': 'POTPAW_LDA_52', 'LDA_54': 'POT_LDA_PAW_54', 'LDA_54_W_HASH': 'POTPAW_LDA_54', 'LDA_64': 'POT_LDA_PAW_64', 'LDA_US': 'POT_LDA_US', 'PBE': 'POT_GGA_PAW_PBE', 'PBE_52': 'POT_GGA_PAW_PBE_52', 'PBE_52_W_HASH': 'POTPAW_PBE_52', 'PBE_54': 'POT_GGA_PAW_PBE_54', 'PBE_54_W_HASH': 'POTPAW_PBE_54', 'PBE_64': 'POT_PAW_PBE_64', 'PW91': 'POT_GGA_PAW_PW91', 'PW91_US': 'POT_GGA_US_PW91', 'Perdew_Zunger81': 'POT_LDA_PAW'}[source]
                                                                                      -functional_tags: ClassVar[dict[str, dict[Literal['name', 'class'], str]]] = {'91': {'class': 'GGA', 'name': 'PW91'}, 'am': {'class': 'GGA', 'name': 'AM05'}, 'ca': {'class': 'LDA', 'name': 'Perdew-Zunger81'}, 'hl': {'class': 'LDA', 'name': 'Hedin-Lundquist'}, 'lm': {'class': 'GGA', 'name': 'Langreth-Mehl-Hu'}, 'pb': {'class': 'GGA', 'name': 'Perdew-Becke'}, 'pe': {'class': 'GGA', 'name': 'PBE'}, 'ps': {'class': 'GGA', 'name': 'PBEsol'}, 'pw': {'class': 'GGA', 'name': 'PW86'}, 'rp': {'class': 'GGA', 'name': 'revPBE'}, 'wi': {'class': 'LDA', 'name': 'Wigner Interpolation'}}[source]
                                                                                      +functional_tags: ClassVar[dict[str, dict[Literal['name', 'class'], str]]] = {'91': {'class': 'GGA', 'name': 'PW91'}, 'am': {'class': 'GGA', 'name': 'AM05'}, 'ca': {'class': 'LDA', 'name': 'Perdew-Zunger81'}, 'hl': {'class': 'LDA', 'name': 'Hedin-Lundquist'}, 'lm': {'class': 'GGA', 'name': 'Langreth-Mehl-Hu'}, 'pb': {'class': 'GGA', 'name': 'Perdew-Becke'}, 'pe': {'class': 'GGA', 'name': 'PBE'}, 'ps': {'class': 'GGA', 'name': 'PBEsol'}, 'pw': {'class': 'GGA', 'name': 'PW86'}, 'rp': {'class': 'GGA', 'name': 'revPBE'}, 'wi': {'class': 'LDA', 'name': 'Wigner Interpolation'}}[source]
                                                                                      -property hash_sha256_from_file: str | None[source]
                                                                                      +property hash_sha256_from_file: str | None[source]

                                                                                      SHA256 hash of the POTCAR file as read from the file. None if no SHA256 hash is found.

                                                                                      -identify_potcar(mode: Literal['data', 'file'] = 'data', data_tol: float = 1e-06) → tuple[list[str], list[str]][source]
                                                                                      +identify_potcar(mode: Literal['data', 'file'] = 'data', data_tol: float = 1e-06) → tuple[list[str], list[str]][source]

                                                                                      Identify the symbol and compatible functionals associated with this PotcarSingle.

                                                                                      This method checks the summary statistics of either the POTCAR metadadata (PotcarSingle._summary_stats[key][“header”] for key in (“keywords”, “stats”) ) @@ -2033,7 +2033,7 @@

                                                                                      Submodules
                                                                                      -identify_potcar_hash_based(mode: Literal['data', 'file'] = 'data') → tuple[list[str], list[str]][source]
                                                                                      +identify_potcar_hash_based(mode: Literal['data', 'file'] = 'data') → tuple[list[str], list[str]][source]

                                                                                      Identify the symbol and compatible functionals associated with this PotcarSingle.

                                                                                      This method checks the MD5 hash of either the POTCAR metadadata (PotcarSingle.md5_header_hash) or the entire POTCAR file (PotcarSingle.md5_computed_file_hash) against a database @@ -2059,7 +2059,7 @@

                                                                                      Submodules
                                                                                      -property is_valid: bool[source]
                                                                                      +property is_valid: bool[source]

                                                                                      Check that POTCAR matches reference metadata. Parsed metadata is stored in self._summary_stats as a human-readable dict,

                                                                                      @@ -2110,30 +2110,30 @@

                                                                                      Submodules
                                                                                      -property md5_computed_file_hash: str[source]
                                                                                      +property md5_computed_file_hash: str[source]

                                                                                      MD5 hash of the entire PotcarSingle.

                                                                                      -property md5_header_hash: str[source]
                                                                                      +property md5_header_hash: str[source]

                                                                                      MD5 hash of the metadata defining the PotcarSingle.

                                                                                      -property nelectrons: float[source]
                                                                                      +property nelectrons: float[source]

                                                                                      Number of electrons.

                                                                                      -parse_functions: ClassVar[dict[str, Any]] = {'COPYR': <method 'strip' of 'str' objects>, 'DEXC': <function _parse_float>, 'EATOM': <function _parse_float>, 'EAUG': <function _parse_float>, 'EMMIN': <function _parse_float>, 'ENMAX': <function _parse_float>, 'ENMIN': <function _parse_float>, 'GGA': <function _parse_list>, 'ICORE': <function _parse_int>, 'IUNSCR': <function _parse_int>, 'LCOR': <function _parse_bool>, 'LEXCH': <method 'strip' of 'str' objects>, 'LPAW': <function _parse_bool>, 'LULTRA': <function _parse_bool>, 'LUNSCR': <function _parse_bool>, 'NDATA': <function _parse_int>, 'POMASS': <function _parse_float>, 'QCUT': <function _parse_float>, 'QGAM': <function _parse_float>, 'RAUG': <function _parse_float>, 'RCLOC': <function _parse_float>, 'RCORE': <function _parse_float>, 'RDEP': <function _parse_float>, 'RDEPT': <function _parse_float>, 'RMAX': <function _parse_float>, 'RPACOR': <function _parse_float>, 'RRKJ': <function _parse_list>, 'RWIGS': <function _parse_float>, 'SHA256': <method 'strip' of 'str' objects>, 'STEP': <function _parse_list>, 'TITEL': <method 'strip' of 'str' objects>, 'VRHFIN': <method 'strip' of 'str' objects>, 'ZVAL': <function _parse_float>}[source]
                                                                                      +parse_functions: ClassVar[dict[str, Any]] = {'COPYR': <method 'strip' of 'str' objects>, 'DEXC': <function _parse_float>, 'EATOM': <function _parse_float>, 'EAUG': <function _parse_float>, 'EMMIN': <function _parse_float>, 'ENMAX': <function _parse_float>, 'ENMIN': <function _parse_float>, 'GGA': <function _parse_list>, 'ICORE': <function _parse_int>, 'IUNSCR': <function _parse_int>, 'LCOR': <function _parse_bool>, 'LEXCH': <method 'strip' of 'str' objects>, 'LPAW': <function _parse_bool>, 'LULTRA': <function _parse_bool>, 'LUNSCR': <function _parse_bool>, 'NDATA': <function _parse_int>, 'POMASS': <function _parse_float>, 'QCUT': <function _parse_float>, 'QGAM': <function _parse_float>, 'RAUG': <function _parse_float>, 'RCLOC': <function _parse_float>, 'RCORE': <function _parse_float>, 'RDEP': <function _parse_float>, 'RDEPT': <function _parse_float>, 'RMAX': <function _parse_float>, 'RPACOR': <function _parse_float>, 'RRKJ': <function _parse_list>, 'RWIGS': <function _parse_float>, 'SHA256': <method 'strip' of 'str' objects>, 'STEP': <function _parse_list>, 'TITEL': <method 'strip' of 'str' objects>, 'VRHFIN': <method 'strip' of 'str' objects>, 'ZVAL': <function _parse_float>}[source]
                                                                                      -property potential_type: Literal['NC', 'PAW', 'US'][source]
                                                                                      +property potential_type: Literal['NC', 'PAW', 'US'][source]

                                                                                      NC (Norm-conserving), US (Ultra-soft), PAW (Projector augmented wave).

                                                                                      Type:
                                                                                      @@ -2144,19 +2144,19 @@

                                                                                      Submodules
                                                                                      -property sha256_computed_file_hash: str[source]
                                                                                      +property sha256_computed_file_hash: str[source]

                                                                                      Compute a SHA256 hash of the PotcarSingle EXCLUDING lines starting with ‘SHA256’ and ‘COPYR’.

                                                                                      -property symbol: str[source]
                                                                                      +property symbol: str[source]

                                                                                      The POTCAR symbol, e.g. W_pv.

                                                                                      -verify_potcar() → tuple[bool, bool][source]
                                                                                      +verify_potcar() → tuple[bool, bool][source]

                                                                                      Attempt to verify the integrity of the POTCAR data.

                                                                                      This method checks the whole file (removing only the SHA256 metadata) against the SHA256 hash in the header if this is found. @@ -2174,7 +2174,7 @@

                                                                                      Submodules
                                                                                      -write_file(filename: str) → None[source]
                                                                                      +write_file(filename: str) → None[source]

                                                                                      Write PotcarSingle to a file.

                                                                                      Parameters:
                                                                                      @@ -2187,14 +2187,14 @@

                                                                                      Submodules
                                                                                      -exception UnknownPotcarWarning[source]
                                                                                      +exception UnknownPotcarWarning[source]

                                                                                      Bases: UserWarning

                                                                                      Warning raised when POTCAR hashes do not pass validation.

                                                                                      -class VaspInput(incar: dict | Incar, kpoints: Kpoints | None, poscar: Poscar, potcar: Potcar | str | None, potcar_spec: bool = False, optional_files: dict[PathLike, object] | None = None, **kwargs)[source]
                                                                                      +class VaspInput(incar: dict | Incar, kpoints: Kpoints | None, poscar: Poscar, potcar: Potcar | str | None, potcar_spec: bool = False, optional_files: dict[PathLike, object] | None = None, **kwargs)[source]

                                                                                      Bases: dict, MSONable

                                                                                      Contain a set of vasp input objects corresponding to a run.

                                                                                      Initialize a VaspInput object with the given input files.

                                                                                      @@ -2217,19 +2217,19 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      MSONable dict.

                                                                                      -copy(deep: bool = True) → Self[source]
                                                                                      +copy(deep: bool = True) → Self[source]

                                                                                      Deep copy of VaspInput.

                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -2242,7 +2242,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_directory(input_dir: PathLike, optional_files: dict | None = None) → Self[source]
                                                                                      +classmethod from_directory(input_dir: PathLike, optional_files: dict | None = None) → Self[source]

                                                                                      Read in a set of VASP inputs from a directory. Note that only the standard INCAR, POSCAR, POTCAR and KPOINTS files are read unless optional_filenames is specified.

                                                                                      @@ -2260,31 +2260,31 @@

                                                                                      Submodules
                                                                                      -property incar: Incar[source]
                                                                                      +property incar: Incar[source]

                                                                                      INCAR object.

                                                                                      -property kpoints: Kpoints | None[source]
                                                                                      +property kpoints: Kpoints | None[source]

                                                                                      KPOINTS object.

                                                                                      -property poscar: Poscar[source]
                                                                                      +property poscar: Poscar[source]

                                                                                      POSCAR object.

                                                                                      -property potcar: Potcar | str | None[source]
                                                                                      +property potcar: Potcar | str | None[source]

                                                                                      POTCAR or POTCAR.spec object.

                                                                                      -run_vasp(run_dir: PathLike = '.', vasp_cmd: list | None = None, output_file: PathLike = 'vasp.out', err_file: PathLike = 'vasp.err') → None[source]
                                                                                      +run_vasp(run_dir: PathLike = '.', vasp_cmd: list | None = None, output_file: PathLike = 'vasp.out', err_file: PathLike = 'vasp.err') → None[source]

                                                                                      Write input files and run VASP.

                                                                                      Parameters:
                                                                                      @@ -2301,7 +2301,7 @@

                                                                                      Submodules
                                                                                      -write_input(output_dir: PathLike = '.', make_dir_if_not_present: bool = True, cif_name: str | None = None, zip_name: str | None = None, files_to_transfer: dict | None = None) → None[source]
                                                                                      +write_input(output_dir: PathLike = '.', make_dir_if_not_present: bool = True, cif_name: str | None = None, zip_name: str | None = None, files_to_transfer: dict | None = None) → None[source]

                                                                                      Write VASP inputs to a directory.

                                                                                      Parameters:
                                                                                      @@ -2334,7 +2334,7 @@

                                                                                      Submodules
                                                                                      -class DielectricFunctionCalculator(cder_real: NDArray, cder_imag: NDArray, eigs: NDArray, kweights: NDArray, nedos: int, deltae: float, ismear: int, sigma: float, efermi: float, cshift: float, ispin: int, volume: float)[source]
                                                                                      +class DielectricFunctionCalculator(cder_real: NDArray, cder_imag: NDArray, eigs: NDArray, kweights: NDArray, nedos: int, deltae: float, ismear: int, sigma: float, efermi: float, cshift: float, ispin: int, volume: float)[source]

                                                                                      Bases: MSONable

                                                                                      Post-process VASP optical properties calculations.

                                                                                      This objects helps load the different parameters from the vasprun.xml file but allows users to override @@ -2358,50 +2358,50 @@

                                                                                      Submodules
                                                                                      -property cder[source]
                                                                                      +property cder[source]

                                                                                      Complex CDER from WAVEDER.

                                                                                      -cder_imag: NDArray[source]
                                                                                      +cder_imag: NDArray[source]
                                                                                      -cder_real: NDArray[source]
                                                                                      +cder_real: NDArray[source]
                                                                                      -cshift: float[source]
                                                                                      +cshift: float[source]
                                                                                      -deltae: float[source]
                                                                                      +deltae: float[source]
                                                                                      -efermi: float[source]
                                                                                      +efermi: float[source]
                                                                                      -eigs: NDArray[source]
                                                                                      +eigs: NDArray[source]
                                                                                      -classmethod from_directory(directory: PathLike) → Self[source]
                                                                                      +classmethod from_directory(directory: PathLike) → Self[source]

                                                                                      Construct a DielectricFunction from a directory containing vasprun.xml and WAVEDER files.

                                                                                      -classmethod from_vasp_objects(vrun: Vasprun, waveder: Waveder) → Self[source]
                                                                                      +classmethod from_vasp_objects(vrun: Vasprun, waveder: Waveder) → Self[source]

                                                                                      Construct a DielectricFunction from Vasprun, Kpoint, and Waveder.

                                                                                      Parameters:
                                                                                      @@ -2416,7 +2416,7 @@

                                                                                      Submodules
                                                                                      -get_epsilon(idir: int, jdir: int, efermi: float | None = None, nedos: int | None = None, deltae: float | None = None, ismear: int | None = None, sigma: float | None = None, cshift: float | None = None, mask: NDArray | None = None) → tuple[NDArray, NDArray][source]
                                                                                      +get_epsilon(idir: int, jdir: int, efermi: float | None = None, nedos: int | None = None, deltae: float | None = None, ismear: int | None = None, sigma: float | None = None, cshift: float | None = None, mask: NDArray | None = None) → tuple[NDArray, NDArray][source]

                                                                                      Compute the frequency dependent dielectric function.

                                                                                      Parameters:
                                                                                      @@ -2437,27 +2437,27 @@

                                                                                      Submodules
                                                                                      -ismear: int[source]
                                                                                      +ismear: int[source]

                                                                                      -ispin: int[source]
                                                                                      +ispin: int[source]
                                                                                      -kweights: NDArray[source]
                                                                                      +kweights: NDArray[source]
                                                                                      -nedos: int[source]
                                                                                      +nedos: int[source]
                                                                                      -plot_weighted_transition_data(idir: int, jdir: int, mask: NDArray | None = None, min_val: float = 0.0)[source]
                                                                                      +plot_weighted_transition_data(idir: int, jdir: int, mask: NDArray | None = None, min_val: float = 0.0)[source]

                                                                                      Data for plotting the weight matrix elements as a scatter plot.

                                                                                      Since the computation of the final spectrum (especially the smearing part) is still fairly expensive. This function can be used to check the values @@ -2479,25 +2479,25 @@

                                                                                      Submodules
                                                                                      -sigma: float[source]
                                                                                      +sigma: float[source]

                                                                                      -volume: float[source]
                                                                                      +volume: float[source]

                                                                                      -delta_func(x: NDArray, ismear: int) → NDArray[source]
                                                                                      +delta_func(x: NDArray, ismear: int) → NDArray[source]

                                                                                      Replication of VASP’s delta function.

                                                                                      -delta_methfessel_paxton(x: NDArray, n: int) → NDArray[source]
                                                                                      +delta_methfessel_paxton(x: NDArray, n: int) → NDArray[source]

                                                                                      D_n (x) = exp -x^2 * sum_i=0^n A_i H_2i(x) where H is a Hermite polynomial and A_i = (-1)^i / ( i! 4^i sqrt(pi) ).

                                                                                      @@ -2505,7 +2505,7 @@

                                                                                      Submodules
                                                                                      -epsilon_imag(cder: NDArray, eigs: NDArray, kweights: ArrayLike, efermi: float, nedos: int, deltae: float, ismear: int, sigma: float, idir: int, jdir: int, mask: NDArray | None = None) → tuple[NDArray, NDArray][source]
                                                                                      +epsilon_imag(cder: NDArray, eigs: NDArray, kweights: ArrayLike, efermi: float, nedos: int, deltae: float, ismear: int, sigma: float, idir: int, jdir: int, mask: NDArray | None = None) → tuple[NDArray, NDArray][source]

                                                                                      Replicate the EPSILON_IMAG function of VASP.

                                                                                      Parameters:
                                                                                      @@ -2534,7 +2534,7 @@

                                                                                      Submodules
                                                                                      -get_delta(x0: float, sigma: float, nx: int, dx: float, ismear: int = 3) → NDArray[source]
                                                                                      +get_delta(x0: float, sigma: float, nx: int, dx: float, ismear: int = 3) → NDArray[source]

                                                                                      Get the smeared delta function to be added to form the spectrum.

                                                                                      This replaces the SLOT function from VASP. Uses finite differences instead of evaluating the delta function since the step function is more likely to have analytic form.

                                                                                      @@ -2559,7 +2559,7 @@

                                                                                      Submodules
                                                                                      -get_step(x0: float, sigma: float, nx: int, dx: float, ismear: int) → float[source]
                                                                                      +get_step(x0: float, sigma: float, nx: int, dx: float, ismear: int) → float[source]

                                                                                      Get the smeared step function to be added to form the spectrum.

                                                                                      This replaces the SLOT function from VASP.

                                                                                      @@ -2583,7 +2583,7 @@

                                                                                      Submodules
                                                                                      -kramers_kronig(eps: NDArray, nedos: int, deltae: float, cshift: float = 0.1) → NDArray[source]
                                                                                      +kramers_kronig(eps: NDArray, nedos: int, deltae: float, cshift: float = 0.1) → NDArray[source]

                                                                                      Perform the Kramers-Kronig transformation.

                                                                                      Perform the Kramers-Kronig transformation exactly as VASP does it. The input eps should be complex and the imaginary part of the dielectric function @@ -2610,13 +2610,13 @@

                                                                                      Submodules
                                                                                      -step_func(x: NDArray, ismear: int) → NDArray[source]
                                                                                      +step_func(x: NDArray, ismear: int) → NDArray[source]

                                                                                      Replication of VASP’s step function.

                                                                                      -step_methfessel_paxton(x: NDArray, n: int) → NDArray[source]
                                                                                      +step_methfessel_paxton(x: NDArray, n: int) → NDArray[source]

                                                                                      S_n (x) = (1 + erf x)/2 - exp -x^2 * sum_i=1^n A_i H_{2i-1}(x) where H is a Hermite polynomial and A_i = (-1)^i / ( i! 4^i sqrt(pi) ).

                                                                                      @@ -2628,7 +2628,7 @@

                                                                                      Submodules
                                                                                      -class BSVasprun(filename: PathLike, parse_projected_eigen: bool | str = False, parse_potcar_file: bool | str = False, occu_tol: float = 1e-08, separate_spins: bool = False)[source]
                                                                                      +class BSVasprun(filename: PathLike, parse_projected_eigen: bool | str = False, parse_potcar_file: bool | str = False, occu_tol: float = 1e-08, separate_spins: bool = False)[source]

                                                                                      Bases: Vasprun

                                                                                      A highly optimized version of Vasprun that parses only eigenvalues for bandstructures. All other properties like structures, parameters, @@ -2659,7 +2659,7 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      JSON-serializable dict representation.

                                                                                      @@ -2667,7 +2667,7 @@

                                                                                      Submodules
                                                                                      -class Chgcar(poscar: Poscar | Structure, data: dict[str, NDArray], data_aug: NDArray | None = None)[source]
                                                                                      +class Chgcar(poscar: Poscar | Structure, data: dict[str, NDArray], data_aug: NDArray | None = None)[source]

                                                                                      Bases: VolumetricData

                                                                                      CHGCAR file reader.

                                                                                      @@ -2681,7 +2681,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_file(filename: str) → Self[source]
                                                                                      +classmethod from_file(filename: str) → Self[source]

                                                                                      Read a CHGCAR file.

                                                                                      Parameters:
                                                                                      @@ -2695,7 +2695,7 @@

                                                                                      Submodules
                                                                                      -property net_magnetization: float | None[source]
                                                                                      +property net_magnetization: float | None[source]

                                                                                      Net magnetic moment from Chgcar.

                                                                                      @@ -2703,12 +2703,12 @@

                                                                                      Submodules
                                                                                      -class Dynmat(filename: PathLike)[source]
                                                                                      +class Dynmat(filename: PathLike)[source]

                                                                                      Bases: object

                                                                                      DYNMAT file reader.

                                                                                      -data[source]
                                                                                      +data[source]

                                                                                      A nested dict containing the DYNMAT data of the form: [atom <int>][disp <int>][‘dispvec’] =

                                                                                      @@ -2733,7 +2733,7 @@

                                                                                      Submodules
                                                                                      -get_phonon_frequencies() → list[source]
                                                                                      +get_phonon_frequencies() → list[source]

                                                                                      Calculate phonon frequencies.

                                                                                      WARNING: This method is most likely incorrect or suboptimal, hence for demonstration purposes only.

                                                                                      @@ -2741,25 +2741,25 @@

                                                                                      Submodules
                                                                                      -property masses: list[float][source]
                                                                                      +property masses: list[float][source]

                                                                                      The list of atomic masses.

                                                                                      -property natoms: int[source]
                                                                                      +property natoms: int[source]

                                                                                      The number of atoms.

                                                                                      -property ndisps: int[source]
                                                                                      +property ndisps: int[source]

                                                                                      The number of displacements.

                                                                                      -property nspecs: int[source]
                                                                                      +property nspecs: int[source]

                                                                                      The number of species.

                                                                                      @@ -2767,12 +2767,12 @@

                                                                                      Submodules
                                                                                      -class Eigenval(filename: PathLike, occu_tol: float = 1e-08, separate_spins: bool = False)[source]
                                                                                      +class Eigenval(filename: PathLike, occu_tol: float = 1e-08, separate_spins: bool = False)[source]

                                                                                      Bases: object

                                                                                      EIGENVAL file reader.

                                                                                      -filename[source]
                                                                                      +filename[source]

                                                                                      The input file.

                                                                                      Type:
                                                                                      @@ -2783,7 +2783,7 @@

                                                                                      Submodules
                                                                                      -occu_tol[source]
                                                                                      +occu_tol[source]

                                                                                      Tolerance for determining occupation in band properties.

                                                                                      Type:
                                                                                      @@ -2794,7 +2794,7 @@

                                                                                      Submodules
                                                                                      -ispin[source]
                                                                                      +ispin[source]

                                                                                      Spin polarization tag.

                                                                                      Type:
                                                                                      @@ -2805,7 +2805,7 @@

                                                                                      Submodules
                                                                                      -nelect[source]
                                                                                      +nelect[source]

                                                                                      Number of electrons.

                                                                                      Type:
                                                                                      @@ -2816,7 +2816,7 @@

                                                                                      Submodules
                                                                                      -nkpt[source]
                                                                                      +nkpt[source]

                                                                                      Number of kpoints.

                                                                                      Type:
                                                                                      @@ -2827,7 +2827,7 @@

                                                                                      Submodules
                                                                                      -nbands[source]
                                                                                      +nbands[source]

                                                                                      Number of bands.

                                                                                      Type:
                                                                                      @@ -2838,7 +2838,7 @@

                                                                                      Submodules
                                                                                      -kpoints[source]
                                                                                      +kpoints[source]

                                                                                      List of kpoints.

                                                                                      Type:
                                                                                      @@ -2849,7 +2849,7 @@

                                                                                      Submodules
                                                                                      -kpoints_weights[source]
                                                                                      +kpoints_weights[source]

                                                                                      Weights of each kpoint in the BZ, should sum to 1.

                                                                                      Type:
                                                                                      @@ -2860,7 +2860,7 @@

                                                                                      Submodules
                                                                                      -eigenvalues[source]
                                                                                      +eigenvalues[source]

                                                                                      Eigenvalues as a dict of {(spin): np.ndarray(shape=(nkpt, nbands, 2))}. This representation is based on actual ordering in VASP and is meant as an intermediate representation to be converted into proper objects. The kpoint index is 0-based (unlike the 1-based indexing in VASP).

                                                                                      @@ -2886,7 +2886,7 @@

                                                                                      Submodules
                                                                                      -property eigenvalue_band_properties: tuple[float, float, float, bool] | tuple[tuple[float, float], tuple[float, float], tuple[float, float], tuple[bool, bool]][source]
                                                                                      +property eigenvalue_band_properties: tuple[float, float, float, bool] | tuple[tuple[float, float], tuple[float, float], tuple[float, float], tuple[bool, bool]][source]

                                                                                      Band properties from the eigenvalues as a tuple of (band gap, cbm, vbm, is_band_gap_direct). In the case of separate_spins=True, @@ -2899,7 +2899,7 @@

                                                                                      Submodules
                                                                                      -class Elfcar(poscar: Poscar | Structure, data: dict[str, NDArray])[source]
                                                                                      +class Elfcar(poscar: Poscar | Structure, data: dict[str, NDArray])[source]

                                                                                      Bases: VolumetricData

                                                                                      Read an ELFCAR file which contains the Electron Localization Function (ELF).

                                                                                      For ELF, “total” key refers to Spin.up, and “diff” refers to Spin.down.

                                                                                      @@ -2914,7 +2914,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_file(filename: str) → Self[source]
                                                                                      +classmethod from_file(filename: str) → Self[source]

                                                                                      Read a ELFCAR file.

                                                                                      Parameters:
                                                                                      @@ -2928,7 +2928,7 @@

                                                                                      Submodules
                                                                                      -get_alpha() → VolumetricData[source]
                                                                                      +get_alpha() → VolumetricData[source]

                                                                                      Get the parameter alpha where ELF = 1/(1 + alpha^2).

                                                                                      @@ -2936,69 +2936,69 @@

                                                                                      Submodules
                                                                                      -class KpointOptProps(tdos: Dos | None = None, idos: Dos | None = None, pdos: list | None = None, efermi: float | None = None, eigenvalues: dict | None = None, projected_eigenvalues: dict | None = None, projected_magnetisation: ndarray | None = None, kpoints: Kpoints | None = None, actual_kpoints: list | None = None, actual_kpoints_weights: list | None = None, dos_has_errors: bool | None = None)[source]
                                                                                      +class KpointOptProps(tdos: Dos | None = None, idos: Dos | None = None, pdos: list | None = None, efermi: float | None = None, eigenvalues: dict | None = None, projected_eigenvalues: dict | None = None, projected_magnetisation: ndarray | None = None, kpoints: Kpoints | None = None, actual_kpoints: list | None = None, actual_kpoints_weights: list | None = None, dos_has_errors: bool | None = None)[source]

                                                                                      Bases: object

                                                                                      Simple container class to store KPOINTS_OPT data in a separate namespace. Used by Vasprun.

                                                                                      -actual_kpoints: list | None = None[source]
                                                                                      +actual_kpoints: list | None = None[source]
                                                                                      -actual_kpoints_weights: list | None = None[source]
                                                                                      +actual_kpoints_weights: list | None = None[source]
                                                                                      -dos_has_errors: bool | None = None[source]
                                                                                      +dos_has_errors: bool | None = None[source]
                                                                                      -efermi: float | None = None[source]
                                                                                      +efermi: float | None = None[source]
                                                                                      -eigenvalues: dict | None = None[source]
                                                                                      +eigenvalues: dict | None = None[source]
                                                                                      -idos: Dos | None = None[source]
                                                                                      +idos: Dos | None = None[source]
                                                                                      -kpoints: Kpoints | None = None[source]
                                                                                      +kpoints: Kpoints | None = None[source]
                                                                                      -pdos: list | None = None[source]
                                                                                      +pdos: list | None = None[source]
                                                                                      -projected_eigenvalues: dict | None = None[source]
                                                                                      +projected_eigenvalues: dict | None = None[source]
                                                                                      -projected_magnetisation: ndarray | None = None[source]
                                                                                      +projected_magnetisation: ndarray | None = None[source]
                                                                                      -tdos: Dos | None = None[source]
                                                                                      +tdos: Dos | None = None[source]

                                                                                      -class Locpot(poscar: Poscar, data: ndarray, **kwargs)[source]
                                                                                      +class Locpot(poscar: Poscar, data: ndarray, **kwargs)[source]

                                                                                      Bases: VolumetricData

                                                                                      LOCPOT file reader.

                                                                                      @@ -3011,7 +3011,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_file(filename: PathLike, **kwargs) → Self[source]
                                                                                      +classmethod from_file(filename: PathLike, **kwargs) → Self[source]

                                                                                      Read a LOCPOT file.

                                                                                      Parameters:
                                                                                      @@ -3027,7 +3027,7 @@

                                                                                      Submodules
                                                                                      -class Oszicar(filename: PathLike)[source]
                                                                                      +class Oszicar(filename: PathLike)[source]

                                                                                      Bases: object

                                                                                      OSZICAR parser for VASP.

                                                                                      In general, while OSZICAR is useful for a quick look at the @@ -3035,7 +3035,7 @@

                                                                                      Submodules
                                                                                      -electronic_steps[source]
                                                                                      +electronic_steps[source]

                                                                                      All electronic steps as a list of list of dict. e.g. [[{“rms”: 160.0, “E”: 4507.24605593, “dE”: 4507.2, “N”: 1, “deps”: -17777.0, “ncg”: 16576}, …], [….] where electronic_steps[index] refers the list of electronic steps in one ionic_step, @@ -3051,7 +3051,7 @@

                                                                                      Submodules
                                                                                      -ionic_steps[source]
                                                                                      +ionic_steps[source]

                                                                                      All ionic_steps as a list of dict, e.g. [{“dE”: -526.36, “E0”: -526.36024, “mag”: 0.0, “F”: -526.36024}, …] This is the typical output from VASP at the end of each ionic step. The stored dict might be different @@ -3070,7 +3070,7 @@

                                                                                      Submodules
                                                                                      -property all_energies: tuple[tuple[float | str, ...], ...][source]
                                                                                      +property all_energies: tuple[tuple[float | str, ...], ...][source]

                                                                                      Compilation of all energies from all electronic steps and ionic steps as a tuple of list of energies, e.g. ((4507.24605593, 143.824705755, -512.073149912, …), …).

                                                                                      @@ -3078,20 +3078,20 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[str, list][source]
                                                                                      +as_dict() → dict[str, list][source]

                                                                                      MSONable dict.

                                                                                      -property final_energy[source]
                                                                                      +property final_energy[source]

                                                                                      -class Outcar(filename: PathLike)[source]
                                                                                      +class Outcar(filename: PathLike)[source]

                                                                                      Bases: object

                                                                                      Parser for data in OUTCAR that is not available in Vasprun.xml.

                                                                                      Note, this class works a bit differently than most of the other @@ -3101,7 +3101,7 @@

                                                                                      Submodules
                                                                                      -magnetization[source]
                                                                                      +magnetization[source]

                                                                                      Magnetization on each ion as a tuple of dict, e.g. ({“d”: 0.0, “p”: 0.003, “s”: 0.002, “tot”: 0.005}, … )

                                                                                      @@ -3113,7 +3113,7 @@

                                                                                      Submodules
                                                                                      -chemical_shielding[source]
                                                                                      +chemical_shielding[source]

                                                                                      Chemical shielding on each ion as a dictionary with core and valence contributions.

                                                                                      Type:
                                                                                      @@ -3124,7 +3124,7 @@

                                                                                      Submodules
                                                                                      -unsym_cs_tensor[source]
                                                                                      +unsym_cs_tensor[source]

                                                                                      Unsymmetrized chemical shielding tensor matrixes on each ion as a list. e.g. [[[sigma11, sigma12, sigma13], [sigma21, sigma22, sigma23], [sigma31, sigma32, sigma33]], …]

                                                                                      @@ -3136,7 +3136,7 @@

                                                                                      Submodules
                                                                                      -cs_g0_contribution[source]
                                                                                      +cs_g0_contribution[source]

                                                                                      G=0 contribution to chemical shielding. 2D rank 3 matrix.

                                                                                      Type:
                                                                                      @@ -3147,7 +3147,7 @@

                                                                                      Submodules
                                                                                      -cs_core_contribution[source]
                                                                                      +cs_core_contribution[source]

                                                                                      Core contribution to chemical shielding. dict. e.g. {‘Mg’: -412.8, ‘C’: -200.5, ‘O’: -271.1}

                                                                                      @@ -3159,7 +3159,7 @@

                                                                                      Submodules
                                                                                      -efg[source]
                                                                                      +efg[source]

                                                                                      Electric Field Gradient (EFG) tensor on each ion as a tuple of dict, e.g. ({“cq”: 0.1, “eta”, 0.2, “nuclear_quadrupole_moment”: 0.3}, {“cq”: 0.7, “eta”, 0.8, “nuclear_quadrupole_moment”: 0.9}, …)

                                                                                      @@ -3172,7 +3172,7 @@

                                                                                      Submodules
                                                                                      -charge[source]
                                                                                      +charge[source]

                                                                                      Charge on each ion as a tuple of dict, e.g. ({“p”: 0.154, “s”: 0.078, “d”: 0.0, “tot”: 0.232}, …)

                                                                                      @@ -3184,7 +3184,7 @@

                                                                                      Submodules
                                                                                      -is_stopped[source]
                                                                                      +is_stopped[source]

                                                                                      True if OUTCAR is from a stopped run (using STOPCAR, see VASP Manual).

                                                                                      Type:
                                                                                      @@ -3195,7 +3195,7 @@

                                                                                      Submodules
                                                                                      -run_stats[source]
                                                                                      +run_stats[source]

                                                                                      Various useful run stats as a dict including “System time (sec)”, “Total CPU time used (sec)”, “Elapsed time (sec)”, “Maximum memory used (kb)”, “Average memory used (kb)”, “User time (sec)”, “cores”.

                                                                                      @@ -3207,7 +3207,7 @@

                                                                                      Submodules
                                                                                      -elastic_tensor[source]
                                                                                      +elastic_tensor[source]

                                                                                      Total elastic moduli (Kbar) is given in a 6x6 array matrix.

                                                                                      Type:
                                                                                      @@ -3218,7 +3218,7 @@

                                                                                      Submodules
                                                                                      -drift[source]
                                                                                      +drift[source]

                                                                                      Total drift for each step in eV/Atom.

                                                                                      Type:
                                                                                      @@ -3229,7 +3229,7 @@

                                                                                      Submodules
                                                                                      -ngf[source]
                                                                                      +ngf[source]

                                                                                      Dimensions for the Augmentation grid.

                                                                                      Type:
                                                                                      @@ -3240,7 +3240,7 @@

                                                                                      Submodules
                                                                                      -sampling_radii[source]
                                                                                      +sampling_radii[source]

                                                                                      Size of the sampling radii in VASP for the test charges for the electrostatic potential at each atom. Total array size is the number of elements present in the calculation.

                                                                                      @@ -3252,7 +3252,7 @@

                                                                                      Submodules
                                                                                      -electrostatic_potential[source]
                                                                                      +electrostatic_potential[source]

                                                                                      Average electrostatic potential at each atomic position in order of the atoms in POSCAR.

                                                                                      @@ -3264,7 +3264,7 @@

                                                                                      Submodules
                                                                                      -final_energy_contribs[source]
                                                                                      +final_energy_contribs[source]

                                                                                      Individual contributions to the total final energy as a dictionary. Include contributions from keys, e.g.: {‘DENC’: -505778.5184347, ‘EATOM’: 15561.06492564, ‘EBANDS’: -804.53201231, ‘EENTRO’: -0.08932659, @@ -3279,7 +3279,7 @@

                                                                                      Submodules
                                                                                      -efermi[source]
                                                                                      +efermi[source]

                                                                                      Fermi energy.

                                                                                      Type:
                                                                                      @@ -3290,7 +3290,7 @@

                                                                                      Submodules
                                                                                      -filename[source]
                                                                                      +filename[source]

                                                                                      Filename.

                                                                                      Type:
                                                                                      @@ -3301,7 +3301,7 @@

                                                                                      Submodules
                                                                                      -final_energy[source]
                                                                                      +final_energy[source]

                                                                                      Final energy after extrapolation of sigma back to 0, i.e. energy(sigma->0).

                                                                                      Type:
                                                                                      @@ -3312,7 +3312,7 @@

                                                                                      Submodules
                                                                                      -final_energy_wo_entrp[source]
                                                                                      +final_energy_wo_entrp[source]

                                                                                      Final energy before extrapolation of sigma, i.e. energy without entropy.

                                                                                      Type:
                                                                                      @@ -3323,7 +3323,7 @@

                                                                                      Submodules
                                                                                      -final_fr_energy[source]
                                                                                      +final_fr_energy[source]

                                                                                      Final “free energy”, i.e. free energy TOTEN.

                                                                                      Type:
                                                                                      @@ -3334,7 +3334,7 @@

                                                                                      Submodules
                                                                                      -has_onsite_density_matrices[source]
                                                                                      +has_onsite_density_matrices[source]

                                                                                      Boolean for if onsite density matrices have been set.

                                                                                      Type:
                                                                                      @@ -3345,7 +3345,7 @@

                                                                                      Submodules
                                                                                      -lcalcpol[source]
                                                                                      +lcalcpol[source]

                                                                                      If LCALCPOL has been set.

                                                                                      Type:
                                                                                      @@ -3356,7 +3356,7 @@

                                                                                      Submodules
                                                                                      -lepsilon[source]
                                                                                      +lepsilon[source]

                                                                                      If LEPSILON has been set.

                                                                                      Type:
                                                                                      @@ -3367,7 +3367,7 @@

                                                                                      Submodules
                                                                                      -nelect[source]
                                                                                      +nelect[source]

                                                                                      Returns the number of electrons in the calculation.

                                                                                      Type:
                                                                                      @@ -3378,7 +3378,7 @@

                                                                                      Submodules
                                                                                      -spin[source]
                                                                                      +spin[source]

                                                                                      If spin-polarization was enabled via ISPIN.

                                                                                      Type:
                                                                                      @@ -3389,7 +3389,7 @@

                                                                                      Submodules
                                                                                      -total_mag[source]
                                                                                      +total_mag[source]

                                                                                      Total magnetization (in terms of the number of unpaired electrons).

                                                                                      Type:
                                                                                      @@ -3410,13 +3410,13 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      MSONable dict.

                                                                                      -read_avg_core_poten() → list[list][source]
                                                                                      +read_avg_core_poten() → list[list][source]

                                                                                      Read the core potential at each ionic step.

                                                                                      Returns:
                                                                                      @@ -3431,7 +3431,7 @@

                                                                                      Submodules
                                                                                      -read_chemical_shielding() → None[source]
                                                                                      +read_chemical_shielding() → None[source]

                                                                                      Parse the NMR chemical shieldings data. Only the second part “absolute, valence and core” will be parsed. And only the three right most field (ISO_SHIELDING, SPAN, SKEW) will be retrieved.

                                                                                      @@ -3442,7 +3442,7 @@

                                                                                      Submodules
                                                                                      -read_core_state_eigen() → list[dict][source]
                                                                                      +read_core_state_eigen() → list[dict][source]

                                                                                      Read the core state eigenenergies at each ionic step.

                                                                                      Returns:
                                                                                      @@ -3461,7 +3461,7 @@

                                                                                      Submodules
                                                                                      -read_corrections(reverse: bool = True, terminate_on_match: bool = True) → None[source]
                                                                                      +read_corrections(reverse: bool = True, terminate_on_match: bool = True) → None[source]

                                                                                      Read the dipol qudropol corrections into self.data[“dipol_quadrupol_correction”].

                                                                                      @@ -3476,7 +3476,7 @@

                                                                                      Submodules
                                                                                      -read_cs_core_contribution() → None[source]
                                                                                      +read_cs_core_contribution() → None[source]

                                                                                      Parse the core contribution of NMR chemical shielding.

                                                                                      Set self.data[“cs_core_contribution”] as:

                                                                                      list[list]: G0 contribution matrix.

                                                                                      @@ -3486,7 +3486,7 @@

                                                                                      Submodules
                                                                                      -read_cs_g0_contribution() → None[source]
                                                                                      +read_cs_g0_contribution() → None[source]

                                                                                      Parse the G0 contribution of NMR chemical shielding.

                                                                                      Set self.data[“cs_g0_contribution”] as:

                                                                                      list[list]: G0 contribution matrix.

                                                                                      @@ -3496,7 +3496,7 @@

                                                                                      Submodules
                                                                                      -read_cs_raw_symmetrized_tensors() → None[source]
                                                                                      +read_cs_raw_symmetrized_tensors() → None[source]

                                                                                      Parse the matrix form of NMR tensor before corrected to table.

                                                                                      Returns:
                                                                                      @@ -3507,7 +3507,7 @@

                                                                                      Submodules
                                                                                      -read_elastic_tensor() → None[source]
                                                                                      +read_elastic_tensor() → None[source]

                                                                                      Parse the elastic tensor data.

                                                                                      Set self.data[“elastic_tensor”] as:

                                                                                      6x6 array corresponding to the elastic tensor from the OUTCAR.

                                                                                      @@ -3517,13 +3517,13 @@

                                                                                      Submodules
                                                                                      -read_electrostatic_potential() → None[source]
                                                                                      +read_electrostatic_potential() → None[source]

                                                                                      Parse the eletrostatic potential for the last ionic step.

                                                                                      -read_fermi_contact_shift() → None[source]
                                                                                      +read_fermi_contact_shift() → None[source]

                                                                                      Read Fermi contact (isotropic) hyperfine coupling parameter.

                                                                                      Output example: Fermi contact (isotropic) hyperfine coupling parameter (MHz) @@ -3543,7 +3543,7 @@

                                                                                      Submodules
                                                                                      -read_freq_dielectric() → None[source]
                                                                                      +read_freq_dielectric() → None[source]

                                                                                      Parse the frequency dependent dielectric function (obtained with LOPTICS). Frequencies (in eV) are in self.frequencies, and dielectric tensor function is given as self.dielectric_tensor_function.

                                                                                      @@ -3551,7 +3551,7 @@

                                                                                      Submodules
                                                                                      -read_igpar() → None[source]
                                                                                      +read_igpar() → None[source]

                                                                                      Read IGPAR.

                                                                                      See VASP sections “LBERRY, IGPAR, NPPSTR, DIPOL” for info on what these are.

                                                                                      @@ -3568,7 +3568,7 @@

                                                                                      Submodules
                                                                                      -read_internal_strain_tensor()[source]
                                                                                      +read_internal_strain_tensor()[source]

                                                                                      Read the internal strain tensor and populates self.internal_strain_tensor with an array of voigt notation tensors for each site.

                                                                                      @@ -3576,28 +3576,28 @@

                                                                                      Submodules
                                                                                      -read_lcalcpol() → None[source]
                                                                                      +read_lcalcpol() → None[source]

                                                                                      Read the LCALCPOL.

                                                                                      TODO: Document the actual variables.

                                                                                      -read_lepsilon() → None[source]
                                                                                      +read_lepsilon() → None[source]

                                                                                      Read a LEPSILON run.

                                                                                      TODO: Document the actual variables.

                                                                                      -read_lepsilon_ionic() → None[source]
                                                                                      +read_lepsilon_ionic() → None[source]

                                                                                      Read the ionic component of a LEPSILON run.

                                                                                      TODO: Document the actual variables.

                                                                                      -read_neb(reverse: bool = True, terminate_on_match: bool = True) → None[source]
                                                                                      +read_neb(reverse: bool = True, terminate_on_match: bool = True) → None[source]

                                                                                      Read NEB data. This only works with OUTCARs from both normal VASP NEB calculations or from the CI NEB method implemented by Henkelman et al.

                                                                                      @@ -3624,7 +3624,7 @@

                                                                                      Submodules
                                                                                      -read_nmr_efg() → None[source]
                                                                                      +read_nmr_efg() → None[source]

                                                                                      Parse the NMR Electric Field Gradient interpreted values.

                                                                                      Set self.data[“efg”] as:

                                                                                      Electric Field Gradient tensors as a list of dict in the order of atoms from OUTCAR. @@ -3635,7 +3635,7 @@

                                                                                      Submodules
                                                                                      -read_nmr_efg_tensor() → list[NDArray][source]
                                                                                      +read_nmr_efg_tensor() → list[NDArray][source]

                                                                                      Parses the NMR Electric Field Gradient Raw Tensors.

                                                                                      Returns:
                                                                                      @@ -3646,7 +3646,7 @@

                                                                                      Submodules
                                                                                      -read_onsite_density_matrices() → None[source]
                                                                                      +read_onsite_density_matrices() → None[source]

                                                                                      Parse the onsite density matrices.

                                                                                      Set self.data[“onsite_density_matrices”] as:

                                                                                      List with index corresponding to atom index in Structure.

                                                                                      @@ -3656,7 +3656,7 @@

                                                                                      Submodules
                                                                                      -read_pattern(patterns: dict[str, str], reverse: bool = False, terminate_on_match: bool = False, postprocess: Callable = <class 'str'>) → None[source]
                                                                                      +read_pattern(patterns: dict[str, str], reverse: bool = False, terminate_on_match: bool = False, postprocess: Callable = <class 'str'>) → None[source]

                                                                                      General pattern reading. Use monty’s regrep method and take the same arguments.

                                                                                      @@ -3686,19 +3686,19 @@

                                                                                      Submodules
                                                                                      -read_piezo_tensor() → None[source]
                                                                                      +read_piezo_tensor() → None[source]

                                                                                      Parse the piezo tensor data.

                                                                                      -read_pseudo_zval() → None[source]
                                                                                      +read_pseudo_zval() → None[source]

                                                                                      Create a pseudopotential ZVAL dictionary.

                                                                                      -read_table_pattern(header_pattern: str, row_pattern: str, footer_pattern: str, postprocess: Callable = <class 'str'>, attribute_name: str | None = None, last_one_only: bool = True, first_one_only: bool = False) → list[source]
                                                                                      +read_table_pattern(header_pattern: str, row_pattern: str, footer_pattern: str, postprocess: Callable = <class 'str'>, attribute_name: str | None = None, last_one_only: bool = True, first_one_only: bool = False) → list[source]
                                                                                      Parse table-like data. A table composes of three parts: header,

                                                                                      main body, footer. All the data matches “row pattern” in the main body will be returned.

                                                                                      @@ -3753,12 +3753,12 @@

                                                                                      Submodules
                                                                                      -class Procar(filename: PathLike)[source]
                                                                                      +class Procar(filename: PathLike)[source]

                                                                                      Bases: object

                                                                                      PROCAR file reader.

                                                                                      -data[source]
                                                                                      +data[source]

                                                                                      The PROCAR data of the form below. It should VASP uses 1-based indexing, but all indices are converted to 0-based here. { spin: nd.array accessed with (k-point index, band index, ion index, orbital index) }

                                                                                      @@ -3771,7 +3771,7 @@

                                                                                      Submodules
                                                                                      -weights[source]
                                                                                      +weights[source]

                                                                                      The weights associated with each k-point as an nd.array of length nkpoints.

                                                                                      Type:
                                                                                      @@ -3782,7 +3782,7 @@

                                                                                      Submodules
                                                                                      -phase_factors[source]
                                                                                      +phase_factors[source]

                                                                                      Phase factors, where present (e.g. LORBIT = 12). A dict of the form: { spin: complex nd.array accessed with (k-point index, band index, ion index, orbital index) }

                                                                                      @@ -3794,7 +3794,7 @@

                                                                                      Submodules
                                                                                      -nbands[source]
                                                                                      +nbands[source]

                                                                                      Number of bands.

                                                                                      Type:
                                                                                      @@ -3805,7 +3805,7 @@

                                                                                      Submodules
                                                                                      -nkpoints[source]
                                                                                      +nkpoints[source]

                                                                                      Number of k-points.

                                                                                      Type:
                                                                                      @@ -3816,7 +3816,7 @@

                                                                                      Submodules
                                                                                      -nions[source]
                                                                                      +nions[source]

                                                                                      Number of ions.

                                                                                      Type:
                                                                                      @@ -3832,7 +3832,7 @@

                                                                                      Submodules
                                                                                      -get_occupation(atom_index: int, orbital: str) → dict[source]
                                                                                      +get_occupation(atom_index: int, orbital: str) → dict[source]

                                                                                      Get the occupation for a particular orbital of a particular atom.

                                                                                      Parameters:
                                                                                      @@ -3856,7 +3856,7 @@

                                                                                      Submodules
                                                                                      -get_projection_on_elements(structure: Structure) → dict[Spin, list][source]
                                                                                      +get_projection_on_elements(structure: Structure) → dict[Spin, list][source]

                                                                                      Get a dict of projections on elements.

                                                                                      Parameters:
                                                                                      @@ -3875,21 +3875,21 @@

                                                                                      Submodules
                                                                                      -exception UnconvergedVASPWarning[source]
                                                                                      +exception UnconvergedVASPWarning[source]

                                                                                      Bases: Warning

                                                                                      Warning for unconverged VASP run.

                                                                                      -exception VaspParseError[source]
                                                                                      +exception VaspParseError[source]

                                                                                      Bases: ParseError

                                                                                      Exception class for VASP parsing.

                                                                                      -class Vasprun(filename: PathLike, ionic_step_skip: int | None = None, ionic_step_offset: int = 0, parse_dos: bool = True, parse_eigen: bool = True, parse_projected_eigen: bool = False, parse_potcar_file: PathLike | bool = True, occu_tol: float = 1e-08, separate_spins: bool = False, exception_on_bad_xml: bool = True)[source]
                                                                                      +class Vasprun(filename: PathLike, ionic_step_skip: int | None = None, ionic_step_offset: int = 0, parse_dos: bool = True, parse_eigen: bool = True, parse_projected_eigen: bool = False, parse_potcar_file: PathLike | bool = True, occu_tol: float = 1e-08, separate_spins: bool = False, exception_on_bad_xml: bool = True)[source]

                                                                                      Bases: MSONable

                                                                                      Vastly improved cElementTree-based parser for vasprun.xml files. Uses iterparse to support incremental parsing of large files. @@ -3898,7 +3898,7 @@

                                                                                      Submodules
                                                                                      -ionic_steps[source]
                                                                                      +ionic_steps[source]

                                                                                      All ionic steps in the run as a list of {“structure”: structure at end of run, “electronic_steps”: {All electronic step data in vasprun file}, “stresses”: stress matrix}.

                                                                                      @@ -3910,7 +3910,7 @@

                                                                                      Submodules
                                                                                      -tdos[source]
                                                                                      +tdos[source]

                                                                                      Total dos calculated at the end of run.

                                                                                      Type:
                                                                                      @@ -3921,7 +3921,7 @@

                                                                                      Submodules
                                                                                      -idos[source]
                                                                                      +idos[source]

                                                                                      Integrated dos calculated at the end of run.

                                                                                      Type:
                                                                                      @@ -3932,7 +3932,7 @@

                                                                                      Submodules
                                                                                      -pdos[source]
                                                                                      +pdos[source]

                                                                                      List of list of PDos objects. Access as pdos[atomindex][orbitalindex].

                                                                                      Type:
                                                                                      @@ -3943,7 +3943,7 @@

                                                                                      Submodules
                                                                                      -efermi[source]
                                                                                      +efermi[source]

                                                                                      Fermi energy.

                                                                                      Type:
                                                                                      @@ -3954,7 +3954,7 @@

                                                                                      Submodules
                                                                                      -eigenvalues[source]
                                                                                      +eigenvalues[source]

                                                                                      Final eigenvalues as a dict of {(spin, kpoint index):[[eigenvalue, occu]]}. The kpoint index is 0-based (unlike the 1-based indexing in VASP).

                                                                                      @@ -3966,7 +3966,7 @@

                                                                                      Submodules
                                                                                      -projected_eigenvalues[source]
                                                                                      +projected_eigenvalues[source]

                                                                                      Final projected eigenvalues as a dict of {spin: nd-array}. To access a particular value, you need to do Vasprun.projected_eigenvalues[spin][kpoint index][band index][atom index][orbital_index]. @@ -3980,7 +3980,7 @@

                                                                                      Submodules
                                                                                      -projected_magnetisation[source]
                                                                                      +projected_magnetisation[source]

                                                                                      Final projected magnetization as a numpy array with the shape (nkpoints, nbands, natoms, norbitals, 3). Where the last axis is the contribution in the 3 Cartesian directions. This attribute is only set if spin-orbit coupling (LSORBIT = True) or @@ -3994,7 +3994,7 @@

                                                                                      Submodules
                                                                                      -other_dielectric[source]
                                                                                      +other_dielectric[source]

                                                                                      Dictionary, with the tag comment as key, containing other variants of the real and imaginary part of the dielectric constant (e.g., computed by RPA) in function of the energy (frequency). Optical properties (e.g. absorption coefficient) can be obtained through this. @@ -4010,7 +4010,7 @@

                                                                                      Submodules
                                                                                      -nionic_steps[source]
                                                                                      +nionic_steps[source]

                                                                                      The total number of ionic steps. This number is always equal to the total number of steps in the actual run even if ionic_step_skip is used.

                                                                                      @@ -4022,7 +4022,7 @@

                                                                                      Submodules
                                                                                      -force_constants[source]
                                                                                      +force_constants[source]

                                                                                      Force constants computed in phonon DFPT run(IBRION = 8). The data is a 4D numpy array of shape (natoms, natoms, 3, 3).

                                                                                      @@ -4034,7 +4034,7 @@

                                                                                      Submodules
                                                                                      -normalmode_eigenvals[source]
                                                                                      +normalmode_eigenvals[source]

                                                                                      Normal mode frequencies. 1D numpy array of size 3*natoms.

                                                                                      Type:
                                                                                      @@ -4045,7 +4045,7 @@

                                                                                      Submodules
                                                                                      -normalmode_eigenvecs[source]
                                                                                      +normalmode_eigenvecs[source]

                                                                                      Normal mode eigen vectors. 3D numpy array of shape (3*natoms, natoms, 3).

                                                                                      Type:
                                                                                      @@ -4056,7 +4056,7 @@

                                                                                      Submodules
                                                                                      -md_data[source]
                                                                                      +md_data[source]

                                                                                      Available only for ML MD runs, i.e., INCAR with ML_LMLFF = .TRUE. md_data is a list of dict with the following format: [{‘energy’: {‘e_0_energy’: -525.07195568, ‘e_fr_energy’: -525.07195568, ‘e_wo_entrp’: -525.07195568, ‘kinetic’: 3.17809233, ‘lattice kinetic’: 0.0, ‘nosekinetic’: 1.323e-5, @@ -4071,7 +4071,7 @@

                                                                                      Submodules
                                                                                      -incar[source]
                                                                                      +incar[source]

                                                                                      Incar object for parameters specified in INCAR file.

                                                                                      Type:
                                                                                      @@ -4082,7 +4082,7 @@

                                                                                      Submodules
                                                                                      -parameters[source]
                                                                                      +parameters[source]

                                                                                      Incar object with parameters that VASP actually used, including all defaults.

                                                                                      Type:
                                                                                      @@ -4093,7 +4093,7 @@

                                                                                      Submodules
                                                                                      -kpoints[source]
                                                                                      +kpoints[source]

                                                                                      Kpoints object for KPOINTS specified in run.

                                                                                      Type:
                                                                                      @@ -4104,7 +4104,7 @@

                                                                                      Submodules
                                                                                      -actual_kpoints[source]
                                                                                      +actual_kpoints[source]

                                                                                      List of actual kpoints, e.g. [[0.25, 0.125, 0.08333333], [-0.25, 0.125, 0.08333333], [0.25, 0.375, 0.08333333], ….].

                                                                                      @@ -4116,7 +4116,7 @@

                                                                                      Submodules
                                                                                      -actual_kpoints_weights[source]
                                                                                      +actual_kpoints_weights[source]

                                                                                      List of kpoint weights, e.g. [0.04166667, 0.04166667, 0.04166667, 0.04166667, 0.04166667, ….].

                                                                                      @@ -4128,7 +4128,7 @@

                                                                                      Submodules
                                                                                      -atomic_symbols[source]
                                                                                      +atomic_symbols[source]

                                                                                      List of atomic symbols, e.g. [“Li”, “Fe”, “Fe”, “P”, “P”, “P”].

                                                                                      Type:
                                                                                      @@ -4139,7 +4139,7 @@

                                                                                      Submodules
                                                                                      -potcar_symbols[source]
                                                                                      +potcar_symbols[source]

                                                                                      List of POTCAR symbols. e.g. [“PAW_PBE Li 17Jan2003”, “PAW_PBE Fe 06Sep2000”, ..].

                                                                                      Type:
                                                                                      @@ -4150,7 +4150,7 @@

                                                                                      Submodules
                                                                                      -kpoints_opt_props[source]
                                                                                      +kpoints_opt_props[source]

                                                                                      Object whose attributes are the data from KPOINTS_OPT (if present, else None). Attributes of the same name have the same format and meaning as Vasprun (or they are None if absent). Attributes are: tdos, idos, pdos, efermi, eigenvalues, projected_eigenvalues, @@ -4214,13 +4214,13 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      JSON-serializable dict representation.

                                                                                      -calculate_efermi(tol: float = 0.001) → float[source]
                                                                                      +calculate_efermi(tol: float = 0.001) → float[source]

                                                                                      Calculate the Fermi level using a robust algorithm.

                                                                                      Sometimes VASP can set the Fermi level inside a band due to issues in the way band occupancies are handled. @@ -4230,13 +4230,13 @@

                                                                                      Submodules
                                                                                      -property complete_dos: CompleteDos[source]
                                                                                      +property complete_dos: CompleteDos[source]

                                                                                      A CompleteDos object which incorporates the total DOS and all projected DOS.

                                                                                      -property complete_dos_normalized: CompleteDos[source]
                                                                                      +property complete_dos_normalized: CompleteDos[source]

                                                                                      A CompleteDos object which incorporates the total DOS and all projected DOS. Normalized by the volume of the unit cell with units of states/eV/unit cell volume.

                                                                                      @@ -4244,20 +4244,20 @@

                                                                                      Submodules
                                                                                      -property converged: bool[source]
                                                                                      +property converged: bool[source]

                                                                                      Whether a relaxation run has both ionically and electronically converged.

                                                                                      -property converged_electronic: bool[source]
                                                                                      +property converged_electronic: bool[source]

                                                                                      Whether electronic step converged in the final ionic step.

                                                                                      -property converged_ionic: bool[source]
                                                                                      +property converged_ionic: bool[source]

                                                                                      Whether ionic step convergence has been reached, i.e. VASP exited before reaching the max ionic steps for a relaxation run. In case IBRION=0 (MD) or EDIFFG=0, returns True if the max ionic @@ -4266,7 +4266,7 @@

                                                                                      Submodules
                                                                                      -property dielectric: tuple[list, list, list][source]
                                                                                      +property dielectric: tuple[list, list, list][source]

                                                                                      The real and imaginary part of the dielectric constant (e.g., computed by RPA) in function of the energy (frequency). Optical properties (e.g. absorption coefficient) can be obtained through this.

                                                                                      @@ -4283,7 +4283,7 @@

                                                                                      Submodules
                                                                                      -property eigenvalue_band_properties: tuple[float, float, float, bool] | tuple[tuple[float, float], tuple[float, float], tuple[float, float], tuple[bool, bool]][source]
                                                                                      +property eigenvalue_band_properties: tuple[float, float, float, bool] | tuple[tuple[float, float], tuple[float, float], tuple[float, float], tuple[bool, bool]][source]

                                                                                      Band properties from the eigenvalues as a tuple, (band gap, cbm, vbm, is_band_gap_direct). In the case of separate_spins=True, the band gap, cbm, vbm, and is_band_gap_direct are each @@ -4293,33 +4293,33 @@

                                                                                      Submodules
                                                                                      -property epsilon_ionic: list[float][source]
                                                                                      +property epsilon_ionic: list[float][source]

                                                                                      The ionic part of the static dielectric constant. Present when it’s a DFPT run (LEPSILON=TRUE) and IBRION=5, 6, 7 or 8.

                                                                                      -property epsilonassets: list[float][source]
                                                                                      +property epsilonassets: list[float][source]

                                                                                      The static part of the dielectric constant. Present only when it’s a DFPT run (LEPSILON=TRUE).

                                                                                      -property epsilonassets_wolfe: list[float][source]
                                                                                      +property epsilonassets_wolfe: list[float][source]

                                                                                      The static part of the dielectric constant without any local field effects. Present only when it’s a DFPT run (LEPSILON=TRUE).

                                                                                      -property final_energy[source]
                                                                                      +property final_energy[source]
                                                                                      -get_band_structure(kpoints_filename: str | None = None, efermi: float | Literal['smart'] | None = None, line_mode: bool = False, force_hybrid_mode: bool = False, ignore_kpoints_opt: bool = False) → BandStructureSymmLine | BandStructure[source]
                                                                                      +get_band_structure(kpoints_filename: str | None = None, efermi: float | Literal['smart'] | None = None, line_mode: bool = False, force_hybrid_mode: bool = False, ignore_kpoints_opt: bool = False) → BandStructureSymmLine | BandStructure[source]

                                                                                      Get the band structure.

                                                                                      Parameters:
                                                                                      @@ -4365,7 +4365,7 @@

                                                                                      Submodules
                                                                                      -get_computed_entry(inc_structure: bool = True, parameters: list[str] | None = None, data: dict | None = None, entry_id: str | None = None) → ComputedStructureEntry | ComputedEntry[source]
                                                                                      +get_computed_entry(inc_structure: bool = True, parameters: list[str] | None = None, data: dict | None = None, entry_id: str | None = None) → ComputedStructureEntry | ComputedEntry[source]

                                                                                      Get a ComputedEntry or ComputedStructureEntry from the Vasprun.

                                                                                      Parameters:
                                                                                      @@ -4390,7 +4390,7 @@

                                                                                      Submodules
                                                                                      -get_potcars(path: PathLike | bool) → Potcar | None[source]
                                                                                      +get_potcars(path: PathLike | bool) → Potcar | None[source]

                                                                                      Get the POTCAR from the specified path.

                                                                                      Parameters:
                                                                                      @@ -4408,7 +4408,7 @@

                                                                                      Submodules
                                                                                      -get_trajectory() → Trajectory[source]
                                                                                      +get_trajectory() → Trajectory[source]

                                                                                      Get a Trajectory, an alternative representation of self.structures as a single object. Forces are added as site properties.

                                                                                      @@ -4420,32 +4420,32 @@

                                                                                      Submodules
                                                                                      -property hubbards: dict[str, float][source]
                                                                                      +property hubbards: dict[str, float][source]

                                                                                      Hubbard U values used for a GGA+U run, otherwise an empty dict.

                                                                                      -property is_hubbard: bool[source]
                                                                                      +property is_hubbard: bool[source]

                                                                                      Whether is a DFT+U run.

                                                                                      -property is_spin: bool[source]
                                                                                      +property is_spin: bool[source]

                                                                                      Whether is spin-polarized.

                                                                                      -property md_n_steps: int[source]
                                                                                      +property md_n_steps: int[source]

                                                                                      Number of steps for MD runs.

                                                                                      Count all the actual MD steps if ML enabled.

                                                                                      -property optical_absorption_coeff: list[float] | None[source]
                                                                                      +property optical_absorption_coeff: list[float] | None[source]

                                                                                      The optical absorption coefficient from the dielectric constants. Note that this method is only implemented for optical properties calculated with GGA and BSE.

                                                                                      @@ -4453,7 +4453,7 @@

                                                                                      Submodules
                                                                                      -property run_type: str[source]
                                                                                      +property run_type: str[source]

                                                                                      The run type. Currently detects GGA, metaGGA, HF, HSE, B3LYP, and hybrid functionals based on relevant INCAR tags. LDA is assigned if PAW POTCARs are used and no other functional is detected.

                                                                                      @@ -4462,13 +4462,13 @@

                                                                                      Submodules
                                                                                      -property structures: list[Structure][source]
                                                                                      +property structures: list[Structure][source]

                                                                                      List of Structures for each ionic step.

                                                                                      -update_charge_from_potcar(path: PathLike | bool) → None[source]
                                                                                      +update_charge_from_potcar(path: PathLike | bool) → None[source]

                                                                                      Update the charge of a structure based on the POTCARs found.

                                                                                      Parameters:
                                                                                      @@ -4479,7 +4479,7 @@

                                                                                      Submodules
                                                                                      -update_potcar_spec(path: PathLike | bool) → None[source]
                                                                                      +update_potcar_spec(path: PathLike | bool) → None[source]

                                                                                      Update the specs based on the POTCARs found.

                                                                                      Parameters:
                                                                                      @@ -4492,7 +4492,7 @@

                                                                                      Submodules
                                                                                      -class VolumetricData(structure: Structure, data: dict[str, ndarray], distance_matrix: ndarray | None = None, data_aug: ndarray | None = None)[source]
                                                                                      +class VolumetricData(structure: Structure, data: dict[str, ndarray], distance_matrix: ndarray | None = None, data_aug: ndarray | None = None)[source]

                                                                                      Bases: VolumetricData

                                                                                      Container for volumetric data that allows for reading/writing with Poscar-type data.

                                                                                      @@ -4514,7 +4514,7 @@

                                                                                      Submodules
                                                                                      -static parse_file(filename: PathLike) → tuple[Poscar, dict, dict][source]
                                                                                      +static parse_file(filename: PathLike) → tuple[Poscar, dict, dict][source]

                                                                                      Parse a generic volumetric data file in the VASP like format. Used by subclasses for parsing files.

                                                                                      @@ -4532,7 +4532,7 @@

                                                                                      Submodules
                                                                                      -write_file(file_name: str | Path, vasp4_compatible: bool = False) → None[source]
                                                                                      +write_file(file_name: str | Path, vasp4_compatible: bool = False) → None[source]

                                                                                      Write the VolumetricData object to a VASP compatible file.

                                                                                      Parameters:
                                                                                      @@ -4548,7 +4548,7 @@

                                                                                      Submodules
                                                                                      -class WSWQ(nspin: int, nkpoints: int, nbands: int, me_real: ndarray, me_imag: ndarray)[source]
                                                                                      +class WSWQ(nspin: int, nkpoints: int, nbands: int, me_real: ndarray, me_imag: ndarray)[source]

                                                                                      Bases: MSONable

                                                                                      Read a WSWQ file. The WSWQ file is used to calculation the wave function overlaps between:

                                                                                      @@ -4574,7 +4574,7 @@

                                                                                      Submodules
                                                                                      -nspin[source]
                                                                                      +nspin[source]

                                                                                      Number of spin channels

                                                                                      Type:
                                                                                      @@ -4585,7 +4585,7 @@

                                                                                      Submodules
                                                                                      -nkpoints[source]
                                                                                      +nkpoints[source]

                                                                                      Number of k-points

                                                                                      Type:
                                                                                      @@ -4596,7 +4596,7 @@

                                                                                      Submodules
                                                                                      -nbands[source]
                                                                                      +nbands[source]

                                                                                      Number of bands

                                                                                      Type:
                                                                                      @@ -4607,7 +4607,7 @@

                                                                                      Submodules
                                                                                      -me_real[source]
                                                                                      +me_real[source]

                                                                                      Real part of the overlap matrix elements

                                                                                      Type:
                                                                                      @@ -4618,7 +4618,7 @@

                                                                                      Submodules
                                                                                      -me_imag[source]
                                                                                      +me_imag[source]

                                                                                      Imaginary part of the overlap matrix elements

                                                                                      Type:
                                                                                      @@ -4629,13 +4629,13 @@

                                                                                      Submodules
                                                                                      -property data: ndarray[source]
                                                                                      +property data: ndarray[source]

                                                                                      Complex overlap matrix.

                                                                                      -classmethod from_file(filename: str) → Self[source]
                                                                                      +classmethod from_file(filename: str) → Self[source]

                                                                                      Construct a WSWQ object from a file.

                                                                                      Parameters:
                                                                                      @@ -4649,34 +4649,34 @@

                                                                                      Submodules
                                                                                      -me_imag: ndarray[source]
                                                                                      +me_imag: ndarray[source]

                                                                                      -me_real: ndarray[source]
                                                                                      +me_real: ndarray[source]
                                                                                      -nbands: int[source]
                                                                                      +nbands: int[source]
                                                                                      -nkpoints: int[source]
                                                                                      +nkpoints: int[source]
                                                                                      -nspin: int[source]
                                                                                      +nspin: int[source]
                                                                                      -class Wavecar(filename: PathLike = 'WAVECAR', verbose: bool = False, precision: Literal['normal', 'accurate'] = 'normal', vasp_type: Literal['std', 'gam', 'ncl'] | None = None)[source]
                                                                                      +class Wavecar(filename: PathLike = 'WAVECAR', verbose: bool = False, precision: Literal['normal', 'accurate'] = 'normal', vasp_type: Literal['std', 'gam', 'ncl'] | None = None)[source]

                                                                                      Bases: object

                                                                                      Container for the (pseudo-) wavefunctions from VASP.

                                                                                      Coefficients are read from the given WAVECAR file and the corresponding @@ -4692,7 +4692,7 @@

                                                                                      Submoduleshttps://doi.org/10.1103/PhysRevMaterials.1.065001).

                                                                                      -vasp_type[source]
                                                                                      +vasp_type[source]

                                                                                      String that determines VASP type the WAVECAR was generated with. One of ‘std’, ‘gam’, ‘ncl’.

                                                                                      @@ -4704,7 +4704,7 @@

                                                                                      Submodules
                                                                                      -nk[source]
                                                                                      +nk[source]

                                                                                      Number of k-points from the WAVECAR.

                                                                                      Type:
                                                                                      @@ -4715,7 +4715,7 @@

                                                                                      Submodules
                                                                                      -nb[source]
                                                                                      +nb[source]

                                                                                      Number of bands per k-point.

                                                                                      Type:
                                                                                      @@ -4726,7 +4726,7 @@

                                                                                      Submodules
                                                                                      -encut[source]
                                                                                      +encut[source]

                                                                                      Energy cutoff (used to define G_{cut}).

                                                                                      Type:
                                                                                      @@ -4737,7 +4737,7 @@

                                                                                      Submodules
                                                                                      -efermi[source]
                                                                                      +efermi[source]

                                                                                      Fermi energy.

                                                                                      Type:
                                                                                      @@ -4748,7 +4748,7 @@

                                                                                      Submodules
                                                                                      -a[source]
                                                                                      +a[source]

                                                                                      Primitive lattice vectors of the cell (e.g. a_1 = self.a[0, :]).

                                                                                      Type:
                                                                                      @@ -4759,7 +4759,7 @@

                                                                                      Submodules
                                                                                      -b[source]
                                                                                      +b[source]

                                                                                      Reciprocal lattice vectors of the cell (e.g. b_1 = self.b[0, :]).

                                                                                      Type:
                                                                                      @@ -4770,7 +4770,7 @@

                                                                                      Submodules
                                                                                      -vol[source]
                                                                                      +vol[source]

                                                                                      The volume of the unit cell in real space.

                                                                                      Type:
                                                                                      @@ -4781,7 +4781,7 @@

                                                                                      Submodules
                                                                                      -kpoints[source]
                                                                                      +kpoints[source]

                                                                                      The list of k-points read from the WAVECAR file.

                                                                                      Type:
                                                                                      @@ -4792,7 +4792,7 @@

                                                                                      Submodules
                                                                                      -band_energy[source]
                                                                                      +band_energy[source]

                                                                                      The list of band eigenenergies (and corresponding occupancies) for each kpoint, where the first index corresponds to the index of the k-point (e.g. self.band_energy[kp]).

                                                                                      @@ -4804,7 +4804,7 @@

                                                                                      Submodules
                                                                                      -Gpoints[source]
                                                                                      +Gpoints[source]

                                                                                      The list of generated G-points for each k-point (a double list), which are used with the coefficients for each k-point and band to recreate the wavefunction (e.g. self.Gpoints[kp] is the list of G-points for @@ -4822,7 +4822,7 @@

                                                                                      Submodules
                                                                                      -coeffs[source]
                                                                                      +coeffs[source]

                                                                                      The list of coefficients for each k-point and band for reconstructing the wavefunction. For non-spin-polarized, the first index corresponds to the kpoint and the second corresponds to the band (e.g. self.coeffs[kp][b] corresponds to k-point kp and band b). For spin-polarized calculations, @@ -4858,7 +4858,7 @@

                                                                                      Submodules
                                                                                      -evaluate_wavefunc(kpoint: int, band: int, r: ndarray, spin: int = 0, spinor: int = 0) → complex64[source]
                                                                                      +evaluate_wavefunc(kpoint: int, band: int, r: ndarray, spin: int = 0, spinor: int = 0) → complex64[source]

                                                                                      Evaluate the wavefunction for a given position, r.

                                                                                      The wavefunction is given by the k-point and band. It is evaluated at the given position by summing over the components. Formally,

                                                                                      @@ -4889,7 +4889,7 @@

                                                                                      Submodules
                                                                                      -fft_mesh(kpoint: int, band: int, spin: int = 0, spinor: int = 0, shift: bool = True) → ndarray[source]
                                                                                      +fft_mesh(kpoint: int, band: int, spin: int = 0, spinor: int = 0, shift: bool = True) → ndarray[source]

                                                                                      Place the coefficients of a wavefunction onto an fft mesh.

                                                                                      Once the mesh has been obtained, a discrete fourier transform can be used to obtain real-space evaluation of the wavefunction. The output @@ -4918,7 +4918,7 @@

                                                                                      Submodules
                                                                                      -get_parchg(poscar: Poscar, kpoint: int, band: int, spin: int | None = None, spinor: int | None = None, phase: bool = False, scale: int = 2) → Chgcar[source]
                                                                                      +get_parchg(poscar: Poscar, kpoint: int, band: int, spin: int | None = None, spinor: int | None = None, phase: bool = False, scale: int = 2) → Chgcar[source]

                                                                                      Generate a Chgcar object, which is the charge density of the specified wavefunction.

                                                                                      This function generates a Chgcar object with the charge density of the @@ -4960,7 +4960,7 @@

                                                                                      Submodules
                                                                                      -write_unks(directory: PathLike) → None[source]
                                                                                      +write_unks(directory: PathLike) → None[source]

                                                                                      Write the UNK files to the given directory.

                                                                                      Write the cell-periodic part of the Bloch wavefunctions from the WAVECAR file to each of the UNK files. There will be one UNK file for @@ -4982,7 +4982,7 @@

                                                                                      Submodules
                                                                                      -class Waveder(cder_real: ndarray, cder_imag: ndarray)[source]
                                                                                      +class Waveder(cder_real: ndarray, cder_imag: ndarray)[source]

                                                                                      Bases: MSONable

                                                                                      Representation of the WAVEDER file.

                                                                                      The LOPTICS tag produces a WAVEDER file which contains the derivative of the orbitals with respect to k. @@ -5009,7 +5009,7 @@

                                                                                      Submodules
                                                                                      -cder_real[source]
                                                                                      +cder_real[source]

                                                                                      Real part of the derivative of the orbitals with respect to k.

                                                                                      Type:
                                                                                      @@ -5020,7 +5020,7 @@

                                                                                      Submodules
                                                                                      -cder_imag[source]
                                                                                      +cder_imag[source]

                                                                                      Imaginary part of the derivative of the orbitals with respect to k.

                                                                                      Type:
                                                                                      @@ -5032,23 +5032,23 @@

                                                                                      Submodules
                                                                                      -property cder: ndarray[source]
                                                                                      +property cder: ndarray[source]

                                                                                      The complex derivative of the orbitals with respect to k.

                                                                                      -cder_imag: ndarray[source]
                                                                                      +cder_imag: ndarray[source]
                                                                                      -cder_real: ndarray[source]
                                                                                      +cder_real: ndarray[source]
                                                                                      -classmethod from_binary(filename: PathLike, data_type: Literal['complex64', 'float64', 'float32'] = 'complex64') → Self[source]
                                                                                      +classmethod from_binary(filename: PathLike, data_type: Literal['complex64', 'float64', 'float32'] = 'complex64') → Self[source]

                                                                                      Read the WAVEDER file.

                                                                                      Parameters:
                                                                                      @@ -5067,7 +5067,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_formatted(filename: PathLike) → Self[source]
                                                                                      +classmethod from_formatted(filename: PathLike) → Self[source]

                                                                                      Read the WAVEDERF file.

                                                                                      Note: This file is only produced when LOPTICS is true and VASP has been recompiled after uncommenting the line that calls @@ -5086,7 +5086,7 @@

                                                                                      Submodules
                                                                                      -get_orbital_derivative_between_states(band_i: int, band_j: int, kpoint: int, spin: Literal[0, 1], cart_dir: Literal[0, 1, 2]) → float[source]
                                                                                      +get_orbital_derivative_between_states(band_i: int, band_j: int, kpoint: int, spin: Literal[0, 1], cart_dir: Literal[0, 1, 2]) → float[source]

                                                                                      Get a float between bands band_i and band_j for k-point index, spin-channel and Cartesian direction.

                                                                                      @@ -5107,19 +5107,19 @@

                                                                                      Submodules
                                                                                      -property nbands: int[source]
                                                                                      +property nbands: int[source]

                                                                                      The number of bands.

                                                                                      -property nkpoints: int[source]
                                                                                      +property nkpoints: int[source]

                                                                                      The number of k-points.

                                                                                      -property nspin: int[source]
                                                                                      +property nspin: int[source]

                                                                                      The number of spin channels.

                                                                                      @@ -5127,12 +5127,12 @@

                                                                                      Submodules
                                                                                      -class Xdatcar(filename: PathLike, ionicstep_start: int = 1, ionicstep_end: int | None = None, comment: str | None = None)[source]
                                                                                      +class Xdatcar(filename: PathLike, ionicstep_start: int = 1, ionicstep_end: int | None = None, comment: str | None = None)[source]

                                                                                      Bases: object

                                                                                      XDATCAR parser. Only tested with VASP 5.x files.

                                                                                      -structures[source]
                                                                                      +structures[source]

                                                                                      List of structures parsed from XDATCAR.

                                                                                      Type:
                                                                                      @@ -5143,7 +5143,7 @@

                                                                                      Submodules
                                                                                      -comment[source]
                                                                                      +comment[source]

                                                                                      Optional comment string.

                                                                                      Type:
                                                                                      @@ -5166,7 +5166,7 @@

                                                                                      Submodules
                                                                                      -concatenate(filename: PathLike, ionicstep_start: int = 1, ionicstep_end: int | None = None) → None[source]
                                                                                      +concatenate(filename: PathLike, ionicstep_start: int = 1, ionicstep_end: int | None = None) → None[source]

                                                                                      Concatenate structures in file to Xdatcar.

                                                                                      Parameters:
                                                                                      @@ -5185,7 +5185,7 @@

                                                                                      Submodules
                                                                                      -get_str(ionicstep_start: int = 1, ionicstep_end: int | None = None, significant_figures: int = 8) → str[source]
                                                                                      +get_str(ionicstep_start: int = 1, ionicstep_end: int | None = None, significant_figures: int = 8) → str[source]

                                                                                      Write Xdatcar to a string.

                                                                                      Parameters:
                                                                                      @@ -5200,21 +5200,21 @@

                                                                                      Submodules
                                                                                      -property natoms: list[int][source]
                                                                                      +property natoms: list[int][source]

                                                                                      Sequence of number of sites of each type associated with the Poscar. Similar to 7th line in VASP 5+ Xdatcar.

                                                                                      -property site_symbols: list[str][source]
                                                                                      +property site_symbols: list[str][source]

                                                                                      Sequence of symbols associated with the Xdatcar. Similar to 6th line in VASP 5+ Xdatcar.

                                                                                      -write_file(filename: PathLike, **kwargs) → None[source]
                                                                                      +write_file(filename: PathLike, **kwargs) → None[source]

                                                                                      Write Xdatcar into a file.

                                                                                      Parameters:
                                                                                      @@ -5231,7 +5231,7 @@

                                                                                      Submodules
                                                                                      -get_adjusted_fermi_level(efermi: float, cbm: float, band_structure: BandStructureSymmLine, energy_step: float = 0.01) → float[source]
                                                                                      +get_adjusted_fermi_level(efermi: float, cbm: float, band_structure: BandStructureSymmLine, energy_step: float = 0.01) → float[source]

                                                                                      When running a band structure computation, the Fermi level needs to be taken from the static run that gave the charge density used for the non-self consistent band structure run. Sometimes this Fermi level is too low @@ -5263,7 +5263,7 @@

                                                                                      Submodules
                                                                                      -get_band_structure_from_vasp_multiple_branches(dir_name: str, efermi: float | None = None, projections: bool = False) → BandStructureSymmLine | BandStructure | None[source]
                                                                                      +get_band_structure_from_vasp_multiple_branches(dir_name: str, efermi: float | None = None, projections: bool = False) → BandStructureSymmLine | BandStructure | None[source]

                                                                                      Get band structure info from a VASP directory.

                                                                                      It takes into account that a run can be divided in several branches named “branch_x”. If the run has not been divided in branches the method will @@ -5314,21 +5314,21 @@

                                                                                      Submodules
                                                                                      -exception BadInputSetWarning[source]
                                                                                      +exception BadInputSetWarning[source]

                                                                                      Bases: UserWarning

                                                                                      Warning class for bad but legal VASP inputs.

                                                                                      -class DictSet(*args, **kwargs)[source]
                                                                                      +class DictSet(*args, **kwargs)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Alias for VaspInputSet.

                                                                                      -class LobsterSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_54', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'), isym: int = 0, ismear: int = -5, reciprocal_density: int | None = None, address_basis_file: str | None = None, user_supplied_basis: dict | None = None)[source]
                                                                                      +class LobsterSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_54', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'), isym: int = 0, ismear: int = -5, reciprocal_density: int | None = None, address_basis_file: str | None = None, user_supplied_basis: dict | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Input set to prepare VASP runs that can be digested by Lobster (See cohp.de).

                                                                                      @@ -5352,56 +5352,56 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -address_basis_file: str | None = None[source]
                                                                                      +address_basis_file: str | None = None[source]
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -ismear: int = -5[source]
                                                                                      +ismear: int = -5[source]
                                                                                      -isym: int = 0[source]
                                                                                      +isym: int = 0[source]
                                                                                      -property kpoints_updates: dict[str, int][source]
                                                                                      +property kpoints_updates: dict[str, int][source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      -reciprocal_density: int | None = None[source]
                                                                                      +reciprocal_density: int | None = None[source]
                                                                                      -user_potcar_functional: UserPotcarFunctional = 'PBE_54'[source]
                                                                                      +user_potcar_functional: UserPotcarFunctional = 'PBE_54'[source]
                                                                                      -user_supplied_basis: dict | None = None[source]
                                                                                      +user_supplied_basis: dict | None = None[source]
                                                                                      -class MITMDSet(structure: Structure | None = None, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, start_temp: float = 0.0, end_temp: float = 300.0, nsteps: int = 1000, time_step: float = 2, spin_polarized: bool = False)[source]
                                                                                      +class MITMDSet(structure: Structure | None = None, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, start_temp: float = 0.0, end_temp: float = 300.0, nsteps: int = 1000, time_step: float = 2, spin_polarized: bool = False)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Write a VASP MD run. This DOES NOT do multiple stage runs.

                                                                                      @@ -5421,56 +5421,56 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -end_temp: float = 300.0[source]
                                                                                      +end_temp: float = 300.0[source]
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -property kpoints_updates: Kpoints[source]
                                                                                      +property kpoints_updates: Kpoints[source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      -nsteps: int = 1000[source]
                                                                                      +nsteps: int = 1000[source]
                                                                                      -spin_polarized: bool = False[source]
                                                                                      +spin_polarized: bool = False[source]
                                                                                      -start_temp: float = 0.0[source]
                                                                                      +start_temp: float = 0.0[source]
                                                                                      -structure: Structure | None = None[source]
                                                                                      +structure: Structure | None = None[source]
                                                                                      -time_step: float = 2[source]
                                                                                      +time_step: float = 2[source]
                                                                                      -class MITNEBSet(structures: list[Structure], unset_encut: bool = False, **kwargs)[source]
                                                                                      +class MITNEBSet(structures: list[Structure], unset_encut: bool = False, **kwargs)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Write NEB inputs.

                                                                                      Note that EDIFF is not on a per atom basis for this input set.

                                                                                      @@ -5485,19 +5485,19 @@

                                                                                      Submodules
                                                                                      -property poscar: Poscar[source]
                                                                                      +property poscar: Poscar[source]

                                                                                      Poscar for structure of first end point.

                                                                                      -property poscars: list[Poscar][source]
                                                                                      +property poscars: list[Poscar][source]

                                                                                      List of Poscars.

                                                                                      -write_input(output_dir: PathLike, make_dir_if_not_present: bool = True, write_cif: bool = False, write_path_cif: bool = False, write_endpoint_inputs: bool = False) → None[source]
                                                                                      +write_input(output_dir: PathLike, make_dir_if_not_present: bool = True, write_cif: bool = False, write_path_cif: bool = False, write_endpoint_inputs: bool = False) → None[source]

                                                                                      NEB inputs has a special directory structure where inputs are in 00, 01, 02, ….

                                                                                      @@ -5520,7 +5520,7 @@

                                                                                      Submodules
                                                                                      -class MITRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
                                                                                      +class MITRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Standard implementation of VaspInputSet utilizing parameters in the MIT High-throughput project. @@ -5545,14 +5545,14 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -class MPAbsorptionSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = True, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, mode: str = 'IPA', copy_wavecar: bool = True, nbands_factor: float = 2, reciprocal_density: float = 400, nkred: Tuple3Ints | None = None, nedos: int = 2001, nbands: int | None = None)[source]
                                                                                      +class MPAbsorptionSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = True, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, mode: str = 'IPA', copy_wavecar: bool = True, nbands_factor: float = 2, reciprocal_density: float = 400, nkred: Tuple3Ints | None = None, nedos: int = 2001, nbands: int | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      MP input set for generating frequency dependent dielectrics.

                                                                                      Two modes are supported: “IPA” or “RPA”. @@ -5586,38 +5586,38 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -SUPPORTED_MODES = ('IPA', 'RPA')[source]
                                                                                      +SUPPORTED_MODES = ('IPA', 'RPA')[source]
                                                                                      -copy_wavecar: bool = True[source]
                                                                                      +copy_wavecar: bool = True[source]
                                                                                      -force_gamma: bool = True[source]
                                                                                      +force_gamma: bool = True[source]
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -inherit_incar: bool = True[source]
                                                                                      +inherit_incar: bool = True[source]
                                                                                      -property kpoints_updates: dict[str, float][source]
                                                                                      +property kpoints_updates: dict[str, float][source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      Generate gamma center k-points mesh grid for optical calculation. It is not mandatory for ‘ALGO = Exact’, but is requested by ‘ALGO = CHI’ calculation.

                                                                                      @@ -5625,39 +5625,39 @@

                                                                                      Submodules
                                                                                      -mode: str = 'IPA'[source]
                                                                                      +mode: str = 'IPA'[source]

                                                                                      -nbands: int | None = None[source]
                                                                                      +nbands: int | None = None[source]
                                                                                      -nbands_factor: float = 2[source]
                                                                                      +nbands_factor: float = 2[source]
                                                                                      -nedos: int = 2001[source]
                                                                                      +nedos: int = 2001[source]
                                                                                      -nkred: Tuple3Ints | None = None[source]
                                                                                      +nkred: Tuple3Ints | None = None[source]
                                                                                      -reciprocal_density: float = 400[source]
                                                                                      +reciprocal_density: float = 400[source]
                                                                                      -class MPHSEBSSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, added_kpoints: list[Vector3D] = <factory>, mode: str = 'gap', reciprocal_density: float = 50, copy_chgcar: bool = True, kpoints_line_density: float = 20, nbands_factor: float = 1.2, zero_weighted_reciprocal_density: float = 100, dedos: float = 0.02, optics: bool = False)[source]
                                                                                      +class MPHSEBSSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, added_kpoints: list[Vector3D] = <factory>, mode: str = 'gap', reciprocal_density: float = 50, copy_chgcar: bool = True, kpoints_line_density: float = 20, nbands_factor: float = 1.2, zero_weighted_reciprocal_density: float = 100, dedos: float = 0.02, optics: bool = False)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Implementation of a VaspInputSet for HSE band structure computations.

                                                                                      Remember that HSE band structures must be self-consistent in VASP. A band structure @@ -5697,83 +5697,83 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'All', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'HFSCREEN': 0.2, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'LHFCALC': True, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'PRECFOCK': 'Fast', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 50}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'All', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'HFSCREEN': 0.2, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'LHFCALC': True, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'PRECFOCK': 'Fast', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 50}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]

                                                                                      -added_kpoints: list[Vector3D][source]
                                                                                      +added_kpoints: list[Vector3D][source]
                                                                                      -copy_chgcar: bool = True[source]
                                                                                      +copy_chgcar: bool = True[source]
                                                                                      -dedos: float = 0.02[source]
                                                                                      +dedos: float = 0.02[source]
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -kpoints_line_density: float = 20[source]
                                                                                      +kpoints_line_density: float = 20[source]
                                                                                      -property kpoints_updates: dict[str, Any][source]
                                                                                      +property kpoints_updates: dict[str, Any][source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      -mode: str = 'gap'[source]
                                                                                      +mode: str = 'gap'[source]
                                                                                      -nbands_factor: float = 1.2[source]
                                                                                      +nbands_factor: float = 1.2[source]
                                                                                      -optics: bool = False[source]
                                                                                      +optics: bool = False[source]
                                                                                      -reciprocal_density: float = 50[source]
                                                                                      +reciprocal_density: float = 50[source]
                                                                                      -zero_weighted_reciprocal_density: float = 100[source]
                                                                                      +zero_weighted_reciprocal_density: float = 100[source]

                                                                                      -class MPHSERelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
                                                                                      +class MPHSERelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Same as the MPRelaxSet, but with HSE parameters.

                                                                                      -CONFIG = {'INCAR': {'ALGO': 'All', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'HFSCREEN': 0.2, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'LHFCALC': True, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'PRECFOCK': 'Fast', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 50}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'All', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'HFSCREEN': 0.2, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'LHFCALC': True, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'PRECFOCK': 'Fast', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 50}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
                                                                                      -class MPMDSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, start_temp: float = 0.0, end_temp: float = 300.0, nsteps: int = 1000, time_step: float | None = None, spin_polarized: bool = False)[source]
                                                                                      +class MPMDSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, start_temp: float = 0.0, end_temp: float = 300.0, nsteps: int = 1000, time_step: float | None = None, spin_polarized: bool = False)[source]

                                                                                      Bases: VaspInputSet

                                                                                      This a modified version of the old MITMDSet pre 2018/03/12.

                                                                                      This set serves as the basis for the amorphous skyline paper.

                                                                                      @@ -5803,69 +5803,69 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -end_temp: float = 300.0[source]
                                                                                      +end_temp: float = 300.0[source]
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -property kpoints_updates: Kpoints[source]
                                                                                      +property kpoints_updates: Kpoints[source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      -nsteps: int = 1000[source]
                                                                                      +nsteps: int = 1000[source]
                                                                                      -spin_polarized: bool = False[source]
                                                                                      +spin_polarized: bool = False[source]
                                                                                      -start_temp: float = 0.0[source]
                                                                                      +start_temp: float = 0.0[source]
                                                                                      -time_step: float | None = None[source]
                                                                                      +time_step: float | None = None[source]

                                                                                      -class MPMetalRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
                                                                                      +class MPMetalRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Implementation of VaspInputSet utilizing parameters in the public Materials Project, but with tuning for metals. Key things are a denser k point density, and a.

                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      -property incar_updates: dict[source]
                                                                                      +property incar_updates: dict[source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -property kpoints_updates: dict[source]
                                                                                      +property kpoints_updates: dict[source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      @@ -5873,7 +5873,7 @@

                                                                                      Submodules
                                                                                      -class MPNMRSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, mode: Literal['cs', 'efg'] = 'cs', isotopes: list = <factory>, reciprocal_density: int = 100, small_gap_multiply: tuple[float, float] | None = None)[source]
                                                                                      +class MPNMRSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, mode: Literal['cs', 'efg'] = 'cs', isotopes: list = <factory>, reciprocal_density: int = 100, small_gap_multiply: tuple[float, float] | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Init a MPNMRSet.

                                                                                      @@ -5901,51 +5901,51 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -inherit_incar: bool = True[source]
                                                                                      +inherit_incar: bool = True[source]
                                                                                      -isotopes: list[source]
                                                                                      +isotopes: list[source]
                                                                                      -property kpoints_updates: dict[str, Any][source]
                                                                                      +property kpoints_updates: dict[str, Any][source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      -mode: Literal['cs', 'efg'] = 'cs'[source]
                                                                                      +mode: Literal['cs', 'efg'] = 'cs'[source]
                                                                                      -reciprocal_density: int = 100[source]
                                                                                      +reciprocal_density: int = 100[source]
                                                                                      -small_gap_multiply: tuple[float, float] | None = None[source]
                                                                                      +small_gap_multiply: tuple[float, float] | None = None[source]

                                                                                      -class MPNonSCFSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, mode: str = 'line', nedos: int = 2001, dedos: float = 0.005, reciprocal_density: float = 100, kpoints_line_density: float = 20, optics: bool = False, copy_chgcar: bool = True, nbands_factor: float = 1.2, small_gap_multiply: tuple[float, float] | None = None)[source]
                                                                                      +class MPNonSCFSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, mode: str = 'line', nedos: int = 2001, dedos: float = 0.005, reciprocal_density: float = 100, kpoints_line_density: float = 20, optics: bool = False, copy_chgcar: bool = True, nbands_factor: float = 1.2, small_gap_multiply: tuple[float, float] | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Init a MPNonSCFSet. Typically, you would use the classmethod from_prev_calc to initialize from a previous SCF run.

                                                                                      @@ -5976,76 +5976,76 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -copy_chgcar: bool = True[source]
                                                                                      +copy_chgcar: bool = True[source]
                                                                                      -dedos: float = 0.005[source]
                                                                                      +dedos: float = 0.005[source]
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -inherit_incar: bool = True[source]
                                                                                      +inherit_incar: bool = True[source]
                                                                                      -kpoints_line_density: float = 20[source]
                                                                                      +kpoints_line_density: float = 20[source]
                                                                                      -property kpoints_updates: dict[str, Any][source]
                                                                                      +property kpoints_updates: dict[str, Any][source]

                                                                                      Updates to the KPOINTS configuration for this calculation type.

                                                                                      -mode: str = 'line'[source]
                                                                                      +mode: str = 'line'[source]
                                                                                      -nbands_factor: float = 1.2[source]
                                                                                      +nbands_factor: float = 1.2[source]
                                                                                      -nedos: int = 2001[source]
                                                                                      +nedos: int = 2001[source]
                                                                                      -optics: bool = False[source]
                                                                                      +optics: bool = False[source]
                                                                                      -reciprocal_density: float = 100[source]
                                                                                      +reciprocal_density: float = 100[source]
                                                                                      -small_gap_multiply: tuple[float, float] | None = None[source]
                                                                                      +small_gap_multiply: tuple[float, float] | None = None[source]

                                                                                      -class MPRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
                                                                                      +class MPRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Implementation of VaspInputSet utilizing parameters in the public Materials Project. Typically, the pseudopotentials chosen contain more @@ -6064,14 +6064,14 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -class MPSOCSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, saxis: Tuple3Ints = (0, 0, 1), nbands_factor: float = 1.2, lepsilon: bool = False, lcalcpol: bool = False, reciprocal_density: float = 100, small_gap_multiply: tuple[float, float] | None = None, magmom: list[Vector3D] | None = None, copy_chgcar: bool = True)[source]
                                                                                      +class MPSOCSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, saxis: Tuple3Ints = (0, 0, 1), nbands_factor: float = 1.2, lepsilon: bool = False, lcalcpol: bool = False, reciprocal_density: float = 100, small_gap_multiply: tuple[float, float] | None = None, magmom: list[Vector3D] | None = None, copy_chgcar: bool = True)[source]

                                                                                      Bases: VaspInputSet

                                                                                      An input set for running spin-orbit coupling (SOC) calculations.

                                                                                      @@ -6098,69 +6098,69 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -copy_chgcar: bool = True[source]
                                                                                      +copy_chgcar: bool = True[source]
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -inherit_incar: bool = True[source]
                                                                                      +inherit_incar: bool = True[source]
                                                                                      -property kpoints_updates: dict[str, Any][source]
                                                                                      +property kpoints_updates: dict[str, Any][source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      -lcalcpol: bool = False[source]
                                                                                      +lcalcpol: bool = False[source]
                                                                                      -lepsilon: bool = False[source]
                                                                                      +lepsilon: bool = False[source]
                                                                                      -magmom: list[Vector3D] | None = None[source]
                                                                                      +magmom: list[Vector3D] | None = None[source]
                                                                                      -nbands_factor: float = 1.2[source]
                                                                                      +nbands_factor: float = 1.2[source]
                                                                                      -reciprocal_density: float = 100[source]
                                                                                      +reciprocal_density: float = 100[source]
                                                                                      -saxis: Tuple3Ints = (0, 0, 1)[source]
                                                                                      +saxis: Tuple3Ints = (0, 0, 1)[source]
                                                                                      -small_gap_multiply: tuple[float, float] | None = None[source]
                                                                                      +small_gap_multiply: tuple[float, float] | None = None[source]
                                                                                      -property structure: Structure | None[source]
                                                                                      +property structure: Structure | None[source]

                                                                                      Structure.

                                                                                      @@ -6168,7 +6168,7 @@

                                                                                      Submodules
                                                                                      -class MPScanRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_54', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = True, auto_ismear: bool = True, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'))[source]
                                                                                      +class MPScanRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_54', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = True, auto_ismear: bool = True, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'))[source]

                                                                                      Bases: VaspInputSet

                                                                                      Write a relaxation input set using the accurate and numerically efficient r2SCAN variant of the Strongly Constrained and Appropriately Normed @@ -6220,34 +6220,34 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'ALL', 'EDIFF': 1e-05, 'EDIFFG': -0.02, 'ENAUG': 1360, 'ENCUT': 680, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'KSPACING': 0.22, 'LAECHG': True, 'LASPH': True, 'LCHARG': True, 'LELF': False, 'LMIXTAU': True, 'LORBIT': 11, 'LREAL': 'Auto', 'LVTOT': True, 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'METAGGA': 'R2SCAN', 'NELM': 200, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cf': 'Cf', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_sv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_3', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'ALL', 'EDIFF': 1e-05, 'EDIFFG': -0.02, 'ENAUG': 1360, 'ENCUT': 680, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'KSPACING': 0.22, 'LAECHG': True, 'LASPH': True, 'LCHARG': True, 'LELF': False, 'LMIXTAU': True, 'LORBIT': 11, 'LREAL': 'Auto', 'LVTOT': True, 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'METAGGA': 'R2SCAN', 'NELM': 200, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cf': 'Cf', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_sv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_3', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]

                                                                                      -auto_ismear: bool = True[source]
                                                                                      +auto_ismear: bool = True[source]
                                                                                      -auto_kspacing: bool = True[source]
                                                                                      +auto_kspacing: bool = True[source]
                                                                                      -bandgap: float | None = None[source]
                                                                                      +bandgap: float | None = None[source]
                                                                                      -user_potcar_functional: UserPotcarFunctional = 'PBE_54'[source]
                                                                                      +user_potcar_functional: UserPotcarFunctional = 'PBE_54'[source]

                                                                                      -class MPScanStaticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_54', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = True, auto_ismear: bool = True, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'), lepsilon: bool = False, lcalcpol: bool = False)[source]
                                                                                      +class MPScanStaticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_54', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = True, auto_ismear: bool = True, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'), lepsilon: bool = False, lcalcpol: bool = False)[source]

                                                                                      Bases: MPScanRelaxSet

                                                                                      Create input files for a static calculation using the accurate and numerically efficient r2SCAN variant of the Strongly Constrained and Appropriately Normed @@ -6267,35 +6267,35 @@

                                                                                      Submodules
                                                                                      -auto_kspacing: bool = True[source]
                                                                                      +auto_kspacing: bool = True[source]

                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -inherit_incar: bool = True[source]
                                                                                      +inherit_incar: bool = True[source]
                                                                                      -lcalcpol: bool = False[source]
                                                                                      +lcalcpol: bool = False[source]
                                                                                      -lepsilon: bool = False[source]
                                                                                      +lepsilon: bool = False[source]
                                                                                      -class MPStaticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, lepsilon: bool = False, lcalcpol: bool = False, reciprocal_density: int = 100, small_gap_multiply: tuple[float, float] | None = None)[source]
                                                                                      +class MPStaticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, lepsilon: bool = False, lcalcpol: bool = False, reciprocal_density: int = 100, small_gap_multiply: tuple[float, float] | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Create input files for a static calculation.

                                                                                      @@ -6318,51 +6318,51 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -property incar_updates: dict[source]
                                                                                      +property incar_updates: dict[source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -inherit_incar: bool = True[source]
                                                                                      +inherit_incar: bool = True[source]
                                                                                      -property kpoints_updates: dict | Kpoints[source]
                                                                                      +property kpoints_updates: dict | Kpoints[source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      -lcalcpol: bool = False[source]
                                                                                      +lcalcpol: bool = False[source]
                                                                                      -lepsilon: bool = False[source]
                                                                                      +lepsilon: bool = False[source]
                                                                                      -reciprocal_density: int = 100[source]
                                                                                      +reciprocal_density: int = 100[source]
                                                                                      -small_gap_multiply: tuple[float, float] | None = None[source]
                                                                                      +small_gap_multiply: tuple[float, float] | None = None[source]
                                                                                      -class MVLElasticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
                                                                                      +class MVLElasticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      MVL denotes VASP input sets that are implemented by the Materials Virtual Lab (http://materialsvirtuallab.org) for various research.

                                                                                      @@ -6388,25 +6388,25 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -potim: float = 0.015[source]
                                                                                      +potim: float = 0.015[source]

                                                                                      -class MVLGBSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, k_product: int = 40, slab_mode: bool = False, is_metal: bool = True)[source]
                                                                                      +class MVLGBSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, k_product: int = 40, slab_mode: bool = False, is_metal: bool = True)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Write a VASP input files for grain boundary calculations, slab or bulk.

                                                                                      @@ -6428,42 +6428,42 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -is_metal: bool = True[source]
                                                                                      +is_metal: bool = True[source]
                                                                                      -k_product: int = 40[source]
                                                                                      +k_product: int = 40[source]
                                                                                      -property kpoints_updates: Kpoints[source]
                                                                                      +property kpoints_updates: Kpoints[source]

                                                                                      k_product is kpoint number * length for a & b directions, also for c direction in bulk calculations Automatic mesh & Gamma is the default setting.

                                                                                      -slab_mode: bool = False[source]
                                                                                      +slab_mode: bool = False[source]
                                                                                      -class MVLGWSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = True, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, reciprocal_density: float = 100, mode: str = 'STATIC', copy_wavecar: bool = True, nbands_factor: int = 5, ncores: int = 16, nbands: int | None = None)[source]
                                                                                      +class MVLGWSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = True, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, reciprocal_density: float = 100, mode: str = 'STATIC', copy_wavecar: bool = True, nbands_factor: int = 5, ncores: int = 16, nbands: int | None = None)[source]

                                                                                      Bases: VaspInputSet

                                                                                      MVL denotes VASP input sets that are implemented by the Materials Virtual Lab (http://materialsvirtuallab.org) for various research. This is a @@ -6503,27 +6503,27 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'Normal', 'EDIFF': 1e-08, 'IBRION': -1, 'ICHARG': 1, 'ISMEAR': 0, 'ISPIN': 2, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': True, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'PREC': 'Accurate', 'SIGMA': 0.01}, 'KPOINTS': {'reciprocal_density': 100}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag_sv_GW', 'Al': 'Al_GW', 'Ar': 'Ar_GW', 'As': 'As_GW', 'At': 'At_d_GW', 'Au': 'Au_sv_GW', 'B': 'B_GW', 'Ba': 'Ba_sv_GW', 'Be': 'Be_sv_GW', 'Bi': 'Bi_d_GW', 'Br': 'Br_GW', 'C': 'C_GW', 'Ca': 'Ca_sv_GW', 'Cd': 'Cd_sv_GW', 'Ce': 'Ce_GW', 'Cl': 'Cl_GW', 'Co': 'Co_sv_GW', 'Cr': 'Cr_sv_GW', 'Cs': 'Cs_sv_GW', 'Cu': 'Cu_sv_GW', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F_GW', 'Fe': 'Fe_sv_GW', 'Ga': 'Ga_d_GW', 'Gd': 'Gd', 'Ge': 'Ge_d_GW', 'H': 'H_GW', 'He': 'He_GW', 'Hf': 'Hf_sv_GW', 'Hg': 'Hg_sv_GW', 'Ho': 'Ho_3', 'I': 'I_GW', 'In': 'In_d_GW', 'Ir': 'Ir_sv_GW', 'K': 'K_sv_GW', 'Kr': 'Kr_GW', 'La': 'La_GW', 'Li': 'Li_sv_GW', 'Lu': 'Lu_3', 'Mg': 'Mg_sv_GW', 'Mn': 'Mn_sv_GW', 'Mo': 'Mo_sv_GW', 'N': 'N_GW', 'Na': 'Na_sv_GW', 'Nb': 'Nb_sv_GW', 'Nd': 'Nd_3', 'Ne': 'Ne_GW', 'Ni': 'Ni_sv_GW', 'Np': 'Np', 'O': 'O_GW', 'Os': 'Os_sv_GW', 'P': 'P_GW', 'Pa': 'Pa', 'Pb': 'Pb_d_GW', 'Pd': 'Pd_sv_GW', 'Pm': 'Pm_3', 'Po': 'Po_d_GW', 'Pr': 'Pr_3', 'Pt': 'Pt_sv_GW', 'Pu': 'Pu', 'Rb': 'Rb_sv_GW', 'Re': 'Re_sv_GW', 'Rh': 'Rh_sv_GW', 'Rn': 'Rn_d_GW', 'Ru': 'Ru_sv_GW', 'S': 'S_GW', 'Sb': 'Sb_d_GW', 'Sc': 'Sc_sv_GW', 'Se': 'Se_GW', 'Si': 'Si_GW', 'Sm': 'Sm_3', 'Sn': 'Sn_d_GW', 'Sr': 'Sr_sv_GW', 'Ta': 'Ta_sv_GW', 'Tb': 'Tb_3', 'Tc': 'Tc_sv_GW', 'Te': 'Te_GW', 'Th': 'Th', 'Ti': 'Ti_sv_GW', 'Tl': 'Tl_d_GW', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv_GW', 'W': 'W_sv_GW', 'Xe': 'Xe_GW', 'Y': 'Y_sv_GW', 'Yb': 'Yb_3', 'Zn': 'Zn_sv_GW', 'Zr': 'Zr_sv_GW'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'Normal', 'EDIFF': 1e-08, 'IBRION': -1, 'ICHARG': 1, 'ISMEAR': 0, 'ISPIN': 2, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': True, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'PREC': 'Accurate', 'SIGMA': 0.01}, 'KPOINTS': {'reciprocal_density': 100}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag_sv_GW', 'Al': 'Al_GW', 'Ar': 'Ar_GW', 'As': 'As_GW', 'At': 'At_d_GW', 'Au': 'Au_sv_GW', 'B': 'B_GW', 'Ba': 'Ba_sv_GW', 'Be': 'Be_sv_GW', 'Bi': 'Bi_d_GW', 'Br': 'Br_GW', 'C': 'C_GW', 'Ca': 'Ca_sv_GW', 'Cd': 'Cd_sv_GW', 'Ce': 'Ce_GW', 'Cl': 'Cl_GW', 'Co': 'Co_sv_GW', 'Cr': 'Cr_sv_GW', 'Cs': 'Cs_sv_GW', 'Cu': 'Cu_sv_GW', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F_GW', 'Fe': 'Fe_sv_GW', 'Ga': 'Ga_d_GW', 'Gd': 'Gd', 'Ge': 'Ge_d_GW', 'H': 'H_GW', 'He': 'He_GW', 'Hf': 'Hf_sv_GW', 'Hg': 'Hg_sv_GW', 'Ho': 'Ho_3', 'I': 'I_GW', 'In': 'In_d_GW', 'Ir': 'Ir_sv_GW', 'K': 'K_sv_GW', 'Kr': 'Kr_GW', 'La': 'La_GW', 'Li': 'Li_sv_GW', 'Lu': 'Lu_3', 'Mg': 'Mg_sv_GW', 'Mn': 'Mn_sv_GW', 'Mo': 'Mo_sv_GW', 'N': 'N_GW', 'Na': 'Na_sv_GW', 'Nb': 'Nb_sv_GW', 'Nd': 'Nd_3', 'Ne': 'Ne_GW', 'Ni': 'Ni_sv_GW', 'Np': 'Np', 'O': 'O_GW', 'Os': 'Os_sv_GW', 'P': 'P_GW', 'Pa': 'Pa', 'Pb': 'Pb_d_GW', 'Pd': 'Pd_sv_GW', 'Pm': 'Pm_3', 'Po': 'Po_d_GW', 'Pr': 'Pr_3', 'Pt': 'Pt_sv_GW', 'Pu': 'Pu', 'Rb': 'Rb_sv_GW', 'Re': 'Re_sv_GW', 'Rh': 'Rh_sv_GW', 'Rn': 'Rn_d_GW', 'Ru': 'Ru_sv_GW', 'S': 'S_GW', 'Sb': 'Sb_d_GW', 'Sc': 'Sc_sv_GW', 'Se': 'Se_GW', 'Si': 'Si_GW', 'Sm': 'Sm_3', 'Sn': 'Sn_d_GW', 'Sr': 'Sr_sv_GW', 'Ta': 'Ta_sv_GW', 'Tb': 'Tb_3', 'Tc': 'Tc_sv_GW', 'Te': 'Te_GW', 'Th': 'Th', 'Ti': 'Ti_sv_GW', 'Tl': 'Tl_d_GW', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv_GW', 'W': 'W_sv_GW', 'Xe': 'Xe_GW', 'Y': 'Y_sv_GW', 'Yb': 'Yb_3', 'Zn': 'Zn_sv_GW', 'Zr': 'Zr_sv_GW'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]

                                                                                      -SUPPORTED_MODES = ('DIAG', 'GW', 'STATIC', 'BSE')[source]
                                                                                      +SUPPORTED_MODES = ('DIAG', 'GW', 'STATIC', 'BSE')[source]
                                                                                      -copy_wavecar: bool = True[source]
                                                                                      +copy_wavecar: bool = True[source]
                                                                                      -force_gamma: bool = True[source]
                                                                                      +force_gamma: bool = True[source]
                                                                                      -classmethod from_prev_calc(prev_calc_dir: PathLike, mode: str = 'DIAG', **kwargs) → Self[source]
                                                                                      +classmethod from_prev_calc(prev_calc_dir: PathLike, mode: str = 'DIAG', **kwargs) → Self[source]

                                                                                      Generate a set of VASP input files for GW or BSE calculations from a directory of previous Exact Diag VASP run.

                                                                                      @@ -6543,51 +6543,51 @@

                                                                                      Submodules
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -inherit_incar: bool = True[source]
                                                                                      +inherit_incar: bool = True[source]
                                                                                      -property kpoints_updates: dict[str, Any][source]
                                                                                      +property kpoints_updates: dict[str, Any][source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      -mode: str = 'STATIC'[source]
                                                                                      +mode: str = 'STATIC'[source]
                                                                                      -nbands: int | None = None[source]
                                                                                      +nbands: int | None = None[source]
                                                                                      -nbands_factor: int = 5[source]
                                                                                      +nbands_factor: int = 5[source]
                                                                                      -ncores: int = 16[source]
                                                                                      +ncores: int = 16[source]
                                                                                      -reciprocal_density: float = 100[source]
                                                                                      +reciprocal_density: float = 100[source]
                                                                                      -class MVLNPTMDSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, start_temp: float = 0.0, end_temp: float = 300.0, nsteps: int = 1000, time_step: float = 2, spin_polarized: bool = False)[source]
                                                                                      +class MVLNPTMDSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, start_temp: float = 0.0, end_temp: float = 300.0, nsteps: int = 1000, time_step: float = 2, spin_polarized: bool = False)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Write a VASP MD run in NPT ensemble.

                                                                                      Notes

                                                                                      @@ -6595,51 +6595,51 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -end_temp: float = 300.0[source]
                                                                                      +end_temp: float = 300.0[source]
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -property kpoints_updates: Kpoints[source]
                                                                                      +property kpoints_updates: Kpoints[source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      -nsteps: int = 1000[source]
                                                                                      +nsteps: int = 1000[source]
                                                                                      -spin_polarized: bool = False[source]
                                                                                      +spin_polarized: bool = False[source]
                                                                                      -start_temp: float = 0.0[source]
                                                                                      +start_temp: float = 0.0[source]
                                                                                      -time_step: float = 2[source]
                                                                                      +time_step: float = 2[source]

                                                                                      -class MVLRelax52Set(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_52', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'))[source]
                                                                                      +class MVLRelax52Set(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_52', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'))[source]

                                                                                      Bases: VaspInputSet

                                                                                      Implementation of VaspInputSet utilizing the public Materials Project parameters for INCAR & KPOINTS and VASP’s recommended PAW potentials for @@ -6672,19 +6672,19 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At_d', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be', 'Bi': 'Bi_d', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu_2', 'F': 'F', 'Fe': 'Fe', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd_3', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg', 'Mn': 'Mn_pv', 'Mo': 'Mo_sv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_sv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni', 'Np': 'Np', 'O': 'O', 'Os': 'Os', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_sv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At_d', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be', 'Bi': 'Bi_d', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu_2', 'F': 'F', 'Fe': 'Fe', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd_3', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg', 'Mn': 'Mn_pv', 'Mo': 'Mo_sv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_sv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni', 'Np': 'Np', 'O': 'O', 'Os': 'Os', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_sv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]

                                                                                      -user_potcar_functional: UserPotcarFunctional = 'PBE_52'[source]
                                                                                      +user_potcar_functional: UserPotcarFunctional = 'PBE_52'[source]

                                                                                      -class MVLScanRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_52', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'))[source]
                                                                                      +class MVLScanRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_52', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'))[source]

                                                                                      Bases: VaspInputSet

                                                                                      Write a relax input set using Strongly Constrained and Appropriately Normed (SCAN) semilocal density functional.

                                                                                      @@ -6715,25 +6715,25 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -user_potcar_functional: UserPotcarFunctional = 'PBE_52'[source]
                                                                                      +user_potcar_functional: UserPotcarFunctional = 'PBE_52'[source]

                                                                                      -class MVLSlabSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, k_product: int = 50, bulk: bool = False, auto_dipole: bool = False, set_mix: bool = True)[source]
                                                                                      +class MVLSlabSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, k_product: int = 50, bulk: bool = False, auto_dipole: bool = False, set_mix: bool = True)[source]

                                                                                      Bases: VaspInputSet

                                                                                      Write a set of slab VASP runs, including both slabs (along the c direction) and orient unit cells (bulk), to ensure the same KPOINTS, POTCAR and INCAR criterion.

                                                                                      @@ -6753,12 +6753,12 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]

                                                                                      -as_dict(verbosity: int = 2) → dict[str, Any][source]
                                                                                      +as_dict(verbosity: int = 2) → dict[str, Any][source]
                                                                                      Parameters:

                                                                                      verbosity (int) – Verbosity of dict. e.g. whether to include Structure.

                                                                                      @@ -6774,28 +6774,28 @@

                                                                                      Submodules
                                                                                      -auto_dipole: bool = False[source]
                                                                                      +auto_dipole: bool = False[source]

                                                                                      -bulk: bool = False[source]
                                                                                      +bulk: bool = False[source]
                                                                                      -property incar_updates: dict[str, Any][source]
                                                                                      +property incar_updates: dict[str, Any][source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -k_product: int = 50[source]
                                                                                      +k_product: int = 50[source]
                                                                                      -property kpoints_updates: Kpoints[source]
                                                                                      +property kpoints_updates: Kpoints[source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      k_product, default to 50, is kpoint number * length for a & b directions, also for c direction in bulk calculations @@ -6804,14 +6804,14 @@

                                                                                      Submodules
                                                                                      -set_mix: bool = True[source]
                                                                                      +set_mix: bool = True[source]

                                                                                      -class MatPESStaticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: tuple[str, ...] | bool = ('LPEAD', 'NGX', 'NGY', 'NGZ', 'SYMPREC', 'IMIX', 'LMAXMIX', 'KGAMMA', 'ISYM', 'NCORE', 'NPAR', 'NELMIN', 'IOPT', 'NBANDS', 'KPAR', 'AMIN', 'NELMDL', 'BMIX', 'AMIX_MAG', 'BMIX_MAG'), auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: dict | str | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, xc_functional: Literal['R2SCAN', 'PBE', 'PBE+U'] = 'PBE')[source]
                                                                                      +class MatPESStaticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: tuple[str, ...] | bool = ('LPEAD', 'NGX', 'NGY', 'NGZ', 'SYMPREC', 'IMIX', 'LMAXMIX', 'KGAMMA', 'ISYM', 'NCORE', 'NPAR', 'NELMIN', 'IOPT', 'NBANDS', 'KPAR', 'AMIN', 'NELMDL', 'BMIX', 'AMIX_MAG', 'BMIX_MAG'), auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: dict | str | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, xc_functional: Literal['R2SCAN', 'PBE', 'PBE+U'] = 'PBE')[source]

                                                                                      Bases: VaspInputSet

                                                                                      Create input files for a MatPES static calculation.

                                                                                      The goal of MatPES is to generate potential energy surface data. This is a distinctly different @@ -6835,35 +6835,35 @@

                                                                                      Submodules
                                                                                      -CONFIG = {'INCAR': {'ALGO': 'Normal', 'EDIFF': 1e-05, 'ENAUG': 1360, 'ENCUT': 680, 'GGA': 'PE', 'ISMEAR': 0, 'ISPIN': 2, 'KSPACING': 0.22, 'LAECHG': True, 'LASPH': True, 'LCHARG': True, 'LDAU': False, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LMAXMIX': 6, 'LMIXTAU': True, 'LORBIT': 11, 'LREAL': False, 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NSW': 0, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'PARENT': 'PBE64Base', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cf': 'Cf', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_sv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_3', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_64'}[source]
                                                                                      +CONFIG = {'INCAR': {'ALGO': 'Normal', 'EDIFF': 1e-05, 'ENAUG': 1360, 'ENCUT': 680, 'GGA': 'PE', 'ISMEAR': 0, 'ISPIN': 2, 'KSPACING': 0.22, 'LAECHG': True, 'LASPH': True, 'LCHARG': True, 'LDAU': False, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LMAXMIX': 6, 'LMIXTAU': True, 'LORBIT': 11, 'LREAL': False, 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NSW': 0, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'PARENT': 'PBE64Base', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cf': 'Cf', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_sv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_3', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_64'}[source]

                                                                                      -inherit_incar: tuple[str, ...] | bool = ('LPEAD', 'NGX', 'NGY', 'NGZ', 'SYMPREC', 'IMIX', 'LMAXMIX', 'KGAMMA', 'ISYM', 'NCORE', 'NPAR', 'NELMIN', 'IOPT', 'NBANDS', 'KPAR', 'AMIN', 'NELMDL', 'BMIX', 'AMIX_MAG', 'BMIX_MAG')[source]
                                                                                      +inherit_incar: tuple[str, ...] | bool = ('LPEAD', 'NGX', 'NGY', 'NGZ', 'SYMPREC', 'IMIX', 'LMAXMIX', 'KGAMMA', 'ISYM', 'NCORE', 'NPAR', 'NELMIN', 'IOPT', 'NBANDS', 'KPAR', 'AMIN', 'NELMDL', 'BMIX', 'AMIX_MAG', 'BMIX_MAG')[source]
                                                                                      -prev_incar: dict | str | None = None[source]
                                                                                      +prev_incar: dict | str | None = None[source]
                                                                                      -xc_functional: Literal['R2SCAN', 'PBE', 'PBE+U'] = 'PBE'[source]
                                                                                      +xc_functional: Literal['R2SCAN', 'PBE', 'PBE+U'] = 'PBE'[source]

                                                                                      -VaspInputGenerator[source]
                                                                                      +VaspInputGenerator[source]

                                                                                      alias of VaspInputSet

                                                                                      -class VaspInputSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
                                                                                      +class VaspInputSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]

                                                                                      Bases: InputGenerator, ABC

                                                                                      Base class representing a set of VASP input parameters with a structure supplied as init parameters and initialized from a dict of settings. @@ -6985,7 +6985,7 @@

                                                                                      Submodules
                                                                                      -as_dict(verbosity: int = 2) → dict[source]
                                                                                      +as_dict(verbosity: int = 2) → dict[source]
                                                                                      Parameters:
                                                                                      -auto_ispin: bool = False[source]
                                                                                      +auto_ispin: bool = False[source]
                                                                                      -auto_kspacing: bool = False[source]
                                                                                      +auto_kspacing: bool = False[source]
                                                                                      -auto_lreal: bool = False[source]
                                                                                      +auto_lreal: bool = False[source]
                                                                                      -auto_metal_kpoints: bool = False[source]
                                                                                      +auto_metal_kpoints: bool = False[source]
                                                                                      -bandgap: float | None = None[source]
                                                                                      +bandgap: float | None = None[source]
                                                                                      -bandgap_tol: float = 0.0001[source]
                                                                                      +bandgap_tol: float = 0.0001[source]
                                                                                      -calculate_ng(max_prime_factor: int = 7, must_inc_2: bool = True, custom_encut: float | None = None, custom_prec: str | None = None) → tuple[source]
                                                                                      +calculate_ng(max_prime_factor: int = 7, must_inc_2: bool = True, custom_encut: float | None = None, custom_prec: str | None = None) → tuple[source]

                                                                                      Calculate the NGX, NGY, and NGZ values using the information available in the INCAR and POTCAR This is meant to help with making initial guess for the FFT grid so we can interact with the Charge density API.

                                                                                      @@ -7062,17 +7062,17 @@

                                                                                      Submodules
                                                                                      -config_dict: dict[source]
                                                                                      +config_dict: dict[source]

                                                                                      -constrain_total_magmom: bool = False[source]
                                                                                      +constrain_total_magmom: bool = False[source]
                                                                                      -estimate_nbands() → int[source]
                                                                                      +estimate_nbands() → int[source]

                                                                                      Estimate the number of bands that VASP will initialize a calculation with by default. Note that in practice this can depend on # of cores (if not set explicitly).

                                                                                      @@ -7083,17 +7083,17 @@

                                                                                      Submodules
                                                                                      -files_to_transfer: dict[source]
                                                                                      +files_to_transfer: dict[source]

                                                                                      -force_gamma: bool = False[source]
                                                                                      +force_gamma: bool = False[source]
                                                                                      -static from_directory(directory: PathLike, optional_files: dict | None = None) → VaspInput[source]
                                                                                      +static from_directory(directory: PathLike, optional_files: dict | None = None) → VaspInput[source]

                                                                                      Load a set of VASP inputs from a directory.

                                                                                      Note that only the standard INCAR, POSCAR, POTCAR and KPOINTS files are read unless optional_filenames is specified.

                                                                                      @@ -7110,7 +7110,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_prev_calc(prev_calc_dir: PathLike, **kwargs) → Self[source]
                                                                                      +classmethod from_prev_calc(prev_calc_dir: PathLike, **kwargs) → Self[source]

                                                                                      Generate a set of VASP input files for static calculations from a directory of previous VASP run.

                                                                                      @@ -7128,7 +7128,7 @@

                                                                                      Submodules
                                                                                      -get_input_set(structure: Structure | None = None, prev_dir: PathLike | None = None, potcar_spec: bool = False) → VaspInput[source]
                                                                                      +get_input_set(structure: Structure | None = None, prev_dir: PathLike | None = None, potcar_spec: bool = False) → VaspInput[source]

                                                                                      Get a VASP input set.

                                                                                      Note, if both structure and prev_dir are set, then the structure specified will be preferred over the final structure from the last VASP run.

                                                                                      @@ -7156,40 +7156,40 @@

                                                                                      Submodules
                                                                                      -get_vasp_input(**kwargs)[source]
                                                                                      +get_vasp_input(**kwargs)[source]

                                                                                      -property incar: Incar[source]
                                                                                      +property incar: Incar[source]

                                                                                      The INCAR.

                                                                                      -property incar_updates: dict[source]
                                                                                      +property incar_updates: dict[source]

                                                                                      Updates to the INCAR config for this calculation type.

                                                                                      -inherit_incar: bool | list[str] = False[source]
                                                                                      +inherit_incar: bool | list[str] = False[source]
                                                                                      -international_monoclinic: bool = True[source]
                                                                                      +international_monoclinic: bool = True[source]
                                                                                      -property kpoints: Kpoints | None[source]
                                                                                      +property kpoints: Kpoints | None[source]

                                                                                      The KPOINTS file.

                                                                                      -property kpoints_updates: dict[source]
                                                                                      +property kpoints_updates: dict[source]

                                                                                      Updates to the kpoints configuration for this calculation type.

                                                                                      Note, these updates will be ignored if the user has set user_kpoint_settings.

                                                                                      @@ -7208,13 +7208,13 @@

                                                                                      Submodules
                                                                                      -property nelect: float[source]
                                                                                      +property nelect: float[source]

                                                                                      The default number of electrons for a given structure.

                                                                                      -override_from_prev_calc(prev_calc_dir: PathLike = '.') → Self[source]
                                                                                      +override_from_prev_calc(prev_calc_dir: PathLike = '.') → Self[source]

                                                                                      Update the input set to include settings from a previous calculation.

                                                                                      Parameters:
                                                                                      @@ -7235,102 +7235,102 @@

                                                                                      Submodules
                                                                                      -property poscar: Poscar[source]
                                                                                      +property poscar: Poscar[source]

                                                                                      Poscar.

                                                                                      -property potcar: Potcar[source]
                                                                                      +property potcar: Potcar[source]

                                                                                      The input set’s POTCAR.

                                                                                      -property potcar_functional: UserPotcarFunctional[source]
                                                                                      +property potcar_functional: UserPotcarFunctional[source]

                                                                                      The functional used for POTCAR generation.

                                                                                      -property potcar_symbols: list[str][source]
                                                                                      +property potcar_symbols: list[str][source]

                                                                                      List of POTCAR symbols.

                                                                                      -prev_incar: str | dict | None = None[source]
                                                                                      +prev_incar: str | dict | None = None[source]
                                                                                      -prev_kpoints: str | Kpoints | None = None[source]
                                                                                      +prev_kpoints: str | Kpoints | None = None[source]
                                                                                      -reduce_structure: Literal['niggli', 'LLL'] | None = None[source]
                                                                                      +reduce_structure: Literal['niggli', 'LLL'] | None = None[source]
                                                                                      -sort_structure: bool = True[source]
                                                                                      +sort_structure: bool = True[source]
                                                                                      -standardize: bool = False[source]
                                                                                      +standardize: bool = False[source]
                                                                                      -property structure: Structure | None[source]
                                                                                      +property structure: Structure | None[source]

                                                                                      Structure.

                                                                                      -sym_prec: float = 0.1[source]
                                                                                      +sym_prec: float = 0.1[source]
                                                                                      -use_structure_charge: bool = False[source]
                                                                                      +use_structure_charge: bool = False[source]
                                                                                      -user_incar_settings: dict[source]
                                                                                      +user_incar_settings: dict[source]
                                                                                      -user_kpoints_settings: dict[source]
                                                                                      +user_kpoints_settings: dict[source]
                                                                                      -user_potcar_functional: UserPotcarFunctional = None[source]
                                                                                      +user_potcar_functional: UserPotcarFunctional = None[source]
                                                                                      -user_potcar_settings: dict[source]
                                                                                      +user_potcar_settings: dict[source]
                                                                                      -validate_magmom: bool = True[source]
                                                                                      +validate_magmom: bool = True[source]
                                                                                      -vdw: str | None = None[source]
                                                                                      +vdw: str | None = None[source]
                                                                                      -write_input(output_dir: str, make_dir_if_not_present: bool = True, include_cif: bool | str = False, potcar_spec: bool = False, zip_output: bool | str = False) → None[source]
                                                                                      +write_input(output_dir: str, make_dir_if_not_present: bool = True, include_cif: bool | str = False, potcar_spec: bool = False, zip_output: bool | str = False) → None[source]

                                                                                      Write a set of VASP input to a directory.

                                                                                      Parameters:
                                                                                      @@ -7357,13 +7357,13 @@

                                                                                      Submodules
                                                                                      -auto_kspacing(bandgap: float | None, bandgap_tol: float) → float[source]
                                                                                      +auto_kspacing(bandgap: float | None, bandgap_tol: float) → float[source]

                                                                                      Set kspacing based on the bandgap

                                                                                      -batch_write_input(structures: Sequence[Structure], vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: PathLike = '.', make_dir_if_not_present: bool = True, subfolder: Callable | None = None, sanitize: bool = False, include_cif: bool = False, potcar_spec: bool = False, zip_output: bool = False, **kwargs)[source]
                                                                                      +batch_write_input(structures: Sequence[Structure], vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: PathLike = '.', make_dir_if_not_present: bool = True, subfolder: Callable | None = None, sanitize: bool = False, include_cif: bool = False, potcar_spec: bool = False, zip_output: bool = False, **kwargs)[source]

                                                                                      Batch write VASP input for a sequence of structures to output_dir, following the format output_dir/{group}/{formula}_{number}.

                                                                                      @@ -7401,7 +7401,7 @@

                                                                                      Submodules
                                                                                      -get_structure_from_prev_run(vasprun: Vasprun, outcar: Outcar | None = None) → Structure[source]
                                                                                      +get_structure_from_prev_run(vasprun: Vasprun, outcar: Outcar | None = None) → Structure[source]

                                                                                      Process structure from previous run.

                                                                                      Parameters:
                                                                                      @@ -7425,7 +7425,7 @@

                                                                                      Submodules
                                                                                      -get_valid_magmom_struct(structure: Structure, inplace: bool = True, spin_mode: str = 'auto') → Structure[source]
                                                                                      +get_valid_magmom_struct(structure: Structure, inplace: bool = True, spin_mode: str = 'auto') → Structure[source]

                                                                                      Make sure that the structure has valid magmoms based on the kind of calculation.

                                                                                      Fill in missing Magmom values.

                                                                                      @@ -7452,7 +7452,7 @@

                                                                                      Submodules
                                                                                      -get_vasprun_outcar(path: PathLike, parse_dos: bool = True, parse_eigen: bool = True) → tuple[Vasprun, Outcar][source]
                                                                                      +get_vasprun_outcar(path: PathLike, parse_dos: bool = True, parse_eigen: bool = True) → tuple[Vasprun, Outcar][source]

                                                                                      Get a Vasprun and Outcar from a directory.

                                                                                      Parameters:
                                                                                      @@ -7470,7 +7470,7 @@

                                                                                      Submodules
                                                                                      -next_num_with_prime_factors(n: int, max_prime_factor: int, must_inc_2: bool = True) → int[source]
                                                                                      +next_num_with_prime_factors(n: int, max_prime_factor: int, must_inc_2: bool = True) → int[source]

                                                                                      Get the next number greater than or equal to n that only has the desired prime factors.

                                                                                      Parameters:
                                                                                      @@ -7491,13 +7491,13 @@

                                                                                      Submodules
                                                                                      -primes_less_than(max_val: int) → list[int][source]
                                                                                      +primes_less_than(max_val: int) → list[int][source]

                                                                                      Get the primes less than or equal to the max value.

                                                                                      -standardize_structure(structure: Structure, sym_prec: float = 0.1, international_monoclinic: bool = True) → Structure[source]
                                                                                      +standardize_structure(structure: Structure, sym_prec: float = 0.1, international_monoclinic: bool = True) → Structure[source]

                                                                                      Get the symmetrically standardized structure.

                                                                                      Parameters:
                                                                                      diff --git a/docs/pymatgen.io.xtb.html b/docs/pymatgen.io.xtb.html index 0006f4b566c..93951a6840d 100644 --- a/docs/pymatgen.io.xtb.html +++ b/docs/pymatgen.io.xtb.html @@ -4,7 +4,7 @@ - pymatgen.io.xtb package — pymatgen 2024.6.4 documentation + pymatgen.io.xtb package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                      - 2024.6.4 + 2024.6.10
                                                                                      @@ -100,7 +100,7 @@

                                                                                      Submodules
                                                                                      -class CRESTInput(molecule: Molecule, working_dir: str = '.', coords_filename: str | None = 'crest_in.xyz', constraints: dict[str, list[int] | float] | None = None)[source]
                                                                                      +class CRESTInput(molecule: Molecule, working_dir: str = '.', coords_filename: str | None = 'crest_in.xyz', constraints: dict[str, list[int] | float] | None = None)[source]

                                                                                      Bases: MSONable

                                                                                      An object representing CREST input files. Because CREST is controlled through command line flags and external @@ -120,7 +120,7 @@

                                                                                      Submodules
                                                                                      -static constrains_template(molecule, reference_fnm, constraints) → str[source]
                                                                                      +static constrains_template(molecule, reference_fnm, constraints) → str[source]
                                                                                      Parameters:
                                                                                      @@ -153,7 +153,7 @@

                                                                                      Submodules
                                                                                      -class CRESTOutput(output_filename, path='.')[source]
                                                                                      +class CRESTOutput(output_filename, path='.')[source]

                                                                                      Bases: MSONable

                                                                                      Parse CREST output files.

                                                                                      Assumes runtype is iMTD-GC [default].

                                                                                      diff --git a/docs/pymatgen.optimization.html b/docs/pymatgen.optimization.html index eb669390051..643bcf1e2b9 100644 --- a/docs/pymatgen.optimization.html +++ b/docs/pymatgen.optimization.html @@ -4,7 +4,7 @@ - pymatgen.optimization package — pymatgen 2024.6.4 documentation + pymatgen.optimization package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                      - 2024.6.4 + 2024.6.10
                                                                                      @@ -96,7 +96,7 @@

                                                                                      Submodules
                                                                                      -class LinearAssignment(costs, epsilon=1e-13)[source]
                                                                                      +class LinearAssignment(costs, epsilon=1e-13)[source]

                                                                                      Bases: object

                                                                                      This class finds the solution to the Linear Assignment Problem. It finds a minimum cost matching between two sets, given a cost @@ -122,7 +122,7 @@

                                                                                      Submodules

                                                                                      pymatgen.optimization.neighbors module

                                                                                      -find_points_in_spheres(all_coords, center_coords, r, pbc, lattice, tol=1e-08, min_r=1.0)[source]
                                                                                      +find_points_in_spheres(all_coords, center_coords, r, pbc, lattice, tol=1e-08, min_r=1.0)[source]

                                                                                      For each point in center_coords, get all the neighboring points in all_coords that are within the cutoff radius r. All the coordinates should be Cartesian.

                                                                                      diff --git a/docs/pymatgen.phonon.html b/docs/pymatgen.phonon.html index a8a8eeb7e6c..2153d60c00c 100644 --- a/docs/pymatgen.phonon.html +++ b/docs/pymatgen.phonon.html @@ -4,7 +4,7 @@ - pymatgen.phonon package — pymatgen 2024.6.4 documentation + pymatgen.phonon package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                      - 2024.6.4 + 2024.6.10
                                                                                      @@ -258,7 +258,7 @@

                                                                                      Submodules
                                                                                      -class PhononBandStructure(qpoints: Sequence[Kpoint], frequencies: ArrayLike, lattice: Lattice, nac_frequencies: Sequence[Sequence] | None = None, eigendisplacements: ArrayLike = None, nac_eigendisplacements: Sequence[Sequence] | None = None, labels_dict: dict | None = None, coords_are_cartesian: bool = False, structure: Structure | None = None)[source]
                                                                                      +class PhononBandStructure(qpoints: Sequence[Kpoint], frequencies: ArrayLike, lattice: Lattice, nac_frequencies: Sequence[Sequence] | None = None, eigendisplacements: ArrayLike = None, nac_eigendisplacements: Sequence[Sequence] | None = None, labels_dict: dict | None = None, coords_are_cartesian: bool = False, structure: Structure | None = None)[source]

                                                                                      Bases: MSONable

                                                                                      This is the most generic phonon band structure data possible it’s defined by a list of qpoints + frequencies for each of them. @@ -302,13 +302,13 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[str, Any][source]
                                                                                      +as_dict() → dict[str, Any][source]

                                                                                      MSONable dict.

                                                                                      -asr_breaking(tol_eigendisplacements: float = 1e-05) → ndarray | None[source]
                                                                                      +asr_breaking(tol_eigendisplacements: float = 1e-05) → ndarray | None[source]

                                                                                      Get the breaking of the acoustic sum rule for the three acoustic modes, if Gamma is present. None otherwise. If eigendisplacements are available they are used to determine the acoustic @@ -320,7 +320,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                                      +classmethod from_dict(dct: dict[str, Any]) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation of PhononBandStructure.

                                                                                      @@ -333,13 +333,13 @@

                                                                                      Submodules
                                                                                      -get_gamma_point() → Kpoint | None[source]
                                                                                      +get_gamma_point() → Kpoint | None[source]

                                                                                      Get the Gamma q-point as a Kpoint object (or None if not found).

                                                                                      -get_nac_eigendisplacements_along_dir(direction) → ndarray | None[source]
                                                                                      +get_nac_eigendisplacements_along_dir(direction) → ndarray | None[source]

                                                                                      Get the nac_eigendisplacements for the given direction (not necessarily a versor). None if the direction is not present or nac_eigendisplacements has not been calculated.

                                                                                      @@ -355,7 +355,7 @@

                                                                                      Submodules
                                                                                      -get_nac_frequencies_along_dir(direction: Sequence) → np.ndarray | None[source]
                                                                                      +get_nac_frequencies_along_dir(direction: Sequence) → np.ndarray | None[source]

                                                                                      Get the nac_frequencies for the given direction (not necessarily a versor). None if the direction is not present or nac_frequencies has not been calculated.

                                                                                      @@ -371,13 +371,13 @@

                                                                                      Submodules
                                                                                      -property has_eigendisplacements: bool[source]
                                                                                      +property has_eigendisplacements: bool[source]

                                                                                      True if eigendisplacements are present.

                                                                                      -has_imaginary_freq(tol: float = 0.01) → bool[source]
                                                                                      +has_imaginary_freq(tol: float = 0.01) → bool[source]

                                                                                      True if imaginary frequencies are present anywhere in the band structure. Always True if has_imaginary_gamma_freq is True.

                                                                                      @@ -389,7 +389,7 @@

                                                                                      Submodules
                                                                                      -has_imaginary_gamma_freq(tol: float = 0.01) → bool[source]
                                                                                      +has_imaginary_gamma_freq(tol: float = 0.01) → bool[source]

                                                                                      Check if there are imaginary modes at the gamma point and all close points.

                                                                                      Parameters:
                                                                                      @@ -400,26 +400,26 @@

                                                                                      Submodules
                                                                                      -property has_nac: bool[source]
                                                                                      +property has_nac: bool[source]

                                                                                      True if nac_frequencies are present (i.e. the band structure has been calculated taking into account Born-charge-derived non-analytical corrections at Gamma).

                                                                                      -max_freq() → tuple[Kpoint, float][source]
                                                                                      +max_freq() → tuple[Kpoint, float][source]

                                                                                      Get the q-point where the maximum frequency is reached and its value.

                                                                                      -min_freq() → tuple[Kpoint, float][source]
                                                                                      +min_freq() → tuple[Kpoint, float][source]

                                                                                      Get the q-point where the minimum frequency is reached and its value.

                                                                                      -width(with_imaginary: bool = False) → float[source]
                                                                                      +width(with_imaginary: bool = False) → float[source]

                                                                                      Get the difference between the maximum and minimum frequencies anywhere in the band structure, not necessarily at identical same q-points. If with_imaginary is False, only positive frequencies are considered.

                                                                                      @@ -429,7 +429,7 @@

                                                                                      Submodules
                                                                                      -class PhononBandStructureSymmLine(qpoints: Sequence[Kpoint], frequencies: ArrayLike, lattice: Lattice, has_nac: bool = False, eigendisplacements: ArrayLike = None, labels_dict: dict | None = None, coords_are_cartesian: bool = False, structure: Structure | None = None)[source]
                                                                                      +class PhononBandStructureSymmLine(qpoints: Sequence[Kpoint], frequencies: ArrayLike, lattice: Lattice, has_nac: bool = False, eigendisplacements: ArrayLike = None, labels_dict: dict | None = None, coords_are_cartesian: bool = False, structure: Structure | None = None)[source]

                                                                                      Bases: PhononBandStructure

                                                                                      Store phonon band structures along selected (symmetry) lines in the Brillouin zone. We call the different symmetry lines (ex: \Gamma to Z) “branches”.

                                                                                      @@ -463,26 +463,26 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      Get MSONable dict.

                                                                                      -as_phononwebsite() → dict[source]
                                                                                      +as_phononwebsite() → dict[source]

                                                                                      Return a dictionary with the phononwebsite format: http://henriquemiranda.github.io/phononwebsite.

                                                                                      -band_reorder() → None[source]
                                                                                      +band_reorder() → None[source]

                                                                                      Re-order the eigenvalues according to the similarity of the eigenvectors.

                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -495,7 +495,7 @@

                                                                                      Submodules
                                                                                      -get_branch(index: int) → list[dict[str, str | int]][source]
                                                                                      +get_branch(index: int) → list[dict[str, str | int]][source]

                                                                                      Get in what branch(es) is the qpoint. There can be several branches.

                                                                                      Parameters:
                                                                                      @@ -517,7 +517,7 @@

                                                                                      Submodules
                                                                                      -get_equivalent_qpoints(index: int) → list[int][source]
                                                                                      +get_equivalent_qpoints(index: int) → list[int][source]

                                                                                      Get the list of qpoint indices equivalent (meaning they are the same frac coords) to the given one.

                                                                                      @@ -537,7 +537,7 @@

                                                                                      Submodules
                                                                                      -write_phononwebsite(filename: str | PathLike) → None[source]
                                                                                      +write_phononwebsite(filename: str | PathLike) → None[source]

                                                                                      Write a JSON file for the phononwebsite: http://henriquemiranda.github.io/phononwebsite.

                                                                                      @@ -546,19 +546,19 @@

                                                                                      Submodules
                                                                                      -eigenvectors_from_displacements(disp: ndarray, masses: ndarray) → ndarray[source]
                                                                                      +eigenvectors_from_displacements(disp: ndarray, masses: ndarray) → ndarray[source]

                                                                                      Calculate the eigenvectors from the atomic displacements.

                                                                                      -estimate_band_connection(prev_eigvecs, eigvecs, prev_band_order) → list[int][source]
                                                                                      +estimate_band_connection(prev_eigvecs, eigvecs, prev_band_order) → list[int][source]

                                                                                      A function to order the phonon eigenvectors taken from phonopy.

                                                                                      -get_reasonable_repetitions(n_atoms: int) → Tuple3Ints[source]
                                                                                      +get_reasonable_repetitions(n_atoms: int) → Tuple3Ints[source]

                                                                                      Choose the number of repetitions in a supercell according to the number of atoms in the system.

                                                                                      @@ -569,12 +569,12 @@

                                                                                      Submodules
                                                                                      -class CompletePhononDos(structure: Structure, total_dos, ph_doses: dict)[source]
                                                                                      +class CompletePhononDos(structure: Structure, total_dos, ph_doses: dict)[source]

                                                                                      Bases: PhononDos

                                                                                      This wrapper class defines a total dos, and also provides a list of PDos.

                                                                                      -pdos[source]
                                                                                      +pdos[source]

                                                                                      Dict of partial densities of the form {Site:Densities}. Densities are a dict of {Orbital:Values} where Values are a list of floats. Site is a pymatgen.core.sites.Site object.

                                                                                      @@ -596,19 +596,19 @@

                                                                                      Submodules
                                                                                      -as_dict()[source]
                                                                                      +as_dict()[source]

                                                                                      JSON-serializable dict representation of CompletePhononDos.

                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]

                                                                                      Get CompleteDos object from dict representation.

                                                                                      -get_element_dos() → dict[source]
                                                                                      +get_element_dos() → dict[source]

                                                                                      Get element projected Dos.

                                                                                      Returns:
                                                                                      @@ -622,7 +622,7 @@

                                                                                      Submodules
                                                                                      -get_site_dos(site) → PhononDos[source]
                                                                                      +get_site_dos(site) → PhononDos[source]

                                                                                      Get the Dos for a site.

                                                                                      Parameters:
                                                                                      @@ -641,7 +641,7 @@

                                                                                      Submodules
                                                                                      -class PhononDos(frequencies: Sequence, densities: Sequence)[source]
                                                                                      +class PhononDos(frequencies: Sequence, densities: Sequence)[source]

                                                                                      Bases: MSONable

                                                                                      Basic DOS object. All other DOS objects are extended versions of this object.

                                                                                      @@ -654,13 +654,13 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      JSON-serializable dict representation of PhononDos.

                                                                                      -cv(temp: float | None = None, structure: Structure | None = None, **kwargs) → float[source]
                                                                                      +cv(temp: float | None = None, structure: Structure | None = None, **kwargs) → float[source]

                                                                                      Constant volume specific heat C_v at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number @@ -687,7 +687,7 @@

                                                                                      Submodules
                                                                                      -entropy(temp: float | None = None, structure: Structure | None = None, **kwargs) → float[source]
                                                                                      +entropy(temp: float | None = None, structure: Structure | None = None, **kwargs) → float[source]

                                                                                      Vibrational entropy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number @@ -714,13 +714,13 @@

                                                                                      Submodules
                                                                                      -classmethod from_dict(dct: dict[str, Sequence]) → Self[source]
                                                                                      +classmethod from_dict(dct: dict[str, Sequence]) → Self[source]

                                                                                      Get PhononDos object from dict representation of PhononDos.

                                                                                      -get_interpolated_value(frequency) → float[source]
                                                                                      +get_interpolated_value(frequency) → float[source]

                                                                                      Get interpolated density for a particular frequency.

                                                                                      Parameters:
                                                                                      @@ -731,7 +731,7 @@

                                                                                      Submodules
                                                                                      -get_last_peak(threshold: float = 0.05) → float[source]
                                                                                      +get_last_peak(threshold: float = 0.05) → float[source]

                                                                                      Find the last peak in the phonon DOS defined as the highest frequency with a DOS value at least threshold * height of the overall highest DOS peak. A peak is any local maximum of the DOS as a function of frequency. @@ -756,7 +756,7 @@

                                                                                      Submodules
                                                                                      -get_smeared_densities(sigma: float) → ndarray[source]
                                                                                      +get_smeared_densities(sigma: float) → ndarray[source]

                                                                                      Get the densities, but with a Gaussian smearing of std dev sigma applied.

                                                                                      @@ -775,7 +775,7 @@

                                                                                      Submodules
                                                                                      -helmholtz_free_energy(temp: float | None = None, structure: Structure | None = None, **kwargs) → float[source]
                                                                                      +helmholtz_free_energy(temp: float | None = None, structure: Structure | None = None, **kwargs) → float[source]

                                                                                      Phonon contribution to the Helmholtz free energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number @@ -802,13 +802,13 @@

                                                                                      Submodules
                                                                                      -ind_zero_freq()[source]
                                                                                      +ind_zero_freq()[source]

                                                                                      Index of the first point for which the frequencies are >= 0.

                                                                                      -internal_energy(temp: float | None = None, structure: Structure | None = None, **kwargs) → float[source]
                                                                                      +internal_energy(temp: float | None = None, structure: Structure | None = None, **kwargs) → float[source]

                                                                                      Phonon contribution to the internal energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number @@ -835,7 +835,7 @@

                                                                                      Submodules
                                                                                      -mae(other: PhononDos, two_sided: bool = True) → float[source]
                                                                                      +mae(other: PhononDos, two_sided: bool = True) → float[source]

                                                                                      Mean absolute error between two DOSs.

                                                                                      Parameters:
                                                                                      @@ -856,7 +856,7 @@

                                                                                      Submodules
                                                                                      -r2_score(other: PhononDos) → float[source]
                                                                                      +r2_score(other: PhononDos) → float[source]

                                                                                      R^2 score between two DOSs.

                                                                                      Parameters:
                                                                                      @@ -873,7 +873,7 @@

                                                                                      Submodules
                                                                                      -zero_point_energy(structure: Structure | None = None) → float[source]
                                                                                      +zero_point_energy(structure: Structure | None = None) → float[source]

                                                                                      Zero point energy of the system. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result @@ -898,7 +898,7 @@

                                                                                      Submodules
                                                                                      -class GruneisenParameter(qpoints: ArrayLike, gruneisen: ArrayLike[ArrayLike], frequencies: ArrayLike[ArrayLike], multiplicities: Sequence | None = None, structure: Structure = None, lattice: Lattice = None)[source]
                                                                                      +class GruneisenParameter(qpoints: ArrayLike, gruneisen: ArrayLike[ArrayLike], frequencies: ArrayLike[ArrayLike], multiplicities: Sequence | None = None, structure: Structure = None, lattice: Lattice = None)[source]

                                                                                      Bases: MSONable

                                                                                      Store the Gruneisen parameter for a single q-point on a regular grid.

                                                                                      @@ -916,14 +916,14 @@

                                                                                      Submodules
                                                                                      -property acoustic_debye_temp: float[source]
                                                                                      +property acoustic_debye_temp: float[source]

                                                                                      Acoustic Debye temperature in K, i.e. the Debye temperature divided by n_sites**(1/3). Adapted from abipy.

                                                                                      -average_gruneisen(t: float | None = None, squared: bool = True, limit_frequencies: Literal['debye', 'acoustic'] | None = None) → float[source]
                                                                                      +average_gruneisen(t: float | None = None, squared: bool = True, limit_frequencies: Literal['debye', 'acoustic'] | None = None) → float[source]

                                                                                      Calculate the average of the Gruneisen based on the values on the regular grid. If squared is True, the average will use the squared value of the Gruneisen and a squared root is performed on the final result. @@ -949,13 +949,13 @@

                                                                                      Submodules
                                                                                      -property debye_temp_limit: float[source]
                                                                                      +property debye_temp_limit: float[source]

                                                                                      Debye temperature in K. Adapted from apipy.

                                                                                      -debye_temp_phonopy(freq_max_fit=None) → float[source]
                                                                                      +debye_temp_phonopy(freq_max_fit=None) → float[source]

                                                                                      Get Debye temperature in K as implemented in phonopy.

                                                                                      Parameters:
                                                                                      @@ -970,19 +970,19 @@

                                                                                      Submodules
                                                                                      -property phdos: PhononDos[source]
                                                                                      +property phdos: PhononDos[source]

                                                                                      The phonon DOS (re)constructed from the gruneisen.yaml file.

                                                                                      -property tdos[source]
                                                                                      +property tdos[source]

                                                                                      The total DOS (re)constructed from the gruneisen.yaml file.

                                                                                      -thermal_conductivity_slack(squared: bool = True, limit_frequencies: Literal['debye', 'acoustic'] | None = None, theta_d: float | None = None, t: float | None = None) → float[source]
                                                                                      +thermal_conductivity_slack(squared: bool = True, limit_frequencies: Literal['debye', 'acoustic'] | None = None, theta_d: float | None = None, t: float | None = None) → float[source]

                                                                                      Calculate the thermal conductivity at the acoustic Debye temperature with the Slack formula, using the average Gruneisen. Adapted from abipy.

                                                                                      @@ -1011,7 +1011,7 @@

                                                                                      Submodules
                                                                                      -class GruneisenPhononBandStructure(qpoints: ArrayLike, frequencies: ArrayLike[ArrayLike], gruneisenparameters: ArrayLike, lattice: Lattice, eigendisplacements: ArrayLike[ArrayLike] = None, labels_dict: dict | None = None, coords_are_cartesian: bool = False, structure: Structure | None = None)[source]
                                                                                      +class GruneisenPhononBandStructure(qpoints: ArrayLike, frequencies: ArrayLike[ArrayLike], gruneisenparameters: ArrayLike, lattice: Lattice, eigendisplacements: ArrayLike[ArrayLike] = None, labels_dict: dict | None = None, coords_are_cartesian: bool = False, structure: Structure | None = None)[source]

                                                                                      Bases: PhononBandStructure

                                                                                      This is the most generic phonon band structure data possible it’s defined by a list of qpoints + frequencies for each of them. @@ -1047,7 +1047,7 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]
                                                                                      Returns:

                                                                                      MSONable dict.

                                                                                      @@ -1060,7 +1060,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -1078,7 +1078,7 @@

                                                                                      Submodules
                                                                                      -class GruneisenPhononBandStructureSymmLine(qpoints: ArrayLike, frequencies: ArrayLike[ArrayLike], gruneisenparameters: ArrayLike, lattice: Lattice, eigendisplacements: ArrayLike[ArrayLike] = None, labels_dict: dict | None = None, coords_are_cartesian: bool = False, structure: Structure | None = None)[source]
                                                                                      +class GruneisenPhononBandStructureSymmLine(qpoints: ArrayLike, frequencies: ArrayLike[ArrayLike], gruneisenparameters: ArrayLike, lattice: Lattice, eigendisplacements: ArrayLike[ArrayLike] = None, labels_dict: dict | None = None, coords_are_cartesian: bool = False, structure: Structure | None = None)[source]

                                                                                      Bases: GruneisenPhononBandStructure, PhononBandStructureSymmLine

                                                                                      Store a GruneisenPhononBandStructureSymmLine together with Grueneisen parameters for every frequency.

                                                                                      @@ -1111,7 +1111,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -1133,7 +1133,7 @@

                                                                                      Submodules
                                                                                      -class IRDielectricTensor(oscillator_strength: ArrayLike, ph_freqs_gamma: ArrayLike, epsilon_infinity: ArrayLike, structure: Structure)[source]
                                                                                      +class IRDielectricTensor(oscillator_strength: ArrayLike, ph_freqs_gamma: ArrayLike, epsilon_infinity: ArrayLike, structure: Structure)[source]

                                                                                      Bases: MSONable

                                                                                      Handle the Ionic Dielectric Tensor The implementation is adapted from Abipy @@ -1151,19 +1151,19 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[source]
                                                                                      +as_dict() → dict[source]

                                                                                      JSON-serializable dict representation of IRDielectricTensor.

                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]

                                                                                      Get IRDielectricTensor from dict representation.

                                                                                      -get_ir_spectra(broad: list | float = 5e-05, emin: float = 0, emax: float | None = None, divs: int = 500) → tuple[source]
                                                                                      +get_ir_spectra(broad: list | float = 5e-05, emin: float = 0, emax: float | None = None, divs: int = 500) → tuple[source]

                                                                                      The IR spectra is obtained for the different directions.

                                                                                      Parameters:
                                                                                      @@ -1191,7 +1191,7 @@

                                                                                      Submodules
                                                                                      -get_plotter(components: Sequence = ('xx',), reim: str = 'reim', broad: list | float = 5e-05, emin: float = 0, emax: float | None = None, divs: int = 500, **kwargs) → SpectrumPlotter[source]
                                                                                      +get_plotter(components: Sequence = ('xx',), reim: str = 'reim', broad: list | float = 5e-05, emin: float = 0, emax: float | None = None, divs: int = 500, **kwargs) → SpectrumPlotter[source]

                                                                                      Return an instance of the Spectrum plotter containing the different requested components.

                                                                                      Parameters:
                                                                                      @@ -1211,7 +1211,7 @@

                                                                                      Submodules
                                                                                      -get_spectrum(component: Sequence | str, reim: str, broad: list | float = 5e-05, emin: float = 0, emax: float | None = None, divs: int = 500, label=None) → Spectrum[source]
                                                                                      +get_spectrum(component: Sequence | str, reim: str, broad: list | float = 5e-05, emin: float = 0, emax: float | None = None, divs: int = 500, label=None) → Spectrum[source]

                                                                                      component: either two indexes or a string like ‘xx’ to plot the (0,0) component reim: only “re” or “im” broad: a list of broadenings or a single broadening for the phonon peaks.

                                                                                      @@ -1219,19 +1219,19 @@

                                                                                      Submodules
                                                                                      -property max_phfreq: float[source]
                                                                                      +property max_phfreq: float[source]

                                                                                      Maximum phonon frequency.

                                                                                      -property nph_freqs: int[source]
                                                                                      +property nph_freqs: int[source]

                                                                                      Number of phonon frequencies.

                                                                                      -plot(components: Sequence = ('xx',), reim: str = 'reim', show_phonon_frequencies: bool = True, xlim: float | None = None, ylim: float | None = None, **kwargs) → Axes[source]
                                                                                      +plot(components: Sequence = ('xx',), reim: str = 'reim', show_phonon_frequencies: bool = True, xlim: float | None = None, ylim: float | None = None, **kwargs) → Axes[source]

                                                                                      Helper function to generate the Spectrum plotter and directly plot the results.

                                                                                      Parameters:
                                                                                      @@ -1287,7 +1287,7 @@

                                                                                      Submodules
                                                                                      -write_json(filename: str | PathLike) → None[source]
                                                                                      +write_json(filename: str | PathLike) → None[source]

                                                                                      Save a JSON file with this data.

                                                                                      @@ -1299,19 +1299,19 @@

                                                                                      Submodules
                                                                                      -class FreqUnits(factor: float, label: str)[source]
                                                                                      +class FreqUnits(factor: float, label: str)[source]

                                                                                      Bases: NamedTuple

                                                                                      Conversion factor from THz to the required units and the label.

                                                                                      Create new instance of FreqUnits(factor, label)

                                                                                      -factor: float[source]
                                                                                      +factor: float[source]

                                                                                      Alias for field number 0

                                                                                      -label: str[source]
                                                                                      +label: str[source]

                                                                                      Alias for field number 1

                                                                                      @@ -1319,7 +1319,7 @@

                                                                                      Submodules
                                                                                      -class GruneisenPhononBSPlotter(bs: GruneisenPhononBandStructureSymmLine)[source]
                                                                                      +class GruneisenPhononBSPlotter(bs: GruneisenPhononBandStructureSymmLine)[source]

                                                                                      Bases: PhononBSPlotter

                                                                                      Plot or get data to facilitate the plot of band structure objects.

                                                                                      @@ -1329,7 +1329,7 @@

                                                                                      Submodules
                                                                                      -bs_plot_data() → dict[str, Any][source]
                                                                                      +bs_plot_data() → dict[str, Any][source]

                                                                                      Get the data nicely formatted for a plot.

                                                                                      Returns:
                                                                                      @@ -1349,7 +1349,7 @@

                                                                                      Submodules
                                                                                      -get_plot_gs(ylim: float | None = None, **kwargs) → Axes[source]
                                                                                      +get_plot_gs(ylim: float | None = None, **kwargs) → Axes[source]

                                                                                      Get a matplotlib object for the Gruneisen bandstructure plot.

                                                                                      Parameters:
                                                                                      @@ -1364,7 +1364,7 @@

                                                                                      Submodules
                                                                                      -plot_compare_gs(other_plotter: GruneisenPhononBSPlotter) → Axes[source]
                                                                                      +plot_compare_gs(other_plotter: GruneisenPhononBSPlotter) → Axes[source]

                                                                                      Plot two band structure for comparison. One is in red the other in blue. The two band structures need to be defined on the same symmetry lines! and the distance between symmetry lines is @@ -1385,7 +1385,7 @@

                                                                                      Submodules
                                                                                      -save_plot_gs(filename: str | PathLike, img_format: str = 'eps', ylim: float | None = None) → None[source]
                                                                                      +save_plot_gs(filename: str | PathLike, img_format: str = 'eps', ylim: float | None = None) → None[source]

                                                                                      Save matplotlib plot to a file.

                                                                                      Parameters:
                                                                                      @@ -1400,7 +1400,7 @@

                                                                                      Submodules
                                                                                      -show_gs(ylim: float | None = None) → None[source]
                                                                                      +show_gs(ylim: float | None = None) → None[source]

                                                                                      Show the plot using matplotlib.

                                                                                      Parameters:
                                                                                      @@ -1413,7 +1413,7 @@

                                                                                      Submodules
                                                                                      -class GruneisenPlotter(gruneisen: GruneisenParameter)[source]
                                                                                      +class GruneisenPlotter(gruneisen: GruneisenParameter)[source]

                                                                                      Bases: object

                                                                                      Plot GruneisenParameter.

                                                                                      Plot information from GruneisenParameter.

                                                                                      @@ -1424,7 +1424,7 @@

                                                                                      Submodules
                                                                                      -get_plot(marker: str = 'o', markersize: float | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → Axes[source]
                                                                                      +get_plot(marker: str = 'o', markersize: float | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → Axes[source]

                                                                                      Will produce a plot.

                                                                                      Parameters:
                                                                                      @@ -1445,7 +1445,7 @@

                                                                                      Submodules
                                                                                      -save_plot(filename: str | PathLike, img_format: str = 'pdf', units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]
                                                                                      +save_plot(filename: str | PathLike, img_format: str = 'pdf', units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]

                                                                                      Will save the plot to a file.

                                                                                      Parameters:
                                                                                      @@ -1460,7 +1460,7 @@

                                                                                      Submodules
                                                                                      -show(units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]
                                                                                      +show(units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]

                                                                                      Will show the plot.

                                                                                      Parameters:
                                                                                      @@ -1473,7 +1473,7 @@

                                                                                      Submodules
                                                                                      -class PhononBSPlotter(bs: PhononBandStructureSymmLine, label: str | None = None)[source]
                                                                                      +class PhononBSPlotter(bs: PhononBandStructureSymmLine, label: str | None = None)[source]

                                                                                      Bases: object

                                                                                      Plot or get data to facilitate the plot of band structure objects.

                                                                                      @@ -1487,7 +1487,7 @@

                                                                                      Submodules
                                                                                      -bs_plot_data() → dict[str, Any][source]
                                                                                      +bs_plot_data() → dict[str, Any][source]

                                                                                      Get the data nicely formatted for a plot.

                                                                                      Returns:
                                                                                      @@ -1506,7 +1506,7 @@

                                                                                      Submodules
                                                                                      -get_plot(ylim: float | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', **kwargs) → Axes[source]
                                                                                      +get_plot(ylim: float | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', **kwargs) → Axes[source]

                                                                                      Get a matplotlib object for the bandstructure plot.

                                                                                      Parameters:
                                                                                      @@ -1523,7 +1523,7 @@

                                                                                      Submodules
                                                                                      -get_proj_plot(site_comb: str | list[list[int]] = 'element', ylim: tuple[None | float, None | float] | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', rgb_labels: tuple[None | str] | None = None) → Axes[source]
                                                                                      +get_proj_plot(site_comb: str | list[list[int]] = 'element', ylim: tuple[None | float, None | float] | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', rgb_labels: tuple[None | str] | None = None) → Axes[source]

                                                                                      Get a matplotlib object for the bandstructure plot projected along atomic sites.

                                                                                      @@ -1546,7 +1546,7 @@

                                                                                      Submodules
                                                                                      -get_ticks() → dict[str, list][source]
                                                                                      +get_ticks() → dict[str, list][source]

                                                                                      Get all ticks and labels for a band structure plot.

                                                                                      Returns:
                                                                                      @@ -1561,19 +1561,19 @@

                                                                                      Submodules
                                                                                      -property n_bands: int[source]
                                                                                      +property n_bands: int[source]

                                                                                      Number of bands.

                                                                                      -plot_brillouin() → None[source]
                                                                                      +plot_brillouin() → None[source]

                                                                                      Plot the Brillouin zone.

                                                                                      -plot_compare(other_plotter: PhononBSPlotter | dict[str, PhononBSPlotter], units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', self_label: str = 'self', colors: Sequence[str] | None = None, legend_kwargs: dict | None = None, on_incompatible: Literal['raise', 'warn', 'ignore'] = 'raise', other_kwargs: dict | None = None, **kwargs) → Axes[source]
                                                                                      +plot_compare(other_plotter: PhononBSPlotter | dict[str, PhononBSPlotter], units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', self_label: str = 'self', colors: Sequence[str] | None = None, legend_kwargs: dict | None = None, on_incompatible: Literal['raise', 'warn', 'ignore'] = 'raise', other_kwargs: dict | None = None, **kwargs) → Axes[source]

                                                                                      Plot two band structure for comparison. self in blue, others in red, green, … The band structures need to be defined on the same symmetry lines! The distance between symmetry lines is determined by the band structure used to @@ -1603,7 +1603,7 @@

                                                                                      Submodules
                                                                                      -save_plot(filename: str | PathLike, ylim: float | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]
                                                                                      +save_plot(filename: str | PathLike, ylim: float | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]

                                                                                      Save matplotlib plot to a file.

                                                                                      Parameters:
                                                                                      @@ -1618,7 +1618,7 @@

                                                                                      Submodules
                                                                                      -show(ylim: float | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]
                                                                                      +show(ylim: float | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]

                                                                                      Show the plot using matplotlib.

                                                                                      Parameters:
                                                                                      @@ -1632,7 +1632,7 @@

                                                                                      Submodules
                                                                                      -show_proj(site_comb: str | list[list[int]] = 'element', ylim: tuple[None | float, None | float] | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', rgb_labels: tuple[str] | None = None) → None[source]
                                                                                      +show_proj(site_comb: str | list[list[int]] = 'element', ylim: tuple[None | float, None | float] | None = None, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', rgb_labels: tuple[str] | None = None) → None[source]

                                                                                      Show the projected plot using matplotlib.

                                                                                      Parameters:
                                                                                      @@ -1656,7 +1656,7 @@

                                                                                      Submodules
                                                                                      -class PhononDosPlotter(stack: bool = False, sigma: float | None = None)[source]
                                                                                      +class PhononDosPlotter(stack: bool = False, sigma: float | None = None)[source]

                                                                                      Bases: object

                                                                                      Plot phonon DOSs. The interface is very flexible to accommodate the many different ways in which people want to view DOS. @@ -1680,7 +1680,7 @@

                                                                                      Submodules
                                                                                      -add_dos(label: str, dos: PhononDos, **kwargs: Any) → None[source]
                                                                                      +add_dos(label: str, dos: PhononDos, **kwargs: Any) → None[source]

                                                                                      Add a dos for plotting.

                                                                                      Parameters:
                                                                                      @@ -1695,7 +1695,7 @@

                                                                                      Submodules
                                                                                      -add_dos_dict(dos_dict: dict, key_sort_func=None) → None[source]
                                                                                      +add_dos_dict(dos_dict: dict, key_sort_func=None) → None[source]

                                                                                      Add a dictionary of doses, with an optional sorting function for the keys.

                                                                                      @@ -1710,7 +1710,7 @@

                                                                                      Submodules
                                                                                      -get_dos_dict() → dict[source]
                                                                                      +get_dos_dict() → dict[source]

                                                                                      Get the added doses as a json-serializable dict. Note that if you have specified smearing for the DOS plot, the densities returned will be the smeared densities, not the original densities.

                                                                                      @@ -1726,7 +1726,7 @@

                                                                                      Submodules
                                                                                      -get_plot(xlim: float | None = None, ylim: float | None = None, invert_axes: bool = False, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', legend: dict | None = None, ax: Axes | None = None) → Axes[source]
                                                                                      +get_plot(xlim: float | None = None, ylim: float | None = None, invert_axes: bool = False, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz', legend: dict | None = None, ax: Axes | None = None) → Axes[source]

                                                                                      Get a matplotlib plot showing the DOS.

                                                                                      Parameters:
                                                                                      @@ -1747,7 +1747,7 @@

                                                                                      Submodules
                                                                                      -save_plot(filename: str | PathLike, img_format: str = 'eps', xlim: float | None = None, ylim: float | None = None, invert_axes: bool = False, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]
                                                                                      +save_plot(filename: str | PathLike, img_format: str = 'eps', xlim: float | None = None, ylim: float | None = None, invert_axes: bool = False, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]

                                                                                      Save matplotlib plot to a file.

                                                                                      Parameters:
                                                                                      @@ -1767,7 +1767,7 @@

                                                                                      Submodules
                                                                                      -show(xlim: float | None = None, ylim: None = None, invert_axes: bool = False, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]
                                                                                      +show(xlim: float | None = None, ylim: None = None, invert_axes: bool = False, units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1'] = 'thz') → None[source]

                                                                                      Show the plot using matplotlib.

                                                                                      Parameters:
                                                                                      @@ -1787,7 +1787,7 @@

                                                                                      Submodules
                                                                                      -class ThermoPlotter(dos: PhononDos, structure: Structure = None)[source]
                                                                                      +class ThermoPlotter(dos: PhononDos, structure: Structure = None)[source]

                                                                                      Bases: object

                                                                                      Plotter for thermodynamic properties obtained from phonon DOS. If the structure corresponding to the DOS, it will be used to extract the formula unit and provide @@ -1802,7 +1802,7 @@

                                                                                      Submodules
                                                                                      -plot_cv(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]
                                                                                      +plot_cv(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]

                                                                                      Plots the constant volume specific heat C_v in a temperature range.

                                                                                      Parameters:
                                                                                      @@ -1862,7 +1862,7 @@

                                                                                      Submodules
                                                                                      -plot_entropy(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]
                                                                                      +plot_entropy(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]

                                                                                      Plots the vibrational entrpy in a temperature range.

                                                                                      Parameters:
                                                                                      @@ -1922,7 +1922,7 @@

                                                                                      Submodules
                                                                                      -plot_helmholtz_free_energy(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]
                                                                                      +plot_helmholtz_free_energy(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]

                                                                                      Plots the vibrational contribution to the Helmoltz free energy in a temperature range.

                                                                                      Parameters:
                                                                                      @@ -1982,7 +1982,7 @@

                                                                                      Submodules
                                                                                      -plot_internal_energy(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]
                                                                                      +plot_internal_energy(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]

                                                                                      Plots the vibrational internal energy in a temperature range.

                                                                                      Parameters:
                                                                                      @@ -2042,7 +2042,7 @@

                                                                                      Submodules
                                                                                      -plot_thermodynamic_properties(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]
                                                                                      +plot_thermodynamic_properties(tmin: float, tmax: float, ntemp: int, ylim: float | None = None, **kwargs) → Figure[source]

                                                                                      Plots all the thermodynamic properties in a temperature range.

                                                                                      Parameters:
                                                                                      @@ -2104,7 +2104,7 @@

                                                                                      Submodules
                                                                                      -freq_units(units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1']) → FreqUnits[source]
                                                                                      +freq_units(units: Literal['thz', 'ev', 'mev', 'ha', 'cm-1', 'cm^-1']) → FreqUnits[source]
                                                                                      Parameters:

                                                                                      units – str, accepted values: thz, ev, mev, ha, cm-1, cm^-1.

                                                                                      @@ -2121,7 +2121,7 @@

                                                                                      Submodules
                                                                                      -class ThermalDisplacementMatrices(thermal_displacement_matrix_cart: ArrayLike[ArrayLike], structure: Structure, temperature: float | None, thermal_displacement_matrix_cif: ArrayLike[ArrayLike] = None)[source]
                                                                                      +class ThermalDisplacementMatrices(thermal_displacement_matrix_cart: ArrayLike[ArrayLike], structure: Structure, temperature: float | None, thermal_displacement_matrix_cif: ArrayLike[ArrayLike] = None)[source]

                                                                                      Bases: MSONable

                                                                                      Handle thermal displacement matrices This class stores thermal displacement matrices in Ucart format.

                                                                                      @@ -2146,7 +2146,7 @@

                                                                                      Submodules
                                                                                      -property B: ndarray[source]
                                                                                      +property B: ndarray[source]

                                                                                      Computation as described in R. W. Grosse-Kunstleve, P. D. Adams, J Appl Cryst 2002, 35, 477-480.

                                                                                      Returns:
                                                                                      @@ -2160,7 +2160,7 @@

                                                                                      Submodules
                                                                                      -property U1U2U3: list[source]
                                                                                      +property U1U2U3: list[source]

                                                                                      Computation as described in R. W. Grosse-Kunstleve, P. D. Adams, J Appl Cryst 2002, 35, 477-480.

                                                                                      Returns:
                                                                                      @@ -2174,7 +2174,7 @@

                                                                                      Submodules
                                                                                      -property Ucif: ndarray[source]
                                                                                      +property Ucif: ndarray[source]

                                                                                      Computation as described in R. W. Grosse-Kunstleve, P. D. Adams, J Appl Cryst 2002, 35, 477-480.

                                                                                      Returns:
                                                                                      @@ -2188,7 +2188,7 @@

                                                                                      Submodules
                                                                                      -property Ustar: ndarray[source]
                                                                                      +property Ustar: ndarray[source]

                                                                                      Computation as described in R. W. Grosse-Kunstleve, P. D. Adams, J Appl Cryst 2002, 35, 477-480.

                                                                                      Returns:
                                                                                      @@ -2202,7 +2202,7 @@

                                                                                      Submodules
                                                                                      -property beta: list[source]
                                                                                      +property beta: list[source]

                                                                                      Computation as described in R. W. Grosse-Kunstleve, P. D. Adams, J Appl Cryst 2002, 35, 477-480.

                                                                                      Returns:
                                                                                      @@ -2216,7 +2216,7 @@

                                                                                      Submodules
                                                                                      -compute_directionality_quality_criterion(other: ThermalDisplacementMatrices) → list[dict[str, ArrayLike]][source]
                                                                                      +compute_directionality_quality_criterion(other: ThermalDisplacementMatrices) → list[dict[str, ArrayLike]][source]

                                                                                      Will compute directionality of prolate displacement ellipsoids as described in https://doi.org/10.1039/C9CE00794F with the earlier implementation: https://github.com/damMroz/Angle/.

                                                                                      @@ -2245,7 +2245,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_Ucif(thermal_displacement_matrix_cif: ArrayLike[ArrayLike], structure: Structure, temperature: float | None = None) → Self[source]
                                                                                      +classmethod from_Ucif(thermal_displacement_matrix_cif: ArrayLike[ArrayLike], structure: Structure, temperature: float | None = None) → Self[source]

                                                                                      Starting from a numpy array, it will convert Ucif values into Ucart values and initialize the class.

                                                                                      Parameters:
                                                                                      @@ -2267,7 +2267,7 @@

                                                                                      Submodules
                                                                                      -static from_cif_P1(filename: str) → list[ThermalDisplacementMatrices][source]
                                                                                      +static from_cif_P1(filename: str) → list[ThermalDisplacementMatrices][source]

                                                                                      Reads a cif with P1 symmetry including positions and ADPs. Currently, no check of symmetry is performed as CifParser methods cannot be easily reused.

                                                                                      @@ -2282,7 +2282,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_structure_with_site_properties_Ucif(structure: Structure, temperature: float | None = None) → Self[source]
                                                                                      +classmethod from_structure_with_site_properties_Ucif(structure: Structure, temperature: float | None = None) → Self[source]

                                                                                      Will create this object with the help of a structure with site properties.

                                                                                      Parameters:
                                                                                      @@ -2300,7 +2300,7 @@

                                                                                      Submodules
                                                                                      -static get_full_matrix(thermal_displacement: ArrayLike[ArrayLike]) → np.ndarray[np.ndarray][source]
                                                                                      +static get_full_matrix(thermal_displacement: ArrayLike[ArrayLike]) → np.ndarray[np.ndarray][source]

                                                                                      Transfers the reduced matrix to the full matrix (order of reduced matrix U11, U22, U33, U23, U13, U12).

                                                                                      Parameters:
                                                                                      @@ -2314,7 +2314,7 @@

                                                                                      Submodules
                                                                                      -static get_reduced_matrix(thermal_displacement: ArrayLike[ArrayLike]) → np.ndarray[np.ndarray][source]
                                                                                      +static get_reduced_matrix(thermal_displacement: ArrayLike[ArrayLike]) → np.ndarray[np.ndarray][source]

                                                                                      Transfers the full matrix to reduced matrix (order of reduced matrix U11, U22, U33, U23, U13, U12).

                                                                                      Parameters:
                                                                                      @@ -2328,13 +2328,13 @@

                                                                                      Submodules
                                                                                      -property ratio_prolate: ndarray[source]
                                                                                      +property ratio_prolate: ndarray[source]

                                                                                      This will compute ratio between largest and smallest eigenvalue of Ucart.

                                                                                      -to_structure_with_site_properties_Ucif() → Structure[source]
                                                                                      +to_structure_with_site_properties_Ucif() → Structure[source]

                                                                                      Transfers this object into a structure with site properties (Ucif). This is useful for sorting the atoms in the structure including site properties. e.g. with code like this: @@ -2352,7 +2352,7 @@

                                                                                      Submodules
                                                                                      -visualize_directionality_quality_criterion(other: ThermalDisplacementMatrices, filename: str | PathLike = 'visualization.vesta', which_structure: Literal[0, 1] = 0) → None[source]
                                                                                      +visualize_directionality_quality_criterion(other: ThermalDisplacementMatrices, filename: str | PathLike = 'visualization.vesta', which_structure: Literal[0, 1] = 0) → None[source]

                                                                                      Will create a VESTA file for visualization of the directionality criterion.

                                                                                      Parameters:
                                                                                      @@ -2368,7 +2368,7 @@

                                                                                      Submodules
                                                                                      -write_cif(filename: str) → None[source]
                                                                                      +write_cif(filename: str) → None[source]

                                                                                      Write a cif including thermal displacements.

                                                                                      Parameters:
                                                                                      diff --git a/docs/pymatgen.symmetry.html b/docs/pymatgen.symmetry.html index afe805f7fa5..cdd833720aa 100644 --- a/docs/pymatgen.symmetry.html +++ b/docs/pymatgen.symmetry.html @@ -4,7 +4,7 @@ - pymatgen.symmetry package — pymatgen 2024.6.4 documentation + pymatgen.symmetry package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                      - 2024.6.4 + 2024.6.10
                                                                                      @@ -263,7 +263,7 @@

                                                                                      Submodules
                                                                                      -class PointGroupAnalyzer(mol, tolerance=0.3, eigen_tolerance=0.01, matrix_tolerance=0.1)[source]
                                                                                      +class PointGroupAnalyzer(mol, tolerance=0.3, eigen_tolerance=0.01, matrix_tolerance=0.1)[source]

                                                                                      Bases: object

                                                                                      A class to analyze the point group of a molecule.

                                                                                      The general outline of the algorithm is as follows:

                                                                                      @@ -306,7 +306,7 @@

                                                                                      Submodules
                                                                                      -get_equivalent_atoms()[source]
                                                                                      +get_equivalent_atoms()[source]

                                                                                      Get sets of equivalent atoms with symmetry operations.

                                                                                      Returns:
                                                                                      @@ -329,19 +329,19 @@

                                                                                      Submodules
                                                                                      -get_pointgroup()[source]
                                                                                      +get_pointgroup()[source]

                                                                                      Get a PointGroup object for the molecule.

                                                                                      -get_rotational_symmetry_number()[source]
                                                                                      +get_rotational_symmetry_number()[source]

                                                                                      Return the rotational symmetry number.

                                                                                      -get_symmetry_operations()[source]
                                                                                      +get_symmetry_operations()[source]

                                                                                      Return symmetry operations as a list of SymmOp objects. Returns Cartesian coord symmops.

                                                                                      @@ -356,12 +356,12 @@

                                                                                      Submodules
                                                                                      -inversion_op = SymmOp(self.affine_matrix=array([[-1., -0., -0.,  0.],        [-0., -1., -0.,  0.],        [-0., -0., -1.,  0.],        [-0., -0., -0.,  1.]]))[source]
                                                                                      +inversion_op = SymmOp(self.affine_matrix=array([[-1., -0., -0.,  0.],        [-0., -1., -0.,  0.],        [-0., -0., -1.,  0.],        [-0., -0., -0.,  1.]]))[source]

                                                                                      -is_valid_op(symm_op) → bool[source]
                                                                                      +is_valid_op(symm_op) → bool[source]

                                                                                      Check if a particular symmetry operation is a valid symmetry operation for a molecule, i.e., the operation maps all atoms to another equivalent atom.

                                                                                      @@ -379,7 +379,7 @@

                                                                                      Submodules
                                                                                      -symmetrize_molecule()[source]
                                                                                      +symmetrize_molecule()[source]

                                                                                      Get a symmetrized molecule.

                                                                                      The equivalent atoms obtained via get_equivalent_atoms() @@ -414,12 +414,12 @@

                                                                                      Submodules
                                                                                      -class PointGroupOperations(sch_symbol, operations, tol: float = 0.1)[source]
                                                                                      +class PointGroupOperations(sch_symbol, operations, tol: float = 0.1)[source]

                                                                                      Bases: list

                                                                                      Represents a point group, which is a sequence of symmetry operations.

                                                                                      -sch_symbol[source]
                                                                                      +sch_symbol[source]

                                                                                      Schoenflies symbol of the point group.

                                                                                      Type:
                                                                                      @@ -444,7 +444,7 @@

                                                                                      Submodules
                                                                                      -class SpacegroupAnalyzer(structure: Structure, symprec: float | None = 0.01, angle_tolerance: float = 5)[source]
                                                                                      +class SpacegroupAnalyzer(structure: Structure, symprec: float | None = 0.01, angle_tolerance: float = 5)[source]

                                                                                      Bases: object

                                                                                      Takes a pymatgen Structure object and a symprec.

                                                                                      Uses spglib to perform various symmetry finding operations.

                                                                                      @@ -465,7 +465,7 @@

                                                                                      Submodules
                                                                                      -find_primitive(keep_site_properties=False)[source]
                                                                                      +find_primitive(keep_site_properties=False)[source]

                                                                                      Find a primitive version of the unit cell.

                                                                                      Parameters:
                                                                                      @@ -488,7 +488,7 @@

                                                                                      Submodules
                                                                                      -get_conventional_standard_structure(international_monoclinic=True, keep_site_properties=False)[source]
                                                                                      +get_conventional_standard_structure(international_monoclinic=True, keep_site_properties=False)[source]

                                                                                      Get a structure with a conventional cell according to certain standards. The standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: Challenges and tools. Computational @@ -519,7 +519,7 @@

                                                                                      Submodules
                                                                                      -get_conventional_to_primitive_transformation_matrix(international_monoclinic=True)[source]
                                                                                      +get_conventional_to_primitive_transformation_matrix(international_monoclinic=True)[source]

                                                                                      Get the transformation matrix to transform a conventional unit cell to a primitive cell according to certain standards the standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure @@ -538,7 +538,7 @@

                                                                                      Submodules
                                                                                      -get_crystal_system() → CrystalSystem[source]
                                                                                      +get_crystal_system() → CrystalSystem[source]

                                                                                      Get the crystal system for the structure, e.g. (triclinic, orthorhombic, cubic, etc.).

                                                                                      @@ -556,7 +556,7 @@

                                                                                      Submodules
                                                                                      -get_hall() → str[source]
                                                                                      +get_hall() → str[source]

                                                                                      Get Hall symbol for structure.

                                                                                      Returns:
                                                                                      @@ -570,7 +570,7 @@

                                                                                      Submodules
                                                                                      -get_ir_reciprocal_mesh(mesh=(10, 10, 10), is_shift=(0, 0, 0))[source]
                                                                                      +get_ir_reciprocal_mesh(mesh=(10, 10, 10), is_shift=(0, 0, 0))[source]

                                                                                      k-point mesh of the Brillouin zone generated taken into account symmetry.The method returns the irreducible kpoints of the mesh and their weights.

                                                                                      @@ -594,7 +594,7 @@

                                                                                      Submodules
                                                                                      -get_ir_reciprocal_mesh_map(mesh=(10, 10, 10), is_shift=(0, 0, 0))[source]
                                                                                      +get_ir_reciprocal_mesh_map(mesh=(10, 10, 10), is_shift=(0, 0, 0))[source]

                                                                                      Same as ‘get_ir_reciprocal_mesh’ but the full grid together with the mapping that maps a reducible to an irreducible kpoint is returned.

                                                                                      @@ -618,7 +618,7 @@

                                                                                      Submodules
                                                                                      -get_kpoint_weights(kpoints, atol=1e-05)[source]
                                                                                      +get_kpoint_weights(kpoints, atol=1e-05)[source]

                                                                                      Calculate the weights for a list of kpoints.

                                                                                      Parameters:
                                                                                      @@ -637,7 +637,7 @@

                                                                                      Submodules
                                                                                      -get_lattice_type() → LatticeType[source]
                                                                                      +get_lattice_type() → LatticeType[source]

                                                                                      Get the lattice for the structure, e.g. (triclinic, orthorhombic, cubic, etc.).This is the same as the crystal system with the exception of the hexagonal/rhombohedral lattice.

                                                                                      @@ -656,7 +656,7 @@

                                                                                      Submodules
                                                                                      -get_point_group_operations(cartesian=False)[source]
                                                                                      +get_point_group_operations(cartesian=False)[source]

                                                                                      Return symmetry operations as a list of SymmOp objects. By default returns fractional coord symm ops. But Cartesian can be returned too.

                                                                                      @@ -675,7 +675,7 @@

                                                                                      Submodules
                                                                                      -get_point_group_symbol() → str[source]
                                                                                      +get_point_group_symbol() → str[source]

                                                                                      Get the point group associated with the structure.

                                                                                      Returns:
                                                                                      @@ -689,7 +689,7 @@

                                                                                      Submodules
                                                                                      -get_primitive_standard_structure(international_monoclinic=True, keep_site_properties=False)[source]
                                                                                      +get_primitive_standard_structure(international_monoclinic=True, keep_site_properties=False)[source]

                                                                                      Get a structure with a primitive cell according to certain standards. The standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: Challenges and tools. Computational @@ -717,7 +717,7 @@

                                                                                      Submodules
                                                                                      -get_refined_structure(keep_site_properties=False)[source]
                                                                                      +get_refined_structure(keep_site_properties=False)[source]

                                                                                      Get the refined structure based on detected symmetry. The refined structure is a conventional cell setting with atoms moved to the expected symmetry positions.

                                                                                      @@ -739,7 +739,7 @@

                                                                                      Submodules
                                                                                      -get_space_group_number() → int[source]
                                                                                      +get_space_group_number() → int[source]

                                                                                      Get the international spacegroup number (e.g., 62) for structure.

                                                                                      Returns:
                                                                                      @@ -753,7 +753,7 @@

                                                                                      Submodules
                                                                                      -get_space_group_operations() → SpacegroupOperations[source]
                                                                                      +get_space_group_operations() → SpacegroupOperations[source]

                                                                                      Get the SpacegroupOperations for the Structure.

                                                                                      Returns:
                                                                                      @@ -764,7 +764,7 @@

                                                                                      Submodules
                                                                                      -get_space_group_symbol() → str[source]
                                                                                      +get_space_group_symbol() → str[source]

                                                                                      Get the spacegroup symbol (e.g., Pnma) for structure.

                                                                                      Returns:
                                                                                      @@ -778,7 +778,7 @@

                                                                                      Submodules
                                                                                      -get_symmetrized_structure()[source]
                                                                                      +get_symmetrized_structure()[source]

                                                                                      Get a symmetrized structure. A symmetrized structure is one where the sites have been grouped into symmetrically equivalent groups.

                                                                                      @@ -790,7 +790,7 @@

                                                                                      Submodules
                                                                                      -get_symmetry_dataset()[source]
                                                                                      +get_symmetry_dataset()[source]

                                                                                      Get the symmetry dataset as a dict.

                                                                                      Returns:
                                                                                      @@ -817,7 +817,7 @@

                                                                                      Submodules
                                                                                      -get_symmetry_operations(cartesian=False)[source]
                                                                                      +get_symmetry_operations(cartesian=False)[source]

                                                                                      Return symmetry operations as a list of SymmOp objects. By default returns fractional coord sym_ops. But Cartesian can be returned too.

                                                                                      @@ -832,7 +832,7 @@

                                                                                      Submodules
                                                                                      -is_laue() → bool[source]
                                                                                      +is_laue() → bool[source]

                                                                                      Check if the point group of the structure has Laue symmetry (centrosymmetry).

                                                                                      @@ -840,7 +840,7 @@

                                                                                      Submodules
                                                                                      -class SpacegroupOperations(int_symbol, int_number, symmops)[source]
                                                                                      +class SpacegroupOperations(int_symbol, int_number, symmops)[source]

                                                                                      Bases: list

                                                                                      Represents a space group, which is a collection of symmetry operations.

                                                                                      @@ -855,7 +855,7 @@

                                                                                      Submodules
                                                                                      -are_symmetrically_equivalent(sites1, sites2, symm_prec=0.001) → bool[source]
                                                                                      +are_symmetrically_equivalent(sites1, sites2, symm_prec=0.001) → bool[source]

                                                                                      Given two sets of PeriodicSites, test if they are actually symmetrically equivalent under this space group. Useful, for example, if you want to test if selecting atoms 1 and 2 out of a set of 4 atoms are symmetrically the same as @@ -884,7 +884,7 @@

                                                                                      Submodules
                                                                                      -exception SymmetryUndetermined[source]
                                                                                      +exception SymmetryUndetermined[source]

                                                                                      Bases: ValueError

                                                                                      An Exception for when symmetry cannot be determined. This might happen when, for example, atoms are very close together.

                                                                                      @@ -892,7 +892,7 @@

                                                                                      Submodules
                                                                                      -cluster_sites(mol: Molecule, tol: float, give_only_index: bool = False) → tuple[Site | None, dict][source]
                                                                                      +cluster_sites(mol: Molecule, tol: float, give_only_index: bool = False) → tuple[Site | None, dict][source]

                                                                                      Cluster sites based on distance and species type.

                                                                                      Parameters:
                                                                                      @@ -919,7 +919,7 @@

                                                                                      Submodules
                                                                                      -generate_full_symmops(symmops: Sequence[SymmOp], tol: float) → Sequence[SymmOp][source]
                                                                                      +generate_full_symmops(symmops: Sequence[SymmOp], tol: float) → Sequence[SymmOp][source]

                                                                                      Recursive algorithm to permute through all possible combinations of the initially supplied symmetry operations to arrive at a complete set of operations mapping a single atom to all other equivalent atoms in the point group. This assumes that the @@ -942,7 +942,7 @@

                                                                                      Submodules
                                                                                      -iterative_symmetrize(mol, max_n=10, tolerance=0.3, epsilon=0.01)[source]
                                                                                      +iterative_symmetrize(mol, max_n=10, tolerance=0.3, epsilon=0.01)[source]

                                                                                      Get a symmetrized molecule.

                                                                                      The equivalent atoms obtained via get_equivalent_atoms() @@ -992,7 +992,7 @@

                                                                                      Submodules
                                                                                      -class HighSymmKpath(structure, has_magmoms=False, magmom_axis=None, path_type='setyawan_curtarolo', symprec=0.01, angle_tolerance=5, atol=1e-05)[source]
                                                                                      +class HighSymmKpath(structure, has_magmoms=False, magmom_axis=None, path_type='setyawan_curtarolo', symprec=0.01, angle_tolerance=5, atol=1e-05)[source]

                                                                                      Bases: KPathBase

                                                                                      This class generates path along high symmetry lines in the Brillouin zone according to different conventions. @@ -1037,7 +1037,7 @@

                                                                                      Submodules
                                                                                      -property equiv_labels[source]
                                                                                      +property equiv_labels[source]

                                                                                      The correspondence between the kpoint symbols in the Latimer and Munro convention, Setyawan and Curtarolo, and Hinuma conventions respectively. Only generated when path_type = ‘all’.

                                                                                      @@ -1045,7 +1045,7 @@

                                                                                      Submodules
                                                                                      -static get_continuous_path(bandstructure)[source]
                                                                                      +static get_continuous_path(bandstructure)[source]

                                                                                      Obtain a continuous version of an inputted path using graph theory. This routine will attempt to add connections between nodes of odd-degree to ensure a Eulerian path can be formed. Initial @@ -1067,14 +1067,14 @@

                                                                                      Submodules
                                                                                      -property label_index[source]
                                                                                      +property label_index[source]

                                                                                      The correspondence between numbers and kpoint symbols for the combined kpath generated when path_type = ‘all’. None otherwise.

                                                                                      -property path_lengths[source]
                                                                                      +property path_lengths[source]

                                                                                      List of lengths of the Latimer and Munro, Setyawan and Curtarolo, and Hinuma conventions in the combined HighSymmKpath object when path_type = ‘all’ respectively. None otherwise.

                                                                                      @@ -1082,7 +1082,7 @@

                                                                                      Submodules
                                                                                      -property path_type[source]
                                                                                      +property path_type[source]

                                                                                      The type of kpath chosen.

                                                                                      @@ -1096,12 +1096,12 @@

                                                                                      Submodules
                                                                                      -class PointGroup(*args, **kwargs)[source]
                                                                                      +class PointGroup(*args, **kwargs)[source]

                                                                                      Bases: PointGroup

                                                                                      A Point Group, with generators and symmetry operations.

                                                                                      -symbol[source]
                                                                                      +symbol[source]

                                                                                      Full International or Hermann-Mauguin Symbol.

                                                                                      Type:
                                                                                      @@ -1112,7 +1112,7 @@

                                                                                      Submodules
                                                                                      -generators[source]
                                                                                      +generators[source]

                                                                                      List of generator matrices. Note that 3x3 matrices are used for Point Groups.

                                                                                      Type:
                                                                                      @@ -1123,7 +1123,7 @@

                                                                                      Submodules
                                                                                      -symmetry_ops[source]
                                                                                      +symmetry_ops[source]

                                                                                      Full set of symmetry operations as matrices.

                                                                                      Type:
                                                                                      @@ -1142,12 +1142,12 @@

                                                                                      Submodules
                                                                                      -class SpaceGroup(*args, **kwargs)[source]
                                                                                      +class SpaceGroup(*args, **kwargs)[source]

                                                                                      Bases: SpaceGroup

                                                                                      A SpaceGroup.

                                                                                      -symbol[source]
                                                                                      +symbol[source]

                                                                                      Full International or Hermann-Mauguin Symbol.

                                                                                      Type:
                                                                                      @@ -1158,7 +1158,7 @@

                                                                                      Submodules
                                                                                      -int_number[source]
                                                                                      +int_number[source]

                                                                                      International number.

                                                                                      Type:
                                                                                      @@ -1169,7 +1169,7 @@

                                                                                      Submodules
                                                                                      -generators[source]
                                                                                      +generators[source]

                                                                                      List of generator matrices. Note that 4x4 matrices are used for Space Groups.

                                                                                      Type:
                                                                                      @@ -1180,7 +1180,7 @@

                                                                                      Submodules
                                                                                      -order[source]
                                                                                      +order[source]

                                                                                      Order of Space Group.

                                                                                      Type:
                                                                                      @@ -1209,12 +1209,12 @@

                                                                                      Submodules
                                                                                      -class SymmetryGroup[source]
                                                                                      +class SymmetryGroup[source]

                                                                                      Bases: Sequence, Stringify, ABC

                                                                                      Abstract class representing a symmetry group.

                                                                                      -is_subgroup(supergroup: SymmetryGroup) → bool[source]
                                                                                      +is_subgroup(supergroup: SymmetryGroup) → bool[source]

                                                                                      True if this group is a subgroup of the supplied group.

                                                                                      Parameters:
                                                                                      @@ -1231,7 +1231,7 @@

                                                                                      Submodules
                                                                                      -is_supergroup(subgroup: SymmetryGroup) → bool[source]
                                                                                      +is_supergroup(subgroup: SymmetryGroup) → bool[source]

                                                                                      True if this group is a supergroup of the supplied group.

                                                                                      Parameters:
                                                                                      @@ -1248,14 +1248,14 @@

                                                                                      Submodules
                                                                                      -abstract property symmetry_ops: set[SymmOp][source]
                                                                                      +abstract property symmetry_ops: set[SymmOp][source]

                                                                                      Returns: List of symmetry operations associated with the group.

                                                                                      -to_latex_string() → str[source]
                                                                                      +to_latex_string() → str[source]
                                                                                      Returns:

                                                                                      A latex formatted group symbol with proper subscripts and overlines.

                                                                                      @@ -1267,7 +1267,7 @@

                                                                                      Submodules
                                                                                      -in_array_list(array_list: list[ndarray] | ndarray, arr: ndarray, tol: float = 1e-05) → bool[source]
                                                                                      +in_array_list(array_list: list[ndarray] | ndarray, arr: ndarray, tol: float = 1e-05) → bool[source]

                                                                                      Extremely efficient nd-array comparison using numpy’s broadcasting. This function checks if a particular array a, is present in a list of arrays. It works for arrays of any size, e.g. even matrix searches.

                                                                                      @@ -1290,7 +1290,7 @@

                                                                                      Submodules
                                                                                      -sg_symbol_from_int_number(int_number: int, hexagonal: bool = True) → str[source]
                                                                                      +sg_symbol_from_int_number(int_number: int, hexagonal: bool = True) → str[source]

                                                                                      Obtains a SpaceGroup name from its international number.

                                                                                      Parameters:
                                                                                      @@ -1315,7 +1315,7 @@

                                                                                      Submodules
                                                                                      -class KPathBase(structure: Structure, symprec: float = 0.01, angle_tolerance=5, atol=1e-05, *args, **kwargs)[source]
                                                                                      +class KPathBase(structure: Structure, symprec: float = 0.01, angle_tolerance=5, atol=1e-05, *args, **kwargs)[source]

                                                                                      Bases: ABC

                                                                                      This is the base class for classes used to generate high-symmetry paths in reciprocal space (k-paths) for band structure calculations.

                                                                                      @@ -1334,31 +1334,31 @@

                                                                                      Submodules
                                                                                      -get_kpoints(line_density=20, coords_are_cartesian=True)[source]
                                                                                      +get_kpoints(line_density=20, coords_are_cartesian=True)[source]

                                                                                      Get kpoints along the path in Cartesian coordinates together with the critical-point labels.

                                                                                      -property kpath[source]
                                                                                      +property kpath[source]

                                                                                      The symmetry line path in reciprocal space.

                                                                                      -property lattice[source]
                                                                                      +property lattice[source]

                                                                                      The real space lattice.

                                                                                      -property rec_lattice[source]
                                                                                      +property rec_lattice[source]

                                                                                      The reciprocal space lattice.

                                                                                      -property structure[source]
                                                                                      +property structure[source]

                                                                                      The input structure.

                                                                                      @@ -1366,7 +1366,7 @@

                                                                                      Submodules
                                                                                      -class KPathLatimerMunro(structure, has_magmoms=False, magmom_axis=None, symprec=0.01, angle_tolerance=5, atol=1e-05)[source]
                                                                                      +class KPathLatimerMunro(structure, has_magmoms=False, magmom_axis=None, symprec=0.01, angle_tolerance=5, atol=1e-05)[source]

                                                                                      Bases: KPathBase

                                                                                      This class looks for a path along high-symmetry lines in the Brillouin zone. It is based on the method outlined in: @@ -1410,19 +1410,19 @@

                                                                                      Submodules
                                                                                      -static label_points(index)[source]
                                                                                      +static label_points(index)[source]

                                                                                      Axes used in generating labels for Latimer-Munro convention.

                                                                                      -static label_symbol(index)[source]
                                                                                      +static label_symbol(index)[source]

                                                                                      Letters used in generating labels for the Latimer-Munro convention.

                                                                                      -property mag_type[source]
                                                                                      +property mag_type[source]

                                                                                      The type of magnetic space group as a string. Current implementation does not distinguish between types 3 and 4, so return value is ‘3/4’. If has_magmoms is False, returns ‘0’.

                                                                                      @@ -1432,7 +1432,7 @@

                                                                                      Submodules
                                                                                      -class KPathSeek(structure: Structure, symprec: float = 0.01, angle_tolerance=5, atol=1e-05, system_is_tri=True)[source]
                                                                                      +class KPathSeek(structure: Structure, symprec: float = 0.01, angle_tolerance=5, atol=1e-05, system_is_tri=True)[source]

                                                                                      Bases: KPathBase

                                                                                      This class looks for a path along high-symmetry lines in the Brillouin zone. It is based on Hinuma, Y., Pizzi, G., Kumagai, Y., Oba, F., & Tanaka, I. (2017). Band structure diagram paths @@ -1458,7 +1458,7 @@

                                                                                      Submodules
                                                                                      -class KPathSetyawanCurtarolo(structure: Structure, symprec: float = 0.01, angle_tolerance=5, atol=1e-05)[source]
                                                                                      +class KPathSetyawanCurtarolo(structure: Structure, symprec: float = 0.01, angle_tolerance=5, atol=1e-05)[source]

                                                                                      Bases: KPathBase

                                                                                      This class looks for a path along high-symmetry lines in the Brillouin zone. @@ -1489,157 +1489,157 @@

                                                                                      Submodules
                                                                                      -bcc()[source]
                                                                                      +bcc()[source]

                                                                                      BCC Path.

                                                                                      -bctet1(c, a)[source]
                                                                                      +bctet1(c, a)[source]

                                                                                      BCT1 Path.

                                                                                      -bctet2(c, a)[source]
                                                                                      +bctet2(c, a)[source]

                                                                                      BCT2 Path.

                                                                                      -property conventional[source]
                                                                                      +property conventional[source]

                                                                                      The conventional cell structure.

                                                                                      -cubic()[source]
                                                                                      +cubic()[source]

                                                                                      CUB Path.

                                                                                      -fcc()[source]
                                                                                      +fcc()[source]

                                                                                      FCC Path.

                                                                                      -hex()[source]
                                                                                      +hex()[source]

                                                                                      HEX Path.

                                                                                      -mcl(b, c, beta)[source]
                                                                                      +mcl(b, c, beta)[source]

                                                                                      MCL Path.

                                                                                      -mclc1(a, b, c, alpha)[source]
                                                                                      +mclc1(a, b, c, alpha)[source]

                                                                                      MCLC1 Path.

                                                                                      -mclc2(a, b, c, alpha)[source]
                                                                                      +mclc2(a, b, c, alpha)[source]

                                                                                      MCLC2 Path.

                                                                                      -mclc3(a, b, c, alpha)[source]
                                                                                      +mclc3(a, b, c, alpha)[source]

                                                                                      MCLC3 Path.

                                                                                      -mclc4(a, b, c, alpha)[source]
                                                                                      +mclc4(a, b, c, alpha)[source]

                                                                                      MCLC4 Path.

                                                                                      -mclc5(a, b, c, alpha)[source]
                                                                                      +mclc5(a, b, c, alpha)[source]

                                                                                      MCLC5 Path.

                                                                                      -orc()[source]
                                                                                      +orc()[source]

                                                                                      ORC Path.

                                                                                      -orcc(a, b, c)[source]
                                                                                      +orcc(a, b, c)[source]

                                                                                      ORCC Path.

                                                                                      -orcf1(a, b, c)[source]
                                                                                      +orcf1(a, b, c)[source]

                                                                                      ORFC1 Path.

                                                                                      -orcf2(a, b, c)[source]
                                                                                      +orcf2(a, b, c)[source]

                                                                                      ORFC2 Path.

                                                                                      -orcf3(a, b, c)[source]
                                                                                      +orcf3(a, b, c)[source]

                                                                                      ORFC3 Path.

                                                                                      -orci(a, b, c)[source]
                                                                                      +orci(a, b, c)[source]

                                                                                      ORCI Path.

                                                                                      -property prim[source]
                                                                                      +property prim[source]

                                                                                      The primitive cell structure.

                                                                                      -property prim_rec[source]
                                                                                      +property prim_rec[source]

                                                                                      The primitive reciprocal cell structure.

                                                                                      -rhl1(alpha)[source]
                                                                                      +rhl1(alpha)[source]

                                                                                      RHL1 Path.

                                                                                      -rhl2(alpha)[source]
                                                                                      +rhl2(alpha)[source]

                                                                                      RHL2 Path.

                                                                                      -tet()[source]
                                                                                      +tet()[source]

                                                                                      TET Path.

                                                                                      -tria()[source]
                                                                                      +tria()[source]

                                                                                      TRI1a Path.

                                                                                      -trib()[source]
                                                                                      +trib()[source]

                                                                                      TRI1b Path.

                                                                                      @@ -1651,7 +1651,7 @@

                                                                                      Submodules
                                                                                      -class MagneticSpaceGroup(*args, **kwargs)[source]
                                                                                      +class MagneticSpaceGroup(*args, **kwargs)[source]

                                                                                      Bases: MagneticSpaceGroup

                                                                                      Representation of a magnetic space group.

                                                                                      Initialize a MagneticSpaceGroup from its Belov, Neronova and @@ -1736,7 +1736,7 @@

                                                                                      Submodules
                                                                                      -class JonesFaithfulTransformation(P, p)[source]
                                                                                      +class JonesFaithfulTransformation(P, p)[source]

                                                                                      Bases: object

                                                                                      Transformation for space-groups defined in a non-standard setting.

                                                                                      Transform between settings using matrix P and origin shift vector p, @@ -1762,13 +1762,13 @@

                                                                                      Submodules
                                                                                      -property P: list[list[float]][source]
                                                                                      +property P: list[list[float]][source]

                                                                                      Transformation matrix.

                                                                                      -classmethod from_origin_shift(origin_shift: str = '0,0,0') → Self[source]
                                                                                      +classmethod from_origin_shift(origin_shift: str = '0,0,0') → Self[source]

                                                                                      Construct SpaceGroupTransformation from its origin shift string.

                                                                                      Parameters:
                                                                                      @@ -1782,7 +1782,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_transformation_str(transformation_string: str = 'a,b,c;0,0,0') → Self[source]
                                                                                      +classmethod from_transformation_str(transformation_string: str = 'a,b,c;0,0,0') → Self[source]

                                                                                      Construct SpaceGroupTransformation from its transformation string.

                                                                                      Parameters:
                                                                                      @@ -1796,19 +1796,19 @@

                                                                                      Submodules
                                                                                      -property inverse: Self[source]
                                                                                      +property inverse: Self[source]

                                                                                      JonesFaithfulTransformation.

                                                                                      -property p: list[float][source]
                                                                                      +property p: list[float][source]

                                                                                      Translation vector.

                                                                                      -static parse_transformation_string(transformation_string: str = 'a,b,c;0,0,0') → tuple[list[list[float]] | ndarray, list[float]][source]
                                                                                      +static parse_transformation_string(transformation_string: str = 'a,b,c;0,0,0') → tuple[list[list[float]] | ndarray, list[float]][source]
                                                                                      Parameters:

                                                                                      transformation_string (str, optional) – Defaults to “a,b,c;0,0,0”.

                                                                                      @@ -1827,25 +1827,25 @@

                                                                                      Submodules
                                                                                      -transform_coords(coords: list[list[float]] | ndarray) → list[list[float]][source]
                                                                                      +transform_coords(coords: list[list[float]] | ndarray) → list[list[float]][source]

                                                                                      Takes a list of coordinates and transforms them.

                                                                                      -transform_lattice(lattice: Lattice) → Lattice[source]
                                                                                      +transform_lattice(lattice: Lattice) → Lattice[source]

                                                                                      Transforms a lattice.

                                                                                      -transform_symmop(symm_op: SymmOp | MagSymmOp) → SymmOp | MagSymmOp[source]
                                                                                      +transform_symmop(symm_op: SymmOp | MagSymmOp) → SymmOp | MagSymmOp[source]

                                                                                      Takes a symmetry operation and transforms it.

                                                                                      -property transformation_string: str[source]
                                                                                      +property transformation_string: str[source]

                                                                                      Transformation string.

                                                                                      @@ -1857,7 +1857,7 @@

                                                                                      Submodules
                                                                                      -get_shared_symmetry_operations(struct: Structure, pointops: list[list[SymmOp]], tol: float = 0.1)[source]
                                                                                      +get_shared_symmetry_operations(struct: Structure, pointops: list[list[SymmOp]], tol: float = 0.1)[source]

                                                                                      Get all the point group operations shared by a pair of atomic sites in the form [[point operations of site index 1],[],…,[]].

                                                                                      @@ -1876,7 +1876,7 @@

                                                                                      Submodules
                                                                                      -get_site_symmetries(struct: Structure, precision: float = 0.1) → list[list[SymmOp]][source]
                                                                                      +get_site_symmetries(struct: Structure, precision: float = 0.1) → list[list[SymmOp]][source]

                                                                                      Get all the point group operations centered on each atomic site in the form [[point operations of site index 1]…[[point operations of site index N]]].

                                                                                      @@ -1898,7 +1898,7 @@

                                                                                      Submodules
                                                                                      -class SymmetrizedStructure(structure: Structure, spacegroup: SpacegroupOperations, equivalent_positions: Sequence[int], wyckoff_letters: Sequence[str])[source]
                                                                                      +class SymmetrizedStructure(structure: Structure, spacegroup: SpacegroupOperations, equivalent_positions: Sequence[int], wyckoff_letters: Sequence[str])[source]

                                                                                      Bases: Structure

                                                                                      This class represents a symmetrized structure, i.e. a structure where the spacegroup and symmetry operations are defined. This class is @@ -1906,7 +1906,7 @@

                                                                                      Submodules
                                                                                      -equivalent_indices[source]
                                                                                      +equivalent_indices[source]

                                                                                      A list of lists of indices of the sites in the structure that are considered equivalent based on the symmetry operations of the space group.

                                                                                      @@ -1928,19 +1928,19 @@

                                                                                      Submodules
                                                                                      -as_dict()[source]
                                                                                      +as_dict()[source]

                                                                                      MSONable dict.

                                                                                      -copy() → Self[source]
                                                                                      +copy() → Self[source]

                                                                                      Make a copy of the SymmetrizedStructure.

                                                                                      -find_equivalent_sites(site: PeriodicSite) → list[PeriodicSite][source]
                                                                                      +find_equivalent_sites(site: PeriodicSite) → list[PeriodicSite][source]

                                                                                      Find all symmetrically equivalent sites for a particular site.

                                                                                      Parameters:
                                                                                      @@ -1960,7 +1960,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      diff --git a/docs/pymatgen.transformations.html b/docs/pymatgen.transformations.html index a52156ef213..184f1959387 100644 --- a/docs/pymatgen.transformations.html +++ b/docs/pymatgen.transformations.html @@ -4,7 +4,7 @@ - pymatgen.transformations package — pymatgen 2024.6.4 documentation + pymatgen.transformations package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -36,7 +36,7 @@
                                                                                      - 2024.6.4 + 2024.6.10
                                                                                      @@ -303,7 +303,7 @@

                                                                                      Submodules
                                                                                      -class AddAdsorbateTransformation(adsorbate, selective_dynamics=False, height=0.9, mi_vec=None, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]
                                                                                      +class AddAdsorbateTransformation(adsorbate, selective_dynamics=False, height=0.9, mi_vec=None, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Create adsorbate structures.

                                                                                      Use AdsorbateSiteFinder to add an adsorbate to a slab.

                                                                                      @@ -332,7 +332,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      Parameters:
                                                                                      @@ -361,7 +361,7 @@

                                                                                      Submodules
                                                                                      -class ChargeBalanceTransformation(charge_balance_sp)[source]
                                                                                      +class ChargeBalanceTransformation(charge_balance_sp)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This is a transformation that disorders a structure to make it charge balanced, given an oxidation state-decorated structure.

                                                                                      @@ -373,7 +373,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure)[source]
                                                                                      +apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -389,7 +389,7 @@

                                                                                      Submodules
                                                                                      -class CubicSupercellTransformation(min_atoms: int | None = None, max_atoms: int | None = None, min_length: float = 15.0, force_diagonal: bool = False, force_90_degrees: bool = False, angle_tolerance: float = 0.001)[source]
                                                                                      +class CubicSupercellTransformation(min_atoms: int | None = None, max_atoms: int | None = None, min_length: float = 15.0, force_diagonal: bool = False, force_90_degrees: bool = False, angle_tolerance: float = 0.001)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      A transformation that aims to generate a nearly cubic supercell structure from a structure.

                                                                                      @@ -419,7 +419,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure) → Structure[source]
                                                                                      +apply_transformation(structure: Structure) → Structure[source]

                                                                                      The algorithm solves for a transformation matrix that makes the supercell cubic. The matrix must have integer entries, so entries are rounded (in such a way that forces the matrix to be non-singular). From @@ -444,7 +444,7 @@

                                                                                      Submodules
                                                                                      -class DisorderOrderedTransformation(max_sites_to_merge=2)[source]
                                                                                      +class DisorderOrderedTransformation(max_sites_to_merge=2)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Not to be confused with OrderDisorderedTransformation, this transformation attempts to obtain a @@ -462,7 +462,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      Parameters:
                                                                                      @@ -488,7 +488,7 @@

                                                                                      Submodules
                                                                                      -class DopingTransformation(dopant, ionic_radius_tol=inf, min_length=10, alio_tol=0, codopant=False, max_structures_per_enum=100, allowed_doping_species=None, **kwargs)[source]
                                                                                      +class DopingTransformation(dopant, ionic_radius_tol=inf, min_length=10, alio_tol=0, codopant=False, max_structures_per_enum=100, allowed_doping_species=None, **kwargs)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      A transformation that performs doping of a structure.

                                                                                      @@ -521,7 +521,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      Parameters:
                                                                                      @@ -549,7 +549,7 @@

                                                                                      Submodules
                                                                                      -class EnumerateStructureTransformation(min_cell_size: int = 1, max_cell_size: int = 1, symm_prec: float = 0.1, refine_structure: bool = False, enum_precision_parameter: float = 0.001, check_ordered_symmetry: bool = True, max_disordered_sites: int | None = None, sort_criteria: str | Callable = 'ewald', timeout: float | None = None, n_jobs: int = -1)[source]
                                                                                      +class EnumerateStructureTransformation(min_cell_size: int = 1, max_cell_size: int = 1, symm_prec: float = 0.1, refine_structure: bool = False, enum_precision_parameter: float = 0.001, check_ordered_symmetry: bool = True, max_disordered_sites: int | None = None, sort_criteria: str | Callable = 'ewald', timeout: float | None = None, n_jobs: int = -1)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Order a disordered structure using enumlib. For complete orderings, this generally produces fewer structures that the OrderDisorderedStructure @@ -601,7 +601,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False) → Structure | list[dict][source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False) → Structure | list[dict][source]

                                                                                      Get either a single ordered structure or a sequence of all ordered structures.

                                                                                      @@ -628,7 +628,7 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Transform one structure to many.

                                                                                      @@ -636,7 +636,7 @@

                                                                                      Submodules
                                                                                      -class GrainBoundaryTransformation(rotation_axis, rotation_angle, expand_times=4, vacuum_thickness=0.0, ab_shift: tuple[float, float] | None = None, normal=False, ratio=True, plane=None, max_search=20, tol_coi=1e-08, rm_ratio=0.7, quick_gen=False)[source]
                                                                                      +class GrainBoundaryTransformation(rotation_axis, rotation_angle, expand_times=4, vacuum_thickness=0.0, ab_shift: tuple[float, float] | None = None, normal=False, ratio=True, plane=None, max_search=20, tol_coi=1e-08, rm_ratio=0.7, quick_gen=False)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      A transformation that creates a gb from a bulk structure.

                                                                                      @@ -702,7 +702,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure)[source]
                                                                                      +apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -722,7 +722,7 @@

                                                                                      Submodules
                                                                                      -class MagOrderParameterConstraint(order_parameter, species_constraints=None, site_constraint_name=None, site_constraints=None)[source]
                                                                                      +class MagOrderParameterConstraint(order_parameter, species_constraints=None, site_constraint_name=None, site_constraints=None)[source]

                                                                                      Bases: MSONable

                                                                                      This class can be used to supply MagOrderingTransformation to just a specific subset of species or sites that satisfy the @@ -746,7 +746,7 @@

                                                                                      Submodules
                                                                                      -satisfies_constraint(site)[source]
                                                                                      +satisfies_constraint(site)[source]

                                                                                      Check if a periodic site satisfies the constraint.

                                                                                      @@ -754,7 +754,7 @@

                                                                                      Submodules
                                                                                      -class MagOrderingTransformation(mag_species_spin, order_parameter=0.5, energy_model=None, **kwargs)[source]
                                                                                      +class MagOrderingTransformation(mag_species_spin, order_parameter=0.5, energy_model=None, **kwargs)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation takes a structure and returns a list of collinear magnetic orderings. For disordered structures, make an ordered @@ -783,7 +783,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False) → Structure | list[Structure][source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False) → Structure | list[Structure][source]

                                                                                      Apply MagOrderTransformation to an input structure.

                                                                                      Parameters:
                                                                                      @@ -807,14 +807,14 @@

                                                                                      Submodules
                                                                                      -static determine_min_cell(disordered_structure)[source]
                                                                                      +static determine_min_cell(disordered_structure)[source]

                                                                                      Determine the smallest supercell that is able to enumerate the provided structure with the given order parameter.

                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Transform one structure to many.

                                                                                      @@ -822,7 +822,7 @@

                                                                                      Submodules
                                                                                      -class MonteCarloRattleTransformation(rattle_std: float, min_distance: float, seed: int | None = None, **kwargs)[source]
                                                                                      +class MonteCarloRattleTransformation(rattle_std: float, min_distance: float, seed: int | None = None, **kwargs)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Uses a Monte Carlo rattle procedure to randomly perturb the sites in a structure.

                                                                                      @@ -853,7 +853,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure) → Structure[source]
                                                                                      +apply_transformation(structure: Structure) → Structure[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -869,7 +869,7 @@

                                                                                      Submodules
                                                                                      -class MultipleSubstitutionTransformation(sp_to_replace, r_fraction, substitution_dict, charge_balance_species=None, order=True)[source]
                                                                                      +class MultipleSubstitutionTransformation(sp_to_replace, r_fraction, substitution_dict, charge_balance_species=None, order=True)[source]

                                                                                      Bases: object

                                                                                      Perform multiple substitutions on a structure. For example, can do a fractional replacement of Ge in LiGePS with a list of species, creating one @@ -903,7 +903,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -922,7 +922,7 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Transform one structure to many.

                                                                                      @@ -930,7 +930,7 @@

                                                                                      Submodules
                                                                                      -class SQSTransformation(scaling: int | list[int], cluster_size_and_shell: dict[int, int] | None = None, search_time: float = 60, directory: str | None = None, instances: int | None = None, temperature: float = 1, wr: float = 1, wn: float = 1, wd: float = 0.5, tol: float = 0.001, icet_sqs_kwargs: dict[str, Any] | None = None, best_only: bool = True, remove_duplicate_structures: bool = True, reduction_algo: Literal['niggli', 'LLL'] = 'LLL', sqs_method: Literal['mcsqs', 'icet-enumeration', 'icet-monte_carlo'] = 'mcsqs')[source]
                                                                                      +class SQSTransformation(scaling: int | list[int], cluster_size_and_shell: dict[int, int] | None = None, search_time: float = 60, directory: str | None = None, instances: int | None = None, temperature: float = 1, wr: float = 1, wn: float = 1, wd: float = 0.5, tol: float = 0.001, icet_sqs_kwargs: dict[str, Any] | None = None, best_only: bool = True, remove_duplicate_structures: bool = True, reduction_algo: Literal['niggli', 'LLL'] = 'LLL', sqs_method: Literal['mcsqs', 'icet-enumeration', 'icet-monte_carlo'] = 'mcsqs')[source]

                                                                                      Bases: AbstractTransformation

                                                                                      A transformation that creates a special quasi-random structure (SQS) from a structure with partial occupancies.

                                                                                      @@ -978,7 +978,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]

                                                                                      Apply SQS transformation.

                                                                                      Parameters:
                                                                                      @@ -997,7 +997,7 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Transform one structure to many.

                                                                                      @@ -1005,7 +1005,7 @@

                                                                                      Submodules
                                                                                      -class SlabTransformation(miller_index, min_slab_size, min_vacuum_size, lll_reduce=False, center_slab=False, in_unit_planes=False, primitive=True, max_normal_search=None, shift=0, tol=0.1)[source]
                                                                                      +class SlabTransformation(miller_index, min_slab_size, min_vacuum_size, lll_reduce=False, center_slab=False, in_unit_planes=False, primitive=True, max_normal_search=None, shift=0, tol=0.1)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      A transformation that creates a slab from a structure.

                                                                                      @@ -1035,7 +1035,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure)[source]
                                                                                      +apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1051,7 +1051,7 @@

                                                                                      Submodules
                                                                                      -class SubstituteSurfaceSiteTransformation(atom, selective_dynamics=False, height=0.9, mi_vec=None, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)[source]
                                                                                      +class SubstituteSurfaceSiteTransformation(atom, selective_dynamics=False, height=0.9, mi_vec=None, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Use AdsorptionSiteFinder to perform substitution-type doping on the surface and returns all possible configurations where one dopant is substituted @@ -1079,7 +1079,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False) → list[dict] | Structure[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False) → list[dict] | Structure[source]
                                                                                      Parameters:
                                                                                      @@ -1108,7 +1108,7 @@

                                                                                      Submodules
                                                                                      -class SubstitutionPredictorTransformation(threshold=0.01, scale_volumes=True, **kwargs)[source]
                                                                                      +class SubstitutionPredictorTransformation(threshold=0.01, scale_volumes=True, **kwargs)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation takes a structure and uses the structure prediction module to find likely site substitutions.

                                                                                      @@ -1123,7 +1123,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1142,7 +1142,7 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Transform one structure to many.

                                                                                      @@ -1150,7 +1150,7 @@

                                                                                      Submodules
                                                                                      -class SuperTransformation(transformations, nstructures_per_trans=1)[source]
                                                                                      +class SuperTransformation(transformations, nstructures_per_trans=1)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This is a transformation that is inherently one-to-many. It is constructed from a list of transformations and returns one structure for each @@ -1170,7 +1170,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1189,7 +1189,7 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Transform one structure to many.

                                                                                      @@ -1197,7 +1197,7 @@

                                                                                      Submodules
                                                                                      -find_codopant(target: Species, oxidation_state: float, allowed_elements: Sequence[str] | None = None) → Species[source]
                                                                                      +find_codopant(target: Species, oxidation_state: float, allowed_elements: Sequence[str] | None = None) → Species[source]

                                                                                      Find the element from “allowed elements” that (i) possesses the desired “oxidation state” and (ii) is closest in ionic radius to the target specie.

                                                                                      @@ -1227,7 +1227,7 @@

                                                                                      Submodules
                                                                                      -class AddSitePropertyTransformation(site_properties)[source]
                                                                                      +class AddSitePropertyTransformation(site_properties)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Simple transformation to add site properties to a given structure.

                                                                                      @@ -1237,7 +1237,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure)[source]
                                                                                      +apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1254,7 +1254,7 @@

                                                                                      Submodules
                                                                                      -class InsertSitesTransformation(species, coords, coords_are_cartesian=False, validate_proximity=True)[source]
                                                                                      +class InsertSitesTransformation(species, coords, coords_are_cartesian=False, validate_proximity=True)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation substitutes certain sites with certain species.

                                                                                      @@ -1272,7 +1272,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure)[source]
                                                                                      +apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1289,7 +1289,7 @@

                                                                                      Submodules
                                                                                      -class PartialRemoveSitesTransformation(indices, fractions, algo=1)[source]
                                                                                      +class PartialRemoveSitesTransformation(indices, fractions, algo=1)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Remove fraction of specie from a structure. Requires an oxidation state decorated structure for Ewald sum to be @@ -1337,27 +1337,27 @@

                                                                                      Submodules
                                                                                      -ALGO_BEST_FIRST = 2[source]
                                                                                      +ALGO_BEST_FIRST = 2[source]

                                                                                      -ALGO_COMPLETE = 1[source]
                                                                                      +ALGO_COMPLETE = 1[source]
                                                                                      -ALGO_ENUMERATE = 3[source]
                                                                                      +ALGO_ENUMERATE = 3[source]
                                                                                      -ALGO_FAST = 0[source]
                                                                                      +ALGO_FAST = 0[source]
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1383,7 +1383,7 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Transform one structure to many.

                                                                                      @@ -1391,7 +1391,7 @@

                                                                                      Submodules
                                                                                      -class RadialSiteDistortionTransformation(site_index: int, displacement: float = 0.1, nn_only: bool = False)[source]
                                                                                      +class RadialSiteDistortionTransformation(site_index: int, displacement: float = 0.1, nn_only: bool = False)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Radially perturbs atoms around a site. Can be used to create spherical distortion due to a point defect.

                                                                                      @@ -1413,7 +1413,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure)[source]
                                                                                      +apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1427,7 +1427,7 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Determine if a Transformation is a one-to-many transformation. If a Transformation is a one-to-many transformation, the apply_transformation method should have a keyword arg @@ -1437,7 +1437,7 @@

                                                                                      Submodules
                                                                                      -property use_multiprocessing[source]
                                                                                      +property use_multiprocessing[source]

                                                                                      Indicates whether the transformation can be applied by a subprocessing pool. This should be overridden to return True for transformations that the transmuter can parallelize.

                                                                                      @@ -1447,7 +1447,7 @@

                                                                                      Submodules
                                                                                      -class RemoveSitesTransformation(indices_to_remove)[source]
                                                                                      +class RemoveSitesTransformation(indices_to_remove)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Remove certain sites in a structure.

                                                                                      @@ -1457,7 +1457,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure)[source]
                                                                                      +apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1474,7 +1474,7 @@

                                                                                      Submodules
                                                                                      -class ReplaceSiteSpeciesTransformation(indices_species_map)[source]
                                                                                      +class ReplaceSiteSpeciesTransformation(indices_species_map)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation substitutes certain sites with certain species.

                                                                                      @@ -1489,7 +1489,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure)[source]
                                                                                      +apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1506,7 +1506,7 @@

                                                                                      Submodules
                                                                                      -class TranslateSitesTransformation(indices_to_move, translation_vector, vector_in_frac_coords=True)[source]
                                                                                      +class TranslateSitesTransformation(indices_to_move, translation_vector, vector_in_frac_coords=True)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This class translates a set of sites by a certain vector.

                                                                                      @@ -1525,7 +1525,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure)[source]
                                                                                      +apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1540,13 +1540,13 @@

                                                                                      Submodules
                                                                                      -as_dict()[source]
                                                                                      +as_dict()[source]

                                                                                      JSON-serializable dict representation.

                                                                                      -property inverse: TranslateSitesTransformation[source]
                                                                                      +property inverse: TranslateSitesTransformation[source]

                                                                                      TranslateSitesTransformation with the reverse translation.

                                                                                      @@ -1561,7 +1561,7 @@

                                                                                      Submodules
                                                                                      -class AutoOxiStateDecorationTransformation(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015)[source]
                                                                                      +class AutoOxiStateDecorationTransformation(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation automatically decorates a structure with oxidation states using a bond valence approach.

                                                                                      @@ -1584,7 +1584,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1600,7 +1600,7 @@

                                                                                      Submodules
                                                                                      -class ChargedCellTransformation(charge=0)[source]
                                                                                      +class ChargedCellTransformation(charge=0)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      The ChargedCellTransformation applies a charge to a structure (or defect object).

                                                                                      @@ -1612,7 +1612,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1626,7 +1626,7 @@

                                                                                      Submodules
                                                                                      -property inverse[source]
                                                                                      +property inverse[source]

                                                                                      NotImplementedError.

                                                                                      Type:
                                                                                      @@ -1639,7 +1639,7 @@

                                                                                      Submodules
                                                                                      -class ConventionalCellTransformation(symprec: float = 0.01, angle_tolerance=5, international_monoclinic=True)[source]
                                                                                      +class ConventionalCellTransformation(symprec: float = 0.01, angle_tolerance=5, international_monoclinic=True)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This class finds the conventional cell of the input structure.

                                                                                      @@ -1654,7 +1654,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Get most primitive cell for structure.

                                                                                      Parameters:
                                                                                      @@ -1670,7 +1670,7 @@

                                                                                      Submodules
                                                                                      -class DeformStructureTransformation(deformation=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]
                                                                                      +class DeformStructureTransformation(deformation=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation deforms a structure by a deformation gradient matrix.

                                                                                      @@ -1680,7 +1680,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1694,7 +1694,7 @@

                                                                                      Submodules
                                                                                      -property inverse[source]
                                                                                      +property inverse[source]

                                                                                      Inverse Transformation.

                                                                                      @@ -1702,7 +1702,7 @@

                                                                                      Submodules
                                                                                      -class DiscretizeOccupanciesTransformation(max_denominator=5, tol: float | None = None, fix_denominator=False)[source]
                                                                                      +class DiscretizeOccupanciesTransformation(max_denominator=5, tol: float | None = None, fix_denominator=False)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Discretizes the site occupancies in a disordered structure; useful for grouping similar structures or as a pre-processing step for order-disorder @@ -1724,7 +1724,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Discretizes the site occupancies in the structure.

                                                                                      Parameters:
                                                                                      @@ -1740,7 +1740,7 @@

                                                                                      Submodules
                                                                                      -class OrderDisorderedStructureTransformation(algo=0, symmetrized_structures=False, no_oxi_states=False)[source]
                                                                                      +class OrderDisorderedStructureTransformation(algo=0, symmetrized_structures=False, no_oxi_states=False)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Order a disordered structure. The disordered structure must be oxidation state decorated for Ewald sum to be computed. No attempt is made to perform @@ -1776,22 +1776,22 @@

                                                                                      Submodules
                                                                                      -ALGO_BEST_FIRST = 2[source]
                                                                                      +ALGO_BEST_FIRST = 2[source]

                                                                                      -ALGO_COMPLETE = 1[source]
                                                                                      +ALGO_COMPLETE = 1[source]
                                                                                      -ALGO_FAST = 0[source]
                                                                                      +ALGO_FAST = 0[source]
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False) → Structure[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False) → Structure[source]

                                                                                      For this transformation, the apply_transformation method will return only the ordered structure with the lowest Ewald energy, to be consistent with the method signature of the other transformations. @@ -1821,13 +1821,13 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Transform one structure to many.

                                                                                      -property lowest_energy_structure[source]
                                                                                      +property lowest_energy_structure[source]

                                                                                      Lowest energy structure found.

                                                                                      @@ -1835,7 +1835,7 @@

                                                                                      Submodules
                                                                                      -class OxidationStateDecorationTransformation(oxidation_states)[source]
                                                                                      +class OxidationStateDecorationTransformation(oxidation_states)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation decorates a structure with oxidation states.

                                                                                      @@ -1848,7 +1848,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1864,13 +1864,13 @@

                                                                                      Submodules
                                                                                      -class OxidationStateRemovalTransformation[source]
                                                                                      +class OxidationStateRemovalTransformation[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation removes oxidation states from a structure.

                                                                                      No arg needed.

                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1886,7 +1886,7 @@

                                                                                      Submodules
                                                                                      -class PartialRemoveSpecieTransformation(specie_to_remove, fraction_to_remove, algo=0)[source]
                                                                                      +class PartialRemoveSpecieTransformation(specie_to_remove, fraction_to_remove, algo=0)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Remove fraction of specie from a structure.

                                                                                      Requires an oxidation state decorated structure for Ewald sum to be @@ -1909,27 +1909,27 @@

                                                                                      Submodules
                                                                                      -ALGO_BEST_FIRST = 2[source]
                                                                                      +ALGO_BEST_FIRST = 2[source]

                                                                                      -ALGO_COMPLETE = 1[source]
                                                                                      +ALGO_COMPLETE = 1[source]
                                                                                      -ALGO_ENUMERATE = 3[source]
                                                                                      +ALGO_ENUMERATE = 3[source]
                                                                                      -ALGO_FAST = 0[source]
                                                                                      +ALGO_FAST = 0[source]
                                                                                      -apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
                                                                                      +apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1956,7 +1956,7 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Transform one structure to many.

                                                                                      @@ -1964,7 +1964,7 @@

                                                                                      Submodules
                                                                                      -class PerturbStructureTransformation(distance: float = 0.01, min_distance: float | None = None)[source]
                                                                                      +class PerturbStructureTransformation(distance: float = 0.01, min_distance: float | None = None)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation perturbs a structure by a specified distance in random directions. Used for breaking symmetries.

                                                                                      @@ -1982,7 +1982,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure) → Structure[source]
                                                                                      +apply_transformation(structure: Structure) → Structure[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -1998,7 +1998,7 @@

                                                                                      Submodules
                                                                                      -class PrimitiveCellTransformation(tolerance=0.5)[source]
                                                                                      +class PrimitiveCellTransformation(tolerance=0.5)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This class finds the primitive cell of the input structure. It returns a structure that is not necessarily orthogonalized @@ -2013,7 +2013,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Get most primitive cell for structure.

                                                                                      Parameters:
                                                                                      @@ -2030,7 +2030,7 @@

                                                                                      Submodules
                                                                                      -class RemoveSpeciesTransformation(species_to_remove)[source]
                                                                                      +class RemoveSpeciesTransformation(species_to_remove)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Remove all occurrences of some species from a structure.

                                                                                      @@ -2040,7 +2040,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -2056,7 +2056,7 @@

                                                                                      Submodules
                                                                                      -class RotationTransformation(axis, angle, angle_in_radians=False)[source]
                                                                                      +class RotationTransformation(axis, angle, angle_in_radians=False)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      The RotationTransformation applies a rotation to a structure.

                                                                                      @@ -2071,7 +2071,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -2085,7 +2085,7 @@

                                                                                      Submodules
                                                                                      -property inverse[source]
                                                                                      +property inverse[source]

                                                                                      Inverse Transformation.

                                                                                      @@ -2093,7 +2093,7 @@

                                                                                      Submodules
                                                                                      -class ScaleToRelaxedTransformation(unrelaxed_structure, relaxed_structure, species_map=None)[source]
                                                                                      +class ScaleToRelaxedTransformation(unrelaxed_structure, relaxed_structure, species_map=None)[source]

                                                                                      Bases: AbstractTransformation

                                                                                      Takes the unrelaxed and relaxed structure and applies its site and volume relaxation to a structurally similar structures (e.g. bulk: NaCl and PbTe @@ -2118,7 +2118,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Get a copy of structure with lattice parameters and sites scaled to the same degree as the relaxed_structure.

                                                                                      @@ -2133,7 +2133,7 @@

                                                                                      Submodules
                                                                                      -class SubstitutionTransformation(species_map: dict[SpeciesLike, SpeciesLike | dict[SpeciesLike, float]] | list[tuple[SpeciesLike, SpeciesLike]])[source]
                                                                                      +class SubstitutionTransformation(species_map: dict[SpeciesLike, SpeciesLike | dict[SpeciesLike, float]] | list[tuple[SpeciesLike, SpeciesLike]])[source]

                                                                                      Bases: AbstractTransformation

                                                                                      This transformation substitutes species for one another.

                                                                                      @@ -2148,7 +2148,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure: Structure) → Structure[source]
                                                                                      +apply_transformation(structure: Structure) → Structure[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -2162,7 +2162,7 @@

                                                                                      Submodules
                                                                                      -property inverse[source]
                                                                                      +property inverse[source]

                                                                                      Inverse Transformation.

                                                                                      @@ -2170,7 +2170,7 @@

                                                                                      Submodules
                                                                                      -class SupercellTransformation(scaling_matrix=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]
                                                                                      +class SupercellTransformation(scaling_matrix=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]

                                                                                      Bases: AbstractTransformation

                                                                                      The SupercellTransformation replicates a unit cell to a supercell.

                                                                                      @@ -2184,7 +2184,7 @@

                                                                                      Submodules
                                                                                      -apply_transformation(structure)[source]
                                                                                      +apply_transformation(structure)[source]

                                                                                      Apply the transformation.

                                                                                      Parameters:
                                                                                      @@ -2198,7 +2198,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_boundary_distance(structure: Structure, min_boundary_dist: float = 6, allow_rotation: bool = False, max_atoms: float = -1) → Self[source]
                                                                                      +classmethod from_boundary_distance(structure: Structure, min_boundary_dist: float = 6, allow_rotation: bool = False, max_atoms: float = -1) → Self[source]

                                                                                      Get a SupercellTransformation according to the desired minimum distance between periodic boundaries of the resulting supercell.

                                                                                      @@ -2223,7 +2223,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_scaling_factors(scale_a: float = 1, scale_b: float = 1, scale_c: float = 1) → Self[source]
                                                                                      +classmethod from_scaling_factors(scale_a: float = 1, scale_b: float = 1, scale_c: float = 1) → Self[source]

                                                                                      Convenience method to get a SupercellTransformation from a simple series of three numbers for scaling each lattice vector. Equivalent to calling the normal with [[scale_a, 0, 0], [0, scale_b, 0], @@ -2244,7 +2244,7 @@

                                                                                      Submodules
                                                                                      -property inverse[source]
                                                                                      +property inverse[source]

                                                                                      NotImplementedError.

                                                                                      Type:
                                                                                      @@ -2261,12 +2261,12 @@

                                                                                      Submodules
                                                                                      -class AbstractTransformation[source]
                                                                                      +class AbstractTransformation[source]

                                                                                      Bases: MSONable, ABC

                                                                                      Abstract transformation class.

                                                                                      -abstract apply_transformation(structure: Structure)[source]
                                                                                      +abstract apply_transformation(structure: Structure)[source]

                                                                                      Apply the transformation to a structure. Depending on whether a transformation is one-to-many, there may be an option to return a ranked list of structures.

                                                                                      @@ -2296,7 +2296,7 @@

                                                                                      Submodules
                                                                                      -property inverse: AbstractTransformation | None[source]
                                                                                      +property inverse: AbstractTransformation | None[source]

                                                                                      The inverse transformation if available. Otherwise, should return None. Defaults to None, so only need to override if applicable.

                                                                                      @@ -2304,7 +2304,7 @@

                                                                                      Submodules
                                                                                      -property is_one_to_many: bool[source]
                                                                                      +property is_one_to_many: bool[source]

                                                                                      Determine if a Transformation is a one-to-many transformation. In that case, the apply_transformation method should have a keyword arg “return_ranked_list” which allows for the transformed structures to be returned as a ranked list. @@ -2313,7 +2313,7 @@

                                                                                      Submodules
                                                                                      -property use_multiprocessing: bool[source]
                                                                                      +property use_multiprocessing: bool[source]

                                                                                      Indicates whether the transformation can be applied by a subprocessing pool. This should be overridden to return True for transformations that the transmuter can parallelize.

                                                                                      diff --git a/docs/pymatgen.util.html b/docs/pymatgen.util.html index 8aeb08e01eb..f6225ae6fb4 100644 --- a/docs/pymatgen.util.html +++ b/docs/pymatgen.util.html @@ -4,7 +4,7 @@ - pymatgen.util package — pymatgen 2024.6.4 documentation + pymatgen.util package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                      - 2024.6.4 + 2024.6.10
                                                                                      @@ -257,12 +257,12 @@

                                                                                      Submodules
                                                                                      -class Simplex(coords)[source]
                                                                                      +class Simplex(coords)[source]

                                                                                      Bases: MSONable

                                                                                      A generalized simplex object. See http://wikipedia.org/wiki/Simplex.

                                                                                      -space_dim[source]
                                                                                      +space_dim[source]

                                                                                      Dimension of the space. Usually, this is 1 more than the simplex_dim.

                                                                                      Type:
                                                                                      @@ -273,7 +273,7 @@

                                                                                      Submodules
                                                                                      -simplex_dim[source]
                                                                                      +simplex_dim[source]

                                                                                      Dimension of the simplex coordinate space.

                                                                                      Type:
                                                                                      @@ -291,7 +291,7 @@

                                                                                      Submodules
                                                                                      -bary_coords(point)[source]
                                                                                      +bary_coords(point)[source]
                                                                                      Parameters:

                                                                                      point (ArrayLike) – Point coordinates.

                                                                                      @@ -304,13 +304,13 @@

                                                                                      Submodules
                                                                                      -property coords: ndarray[source]
                                                                                      +property coords: ndarray[source]

                                                                                      A copy of the vertex coordinates in the simplex.

                                                                                      -in_simplex(point: Sequence[float], tolerance: float = 1e-08) → bool[source]
                                                                                      +in_simplex(point: Sequence[float], tolerance: float = 1e-08) → bool[source]

                                                                                      Check if a point is in the simplex using the standard barycentric coordinate system algorithm.

                                                                                      Taking an arbitrary vertex as an origin, we compute the basis for the @@ -331,7 +331,7 @@

                                                                                      Submodules
                                                                                      -line_intersection(point1: Sequence[float], point2: Sequence[float], tolerance: float = 1e-08)[source]
                                                                                      +line_intersection(point1: Sequence[float], point2: Sequence[float], tolerance: float = 1e-08)[source]

                                                                                      Compute the intersection points of a line with a simplex.

                                                                                      Parameters:
                                                                                      @@ -349,7 +349,7 @@

                                                                                      Submodules
                                                                                      -point_from_bary_coords(bary_coords: ArrayLike)[source]
                                                                                      +point_from_bary_coords(bary_coords: ArrayLike)[source]
                                                                                      Parameters:

                                                                                      bary_coords (ArrayLike) – Barycentric coordinates (d+1, d).

                                                                                      @@ -365,7 +365,7 @@

                                                                                      Submodules
                                                                                      -property volume: float[source]
                                                                                      +property volume: float[source]

                                                                                      Volume of the simplex.

                                                                                      @@ -373,7 +373,7 @@

                                                                                      Submodules
                                                                                      -all_distances(coords1: ArrayLike, coords2: ArrayLike) → np.ndarray[source]
                                                                                      +all_distances(coords1: ArrayLike, coords2: ArrayLike) → np.ndarray[source]

                                                                                      Get the distances between two lists of coordinates.

                                                                                      Parameters:
                                                                                      @@ -391,7 +391,7 @@

                                                                                      Submodules
                                                                                      -barycentric_coords(coords, simplex)[source]
                                                                                      +barycentric_coords(coords, simplex)[source]

                                                                                      Convert a list of coordinates to barycentric coordinates, given a simplex with d+1 points. Only works for d >= 2.

                                                                                      @@ -410,7 +410,7 @@

                                                                                      Submodules
                                                                                      -coord_list_mapping(subset: ArrayLike, superset: ArrayLike, atol: float = 1e-08)[source]
                                                                                      +coord_list_mapping(subset: ArrayLike, superset: ArrayLike, atol: float = 1e-08)[source]

                                                                                      Get the index mapping from a subset to a superset. Subset and superset cannot contain duplicate rows.

                                                                                      @@ -429,7 +429,7 @@

                                                                                      Submodules
                                                                                      -coord_list_mapping_pbc(subset, superset, atol: float = 1e-08, pbc: PbcLike = (True, True, True))[source]
                                                                                      +coord_list_mapping_pbc(subset, superset, atol: float = 1e-08, pbc: PbcLike = (True, True, True))[source]

                                                                                      Get the index mapping from a subset to a superset. Superset cannot contain duplicate matching rows.

                                                                                      @@ -450,7 +450,7 @@

                                                                                      Submodules
                                                                                      -find_in_coord_list(coord_list, coord, atol: float = 1e-08)[source]
                                                                                      +find_in_coord_list(coord_list, coord, atol: float = 1e-08)[source]

                                                                                      Find the indices of matches of a particular coord in a coord_list.

                                                                                      Parameters:
                                                                                      @@ -469,7 +469,7 @@

                                                                                      Submodules
                                                                                      -find_in_coord_list_pbc(frac_coord_list, frac_coord, atol: float = 1e-08, pbc: PbcLike = (True, True, True)) → np.ndarray[source]
                                                                                      +find_in_coord_list_pbc(frac_coord_list, frac_coord, atol: float = 1e-08, pbc: PbcLike = (True, True, True)) → np.ndarray[source]

                                                                                      Get the indices of all points in a fractional coord list that are equal to a fractional coord (with a tolerance), taking into account periodic boundary conditions.

                                                                                      @@ -491,7 +491,7 @@

                                                                                      Submodules
                                                                                      -get_angle(v1: ArrayLike, v2: ArrayLike, units: Literal['degrees', 'radians'] = 'degrees') → float[source]
                                                                                      +get_angle(v1: ArrayLike, v2: ArrayLike, units: Literal['degrees', 'radians'] = 'degrees') → float[source]

                                                                                      Calculate the angle between two vectors.

                                                                                      Parameters:
                                                                                      @@ -509,7 +509,7 @@

                                                                                      Submodules
                                                                                      -get_linear_interpolated_value(x_values: ArrayLike, y_values: ArrayLike, x: float) → float[source]
                                                                                      +get_linear_interpolated_value(x_values: ArrayLike, y_values: ArrayLike, x: float) → float[source]

                                                                                      Get an interpolated value by linear interpolation between two values. This method is written to avoid dependency on scipy, which causes issues on threading servers.

                                                                                      @@ -529,7 +529,7 @@

                                                                                      Submodules
                                                                                      -in_coord_list(coord_list, coord, atol: float = 1e-08) → bool[source]
                                                                                      +in_coord_list(coord_list, coord, atol: float = 1e-08) → bool[source]

                                                                                      Test if a particular coord is within a coord_list.

                                                                                      Parameters:
                                                                                      @@ -551,7 +551,7 @@

                                                                                      Submodules
                                                                                      -in_coord_list_pbc(fcoord_list, fcoord, atol: float = 1e-08, pbc: PbcLike = (True, True, True)) → bool[source]
                                                                                      +in_coord_list_pbc(fcoord_list, fcoord, atol: float = 1e-08, pbc: PbcLike = (True, True, True)) → bool[source]

                                                                                      Test if a particular fractional coord is within a fractional coord_list.

                                                                                      Parameters:
                                                                                      @@ -574,7 +574,7 @@

                                                                                      Submodules
                                                                                      -is_coord_subset(subset: ArrayLike, superset: ArrayLike, atol: float = 1e-08) → bool[source]
                                                                                      +is_coord_subset(subset: ArrayLike, superset: ArrayLike, atol: float = 1e-08) → bool[source]

                                                                                      Test if all coords in subset are contained in superset. Doesn’t use periodic boundary conditions.

                                                                                      @@ -596,7 +596,7 @@

                                                                                      Submodules
                                                                                      -is_coord_subset_pbc(subset, superset, atol: float = 1e-08, mask=None, pbc: PbcLike = (True, True, True)) → bool[source]
                                                                                      +is_coord_subset_pbc(subset, superset, atol: float = 1e-08, mask=None, pbc: PbcLike = (True, True, True)) → bool[source]

                                                                                      Test if all fractional coords in subset are contained in superset.

                                                                                      Parameters:
                                                                                      @@ -622,7 +622,7 @@

                                                                                      Submodules
                                                                                      -lattice_points_in_supercell(supercell_matrix)[source]
                                                                                      +lattice_points_in_supercell(supercell_matrix)[source]

                                                                                      Get the list of points on the original lattice contained in the supercell in fractional coordinates (with the supercell basis). e.g. [[2,0,0],[0,1,0],[0,0,1]] returns [[0,0,0],[0.5,0,0]].

                                                                                      @@ -638,7 +638,7 @@

                                                                                      Submodules
                                                                                      -pbc_diff(frac_coords1: ArrayLike, frac_coords2: ArrayLike, pbc: PbcLike = (True, True, True))[source]
                                                                                      +pbc_diff(frac_coords1: ArrayLike, frac_coords2: ArrayLike, pbc: PbcLike = (True, True, True))[source]

                                                                                      Get the ‘fractional distance’ between two coordinates taking into account periodic boundary conditions.

                                                                                      @@ -663,7 +663,7 @@

                                                                                      Submodules
                                                                                      -pbc_shortest_vectors(lattice, frac_coords1, frac_coords2, mask=None, return_d2: bool = False)[source]
                                                                                      +pbc_shortest_vectors(lattice, frac_coords1, frac_coords2, mask=None, return_d2: bool = False)[source]

                                                                                      Get the shortest vectors between two lists of coordinates taking into account periodic boundary conditions and the lattice.

                                                                                      @@ -700,7 +700,7 @@

                                                                                      Submodules
                                                                                      -coord_list_mapping_pbc(subset, superset, atol=1e-08, pbc=(True, True, True))[source]
                                                                                      +coord_list_mapping_pbc(subset, superset, atol=1e-08, pbc=(True, True, True))[source]

                                                                                      Gives the index mapping from a subset to a superset. Superset cannot contain duplicate matching rows

                                                                                      @@ -720,7 +720,7 @@

                                                                                      Submodules
                                                                                      -is_coord_subset_pbc(subset, superset, atol, mask, pbc=(True, True, True))[source]
                                                                                      +is_coord_subset_pbc(subset, superset, atol, mask, pbc=(True, True, True))[source]

                                                                                      Tests if all fractional coords in subset are contained in superset. Allows specification of a mask determining pairs that are not allowed to match to each other

                                                                                      @@ -741,7 +741,7 @@

                                                                                      Submodules
                                                                                      -pbc_shortest_vectors(lattice, fcoords1, fcoords2, mask=None, return_d2=False, lll_frac_tol=None)[source]
                                                                                      +pbc_shortest_vectors(lattice, fcoords1, fcoords2, mask=None, return_d2=False, lll_frac_tol=None)[source]

                                                                                      Get the shortest vectors between two lists of coordinates taking into account periodic boundary conditions and the lattice.

                                                                                      @@ -787,59 +787,59 @@

                                                                                      Submodules
                                                                                      -BibTeX(*args, **kwargs)[source]
                                                                                      +BibTeX(*args, **kwargs)[source]

                                                                                      Perform no good and no bad.

                                                                                      -Doi(*args, **kwargs)[source]
                                                                                      +Doi(*args, **kwargs)[source]

                                                                                      Perform no good and no bad.

                                                                                      -class InactiveDueCreditCollector[source]
                                                                                      +class InactiveDueCreditCollector[source]

                                                                                      Bases: object

                                                                                      Just a stub at the Collector which would not do anything.

                                                                                      -activate(*args, **kwargs)[source]
                                                                                      +activate(*args, **kwargs)[source]

                                                                                      Perform no good and no bad.

                                                                                      -active = False[source]
                                                                                      +active = False[source]
                                                                                      -add(*args, **kwargs)[source]
                                                                                      +add(*args, **kwargs)[source]

                                                                                      Perform no good and no bad.

                                                                                      -cite(*args, **kwargs)[source]
                                                                                      +cite(*args, **kwargs)[source]

                                                                                      Perform no good and no bad.

                                                                                      -dcite(*args, **kwargs)[source]
                                                                                      +dcite(*args, **kwargs)[source]

                                                                                      If I could cite I would.

                                                                                      -dump(*args, **kwargs)[source]
                                                                                      +dump(*args, **kwargs)[source]

                                                                                      Perform no good and no bad.

                                                                                      -load(*args, **kwargs)[source]
                                                                                      +load(*args, **kwargs)[source]

                                                                                      Perform no good and no bad.

                                                                                      @@ -847,13 +847,13 @@

                                                                                      Submodules
                                                                                      -Text(*args, **kwargs)[source]
                                                                                      +Text(*args, **kwargs)[source]

                                                                                      Perform no good and no bad.

                                                                                      -Url(*args, **kwargs)[source]
                                                                                      +Url(*args, **kwargs)[source]

                                                                                      Perform no good and no bad.

                                                                                      @@ -898,7 +898,7 @@

                                                                                      Submodules
                                                                                      -weisfeiler_lehman_graph_hash(graph: nx.Graph, edge_attr=None, node_attr=None, iterations=3, digest_size=16)[source]
                                                                                      +weisfeiler_lehman_graph_hash(graph: nx.Graph, edge_attr=None, node_attr=None, iterations=3, digest_size=16)[source]

                                                                                      Return Weisfeiler Lehman (WL) graph hash.

                                                                                      The function iteratively aggregates and hashes neighborhoods of each node. After each node’s neighbors are hashed to obtain updated node labels, @@ -960,7 +960,7 @@

                                                                                      Submodules
                                                                                      -weisfeiler_lehman_subgraph_hashes(graph, edge_attr=None, node_attr=None, iterations=3, digest_size=16)[source]
                                                                                      +weisfeiler_lehman_subgraph_hashes(graph, edge_attr=None, node_attr=None, iterations=3, digest_size=16)[source]

                                                                                      Return a dictionary of subgraph hashes by node.

                                                                                      The dictionary is keyed by node to a list of hashes in increasingly sized induced subgraphs containing the nodes within 2*k edges @@ -1050,7 +1050,7 @@

                                                                                      Submodules
                                                                                      -clean_lines(string_list, remove_empty_lines=True)[source]
                                                                                      +clean_lines(string_list, remove_empty_lines=True)[source]

                                                                                      Strips whitespace, carriage returns and empty lines from a list of strings.

                                                                                      Parameters:
                                                                                      @@ -1068,7 +1068,7 @@

                                                                                      Submodules
                                                                                      -micro_pyawk(filename, search, results=None, debug=None, postdebug=None)[source]
                                                                                      +micro_pyawk(filename, search, results=None, debug=None, postdebug=None)[source]

                                                                                      Small awk-mimicking search routine.

                                                                                      ‘file’ is file to search through. ‘search’ is the “search program”, a list of lists/tuples with 3 elements; @@ -1101,7 +1101,7 @@

                                                                                      Submodules
                                                                                      -make_symmetric_matrix_from_upper_tri(val)[source]
                                                                                      +make_symmetric_matrix_from_upper_tri(val)[source]

                                                                                      Given a symmetric matrix in upper triangular matrix form as flat array indexes as: [A_xx,A_yy,A_zz,A_xy,A_xz,A_yz] This will generate the full matrix: @@ -1110,7 +1110,7 @@

                                                                                      Submodules
                                                                                      -round_to_sigfigs(num, sig_figs)[source]
                                                                                      +round_to_sigfigs(num, sig_figs)[source]

                                                                                      Rounds a number rounded to a specific number of significant figures instead of to a specific precision.

                                                                                      @@ -1124,13 +1124,13 @@

                                                                                      Submodules
                                                                                      -jit(func)[source]
                                                                                      +jit(func)[source]

                                                                                      Replacement for numba.jit when numba is not installed that does nothing.

                                                                                      -njit(func)[source]
                                                                                      +njit(func)[source]

                                                                                      Replacement for numba.njit when numba is not installed that does nothing.

                                                                                      @@ -1140,7 +1140,7 @@

                                                                                      Submodules
                                                                                      -add_fig_kwargs(func)[source]
                                                                                      +add_fig_kwargs(func)[source]

                                                                                      Decorator that adds keyword arguments for functions returning matplotlib figures.

                                                                                      The function should return either a matplotlib figure or None to signal @@ -1150,7 +1150,7 @@

                                                                                      Submodules
                                                                                      -format_formula(formula: str) → str[source]
                                                                                      +format_formula(formula: str) → str[source]

                                                                                      Convert str of chemical formula into latex format for labelling purposes.

                                                                                      @@ -1162,7 +1162,7 @@

                                                                                      Submodules
                                                                                      -get_ax3d_fig(ax: Axes = None, **kwargs) → tuple[Axes3D, Figure][source]
                                                                                      +get_ax3d_fig(ax: Axes = None, **kwargs) → tuple[Axes3D, Figure][source]

                                                                                      Helper function used in plot functions supporting an optional Axes3D argument. If ax is None, we build the matplotlib figure and create the Axes3D else we return the current active figure.

                                                                                      @@ -1184,7 +1184,7 @@

                                                                                      Submodules
                                                                                      -get_ax_fig(ax: Axes = None, **kwargs) → tuple[Axes, Figure][source]
                                                                                      +get_ax_fig(ax: Axes = None, **kwargs) → tuple[Axes, Figure][source]

                                                                                      Helper function used in plot functions supporting an optional Axes argument. If ax is None, we build the matplotlib figure and create the Axes else we return the current active figure.

                                                                                      @@ -1206,7 +1206,7 @@

                                                                                      Submodules
                                                                                      -get_axarray_fig_plt(ax_array, nrows=1, ncols=1, sharex: bool = False, sharey: bool = False, squeeze: bool = True, subplot_kw=None, gridspec_kw=None, **fig_kw)[source]
                                                                                      +get_axarray_fig_plt(ax_array, nrows=1, ncols=1, sharex: bool = False, sharey: bool = False, squeeze: bool = True, subplot_kw=None, gridspec_kw=None, **fig_kw)[source]

                                                                                      Helper function used in plot functions that accept an optional array of Axes as argument. If ax_array is None, we build the matplotlib figure and create the array of Axes by calling plt.subplots else we return the @@ -1225,7 +1225,7 @@

                                                                                      Submodules
                                                                                      -periodic_table_heatmap(elemental_data=None, cbar_label='', cbar_label_size=14, show_plot: bool = False, cmap='YlOrRd', cmap_range=None, blank_color='grey', edge_color='white', value_format=None, value_fontsize=10, symbol_fontsize=14, max_row: int = 9, readable_fontcolor=False, pymatviz: bool = True, **kwargs)[source]
                                                                                      +periodic_table_heatmap(elemental_data=None, cbar_label='', cbar_label_size=14, show_plot: bool = False, cmap='YlOrRd', cmap_range=None, blank_color='grey', edge_color='white', value_format=None, value_fontsize=10, symbol_fontsize=14, max_row: int = 9, readable_fontcolor=False, pymatviz: bool = True, **kwargs)[source]

                                                                                      A static method that generates a heat map overlaid on a periodic table.

                                                                                      Parameters:
                                                                                      @@ -1273,7 +1273,7 @@

                                                                                      Submodules
                                                                                      -pretty_plot(width: float = 8, height: float | None = None, ax: Axes = None, dpi: float | None = None, color_cycle: tuple[str, str] = ('qualitative', 'Set1_9')) → Axes[source]
                                                                                      +pretty_plot(width: float = 8, height: float | None = None, ax: Axes = None, dpi: float | None = None, color_cycle: tuple[str, str] = ('qualitative', 'Set1_9')) → Axes[source]

                                                                                      Get a publication quality plot, with nice defaults for font sizes etc.

                                                                                      Parameters:
                                                                                      @@ -1299,7 +1299,7 @@

                                                                                      Submodules
                                                                                      -pretty_plot_two_axis(x, y1, y2, xlabel=None, y1label=None, y2label=None, width: float = 8, height: float | None = None, dpi=300, **plot_kwargs)[source]
                                                                                      +pretty_plot_two_axis(x, y1, y2, xlabel=None, y1label=None, y2label=None, width: float = 8, height: float | None = None, dpi=300, **plot_kwargs)[source]

                                                                                      Variant of pretty_plot that does a dual axis plot. Adapted from matplotlib examples. Makes it easier to create plots with different axes.

                                                                                      @@ -1332,7 +1332,7 @@

                                                                                      Submodules
                                                                                      -pretty_polyfit_plot(x: ArrayLike, y: ArrayLike, deg: int = 1, xlabel=None, ylabel=None, **kwargs)[source]
                                                                                      +pretty_polyfit_plot(x: ArrayLike, y: ArrayLike, deg: int = 1, xlabel=None, ylabel=None, **kwargs)[source]

                                                                                      Convenience method to plot data with trend lines based on polynomial fit.

                                                                                      Parameters:
                                                                                      @@ -1353,7 +1353,7 @@

                                                                                      Submodules
                                                                                      -van_arkel_triangle(list_of_materials: Sequence, annotate: bool = True)[source]
                                                                                      +van_arkel_triangle(list_of_materials: Sequence, annotate: bool = True)[source]

                                                                                      A static method that generates a binary van Arkel-Ketelaar triangle to quantify the ionic, metallic and covalent character of a compound by plotting the electronegativity difference (y) vs average (x). @@ -1396,26 +1396,26 @@

                                                                                      Submodules
                                                                                      -class Author(name: str, email: str)[source]
                                                                                      +class Author(name: str, email: str)[source]

                                                                                      Bases: NamedTuple

                                                                                      An Author contains two fields: name and email. It is meant to represent the author of a Structure or the author of a code that was applied to a Structure.

                                                                                      Create new instance of Author(name, email)

                                                                                      -as_dict()[source]
                                                                                      +as_dict()[source]

                                                                                      Get MSONable dict.

                                                                                      -email: str[source]
                                                                                      +email: str[source]

                                                                                      Alias for field number 1

                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -1428,13 +1428,13 @@

                                                                                      Submodules
                                                                                      -name: str[source]
                                                                                      +name: str[source]

                                                                                      Alias for field number 0

                                                                                      -classmethod parse_author(author) → Self[source]
                                                                                      +classmethod parse_author(author) → Self[source]

                                                                                      Parse an Author object from either a String, dict, or tuple.

                                                                                      Parameters:
                                                                                      @@ -1451,7 +1451,7 @@

                                                                                      Submodules
                                                                                      -class HistoryNode(name: str, url: str, description: str)[source]
                                                                                      +class HistoryNode(name: str, url: str, description: str)[source]

                                                                                      Bases: NamedTuple

                                                                                      A HistoryNode represents a step in the chain of events that lead to a Structure. HistoryNodes leave ‘breadcrumbs’ so that you can trace back how @@ -1463,7 +1463,7 @@

                                                                                      Submodules
                                                                                      -name[source]
                                                                                      +name[source]

                                                                                      The name of a code or resource that this Structure encountered in its history.

                                                                                      Type:
                                                                                      @@ -1474,7 +1474,7 @@

                                                                                      Submodules
                                                                                      -url[source]
                                                                                      +url[source]

                                                                                      The URL of that code/resource.

                                                                                      Type:
                                                                                      @@ -1485,7 +1485,7 @@

                                                                                      Submodules
                                                                                      -description[source]
                                                                                      +description[source]

                                                                                      A free-form description of how the code/resource is related to the Structure.

                                                                                      Type:
                                                                                      @@ -1497,19 +1497,19 @@

                                                                                      Submodules
                                                                                      -as_dict() → dict[str, str][source]
                                                                                      +as_dict() → dict[str, str][source]

                                                                                      Get MSONable dict.

                                                                                      -description: str[source]
                                                                                      +description: str[source]

                                                                                      Alias for field number 2

                                                                                      -classmethod from_dict(dct: dict[str, str]) → Self[source]
                                                                                      +classmethod from_dict(dct: dict[str, str]) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -1522,13 +1522,13 @@

                                                                                      Submodules
                                                                                      -name: str[source]
                                                                                      +name: str[source]

                                                                                      Alias for field number 0

                                                                                      -classmethod parse_history_node(h_node) → Self[source]
                                                                                      +classmethod parse_history_node(h_node) → Self[source]

                                                                                      Parse a History Node object from either a dict or a tuple.

                                                                                      Parameters:
                                                                                      @@ -1542,7 +1542,7 @@

                                                                                      Submodules
                                                                                      -url: str[source]
                                                                                      +url: str[source]

                                                                                      Alias for field number 1

                                                                                      @@ -1550,7 +1550,7 @@

                                                                                      Submodules
                                                                                      -class StructureNL(struct_or_mol, authors, projects=None, references='', remarks=None, data=None, history=None, created_at=None)[source]
                                                                                      +class StructureNL(struct_or_mol, authors, projects=None, references='', remarks=None, data=None, history=None, created_at=None)[source]

                                                                                      Bases: object

                                                                                      The Structure Notation Language (SNL, pronounced ‘snail’) is a container for a pymatgen Structure/Molecule object with some additional fields for enhanced provenance.

                                                                                      @@ -1593,13 +1593,13 @@

                                                                                      Submodules
                                                                                      -as_dict()[source]
                                                                                      +as_dict()[source]

                                                                                      Get MSONable dict.

                                                                                      -classmethod from_dict(dct: dict) → Self[source]
                                                                                      +classmethod from_dict(dct: dict) → Self[source]
                                                                                      Parameters:

                                                                                      dct (dict) – Dict representation.

                                                                                      @@ -1612,7 +1612,7 @@

                                                                                      Submodules
                                                                                      -classmethod from_structures(structures: Sequence[Structure], authors: Sequence[dict[str, str]], projects=None, references='', remarks=None, data=None, histories=None, created_at=None) → list[Self][source]
                                                                                      +classmethod from_structures(structures: Sequence[Structure], authors: Sequence[dict[str, str]], projects=None, references='', remarks=None, data=None, histories=None, created_at=None) → list[Self][source]

                                                                                      A convenience method for getting a list of StructureNL objects by specifying structures and metadata separately. Some of the metadata is applied to all of the structures for ease of use.

                                                                                      @@ -1645,7 +1645,7 @@

                                                                                      Submodules
                                                                                      -is_valid_bibtex(reference: str) → bool[source]
                                                                                      +is_valid_bibtex(reference: str) → bool[source]

                                                                                      Use pybtex to validate that a reference is in proper BibTeX format.

                                                                                      Parameters:
                                                                                      @@ -1663,17 +1663,17 @@

                                                                                      Submodules
                                                                                      -class Stringify[source]
                                                                                      +class Stringify[source]

                                                                                      Bases: object

                                                                                      Mix-in class for string formatting, e.g. superscripting numbers and symbols or superscripting.

                                                                                      -STRING_MODE = 'SUBSCRIPT'[source]
                                                                                      +STRING_MODE = 'SUBSCRIPT'[source]
                                                                                      -to_html_string() → str[source]
                                                                                      +to_html_string() → str[source]

                                                                                      Generate a HTML formatted string. This uses the output from to_latex_string to generate a HTML output.

                                                                                      Returns:
                                                                                      @@ -1684,7 +1684,7 @@

                                                                                      Submodules
                                                                                      -to_latex_string() → str[source]
                                                                                      +to_latex_string() → str[source]

                                                                                      Generate a LaTeX formatted string. The mode is set by the class variable STRING_MODE, which defaults to “SUBSCRIPT”. e.g. Fe2O3 is transformed to Fe$_{2}$O$_{3}$. Setting STRING_MODE to “SUPERSCRIPT” creates superscript, e.g. Fe2+ becomes Fe^{2+}. The initial string is obtained from the class’s __str__ method.

                                                                                      @@ -1700,14 +1700,14 @@

                                                                                      Submodules
                                                                                      -to_pretty_string() → str[source]
                                                                                      +to_pretty_string() → str[source]

                                                                                      A pretty string representation. By default, the __str__ output is used, but this method can be overridden if a different representation from default is desired.

                                                                                      -to_unicode_string()[source]
                                                                                      +to_unicode_string()[source]

                                                                                      Unicode string with proper sub and superscripts. Note that this works only with systems where the sub and superscripts are pure integers.

                                                                                      @@ -1716,7 +1716,7 @@

                                                                                      Submodules
                                                                                      -charge_string(charge, brackets=True, explicit_one=True)[source]
                                                                                      +charge_string(charge, brackets=True, explicit_one=True)[source]

                                                                                      Get a string representing the charge of an Ion. By default, the charge is placed in brackets with the sign preceding the magnitude, e.g. ‘[+2]’. For uncharged species, the string returned is ‘(aq)’.

                                                                                      @@ -1734,7 +1734,7 @@

                                                                                      Submodules
                                                                                      -disordered_formula(disordered_struct, symbols=('x', 'y', 'z'), fmt='plain')[source]
                                                                                      +disordered_formula(disordered_struct, symbols=('x', 'y', 'z'), fmt='plain')[source]

                                                                                      Get a formula of a form like AxB1-x (x=0.5) for disordered structures. Will only return a formula for disordered structures with one @@ -1762,7 +1762,7 @@

                                                                                      Submodules
                                                                                      -formula_double_format(afloat, ignore_ones=True, tol: float = 1e-08)[source]
                                                                                      +formula_double_format(afloat, ignore_ones=True, tol: float = 1e-08)[source]

                                                                                      This function is used to make pretty formulas by formatting the amounts. Instead of Li1.0 Fe1.0 P1.0 O4.0, you get LiFePO4.

                                                                                      @@ -1781,7 +1781,7 @@

                                                                                      Submodules
                                                                                      -htmlify(formula: str) → str[source]
                                                                                      +htmlify(formula: str) → str[source]

                                                                                      Generate a HTML formatted formula, e.g. Fe2O3 is transformed to Fe<sub>2</sub>O</sub>3</sub>.

                                                                                      Note that Composition now has a to_html_string() method that may @@ -1795,7 +1795,7 @@

                                                                                      Submodules
                                                                                      -latexify(formula: str, bold: bool = False)[source]
                                                                                      +latexify(formula: str, bold: bool = False)[source]

                                                                                      Generate a LaTeX formatted formula. e.g. Fe2O3 is transformed to Fe$_{2}$O$_{3}$.

                                                                                      Note that Composition now has a to_latex_string() method that may @@ -1815,7 +1815,7 @@

                                                                                      Submodules
                                                                                      -latexify_spacegroup(spacegroup_symbol)[source]
                                                                                      +latexify_spacegroup(spacegroup_symbol)[source]

                                                                                      Generate a latex formatted spacegroup. e.g. P2_1/c is converted to P2$_{1}$/c and P-1 is converted to P$\overline{1}$.

                                                                                      Note that SymmetryGroup now has a to_latex_string() method that may @@ -1832,7 +1832,7 @@

                                                                                      Submodules
                                                                                      -str_delimited(results, header=None, delimiter='\t')[source]
                                                                                      +str_delimited(results, header=None, delimiter='\t')[source]

                                                                                      Given a tuple of tuples, generate a delimited string form. >>> results = [[“a”, “b”, “c”], [“d”, “e”, “f”], [1, 2, 3]] >>> print(str_delimited(results, delimiter=”,”)) @@ -1855,13 +1855,13 @@

                                                                                      Submodules
                                                                                      -stream_has_colors(stream)[source]
                                                                                      +stream_has_colors(stream)[source]

                                                                                      True if stream supports colors. Python cookbook, #475186.

                                                                                      -transformation_to_string(matrix, translation_vec=(0, 0, 0), components=('x', 'y', 'z'), c='', delim=',')[source]
                                                                                      +transformation_to_string(matrix, translation_vec=(0, 0, 0), components=('x', 'y', 'z'), c='', delim=',')[source]

                                                                                      Convenience method. Given matrix returns string, e.g. x+2y+1/4.

                                                                                      Parameters:
                                                                                      @@ -1882,7 +1882,7 @@

                                                                                      Submodules
                                                                                      -unicodeify(formula: str) → str[source]
                                                                                      +unicodeify(formula: str) → str[source]

                                                                                      Generate a formula with unicode subscripts, e.g. Fe2O3 is transformed to Fe₂O₃. Does not support formulae with decimal points.

                                                                                      Note that Composition now has a to_unicode_string() method that may @@ -1896,7 +1896,7 @@

                                                                                      Submodules
                                                                                      -unicodeify_spacegroup(spacegroup_symbol)[source]
                                                                                      +unicodeify_spacegroup(spacegroup_symbol)[source]

                                                                                      Generate a unicode formatted spacegroup. e.g. P2$_{1}$/c is converted to P2₁/c and P$\overline{1}$ is converted to P̅1.

                                                                                      Note that SymmetryGroup now has a to_unicode_string() method that @@ -1913,7 +1913,7 @@

                                                                                      Submodules
                                                                                      -unicodeify_species(specie_string)[source]
                                                                                      +unicodeify_species(specie_string)[source]

                                                                                      Generate a unicode formatted species string, with appropriate superscripts for oxidation states.

                                                                                      Note that Species now has a to_unicode_string() method that diff --git a/docs/pymatgen.util.testing.html b/docs/pymatgen.util.testing.html index 849cc2d1621..9a50287931a 100644 --- a/docs/pymatgen.util.testing.html +++ b/docs/pymatgen.util.testing.html @@ -4,7 +4,7 @@ - pymatgen.util.testing package — pymatgen 2024.6.4 documentation + pymatgen.util.testing package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@

                                                                                      - 2024.6.4 + 2024.6.10
                                                                                      @@ -100,7 +100,7 @@ right away.

                                                                                      -class PymatgenTest(methodName='runTest')[source]
                                                                                      +class PymatgenTest(methodName='runTest')[source]

                                                                                      Bases: TestCase

                                                                                      Extends unittest.TestCase with several assert methods for array and str comparison.

                                                                                      Create an instance of the class that will use the named test @@ -108,12 +108,12 @@ not have a method with the specified name.

                                                                                      -TEST_STRUCTURES: ClassVar[dict[str | Path, Structure | None]] = {PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/BaNiO3.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/CsCl.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/Graphite.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/He_BCC.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/K2O2.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/La2CoO4F.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/Li10GeP2S12.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/Li2O.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/Li2O2.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/Li3V2(PO4)3.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/LiFePO4.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/NaFePO4.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/Pb2TiZrO6.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/Si.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/SiO2.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/Si_SiO2_Interface.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/Sn.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/SrTiO3.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/TiO2.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/TlBiSe2.json'): None, PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/testing/../structures/VO2.json'): None}[source]
                                                                                      +TEST_STRUCTURES: ClassVar[dict[str | Path, Structure | None]] = {PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/BaNiO3.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/CsCl.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/Graphite.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/He_BCC.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/K2O2.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/La2CoO4F.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/Li10GeP2S12.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/Li2O.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/Li2O2.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/Li3V2(PO4)3.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/LiFePO4.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/NaFePO4.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/Pb2TiZrO6.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/Si.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/SiO2.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/Si_SiO2_Interface.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/Sn.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/SrTiO3.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/TiO2.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/TlBiSe2.json'): None, PosixPath('/Users/shyue/miniconda3/envs/mavrl/lib/python3.11/site-packages/pymatgen/util/testing/../structures/VO2.json'): None}[source]
                                                                                      -assert_msonable(obj: MSONable, test_is_subclass: bool = True) → str[source]
                                                                                      +assert_msonable(obj: MSONable, test_is_subclass: bool = True) → str[source]

                                                                                      Test if obj is MSONable and verify the contract is fulfilled.

                                                                                      By default, the method tests whether obj is an instance of MSONable. This check can be deactivated by setting test_is_subclass=False.

                                                                                      @@ -121,13 +121,13 @@
                                                                                      -static assert_str_content_equal(actual, expected)[source]
                                                                                      +static assert_str_content_equal(actual, expected)[source]

                                                                                      Test if two strings are equal, ignoring things like trailing spaces, etc.

                                                                                      -classmethod get_structure(name: str) → Structure[source]
                                                                                      +classmethod get_structure(name: str) → Structure[source]

                                                                                      Lazily load a structure from pymatgen/util/testing/structures.

                                                                                      Parameters:
                                                                                      @@ -141,7 +141,7 @@
                                                                                      -serialize_with_pickle(objects: Any, protocols: Sequence[int] | None = None, test_eq: bool = True)[source]
                                                                                      +serialize_with_pickle(objects: Any, protocols: Sequence[int] | None = None, test_eq: bool = True)[source]

                                                                                      Test whether the object(s) can be serialized and deserialized with pickle. This method tries to serialize the objects with pickle and the protocols specified in input. Then it deserializes the pickle format @@ -174,7 +174,7 @@

                                                                                      Submodules
                                                                                      -check_band(test_line: str, ref_line: str) → bool[source]
                                                                                      +check_band(test_line: str, ref_line: str) → bool[source]

                                                                                      Check if band lines are the same.

                                                                                      Parameters:
                                                                                      @@ -190,7 +190,7 @@

                                                                                      Submodules
                                                                                      -comp_system(structure: Structure, user_params: dict[str, Any], test_name: str, work_dir: Path, ref_dir: Path, generator_cls: type, properties: list[str] | None = None, prev_dir: str | None | Path = None) → None[source]
                                                                                      +comp_system(structure: Structure, user_params: dict[str, Any], test_name: str, work_dir: Path, ref_dir: Path, generator_cls: type, properties: list[str] | None = None, prev_dir: str | None | Path = None) → None[source]

                                                                                      Compare files generated by tests with ones in reference directories.

                                                                                      Parameters:
                                                                                      @@ -213,7 +213,7 @@

                                                                                      Submodules
                                                                                      -compare_files(test_name: str, work_dir: Path, ref_dir: Path) → None[source]
                                                                                      +compare_files(test_name: str, work_dir: Path, ref_dir: Path) → None[source]

                                                                                      Compare files generated by tests with ones in reference directories.

                                                                                      Parameters:
                                                                                      @@ -231,7 +231,7 @@

                                                                                      Submodules
                                                                                      -compare_single_files(ref_file: str | Path, test_file: str | Path) → None[source]
                                                                                      +compare_single_files(ref_file: str | Path, test_file: str | Path) → None[source]

                                                                                      Compare single files generated by tests with ones in reference directories.

                                                                                      Parameters:
                                                                                      diff --git a/docs/pymatgen.vis.html b/docs/pymatgen.vis.html index be37129c8e4..143c0fde06e 100644 --- a/docs/pymatgen.vis.html +++ b/docs/pymatgen.vis.html @@ -4,7 +4,7 @@ - pymatgen.vis package — pymatgen 2024.6.4 documentation + pymatgen.vis package — pymatgen 2024.6.10 documentation @@ -15,7 +15,7 @@ - + @@ -35,7 +35,7 @@
                                                                                      - 2024.6.4 + 2024.6.10
                                                                                      @@ -154,7 +154,7 @@

                                                                                      Submodules
                                                                                      -class SpectrumPlotter(xshift=0.0, yshift=0.0, stack=False, color_cycle=('qualitative', 'Set1_9'))[source]
                                                                                      +class SpectrumPlotter(xshift=0.0, yshift=0.0, stack=False, color_cycle=('qualitative', 'Set1_9'))[source]

                                                                                      Bases: object

                                                                                      Plot Spectrum objects and subclasses. Note that the interface is extremely flexible given that there are many different ways in which @@ -189,7 +189,7 @@

                                                                                      Submodules
                                                                                      -add_spectra(spectra_dict, key_sort_func=None)[source]
                                                                                      +add_spectra(spectra_dict, key_sort_func=None)[source]

                                                                                      Add a dictionary of Spectrum, with an optional sorting function for the keys.

                                                                                      @@ -204,7 +204,7 @@

                                                                                      Submodules
                                                                                      -add_spectrum(label, spectrum, color=None)[source]
                                                                                      +add_spectrum(label, spectrum, color=None)[source]

                                                                                      Adds a Spectrum for plotting.

                                                                                      Parameters:
                                                                                      @@ -221,7 +221,7 @@

                                                                                      Submodules
                                                                                      -get_plot(xlim=None, ylim=None)[source]
                                                                                      +get_plot(xlim=None, ylim=None)[source]

                                                                                      Get a matplotlib plot showing the DOS.

                                                                                      Parameters:
                                                                                      @@ -236,7 +236,7 @@

                                                                                      Submodules
                                                                                      -save_plot(filename: str, **kwargs)[source]
                                                                                      +save_plot(filename: str, **kwargs)[source]

                                                                                      Save matplotlib plot to a file.

                                                                                      Parameters:
                                                                                      @@ -247,7 +247,7 @@

                                                                                      Submodules
                                                                                      -show(**kwargs)[source]
                                                                                      +show(**kwargs)[source]

                                                                                      Show the plot using matplotlib.

                                                                                      @@ -259,7 +259,7 @@

                                                                                      Submodules
                                                                                      -quick_view(structure, bonds=True, conventional=False, transform=None, show_box=True, bond_tol=0.2, stick_radius=0.1)[source]
                                                                                      +quick_view(structure, bonds=True, conventional=False, transform=None, show_box=True, bond_tol=0.2, stick_radius=0.1)[source]

                                                                                      A function to visualize pymatgen Structure objects in jupyter notebook using chemview package.

                                                                                      Parameters:
                                                                                      @@ -286,19 +286,19 @@

                                                                                      Submodules
                                                                                      -class MultiStructuresInteractorStyle(parent)[source]
                                                                                      +class MultiStructuresInteractorStyle(parent)[source]

                                                                                      Bases: StructureInteractorStyle

                                                                                      Interactor for MultiStructureVis.

                                                                                      -keyPressEvent(obj, event)[source]
                                                                                      +keyPressEvent(obj, event)[source]

                                                                                      -class MultiStructuresVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=False, poly_radii_tol_factor=0.5, excluded_bonding_elements=None, animated_movie_options={'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0})[source]
                                                                                      +class MultiStructuresVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=False, poly_radii_tol_factor=0.5, excluded_bonding_elements=None, animated_movie_options={'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0})[source]

                                                                                      Bases: StructureVis

                                                                                      Visualization for multiple structures.

                                                                                      @@ -328,24 +328,24 @@

                                                                                      Submodules
                                                                                      -DEFAULT_ANIMATED_MOVIE_OPTIONS: ClassVar[dict[str, str | float]] = {'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0}[source]
                                                                                      +DEFAULT_ANIMATED_MOVIE_OPTIONS: ClassVar[dict[str, str | float]] = {'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0}[source]

                                                                                      -apply_tags()[source]
                                                                                      +apply_tags()[source]

                                                                                      Apply tags.

                                                                                      -display_help()[source]
                                                                                      +display_help()[source]

                                                                                      Display the help for various keyboard shortcuts.

                                                                                      -display_info(info)[source]
                                                                                      +display_info(info)[source]
                                                                                      Parameters:

                                                                                      info (str) – Information.

                                                                                      @@ -355,7 +355,7 @@

                                                                                      Submodules
                                                                                      -display_warning(warning)[source]
                                                                                      +display_warning(warning)[source]
                                                                                      Parameters:

                                                                                      warning (str) – Warning.

                                                                                      @@ -365,19 +365,19 @@

                                                                                      Submodules
                                                                                      -erase_info()[source]
                                                                                      +erase_info()[source]

                                                                                      Erase all info.

                                                                                      -erase_warning()[source]
                                                                                      +erase_warning()[source]

                                                                                      Remove warnings.

                                                                                      -set_animated_movie_options(animated_movie_options=None)[source]
                                                                                      +set_animated_movie_options(animated_movie_options=None)[source]
                                                                                      Parameters:

                                                                                      () (animated_movie_options)

                                                                                      @@ -387,7 +387,7 @@

                                                                                      Submodules
                                                                                      -set_structure(structure: Structure, reset_camera=True, to_unit_cell=False)[source]
                                                                                      +set_structure(structure: Structure, reset_camera=True, to_unit_cell=False)[source]

                                                                                      Add a structure to the visualizer.

                                                                                      Parameters:
                                                                                      @@ -403,7 +403,7 @@

                                                                                      Submodules
                                                                                      -set_structures(structures: Sequence[Structure], tags=None)[source]
                                                                                      +set_structures(structures: Sequence[Structure], tags=None)[source]

                                                                                      Add list of structures to the visualizer.

                                                                                      Parameters:
                                                                                      @@ -419,34 +419,34 @@

                                                                                      Submodules
                                                                                      -class StructureInteractorStyle(parent)[source]
                                                                                      +class StructureInteractorStyle(parent)[source]

                                                                                      Bases: object

                                                                                      A custom interactor style for visualizing structures.

                                                                                      -keyPressEvent(obj, _event)[source]
                                                                                      +keyPressEvent(obj, _event)[source]
                                                                                      -leftButtonPressEvent(obj, event)[source]
                                                                                      +leftButtonPressEvent(obj, event)[source]
                                                                                      -leftButtonReleaseEvent(obj, event)[source]
                                                                                      +leftButtonReleaseEvent(obj, event)[source]
                                                                                      -mouseMoveEvent(obj, event)[source]
                                                                                      +mouseMoveEvent(obj, event)[source]

                                                                                      -class StructureVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=True, poly_radii_tol_factor=0.5, excluded_bonding_elements=None)[source]
                                                                                      +class StructureVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=True, poly_radii_tol_factor=0.5, excluded_bonding_elements=None)[source]

                                                                                      Bases: object

                                                                                      Structure visualization using VTK.

                                                                                      Constructs a Structure Visualization.

                                                                                      @@ -492,7 +492,7 @@

                                                                                      Submodules
                                                                                      -add_bonds(neighbors, center, color=None, opacity=None, radius=0.1)[source]
                                                                                      +add_bonds(neighbors, center, color=None, opacity=None, radius=0.1)[source]

                                                                                      Adds bonds for a site.

                                                                                      Parameters:
                                                                                      @@ -509,7 +509,7 @@

                                                                                      Submodules
                                                                                      -add_edges(edges, type='line', linewidth=2, color=(0.0, 0.0, 0.0))[source]
                                                                                      +add_edges(edges, type='line', linewidth=2, color=(0.0, 0.0, 0.0))[source]
                                                                                      Parameters:
                                                                                        @@ -524,7 +524,7 @@

                                                                                        Submodules
                                                                                        -add_faces(faces, color, opacity=0.35)[source]
                                                                                        +add_faces(faces, color, opacity=0.35)[source]

                                                                                        Adding face of polygon.

                                                                                        Parameters:
                                                                                        @@ -539,7 +539,7 @@

                                                                                        Submodules
                                                                                        -add_line(start, end, color=(0.5, 0.5, 0.5), width=1)[source]
                                                                                        +add_line(start, end, color=(0.5, 0.5, 0.5), width=1)[source]

                                                                                        Adds a line.

                                                                                        Parameters:
                                                                                        @@ -555,7 +555,7 @@

                                                                                        Submodules
                                                                                        -add_partial_sphere(coords, radius, color, start=0, end=360, opacity=1.0)[source]
                                                                                        +add_partial_sphere(coords, radius, color, start=0, end=360, opacity=1.0)[source]

                                                                                        Adding a partial sphere (to display partial occupancies.

                                                                                        Parameters:
                                                                                        @@ -573,19 +573,19 @@

                                                                                        Submodules
                                                                                        -add_picker()[source]
                                                                                        +add_picker()[source]

                                                                                        Create a cell picker.

                                                                                        -add_picker_fixed()[source]
                                                                                        +add_picker_fixed()[source]

                                                                                        Create a cell picker.Returns:

                                                                                        -add_polyhedron(neighbors, center, color, opacity=1.0, draw_edges=False, edges_color=(0.0, 0.0, 0.0), edges_linewidth=2)[source]
                                                                                        +add_polyhedron(neighbors, center, color, opacity=1.0, draw_edges=False, edges_color=(0.0, 0.0, 0.0), edges_linewidth=2)[source]

                                                                                        Adds a polyhedron.

                                                                                        Parameters:
                                                                                        @@ -604,7 +604,7 @@

                                                                                        Submodules
                                                                                        -add_site(site)[source]
                                                                                        +add_site(site)[source]

                                                                                        Add a site to the render window. The site is displayed as a sphere, the color of which is determined based on the element. Partially occupied sites are displayed as a single element color, though the site info @@ -618,7 +618,7 @@

                                                                                        Submodules
                                                                                        -add_text(coords, text, color=(0, 0, 0))[source]
                                                                                        +add_text(coords, text, color=(0, 0, 0))[source]

                                                                                        Add text at a coordinate.

                                                                                        Parameters:
                                                                                        @@ -633,7 +633,7 @@

                                                                                        Submodules
                                                                                        -add_triangle(neighbors, color, center=None, opacity=0.4, draw_edges=False, edges_color=(0.0, 0.0, 0.0), edges_linewidth=2)[source]
                                                                                        +add_triangle(neighbors, color, center=None, opacity=0.4, draw_edges=False, edges_color=(0.0, 0.0, 0.0), edges_linewidth=2)[source]

                                                                                        Adds a triangular surface between three atoms.

                                                                                        Parameters:
                                                                                        @@ -652,19 +652,19 @@

                                                                                        Submodules
                                                                                        -display_help()[source]
                                                                                        +display_help()[source]

                                                                                        Display the help for various keyboard shortcuts.

                                                                                        -orthogonalize_structure()[source]
                                                                                        +orthogonalize_structure()[source]

                                                                                        Orthogonalize the structure.

                                                                                        -redraw(reset_camera=False)[source]
                                                                                        +redraw(reset_camera=False)[source]

                                                                                        Redraw the render window.

                                                                                        Parameters:
                                                                                        @@ -676,7 +676,7 @@

                                                                                        Submodules
                                                                                        -rotate_view(axis_ind=0, angle=0)[source]
                                                                                        +rotate_view(axis_ind=0, angle=0)[source]

                                                                                        Rotate the camera view.

                                                                                        Parameters:
                                                                                        @@ -690,7 +690,7 @@

                                                                                        Submodules
                                                                                        -set_structure(structure: Structure, reset_camera=True, to_unit_cell=True)[source]
                                                                                        +set_structure(structure: Structure, reset_camera=True, to_unit_cell=True)[source]

                                                                                        Add a structure to the visualizer.

                                                                                        Parameters:
                                                                                        @@ -706,13 +706,13 @@

                                                                                        Submodules
                                                                                        -show()[source]
                                                                                        +show()[source]

                                                                                        Display the visualizer.

                                                                                        -write_image(filename='image.png', magnification=1, image_format='png')[source]
                                                                                        +write_image(filename='image.png', magnification=1, image_format='png')[source]

                                                                                        Save render window to an image.

                                                                                        Parameters:
                                                                                        @@ -727,7 +727,7 @@

                                                                                        Submodules
                                                                                        -zoom(factor)[source]
                                                                                        +zoom(factor)[source]

                                                                                        Zoom the camera view by a factor.

                                                                                        @@ -735,7 +735,7 @@

                                                                                        Submodules
                                                                                        -make_movie(structures, output_filename='movie.mp4', zoom=1.0, fps=20, bitrate='10000k', quality=1, **kwargs)[source]
                                                                                        +make_movie(structures, output_filename='movie.mp4', zoom=1.0, fps=20, bitrate='10000k', quality=1, **kwargs)[source]

                                                                                        Generate a movie from a sequence of structures using vtk and ffmpeg.

                                                                                        Parameters:
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Weir and Yogesh K. Vohra and Craig A. Vanderborgh and Arthur L. Ruoff\",\n title = \" Structural phase transitions in GaAs to 108 GPa\",\n journal = \" Physical Review B\",\n volume = \"39\",\n year = \"1989\",\n page_first = \"1280\",\n page_last = \"1285\",\n pages = \"1280--1285\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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I. F. David and W. T. A. Harrison and J. M. F. Gunn and O. Moze, A. K. Soper and P. Day and J. D. Jorgensen and D. G. Hinks and M. A. Beno and L. Soderholm and D. W. Capone II and I. K. Schuller and C. U. Segre and K. Zhang and J. D. Grace\",\n title = \" Structure and crystal chemistry of the high-Tc superconductor YBa$_2$Cu$_3$O$_{7-x}$\",\n journal = \" Nature\",\n volume = \"327\",\n year = \"1987\",\n page_first = \"310\",\n page_last = \"312\",\n pages = \"310--312\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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D. Jorgensen and H.-B. Sch\\\"{u}ttler and D. G. Hinks and D. W. Capone, II and K. Zhang and M. B. Brodsky},\n title = \" Lattice instability and high-$T_c$ superconductivity in La$_{2-x}$Ba$_x$CuO$_4$\",\n journal = \" Physical Review Letters\",\n volume = \"58\",\n year = \"1987\",\n page_first = \"1024\",\n page_last = \"1029\",\n pages = \"1024--1029\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Crelling and Ond\\v{r}ej \\v{S}ustai and Milan Dr\\'{a}bek and Zden\\v{e}k Weiss and Mariana Klementov\\'{a},\",\n title = \" Arsenic in iron disulfides in a brown coal from the North Bohemian Basin, Czech Republic\",\n journal = \" International Journal of Coal Geology\",\n volume = \"71\",\n year = \"2007\",\n page_first = \"115\",\n page_last = \"121\",\n pages = \"115--121\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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H. Keesom and K. W. Taconis\",\n title = \" On the crystal structure of chlorine\",\n journal = \" Physica\",\n volume = \"3\",\n year = \"1936\",\n page_first = \"237\",\n page_last = \"242\",\n pages = \"237--242\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Ma and C. R{\\o}mming and B. Lebech and J. Gj{\\o}nnes and J. Taft{\\o}\",\n title = \" Structure Refinement of AI3Zr using Single-Crystal X-ray Diffraction, Powder Neutron Diffraction and CBED\",\n journal = \" Acta Crystallographica B\",\n volume = \"48\",\n year = \"1992\",\n page_first = \"11\",\n page_last = \"16\",\n pages = \"11--16\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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K. van Bever and W. Nieuwenkamp\",\n title = \" Die Kristallstruktur von Calciumchlorid, CaCl$_2$\",\n journal = { Zeitschrift f\\\"{u}r Kristallographie - Crystalline Materials},\n volume = \"90\",\n year = \"1935\",\n page_first = \"374\",\n page_last = \"376\",\n pages = \"374--376\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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O. Brockway\",\n title = \" The Crystal Structure of Stannite, Cu$_2$FeSnS$_4$\",\n journal = { Zeitschrift f\\\"{u}r Kristallographie - Crystalline Materials},\n volume = \"89\",\n year = \"1934\",\n page_first = \"434\",\n page_last = \"441\",\n pages = \"434--441\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Skinner\",\n title = \" Unit-Cell Edges of Natural and Synthetic Sphalerites\",\n journal = \" American Mineralogist\",\n volume = \"46\",\n year = \"1961\",\n page_first = \"1399\",\n page_last = \"1411\",\n pages = \"1399--1411\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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L. Bowman and T. C. Wallace and J. L. Yarnell and R. G. Wenzel\",\n title = \" The crystal structure of niobium monoxide\",\n journal = \" Acta Crystallographica\",\n volume = \"21\",\n year = \"1966\",\n page_first = \"843\",\n page_last = \"843\",\n pages = \"843--843\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Goretzki\",\n title = \" Neutron Diffraction Studies on Titanium-Carbon and Zirconium-Carbon Alloys\",\n journal = \" Physica Status Solidi B\",\n volume = \"20\",\n year = \"1967\",\n page_first = \"K141\",\n page_last = \"K143\",\n pages = \"K141--K143\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Svensson\",\n title = \" The crystal structure of orthorhombic antimony trioxide, Sb$_2$O$_3$\",\n journal = \" Acta Crystallographica B\",\n volume = \"30\",\n year = \"1974\",\n page_first = \"458\",\n page_last = \"461\",\n pages = \"458--461\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Geller and V. M. Wolontis\",\n title = \" The Crystal Structure of Co$_2$Si\",\n journal = \" Acta Crystallographica\",\n volume = \"8\",\n year = \"1955\",\n page_first = \"83\",\n page_last = \"87\",\n pages = \"83--87\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Crain and S. J. Clark and G. J. Ackland and M. C. Payne and V. Milman and P. D. Hatton and B. J. Reid\",\n title = \" Theoretical study of high-density phases of covalent semiconductors. I. {\\em Ab initio treatment}\",\n journal = \" Physical Review B\",\n volume = \"49\",\n year = \"1994\",\n page_first = \"5329\",\n page_last = \"5340\",\n pages = \"5329--5340\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Dasgupta and J. Etourneau and B. Chevalier and S. F. Matar and A. M. Umarji\",\n title = \" Structural, thermal, and electrical properties of CrSi$_2$\",\n journal = \" Journal of Applied Physics\",\n volume = \"103\",\n year = \"2008\",\n page_first = \"113516\",\n page_last = \"113516\",\n pages = \"113516--113516\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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B. Roof\",\n title = \" Concerning the Structure of a High Pressure Phase in Californium Metal\",\n journal = \" Journal of the Less-Common Metals\",\n volume = \"120\",\n year = \"1986\",\n page_first = \"345\",\n page_last = \"349\",\n pages = \"345--349\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Mehl\",\n title = \" Hypothetical cF108 Austenite Structure\",\n journal = \" None\",\n volume = \"0\",\n year = \"2008\",\n page_first = \"0\",\n page_last = \"0\",\n pages = \"0--0\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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S. Miller and A. J. King\",\n title = \" The Structure of Polysuflides: 1 Barium Trisulfide\",\n journal = { Zeitschrift f\\\"{u}r Kristallographie - Crystalline Materials},\n volume = \"94\",\n year = \"1936\",\n page_first = \"439\",\n page_last = \"446\",\n pages = \"439--446\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Reithmayer and W. Steurer and H. Schulz and J. L. de Boer\",\n title = \" High-pressure single-crystal structure study on calaverite, AuTe$_2$\",\n journal = \" Acta Crystallographica B\",\n volume = \"49\",\n year = \"1993\",\n page_first = \"6\",\n page_last = \"11\",\n pages = \"6--11\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Yahia and S. Turrell and G. Turrell and J. P. Mercurio\",\n title = \" Infrared and Raman spectra of hexaborides: force-field calculations, and isotopic effects\",\n journal = \" Journal of Molecular Structure\",\n volume = \"224\",\n year = \"1990\",\n page_first = \"303\",\n page_last = \"312\",\n pages = \"303--312\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Finger and Robert M. Hazen\",\n title = \" Crystal structure and compression of ruby to 46 kbar\",\n journal = \" Journal of Applied Physics\",\n volume = \"49\",\n year = \"1978\",\n page_first = \"5823\",\n page_last = \"5826\",\n pages = \"5823--5826\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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J. Murata\",\n title = \" The Atomic Arrangement and Chemical Composition of Krennerite\",\n journal = \" The American Mineralogist\",\n volume = \"35\",\n year = \"1950\",\n page_first = \"959\",\n page_last = \"984\",\n pages = \"959--984\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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J. Meier and R. B. Helmholdt\",\n title = \" Neutron-diffraction study of $\\alpha$- and $\\beta$-oxygen\",\n journal = \" Physical Review B\",\n volume = \"29\",\n year = \"1984\",\n page_first = \"1387\",\n page_last = \"1393\",\n pages = \"1387--1393\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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H. Zachariasen\",\n title = \" The Crystal Structure of Germanium Disulphide\",\n journal = \" Journal of Chemical Physics\",\n volume = \"4\",\n year = \"1936\",\n page_first = \"618\",\n page_last = \"619\",\n pages = \"618--619\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Sitepu and W. W. Schmal and J. K. Stalick\",\n title = \" Correction of intensities for preferred orientation in neutron-diffraction data of NiTi shape-memory alloy using the generalized spherical-harmonic description\",\n journal = \" Applied Physics A\",\n volume = \"74\",\n year = \"2002\",\n page_first = \"S1719\",\n page_last = \"S1721\",\n pages = \"S1719--S1721\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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H. Johansson and J. O. Linde\",\n title = { Gitterstruktur und elektrisches Leitverm\\\"{o}gen der Mischkristallreihen Au-Cu, Pd-Cu und Pt-Cu},\n journal = \" Annalen der Physik\",\n volume = \"387\",\n year = \"1927\",\n page_first = \"449\",\n page_last = \"478\",\n pages = \"449--478\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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structure description. 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Schubert and H. Pfisterer\",\n title = { Zur Kristallchemie der B-Metall-reichsten Phasen in Legierungen von \\\"{U}\"bergangsmetallen der Eisen- und Platintriaden mit Elementen der vierten Nebengruppe},\n journal = { Zeitschrift f\\\"{u}r Metallkunde},\n volume = \"41\",\n year = \"1950\",\n page_first = \"433\",\n page_last = \"441\",\n pages = \"433--441\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Mehl\",\n title = \" Hypothetical cF128 Austenite Structure\",\n journal = \" None\",\n volume = \"0\",\n year = \"2008\",\n page_first = \"0\",\n page_last = \"0\",\n pages = \"0--0\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Mehl\",\n title = \" Hypothetical cI16 Austenite Structure\",\n journal = \" None\",\n volume = \"0\",\n year = \"2008\",\n page_first = \"0\",\n page_last = \"0\",\n pages = \"0--0\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Boysen and F. Altorfer\",\n title = \" A neutron powder investigation of the high-temperature structure and phase transition in LiNbO$_3$\",\n journal = \" Acta Crystallographica B\",\n volume = \"50\",\n year = \"1994\",\n page_first = \"405\",\n page_last = \"414\",\n pages = \"405--414\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Peacor\",\n title = \" High-temperature single-crystal study of the cristobalite inversion\",\n journal = { Zeitschrift f\\\"{u}r kristallographie},\n volume = \"138\",\n year = \"1973\",\n page_first = \"274\",\n page_last = \"298\",\n pages = \"274--298\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Williams and Thomas Proffen and Sara Hobbs and Gordon J. Miller\",\n title = \" Atomic Distributions in the $\\gamma$-Brass Structure of the Cu-Zn System: A Structural and Theoretical Study\",\n journal = \" Inorganic Chemistry\",\n volume = \"46\",\n year = \"2007\",\n page_first = \"251\",\n page_last = \"260\",\n pages = \"251--260\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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A. Wiegers\",\n title = \" The Crystal Structure of the Low-Temperature Form of Silver Selenide\",\n journal = \" American Mineralogist\",\n volume = \"56\",\n year = \"1971\",\n page_first = \"1882\",\n page_last = \"1888\",\n pages = \"1882--1888\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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N. Eremenko and Yu. I. Buyanov and S. B. Prima\",\n title = \" Phase diagram of the system titanium-copper\",\n journal = \" Soviet Powder Metallurgy and Metal Ceramics\",\n volume = \"5\",\n year = \"1966\",\n page_first = \"494\",\n page_last = \"502\",\n pages = \"494--502\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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T. Waugh and Linus Pauling\",\n title = \" The crystal structure of the metallic phase Mg$_{32}$(Al, Zn)$_{49}$\",\n journal = \" Acta Crystallographica\",\n volume = \"10\",\n year = \"1957\",\n page_first = \"254\",\n page_last = \"259\",\n pages = \"254--259\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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E. Rundle and C. G. Shull and E. O. Wollan\",\n title = \" The crystal structure of thorium and zirconium dihydrides by X-ray and neutron diffraction\",\n journal = \" Acta Crystallographica\",\n volume = \"5\",\n year = \"1952\",\n page_first = \"22\",\n page_last = \"26\",\n pages = \"22--26\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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G. Pinsker and S. V. Kaverin\",\n title = \" Electron-Diffraction Determination of the Structure of Iron Carbide Fe$_4$C\",\n journal = \" Soviet Physics-Crystallography, translated from Kristallografiya\",\n volume = \"1\",\n year = \"1956\",\n page_first = \"48\",\n page_last = \"53\",\n pages = \"48--53\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Jauch and A. J. Schultz and G. Heger\",\n title = \" Single-crystal time-of-flight neutron diffraction of Cr$_3$Si and MnF$_2$ comparison with monochromatic-beam techniques\",\n journal = \" Journal of Applied Crystallography\",\n volume = \"20\",\n year = \"1987\",\n page_first = \"117\",\n page_last = \"119\",\n pages = \"117--119\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Palazzi and S. Jaulmes and P. Laruelle\",\n title = \" Structure cristalline de K$_3$AsS$_4$\",\n journal = \" Acta Crystallographica B\",\n volume = \"30\",\n year = \"1974\",\n page_first = \"2378\",\n page_last = \"2381\",\n pages = \"2378--2381\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Schubert and H. G. Meissner and A. Raman and W. Rossteutscher\",\n title = \" Einige Strukturdaten metallischer Phasen (9)\",\n journal = \" Naturwissenschaften\",\n volume = \"51\",\n year = \"1964\",\n page_first = \"287\",\n page_last = \"287\",\n pages = \"287--287\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Rajamani and C. T. Prewitt\",\n title = \" The Crystal Structure of Millerite\",\n journal = \" Canadian Mineralogist\",\n volume = \"12\",\n year = \"1974\",\n page_first = \"253\",\n page_last = \"257\",\n pages = \"253--257\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Ohba and Y. Kitano and Y. Komura\",\n title = \" The charge-density study of the Laves phases, MgZn$_2$ and MgCu$_2$\",\n journal = \" Acta Crystallographic C\",\n volume = \"40\",\n year = \"1984\",\n page_first = \"1\",\n page_last = \"5\",\n pages = \"1--5\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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J. Meier and R. B. Helmholdt\",\n title = \" Neutron-diffraction study of $\\alpha$- and $\\beta$-oxygen\",\n journal = \" Physical Review B\",\n volume = \"29\",\n year = \"1984\",\n page_first = \"1387\",\n page_last = \"1393\",\n pages = \"1387--1393\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Cosca and Donald R. Peacor\",\n title = \" Chemistry and structure of esseneite (CaFe$^{3+}$AlSiO$_6$), a new pyroxene produced by pyrometamorphism\",\n journal = \" American Mineralogist\",\n volume = \"72\",\n year = \"1987\",\n page_first = \"148\",\n page_last = \"156\",\n pages = \"148--156\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Beamer and Charles R. Maxwell\",\n title = \" Physical Properties of Polonium. II. X-Ray Studies and Crystal Structure\",\n journal = \" Journal of Chemical Physics\",\n volume = \"17\",\n year = \"1949\",\n page_first = \"1293\",\n page_last = \"1298\",\n pages = \"1293--1298\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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A. Yurko and J. W. Barton and J. Gordon Parr\",\n title = \" The crystal structure of Ti$_2$Ni\",\n journal = \" Acta Crystallographica\",\n volume = \"12\",\n year = \"1959\",\n page_first = \"909\",\n page_last = \"911\",\n pages = \"909--911\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication."], "history": [], "created_at": {"@module": "datetime", "@class": "datetime", "string": "2018-01-17 19:44:11.878149"}}}, "tags": {"pearson": "cF96", "aflow": "AB2_cF96_227_e_cf", "strukturbericht": "None", "mineral": ""}}, {"snl": {"@module": "pymatgen.util.provenance", "@class": "StructureNL", "charge": null, "lattice": {"matrix": [[-5.705499999999998, -5.7055, 5.705499999999999], [-5.7055, 5.7055, -5.7055], [5.7055, -5.7055, -5.7055]], "a": 9.882215882584227, "b": 9.882215882584228, "c": 9.882215882584228, "alpha": 109.47122063449069, "beta": 109.47122063449069, "gamma": 109.47122063449069, "volume": 742.9184097654999}, "sites": [{"species": [{"element": "Ga", "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "label": "Ga"}, {"species": [{"element": "Ga", "occu": 1.0}], "abc": [0.0, 0.5, 0.5], "xyz": [0.0, 0.0, -5.7055], "label": "Ga"}, {"species": [{"element": "Ga", "occu": 1.0}], "abc": [0.5, 0.5000000000000001, 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Ellner and K. J. Best and H. Jacobi and K. Schubert\",\n title = \" Struktur von Ni$_3$Ga$_4$\",\n journal = \" Journal of the Less-Common Metals\",\n volume = \"19\",\n year = \"1969\",\n page_first = \"294\",\n page_last = \"296\",\n pages = \"294--296\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Iandelli\",\n title = \" MX$_2$-Verbindungen der Erdalkali- und Seltenen Erdmetalle mit Gallium, Indium und Thallium\",\n journal = { Zeitschrift f\\\"{u}r anorganische und allgemeine Chemie},\n volume = \"330\",\n year = \"1964\",\n page_first = \"221\",\n page_last = \"232\",\n pages = \"221--232\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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A. Rouault and P. Herpin and M. R. Fruchart\",\n title = \" Etude Cristallographique des Carbures Cr$_7$C$_3$ et Mn$_7$C$_3$\",\n journal = \" Annales de Chimie (Paris)\",\n volume = \"5\",\n year = \"1970\",\n page_first = \"461\",\n page_last = \"470\",\n pages = \"461--470\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication."], "history": [], "created_at": {"@module": "datetime", "@class": "datetime", "string": "2018-01-17 19:44:12.036385"}}}, "tags": {"pearson": "oP40", "aflow": "A3B7_oP40_62_cd_3c2d", "strukturbericht": "D10_1", "mineral": ""}}, {"snl": {"@module": "pymatgen.util.provenance", "@class": "StructureNL", "charge": null, "lattice": {"matrix": [[-0.0, -0.0, 3.89], [7.3364, -0.0, 4.492249388632321e-16], [-4.492249388632321e-16, 7.3364, 4.492249388632321e-16]], "a": 3.89, "b": 7.3364, "c": 7.3364, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 209.37055569440003}, "sites": [{"species": [{"element": "U", "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "label": "U"}, {"species": [{"element": "U", "occu": 1.0}], "abc": [1.8942859909597176e-32, 0.49999999999999994, 0.49999999999999994], "xyz": [3.6681999999999992, 3.6681999999999997, 4.492249388632321e-16], "label": "U"}, {"species": [{"element": "U", "occu": 1.0}], "abc": [0.5, 0.18210000000000004, 0.6820999999999999], "xyz": [1.3359584400000002, 5.004158439999999, 1.9450000000000003], "label": "U"}, {"species": [{"element": "U", "occu": 1.0}], "abc": [0.5, 0.6820999999999999, 0.8178999999999998], "xyz": [5.004158439999999, 6.000441559999999, 1.9450000000000007], "label": "U"}, {"species": [{"element": "U", "occu": 1.0}], "abc": [0.5, 0.31789999999999996, 0.18210000000000012], "xyz": [2.33224156, 1.3359584400000009, 1.9450000000000003], "label": "U"}, {"species": [{"element": "U", "occu": 1.0}], "abc": [0.5, 0.8178999999999998, 0.31789999999999996], "xyz": [6.000441559999999, 2.33224156, 1.9450000000000007], "label": "U"}, {"species": [{"element": "Si", "occu": 1.0}], "abc": [3.456403250135232e-32, 0.38409999999999994, 0.8841], "xyz": [2.817911239999999, 6.4861112400000005, 5.697070674663511e-16], "label": "Si"}, {"species": [{"element": "Si", "occu": 1.0}], "abc": [1.0, 0.8841, 0.6159], "xyz": [6.4861112400000005, 4.51848876, 3.890000000000001], "label": "Si"}, {"species": [{"element": "Si", "occu": 1.0}], "abc": [9.81997871594219e-33, 0.1159, 0.38410000000000005], "xyz": [0.8502887599999999, 2.8179112400000004, 2.246124694316161e-16], "label": "Si"}, {"species": [{"element": "Si", "occu": 1.0}], "abc": [1.5996187723063943e-32, 0.6159, 0.1159], "xyz": [4.51848876, 0.8502887600000001, 3.2874281026011335e-16], "label": "Si"}], "about": {"authors": [{"name": "AFLOW Library of Crystallographic Prototypes", "email": ""}], "projects": [], "references": "@article{reference0,\n author = {K. Remschnig and T. Le Bihan and H. No\\\"{e}l and P. Rogl},\n title = \" Structural chemistry and magnetic behavior of binary uranium silicides\",\n journal = \" Journal of Solid State Chemistry\",\n volume = \"97\",\n year = \"1992\",\n page_first = \"391\",\n page_last = \"399\",\n pages = \"391--399\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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H. Zachariasen\",\n title = \" The Crystal Lattice of Germano Sulphide, GeS\",\n journal = \" Physical Review\",\n volume = \"40\",\n year = \"1932\",\n page_first = \"917\",\n page_last = \"922\",\n pages = \"917--922\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Norrby\",\n title = \" A refinement of the crystal structure of copper(II) oxide with a discussion of some exceptional e.s.d.'s\",\n journal = \" Acta Crystallographica B\",\n volume = \"26\",\n year = \"1970\",\n page_first = \"8\",\n page_last = \"15\",\n pages = \"8--15\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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P. Meagher and G. A. Lager\",\n title = \" Polyhedral thermal expansion in the TiO$_2$ polymorphs; refinement of the crystal structures of rutile and brookite at high temperature\",\n journal = \" Canadian Mineralogist\",\n volume = \"17\",\n year = \"1979\",\n page_first = \"77\",\n page_last = \"85\",\n pages = \"77--85\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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J. Bradley and A. Taylor\",\n title = \" The crystal structures of Ni$_2$Al$_3$ and NiAl$_3$\",\n journal = \" Philosophical Magazine\",\n volume = \"23\",\n year = \"1937\",\n page_first = \"1049\",\n page_last = \"1067\",\n pages = \"1049--1067\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Nowotny and W. Sibert\",\n title = { Tern\\\"{a}re Valenzverbindungen in den Systemen Kupfer(Silber)-Arsen(Antimon,Wismut)-Magnesium},\n journal = { Zeitschrift f\\\"{u}r Metallkunde},\n volume = \"33\",\n year = \"1941\",\n page_first = \"391\",\n page_last = \"394\",\n pages = \"391--394\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Hirotsu and S. Nagakura\",\n title = \" Crystal structure and morphology of the carbide precipitated from martensitic high carbon steel during the first stage of tempering\",\n journal = \" Acta Metallurgica\",\n volume = \"20\",\n year = \"1972\",\n page_first = \"645\",\n page_last = \"655\",\n pages = \"645--655\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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W. Hart\",\n title = \" Verifying predictions of the L1$_3$ crystal structure in Cd-Pt and Pd-Pt by exhaustive enumeration\",\n journal = \" Physical Review B\",\n volume = \"80\",\n year = \"2009\",\n page_first = \"014106\",\n page_last = \"014106\",\n pages = \"014106--014106\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Pearson\",\n title = \" Crystal Structure of Sb$_2$Tl$_7$\",\n journal = \" Canadian Journal of Chemistry\",\n volume = \"55\",\n year = \"1977\",\n page_first = \"1120\",\n page_last = \"1122\",\n pages = \"1120--1122\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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L. Hoard\",\n title = \" The Crystal Structure of Potassium Silver Cyanide\",\n journal = { Zeitschrift f\\\"{u}r Kristallographie - Crystalline Materials},\n volume = \"84\",\n year = \"1933\",\n page_first = \"231\",\n page_last = \"255\",\n pages = \"231--255\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Schubert and S. Bhan and W. Burkhardt and R. Gohle and H. G. Meissner and M. P\\\"{o}tzschke and E. Stolz},\n title = \" Einige strukturelle Ergebnisse an metallischen Phasen (5)\",\n journal = \" Naturwissenschaften\",\n volume = \"47\",\n year = \"1960\",\n page_first = \"303\",\n page_last = \"303\",\n pages = \"303--303\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Fleischer\",\n title = \" X-Ray Structure Determination of Cubane\",\n journal = \" Journal of the American Chemical Society\",\n volume = \"86\",\n year = \"1964\",\n page_first = \"3889\",\n page_last = \"3890\",\n pages = \"3889--3890\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Brauer and E. Zintl\",\n title = \" Konstitution von Phosphiden, Arseniden, Antimoniden und Wismutiden des Lithiums, Natriums und Kaliums\",\n journal = { Zeitschrift f\\\"{u}r Physikalische Chemie},\n volume = \"37B\",\n year = \"1937\",\n page_first = \"323\",\n page_last = \"352\",\n pages = \"323--352\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Pertlik\",\n title = { Kristallchemie nat\\\"{u}rlicher Telluride I: Verfeinerung der Kristallstruktur des Sylvanits, AuAgTe$_4$},\n journal = \" Tschermaks mineralogische und petrographische Mitteilungen\",\n volume = \"33\",\n year = \"1984\",\n page_first = \"203\",\n page_last = \"212\",\n pages = \"203--212\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Petrillo and O. Moze and R. M. Ibberson\",\n title = \" High resolution neutron powder diffraction investigation of the low temperature crystal structure of molecular iodine (I$_2$)\",\n journal = \" Physica B\",\n volume = \"180-181\",\n year = \"1992\",\n page_first = \"639\",\n page_last = \"641\",\n pages = \"639--641\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Geist and R. Kloss and H. Follner\",\n title = \" Verfeinerung des $\\beta$-rhomboedrischen Bors\",\n journal = \" Acta Crystallographica B\",\n volume = \"26\",\n year = \"1970\",\n page_first = \"1800\",\n page_last = \"1802\",\n pages = \"1800--1802\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Yadav and R. P. Ram and S Bhan\",\n title = \" On the Thallium-Selenium-Tellurium System\",\n journal = { Zeitschrift f\\\"{u}r Metallkunde},\n volume = \"67\",\n year = \"1976\",\n page_first = \"173\",\n page_last = \"177\",\n pages = \"173--177\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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G. Cotter and J. A. Kohn and R. A. Potter\",\n title = \" Physical and X-Ray Study of the Disilicides of Titanium, Zirconium, and Hafnium\",\n journal = \" Journal of the American Ceramic Society\",\n volume = \"39\",\n year = \"1956\",\n page_first = \"11\",\n page_last = \"12\",\n pages = \"11--12\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Kuriyama and S. Saito and K. Iwamura\",\n title = \" Ultrasonic study on the elastic moduli of the NaTl (B32) structure\",\n journal = \" Journal of Physics and Chemistry of Solids\",\n volume = \"40\",\n year = \"1979\",\n page_first = \"457\",\n page_last = \"461\",\n pages = \"457--461\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Please cite appropriate AFLOW publication."], "history": [], "created_at": {"@module": "datetime", "@class": "datetime", "string": "2018-01-17 19:44:13.941127"}}}, "tags": {"pearson": "cI80", "aflow": "AB3C6_cI80_206_a_d_e", "strukturbericht": "D5_3", "mineral": "Bixbyite (Mn,Fe)2O4"}}, {"snl": {"@module": "pymatgen.util.provenance", "@class": "StructureNL", "charge": null, "lattice": {"matrix": [[-4.455499999999998, -4.4555, 4.455499999999999], [-4.4555, 4.4555, -4.4555], [4.4555, -4.4555, -4.4555]], "a": 7.717152373123131, "b": 7.717152373123133, "c": 7.717152373123133, "alpha": 109.47122063449069, "beta": 109.47122063449069, "gamma": 109.47122063449069, "volume": 353.79308101549987}, "sites": [{"species": [{"element": "Mn", "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "label": "Mn"}, {"species": [{"element": "Mn", "occu": 1.0}], "abc": [0.3642599999999998, 0.36426000000000003, 0.36426000000000014], "xyz": [-1.6229604299999982, -1.6229604299999996, 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A. Oberteuffer and James A. Ibers\",\n title = \" A refinement of the atomic and thermal parameters of $\\alpha$-manganese from a single crystal\",\n journal = \" Acta Crystallographica B\",\n volume = \"26\",\n year = \"1970\",\n page_first = \"1499\",\n page_last = \"1504\",\n pages = \"1499--1504\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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B. Boisen, Jr. and G. V. Gibbs and M. S. T. Bukowinski\",\n title = \" Framework silica structures generated using simulated annealing with a potential energy function based on an H$_6$Si$_2$O$_7$ molecule\",\n journal = \" Physics and Chemistry of Minerals\",\n volume = \"21\",\n year = \"1994\",\n page_first = \"269\",\n page_last = \"284\",\n pages = \"269--284\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Crain and G. J. Ackland and S. J. Clark\",\n title = \" Exotic structures of tetrahedral semiconductors\",\n journal = \" Reports on Progress in Physics\",\n volume = \"58\",\n year = \"1995\",\n page_first = \"705\",\n page_last = \"754\",\n pages = \"705--754\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Hund and R. Fricke\",\n title = \" Der Kristallbau von $\\alpha$-BiF$_3$\",\n journal = { Zeitschrift f\\\"{u}r anorganische Chemie},\n volume = \"258\",\n year = \"1949\",\n page_first = \"198\",\n page_last = \"204\",\n pages = \"198--204\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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A. Rollier and S. B. Hendricks and Louis R. Maxwell\",\n title = \" The Crystal Structure of Polonium by Electron Diffraction\",\n journal = \" Journal of Chemical Physics\",\n volume = \"4\",\n year = \"1936\",\n page_first = \"648\",\n page_last = \"652\",\n pages = \"648--652\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Adams and Michael O'Keeffe and Alexander A. Demkov and Otto F. Sankey and Yin-Min Huang\",\n title = \" Wide-band-gap Si in open fourfold-coordinated clathrate structures\",\n journal = \" Physical Review B\",\n volume = \"49\",\n year = \"1994\",\n page_first = \"8048\",\n page_last = \"8053\",\n pages = \"8048--8053\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Dollase and Werner H. Baur\",\n title = \" The superstructure of meteoritic low tridymite solved by computer simulation\",\n journal = \" American Mineralogist\",\n volume = \"61\",\n year = \"1976\",\n page_first = \"971\",\n page_last = \"978\",\n pages = \"971--978\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Lange\",\n title = \" Ein Vergleich zwischen Bi$_2$Te$_3$ und Bi$_2$Te$_2$S\",\n journal = \" Naturwissenschaften\",\n volume = \"27\",\n year = \"1939\",\n page_first = \"133\",\n page_last = \"134\",\n pages = \"133--134\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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I. Mn$_{1-t}$Co$_t$P ($0.00<=t<=0.30$).\",\n journal = \" Acta Chemica Scandinvaca A\",\n volume = \"38\",\n year = \"1984\",\n page_first = \"563\",\n page_last = \"573\",\n pages = \"563--573\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Schmidt and B. Ewald and Yu. Prots and R. Cardoso-Gil and M. Armbrster and I. Loa and L. Zhang and Ya-Xi Huang and U. Schwarz and R. Kniep\",\n title = \" Growth and Characterization of BPO$_4$ Single Crystals\",\n journal = { Zeitschrift f\\\"{u}r anorganische und allgemeine Chemie},\n volume = \"630\",\n year = \"2004\",\n page_first = \"655\",\n page_last = \"662\",\n pages = \"655--662\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Gregory and Paul M. O'Meara and Alexandra G. Gordon and Jason P. Hodges and Simine Short and James D. Jorgensen\",\n title = \" Structure of Lithium Nitride and Transition-Metal-Doped Derivatives, Li$_{3-x-y}$M$_x$N (M = Ni, Cu): A Powder Neutron Diffraction Study\",\n journal = \" Chemistry of Materials\",\n volume = \"14\",\n year = \"2002\",\n page_first = \"2063\",\n page_last = \"2070\",\n pages = \"2063--2070\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Cameron and Ian M. Threadgold\",\n title = \" Vulcanite, a new copper telluride from Colorado, with notes on certain associated minerals\",\n journal = \" American Mineralogist\",\n volume = \"46\",\n year = \"1961\",\n page_first = \"258\",\n page_last = \"268\",\n pages = \"258--268\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Barth\",\n title = \" Die Kristallstruktur von Perowskit und verwandten Verbidungen\",\n journal = \" Norsk Geologisk Tidsskrift\",\n volume = \"8\",\n year = \"1925\",\n page_first = \"14\",\n page_last = \"19\",\n pages = \"14--19\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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VI. \\\"{U}ber tern\\\"{a}re Chalogenide des Aluminiums, Galliums und Indiums mit Zink, Cadmium und Quecksilber},\n journal = { Zeitschrift f\\\"{u}r anorganische und allgemeine Chemie},\n volume = \"279\",\n year = \"1955\",\n page_first = \"241\",\n page_last = \"270\",\n pages = \"241--270\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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R. Andress and E. Alberti\",\n title = { R\\\"{o}ntgenographische Untersuchung der Legierungsreihe Aluminium-Barium},\n journal = { Zeitschrift f\\\"{u}r Metallkunde},\n volume = \"27\",\n year = \"1935\",\n page_first = \"126\",\n page_last = \"128\",\n pages = \"126--128\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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W. Barsoum and C. J. Rawn and T. El-Raghy and A. T. Procopio and W. D. Porter and H. Wang and C. R. Hubbard\",\n title = \" Thermal Properties of Ti$_4$AlN$_3$\",\n journal = \" Journal of Applied Physics\",\n volume = \"87\",\n year = \"2000\",\n page_first = \"8407\",\n page_last = \"8414\",\n pages = \"8407--8414\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Sch\\\"{o}nfeld and J. J. Huang and S. C. Moss},\n title = \" Anisotropic Mean-Square Displacements (MSD) in single Crystals of 2H- and 3R-MoS$_2$\",\n journal = \" Acta Crystallographica B\",\n volume = \"39\",\n year = \"1983\",\n page_first = \"404\",\n page_last = \"407\",\n pages = \"404--407\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Schefer and P. Fischer and W. H\\\"{a}lg and F. Stucki and L. Schlapbach and J. J. Didisheim and K. Yvon and A. F. Andresen},\n title = \" New structure results for hydrides and deuterides of the hydrogen storage material Mg$_2$Ni\",\n journal = \" Journal of the Less Common Metals\",\n volume = \"74\",\n year = \"1980\",\n page_first = \"65\",\n page_last = \"73\",\n pages = \"65--73\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Davey\",\n title = \" The Lattice Parameter and Density of Pure Tungsten\",\n journal = \" Physical Review\",\n volume = \"26\",\n year = \"1925\",\n page_first = \"736\",\n page_last = \"738\",\n pages = \"736--738\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Consid\\'{e}rations cristallochimiques sur les t\\'{e}traborures\",\n journal = \" Journal of Solid State Chemistry\",\n volume = \"8\",\n year = \"1973\",\n page_first = \"68\",\n page_last = \"85\",\n pages = \"68--85\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication."], "history": [], "created_at": {"@module": "datetime", "@class": "datetime", "string": "2018-01-17 19:44:14.580333"}}}, "tags": {"pearson": "oP20", "aflow": "A4B_oP20_62_2cd_c", "strukturbericht": "None", "mineral": "Magnesium tetraboride"}}, {"snl": {"@module": "pymatgen.util.provenance", "@class": "StructureNL", "charge": null, "lattice": {"matrix": [[4.07925, 0.0, 2.49782022771092e-16], [-2.49782022771092e-16, 4.07925, 2.49782022771092e-16], [0.0, 0.0, 4.07925]], "a": 4.07925, "b": 4.07925, "c": 4.07925, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 67.87986448457812}, "sites": [{"species": [{"element": "Cs", "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "label": "Cs"}, {"species": [{"element": "Cl", "occu": 1.0}], "abc": [0.5, 0.5, 0.5], "xyz": [2.039625, 2.039625, 2.0396250000000005], "label": "Cl"}], "about": {"authors": [{"name": "AFLOW Library of Crystallographic Prototypes", "email": ""}], "projects": [], "references": "@article{reference0,\n author = \"V. Ganesan and K. S. Girirajan\",\n title = \" Lattice parameter and thermal expansion of CsCl and CsBr by x-ray powder diffraction. I. Thermal expansion of CsCl from room temperature to 90$^{\\circ}$ K\",\n journal = \" Paramana -- Journal of Physics\",\n volume = \"27\",\n year = \"1986\",\n page_first = \"469\",\n page_last = \"474\",\n pages = \"469--474\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Vo\\v{c}adlo and K. S. Knight and G. D. Price and I. G. Wood\",\n title = \" Thermal expansion and crystal structure of FeSi between 4 and 1173 K determined by time-of-flight neutron powder diffraction\",\n journal = \" Physics and Chemistry of Minerals\",\n volume = \"29\",\n year = \"2002\",\n page_first = \"132\",\n page_last = \"139\",\n pages = \"132--139\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Levin and Dirk C. Meyer and Peter Paufler and Werner Kochmann\",\n title = \" Microstructure of a Damascene sabre after annealing\",\n journal = \" International Journal of Materials Research\",\n volume = \"97\",\n year = \"2006\",\n page_first = \"1172\",\n page_last = \"1182\",\n pages = \"1172--1182\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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G. Humble\",\n title = \" Establishment of an ordered phase of composition Au$_5$Mn$_2$ in the gold-manganese system\",\n journal = \" Acta Crystallographica\",\n volume = \"17\",\n year = \"1964\",\n page_first = \"1485\",\n page_last = \"1486\",\n pages = \"1485--1486\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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H. Bragg and W. L. Bragg\",\n title = \" The Structure of Diamond\",\n journal = \" Proceedings of the Royal Society of London, Series A\",\n volume = \"89\",\n year = \"1913\",\n page_first = \"277\",\n page_last = \"291\",\n pages = \"277--291\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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A. Owen and Y. H. Liu\",\n title = \" The Thermal Expansion of the Gold-Copper Alloy AuCu$_3$\",\n journal = \" Philosophical Magazine\",\n volume = \"38\",\n year = \"1947\",\n page_first = \"354\",\n page_last = \"360\",\n pages = \"354--360\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Hull and D. A. Keen\",\n title = \" High-pressure polymorphism of the copper(I) halides: A neutron-diffraction study to ~10 GPa\",\n journal = \" Physical Review B\",\n volume = \"50\",\n year = \"1994\",\n page_first = \"5868\",\n page_last = \"5885\",\n pages = \"5868--5885\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Parise\",\n title = \" Structure of Hazelwoodite (Ni$_3$S$_2$\",\n journal = \" Acta Crystallographica B\",\n volume = \"36\",\n year = \"1980\",\n page_first = \"1179\",\n page_last = \"1180\",\n pages = \"1179--1180\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Nowotny\",\n title = \" Die Kristallstruktur von Cu$_2$Te\",\n journal = { Zeitschrift f\\\"{u}r Metallkunde},\n volume = \"37\",\n year = \"1946\",\n page_first = \"40\",\n page_last = \"42\",\n pages = \"40--42\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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III. Mitteilung. \\\"{U}ber die Kristallstruktur des Rheniumtrioxyds},\n journal = { Zeitschrift f\\\"{u}r anorganische und allgemeine Chemie},\n volume = \"207\",\n year = \"1932\",\n page_first = \"121\",\n page_last = \"128\",\n pages = \"121--128\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Chang\",\n title = \" Atomic displacements and crystallographic mechanisms in diffusionless transformation of gold-cadium single crystals containing 47.5 atomic per cent cadmium\",\n journal = \" Acta Crystallographica\",\n volume = \"4\",\n year = \"1951\",\n page_first = \"320\",\n page_last = \"324\",\n pages = \"320--324\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Jeitschko\",\n title = \" Refinement of the crystal structure of TiSi$_2$ and some comments on bonding in TiSi$_2$ and related compounds\",\n journal = \" Acta Crystallographica B\",\n volume = \"33\",\n year = \"1977\",\n page_first = \"2347\",\n page_last = \"2348\",\n pages = \"2347--2348\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Keat and Philip A. Vaughan\",\n title = \" The crystal structure of keatite, a new form of silica\",\n journal = { Zeitschrift f\\\"{u}r Kristallographie},\n volume = \"112\",\n year = \"1959\",\n page_first = \"409\",\n page_last = \"413\",\n pages = \"409--413\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Jeitschko and H. Nowotny and F. Benesovsky\",\n title = { Kohlenstoffhaltige tern\\\"{a}re Verbindungen (H-Phase)},\n journal = { Monatshefte f\\\"{u}r Chemie und verwandte Teile anderer Wissenschaften},\n volume = \"94\",\n year = \"1963\",\n page_first = \"672\",\n page_last = \"676\",\n pages = \"672--676\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Trojer\",\n title = \" Refinement of the Structure of Sulvanite\",\n journal = \" American Mineralogist\",\n volume = \"51\",\n year = \"1966\",\n page_first = \"890\",\n page_last = \"894\",\n pages = \"890--894\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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N{\\o}rlund Christensen and B. Lebech\",\n title = \" The structure of $\\beta$-Vanadium Nitride\",\n journal = \" Acta Crystallographica B\",\n volume = \"35\",\n year = \"1979\",\n page_first = \"2677\",\n page_last = \"2678\",\n pages = \"2677--2678\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Wenski and A. Mewis\",\n title = \" Trigonal-planar koordiniertes Platin: Darstellung und Struktur von SrPtAs (Sb), BaPtP (As, Sb), SrPt$_x$P$_{2-x}$, SrPt$_x$As$_{0.90}$ und BaPt$_x$As$_{0.90}$\",\n journal = { Zeitschrift f\\\"{u}r anorganische und allgemeine Chemie},\n volume = \"535\",\n year = \"1986\",\n page_first = \"110\",\n page_last = \"122\",\n pages = \"110--122\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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L. Mills and A. F. Schuch\",\n title = \" Crystal Structure of Gamma Nitrogen\",\n journal = \" Physical Review Letters\",\n volume = \"23\",\n year = \"1969\",\n page_first = \"1154\",\n page_last = \"1156\",\n pages = \"1154--1156\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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L. Boyer and Efthimios Kaxiras and J. L. Feldman and J. Q. Broughton and M. J. Mehl\",\n title = \" New low-energy crystal structure for silicon\",\n journal = \" Physical Review Letters\",\n volume = \"67\",\n year = \"1991\",\n page_first = \"715\",\n page_last = \"718\",\n pages = \"715--718\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Schiferl and C. S. Barrett\",\n title = \" The crystal structure of arsenic at 4.2, 78 and 299 K\",\n journal = \" Journal of Applied Crystallography\",\n volume = \"2\",\n year = \"1969\",\n page_first = \"30\",\n page_last = \"36\",\n pages = \"30--36\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Fitch\",\n title = \" Crystal structure of the Mg$_{1-x}$Al$_x$B$_2$ superconductors near $x \\approx 0.5$\",\n journal = \" Physical Review B\",\n volume = \"66\",\n year = \"2002\",\n page_first = \"014518\",\n page_last = \"014518\",\n pages = \"014518--014518\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication."], "history": [], "created_at": {"@module": "datetime", "@class": "datetime", "string": "2018-01-17 19:44:15.326979"}}}, "tags": {"pearson": "hP6", "aflow": "AB4C_hP6_191_a_h_b", "strukturbericht": "None", "mineral": ""}}, {"snl": {"@module": "pymatgen.util.provenance", "@class": "StructureNL", "charge": null, "lattice": {"matrix": [[4.0006, 0.0, 2.449660992334451e-16], [-2.449660992334451e-16, 4.0006, 2.449660992334451e-16], [0.0, 0.0, 6.1043]], "a": 4.0006, "b": 4.0006, "c": 6.1043, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 97.69810283754803}, "sites": [{"species": [{"element": "Cu", "occu": 1.0}], "abc": [0.75, 0.25, 0.0], "xyz": [3.0004500000000003, 1.00015, 2.449660992334451e-16], "label": "Cu"}, {"species": [{"element": "Cu", "occu": 1.0}], "abc": [0.25, 0.75, 0.0], "xyz": [1.0001499999999999, 3.0004500000000003, 2.449660992334451e-16], "label": "Cu"}, {"species": [{"element": "Cu", "occu": 1.0}], "abc": [0.25, 0.25, 0.27], "xyz": [1.00015, 1.00015, 1.6481610000000002], "label": "Cu"}, {"species": [{"element": "Cu", "occu": 1.0}], "abc": [0.75, 0.75, 0.73], "xyz": [3.0004500000000003, 3.0004500000000003, 4.456139], "label": "Cu"}, {"species": [{"element": "Sb", "occu": 1.0}], "abc": [0.25, 0.25, 0.7], "xyz": [1.00015, 1.00015, 4.27301], "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1.0}], "abc": [0.75, 0.75, 0.30000000000000004], "xyz": [3.0004500000000003, 3.0004500000000003, 1.8312900000000008], "label": "Sb"}], "about": {"authors": [{"name": "AFLOW Library of Crystallographic Prototypes", "email": ""}], "projects": [], "references": "@article{reference0,\n author = \"W. B. Pearson\",\n title = \" The Cu$_2$Sb and related structures\",\n journal = { Zeitschrift f\\\"{u}r Kristallographie},\n volume = \"171\",\n year = \"1985\",\n page_first = \"23\",\n page_last = \"39\",\n pages = \"23--39\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication."], "history": [], "created_at": {"@module": "datetime", "@class": "datetime", "string": "2018-01-17 19:44:15.337757"}}}, "tags": {"pearson": "tP6", "aflow": "A2B_tP6_129_ac_c", "strukturbericht": "C38", "mineral": ""}}, {"snl": {"@module": "pymatgen.util.provenance", "@class": "StructureNL", "charge": null, "lattice": {"matrix": [[0.0, 0.0, 3.772], [-5.082, 5.082, 1.886], [-5.081999999999999, -5.082, 1.8859999999999992]], "a": 3.772, "b": 7.430373072733293, "c": 7.430373072733292, "alpha": 86.3060954640227, "beta": 75.2961431175098, "gamma": 75.29614311750977, "volume": 194.83680585599996}, "sites": [{"species": [{"element": "Te", "occu": 1.0}], "abc": [0.27970000000000006, 0.6614, 0.7791999999999999], "xyz": [-7.321129199999998, -0.5986595999999997, 3.7719999999999994], "label": "Te"}, {"species": [{"element": "Te", "occu": 1.0}], "abc": [0.7202999999999999, 0.3385999999999998, 0.2208000000000002], "xyz": [-2.8428707999999996, 0.598659599999998, 3.7719999999999994], "label": "Te"}, {"species": [{"element": "Te", "occu": 1.0}], "abc": [0.05889999999999995, 0.22080000000000008, 0.6614], "xyz": [-4.4833403999999994, -2.2391291999999994, 1.8859999999999995], "label": "Te"}, {"species": [{"element": "Te", "occu": 1.0}], "abc": [0.9411, 0.7791999999999999, 0.3386], "xyz": [-5.6806595999999985, 2.239129199999999, 5.6579999999999995], "label": "Te"}, {"species": [{"element": "Ti", "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "label": "Ti"}, {"species": [{"element": "Ti", "occu": 1.0}], "abc": [0.3752, 0.31039999999999995, 0.9391999999999999], "xyz": [-6.350467199999998, -3.1955616, 3.771999999999999], "label": "Ti"}, {"species": [{"element": "Ti", "occu": 1.0}], "abc": [0.6248, 0.6896, 0.06079999999999996], "xyz": [-3.8135327999999995, 3.1955616, 3.772], "label": "Ti"}, {"species": [{"element": "Ti", "occu": 1.0}], "abc": [0.3143999999999999, 0.060799999999999944, 0.3104000000000001], "xyz": [-1.8864384, -1.2684672000000008, 1.8859999999999992], "label": "Ti"}, {"species": [{"element": "Ti", "occu": 1.0}], "abc": [0.6856, 0.9391999999999999, 0.6895999999999999], "xyz": [-8.277561599999999, 1.2684672, 5.657999999999999], "label": "Ti"}], "about": {"authors": [{"name": "AFLOW Library of Crystallographic Prototypes", "email": ""}], "projects": [], "references": "@article{reference0,\n author = \"F. Gr\\onvold and A. Kjekshus and F. Raaum\",\n title = \" The crystal structure of Ti$_5$Te$_4$\",\n journal = \" Acta Crystallographica\",\n volume = \"14\",\n year = \"1961\",\n page_first = \"930\",\n page_last = \"934\",\n pages = \"930--934\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication."], "history": [], "created_at": {"@module": "datetime", "@class": "datetime", "string": "2018-01-17 19:44:15.353613"}}}, "tags": {"pearson": "tI18", "aflow": "A4B5_tI18_87_h_ah", "strukturbericht": "None", "mineral": "Titanium telluride"}}, {"snl": {"@module": "pymatgen.util.provenance", "@class": "StructureNL", "charge": null, "lattice": {"matrix": [[-2.300099999999999, -2.3001, 2.4731499999999995], [-2.3001, 2.3001, -2.47315], [2.3001, -2.3001, -2.47315]], "a": 4.086244111956601, "b": 4.086244111956602, "c": 4.086244111956602, "alpha": 105.50806729351963, "beta": 111.48840768130603, "gamma": 111.48840768130606, "volume": 52.33640469492599}, "sites": [{"species": [{"element": "In", "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "label": "In"}], "about": {"authors": [{"name": "AFLOW Library of Crystallographic Prototypes", "email": ""}], "projects": [], "references": "@article{reference0,\n author = \"V. T. Deshpande and R. R. Pawar\",\n title = \" Anisotropic Thermal Expansion of Indium\",\n journal = \" Acta Crystallographica A\",\n volume = \"25\",\n year = \"1969\",\n page_first = \"415\",\n page_last = \"416\",\n pages = \"415--416\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", "remarks": ["Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication."], "history": [], "created_at": {"@module": "datetime", "@class": "datetime", "string": "2018-01-17 19:44:15.363933"}}}, "tags": {"pearson": "tI2", "aflow": "A_tI2_139_a", "strukturbericht": "A6", "mineral": "Indium"}}] diff --git a/pymatgen/core/periodic_table.json b/pymatgen/core/periodic_table.json deleted file mode 100644 index e22cda7a078..00000000000 --- a/pymatgen/core/periodic_table.json +++ /dev/null @@ -1 +0,0 @@ -{"Ac": {"Atomic mass": 227.0, "Atomic no": 89, "Atomic orbitals": {"1s": -3443.110367, "2p": -572.7627, "2s": -592.622878, "3d": -119.541743, "3p": -137.654394, "3s": -147.320716, "4d": -23.57061, "4f": -12.278225, "4p": -31.761846, "4s": -36.15826, "5d": -3.222752, "5p": -6.06511, "5s": -7.713078, "6d": -0.137786, "6p": -0.744524, "6s": -1.19698, "7s": -0.126551}, "Atomic radius": 1.95, "Atomic radius calculated": "no data", "Boiling point": "3573 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "10070 kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].6d1.7s2", "Ionic radii": {"3": 1.26}, "Liquid range": "2250 K", "Melting point": "1323 K", "Mendeleev no": 48, "Mineral hardness": "no data", "Molar volume": "22.55 cm3", "Name": "Actinium", "Oxidation states": [3], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.26, "ionic_radius": 1.12}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "12 W m-1 K-1", "Van der waals radius": 2.47, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.1, "Youngs modulus": "no data GPa", "Metallic radius": 1.878, "iupac_ordering": 32, "IUPAC ordering": 32, "Ground level": "2D3/2", "Ionization energies": [5.380226, 11.75, 17.431, 44.8, 55.0, 67.0, 79.0, 98.9, 113.9, 143.9, 161.1, 233.0, 255.0, 279.0, 305.0, 330.0, 355.0, 390.0, 416.0, 444.0, 470.0, 610.0, 640.0, 670.0, 710.0, 780.0, 820.0, 920.0, 950.0, 1030.0, 1100.0, 1170.0, 1240.0, 1310.0, 1380.0, 1460.0, 1530.0, 1610.0, 1680.0, 1750.0, 1820.0, 1900.0, 1970.0, 2298.0, 2362.0, 2430.0, 2503.0, 2572.0, 2639.0, 2762.0, 2833.0, 2908.0, 2980.0, 3264.0, 3334.0, 3409.0, 3479.0, 3811.0, 3893.0, 4093.0, 4175.0, 6767.0, 6923.0, 7088.0, 7265.0, 7430.0, 7600.0, 7950.0, 8120.0, 8310.0, 8480.0, 8970.0, 9120.0, 9290.0, 9440.0, 10480.0, 10660.0, 11030.0, 11200.0, 23480.0, 23890.0, 24340.0, 24760.0, 28610.0, 29160.0, 29850.0, 30293.1, 119938.6, 122062.9], "Electron affinity": 0.35}, "Ag": {"Atomic mass": 107.8682, "Atomic no": 47, "Atomic orbitals": {"1s": -900.324578, "2p": -120.913351, "2s": -129.859807, "3d": -13.367803, "3p": -20.06763, "3s": -23.678437, "4d": -0.298706, "4p": -2.086602, "4s": -3.22309, "5s": -0.157407}, "Atomic radius": 1.6, "Atomic radius calculated": 1.65, "Boiling point": "2435 K", "Brinell hardness": "24.5 MN m-2", "Bulk modulus": "100 GPa", "Coefficient of linear thermal expansion": "18.9 x10-6K-1", "Common oxidation states": [1], "Critical temperature": "no data K", "Density of solid": "10490 kg m-3", "Electrical resistivity": "1.63 10-8 Ω m", "Electronic structure": "[Kr].4d10.5s1", "ICSD oxidation states": [1, 2, 3], "Ionic radii": {"1": 1.29, "2": 1.08, "3": 0.89}, "Liquid range": "1200.07 K", "Melting point": "1234.93 K", "Mendeleev no": 71, "Mineral hardness": "2.5", "Molar volume": "10.27 cm3", "Name": "Silver", "Oxidation states": [1, 2, 3], "Poissons ratio": "0.37", "Reflectivity": "97 %", "Refractive index": "no data", "Rigidity modulus": "30 GPa", "Shannon radii": {"1": {"II": {"": {"crystal_radius": 0.81, "ionic_radius": 0.67}}, "IV": {"": {"crystal_radius": 1.14, "ionic_radius": 1.0}}, "IVSQ": {"": {"crystal_radius": 1.16, "ionic_radius": 1.02}}, "V": {"": {"crystal_radius": 1.23, "ionic_radius": 1.09}}, "VI": {"": {"crystal_radius": 1.29, "ionic_radius": 1.15}}, "VII": {"": {"crystal_radius": 1.36, "ionic_radius": 1.22}}, "VIII": {"": {"crystal_radius": 1.42, "ionic_radius": 1.28}}}, "2": {"IVSQ": {"": {"crystal_radius": 0.93, "ionic_radius": 0.79}}, "VI": {"": {"crystal_radius": 1.08, "ionic_radius": 0.94}}}, "3": {"IVSQ": {"": {"crystal_radius": 0.81, "ionic_radius": 0.67}}, "VI": {"": {"crystal_radius": 0.89, "ionic_radius": 0.75}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "430 W m-1 K-1", "Van der waals radius": 2.11, "Velocity of sound": "2600 m s-1", "Vickers hardness": "251 MN m-2", "X": 1.93, "Youngs modulus": "83 GPa", "Metallic radius": 1.445, "iupac_ordering": 72, "IUPAC ordering": 72, "Ground level": "2S1/2", "Ionization energies": [7.576234, 21.4844, 34.8, 49.0, 65.0, 82.0, 106.0, 125.0, 145.1, 167.0, 188.0, 271.46, 294.0, 321.0, 347.0, 381.0, 408.43, 469.0, 500.87, 885.0, 946.0, 1013.0, 1082.0, 1149.0, 1231.0, 1308.0, 1382.0, 1460.0, 1535.0, 1747.0, 1810.5, 1888.0, 1979.0, 2077.0, 2131.0, 2302.0, 2371.99, 5558.0, 5753.0, 5966.0, 6170.0, 6551.0, 6785.0, 7082.0, 7271.298, 30097.318, 30965.698], "Electron affinity": 1.304473}, "Al": {"Atomic mass": 26.9815386, "Atomic no": 13, "Atomic orbitals": {"1s": -55.156044, "2p": -2.564018, "2s": -3.934827, "3p": -0.102545, "3s": -0.286883}, "Atomic radius": 1.25, "Atomic radius calculated": 1.18, "Boiling point": "2792 K", "Brinell hardness": "245 MN m-2", "Bulk modulus": "76 GPa", "Coefficient of linear thermal expansion": "23.1 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "2700 kg m-3", "Electrical resistivity": "2.7 10-8 Ω m", "Electronic structure": "[Ne].3s2.3p1", "ICSD oxidation states": [3], "Ionic radii": {"3": 0.675}, "Liquid range": "1858.53 K", "Melting point": "933.47 K", "Mendeleev no": 80, "Mineral hardness": "2.75", "Molar volume": "10.00 cm3", "Name": "Aluminum", "Oxidation states": [1, 3], "Poissons ratio": "0.35", "Reflectivity": "71 %", "Refractive index": "no data", "Rigidity modulus": "26 GPa", "Shannon radii": {"3": {"IV": {"": {"crystal_radius": 0.53, "ionic_radius": 0.39}}, "V": {"": {"crystal_radius": 0.62, "ionic_radius": 0.48}}, "VI": {"": {"crystal_radius": 0.675, "ionic_radius": 0.535}}}}, "Superconduction temperature": "1.175 K", "Thermal conductivity": "235 W m-1 K-1", "Van der waals radius": 1.84, "Velocity of sound": "5100 m s-1", "Vickers hardness": "167 MN m-2", "X": 1.61, "Youngs modulus": "70 GPa", "NMR Quadrupole Moment": {"Al-27": 146.6}, "Metallic radius": 1.43, "iupac_ordering": 80, "IUPAC ordering": 80, "Ground level": "2P\u00b01/2", "Ionization energies": [5.985769, 18.82855, 28.447642, 119.9924, 153.8252, 190.49, 241.76, 284.64, 330.21, 398.65, 442.005, 2085.97702, 2304.14007], "Electron affinity": 0.432835}, "Am": {"Atomic mass": 243.0, "Atomic no": 95, "Atomic orbitals": "no data", "Atomic radius": 1.75, "Atomic radius calculated": "no data", "Boiling point": "2880 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].5f7.7s2", "Ionic radii": {"2": 1.4, "3": 1.115, "4": 0.99}, "Liquid range": "1431 K", "Melting point": "1449 K", "Mendeleev no": 42, "Mineral hardness": "no data", "Molar volume": "17.63 cm3", "Name": "Americium", "Oxidation states": [2, 3, 4, 5, 6], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"2": {"VII": {"": {"crystal_radius": 1.35, "ionic_radius": 1.21}}, "VIII": {"": {"crystal_radius": 1.4, "ionic_radius": 1.26}}, "IX": {"": {"crystal_radius": 1.45, "ionic_radius": 1.31}}}, "3": {"VI": {"": {"crystal_radius": 1.115, "ionic_radius": 0.975}}, "VIII": {"": {"crystal_radius": 1.23, "ionic_radius": 1.09}}}, "4": {"VI": {"": {"crystal_radius": 0.99, "ionic_radius": 0.85}}, "VIII": {"": {"crystal_radius": 1.09, "ionic_radius": 0.95}}}}, "Superconduction temperature": "0.6 K", "Thermal conductivity": "10 W m-1 K-1", "Van der waals radius": 2.44, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.3, "Youngs modulus": "no data GPa", "Metallic radius": 1.73, "iupac_ordering": 26, "IUPAC ordering": 26, "Ground level": "8S\u00b07/2", "Ionization energies": [5.97381, 11.7, 21.7, 36.8, 50.0, 67.9, 95.0, 110.0, 125.0, 141.0, 163.0, 184.0, 206.0, 225.0, 242.0, 284.0, 305.0, 424.0, 451.0, 481.0, 511.0, 541.0, 571.0, 616.0, 646.0, 680.0, 711.0, 870.0, 900.0, 940.0, 980.0, 1090.0, 1130.0, 1240.0, 1280.0, 1410.0, 1490.0, 1570.0, 1650.0, 1730.0, 1820.0, 1900.0, 1980.0, 2070.0, 2160.0, 2240.0, 2320.0, 2410.0, 2480.0, 2874.0, 2946.0, 3021.0, 3101.0, 3178.0, 3251.0, 3402.0, 3479.0, 3563.0, 3641.0, 3956.0, 4033.0, 4115.0, 4191.0, 4642.0, 4733.0, 4960.0, 5050.0, 8040.0, 8210.0, 8390.0, 8590.0, 8770.0, 8950.0, 9380.0, 9560.0, 9770.0, 9960.0, 10490.0, 10650.0, 10830.0, 11000.0, 12400.0, 12600.0, 13000.0, 13190.0, 27110.0, 27550.0, 28040.0, 28500.0, 33700.0, 34300.0, 35100.0, 35549.4, 139769.5, 142161.0], "Electron affinity": 0.1}, "Ar": {"Atomic mass": 39.948, "Atomic no": 18, "Atomic orbitals": {"1s": -113.800134, "2p": -8.443439, "2s": -10.794172, "3p": -0.38233, "3s": -0.883384}, "Atomic radius": 0.71, "Atomic radius calculated": 0.71, "Boiling point": "87.3 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Critical temperature": "150.8 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Ne].3s2.3p6", "Liquid range": "3.5 K", "Max oxidation state": 0.0, "Melting point": "83.8 K", "Mendeleev no": 3, "Min oxidation state": 0.0, "Mineral hardness": "no data", "Molar volume": "22.56 cm3", "Name": "Argon", "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000281", "Rigidity modulus": "no data GPa", "Superconduction temperature": "no data K", "Thermal conductivity": "0.01772 W m-1 K-1", "Van der waals radius": 1.88, "Velocity of sound": "319 m s-1", "Vickers hardness": "no data MN m-2", "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 3, "IUPAC ordering": 3, "Ground level": "1S0", "Ionization energies": [15.7596119, 27.62967, 40.735, 59.58, 74.84, 91.29, 124.41, 143.4567, 422.6, 479.76, 540.4, 619.0, 685.5, 755.13, 855.5, 918.375, 4120.6657, 4426.2229], "Electron affinity": -1.02}, "As": {"Atomic mass": 74.9216, "Atomic no": 33, "Atomic orbitals": {"1s": -423.336658, "2p": -47.527869, "2s": -53.093086, "3d": -1.542767, "3p": -4.851725, "3s": -6.730755, "4p": -0.197497, "4s": -0.52367}, "Atomic radius": 1.15, "Atomic radius calculated": 1.14, "Boiling point": "887 K", "Brinell hardness": "1440 MN m-2", "Bulk modulus": "22 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-3, 3, 5], "Critical temperature": "1700 K", "Density of solid": "5727 kg m-3", "Electrical resistivity": "33 10-8 Ω m", "Electronic structure": "[Ar].3d10.4s2.4p3", "ICSD oxidation states": [2, 3, 5, -2, -3, -1], "Ionic radii": {"3": 0.72, "5": 0.6}, "Liquid range": "203 K", "Melting point": "1090 K", "Mendeleev no": 89, "Mineral hardness": "3.5", "Molar volume": "12.95 cm3", "Name": "Arsenic", "Oxidation states": [-3, 2, 3, 5], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.001552", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 0.72, "ionic_radius": 0.58}}}, "5": {"IV": {"": {"crystal_radius": 0.475, "ionic_radius": 0.335}}, "VI": {"": {"crystal_radius": 0.6, "ionic_radius": 0.46}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "50 W m-1 K-1", "Van der waals radius": 1.85, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 2.18, "Youngs modulus": "8 GPa", "Metallic radius": "no data", "iupac_ordering": 89, "IUPAC ordering": 89, "Ground level": "4S\u00b03/2", "Ionization energies": [9.78855, 18.5892, 28.349, 50.15, 62.77, 121.19, 147.0, 180.0, 213.0, 247.0, 296.0, 333.0, 375.0, 418.0, 460.0, 587.6, 628.8, 672.9, 728.9, 774.0, 814.0, 911.7, 956.79, 2356.9, 2486.0, 2626.0, 2766.0, 2938.0, 3088.1, 3287.0, 3411.643, 14447.678, 15028.907], "Electron affinity": 0.80482}, "At": {"Atomic mass": 210.0, "Atomic no": 85, "Atomic orbitals": {"1s": -3127.390276, "2p": -513.044243, "2s": -531.81835, "3d": -103.060375, "3p": -119.995013, "3s": -129.035542, "4d": -18.295162, "4f": -8.063483, "4p": -25.778264, "4s": -29.809515, "5d": -1.643758, "5p": -4.027061, "5s": -5.453383, "6p": -0.255453, "6s": -0.560189}, "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-1, 1], "Critical temperature": "no data K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d10.6s2.6p5", "Ionic radii": {"7": 0.76}, "Liquid range": "no data K", "Melting point": "575 K", "Mendeleev no": 96, "Mineral hardness": "no data", "Molar volume": "no data cm3", "Name": "Astatine", "Oxidation states": [-1, 1, 3, 5], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"7": {"VI": {"": {"crystal_radius": 0.76, "ionic_radius": 0.62}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "2 (estimate)W m-1 K-1", "Van der waals radius": 2.02, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 2.2, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 98, "IUPAC ordering": 98, "Ground level": "2P\u00b03/2", "Ionization energies": [9.31751, 17.88, 26.58, 39.65, 50.39, 72.0, 85.1, 130.1, 149.0, 169.0, 192.1, 212.0, 236.0, 263.0, 287.0, 311.0, 335.0, 452.0, 481.0, 510.0, 540.0, 600.0, 630.0, 720.0, 750.0, 790.0, 860.0, 920.0, 990.0, 1050.0, 1120.0, 1180.0, 1250.0, 1320.0, 1380.0, 1450.0, 1510.0, 1590.0, 1650.0, 1948.0, 2007.0, 2071.0, 2139.0, 2203.0, 2266.0, 2373.0, 2439.0, 2510.0, 2576.0, 2841.0, 2905.0, 2977.0, 3042.0, 3312.0, 3388.0, 3573.0, 3649.0, 5976.0, 6122.0, 6279.0, 6445.0, 6604.0, 6759.0, 7068.0, 7230.0, 7410.0, 7570.0, 8030.0, 8180.0, 8330.0, 8480.0, 9330.0, 9500.0, 9830.0, 9990.0, 21210.0, 21600.0, 22030.0, 22420.0, 25580.0, 26090.0, 26730.0, 27139.0, 107923.4, 109886.0], "Electron affinity": 2.415787}, "Au": {"Atomic mass": 196.966569, "Atomic no": 79, "Atomic orbitals": {"1s": -2683.508245, "2p": -430.725701, "2s": -447.888973, "3d": -81.511751, "3p": -96.707, "3s": -104.824516, "4d": -12.131815, "4f": -3.486824, "4p": -18.578652, "4s": -22.078357, "5d": -0.304738, "5p": -2.002495, "5s": -3.113936, "6s": -0.162334}, "Atomic radius": 1.35, "Atomic radius calculated": 1.74, "Boiling point": "3129 K", "Brinell hardness": "2450 MN m-2", "Bulk modulus": "220 GPa", "Coefficient of linear thermal expansion": "14.2 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "19300 kg m-3", "Electrical resistivity": "2.2 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d10.6s1", "Ionic radii": {"1": 1.51, "3": 0.99, "5": 0.71}, "Liquid range": "1791.67 K", "Melting point": "1337.33 K", "Mendeleev no": 70, "Mineral hardness": "2.5", "Molar volume": "10.21 cm3", "Name": "Gold", "Oxidation states": [-1, 1, 2, 3, 5], "Poissons ratio": "0.44", "Reflectivity": "95 %", "Refractive index": "no data", "Rigidity modulus": "27 GPa", "Shannon radii": {"1": {"VI": {"": {"crystal_radius": 1.51, "ionic_radius": 1.37}}}, "3": {"IVSQ": {"": {"crystal_radius": 0.82, "ionic_radius": 0.68}}, "VI": {"": {"crystal_radius": 0.99, "ionic_radius": 0.85}}}, "5": {"VI": {"": {"crystal_radius": 0.71, "ionic_radius": 0.57}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "320 W m-1 K-1", "Van der waals radius": 2.14, "Velocity of sound": "1740 m s-1", "Vickers hardness": "216 MN m-2", "X": 2.54, "Youngs modulus": "78 GPa", "Metallic radius": 1.442, "iupac_ordering": 71, "IUPAC ordering": 71, "Ground level": "2S1/2", "Ionization energies": [9.225554, 20.203, 30.0, 45.0, 60.0, 74.0, 94.0, 112.0, 130.1, 149.0, 168.2, 248.0, 275.0, 299.0, 324.0, 365.0, 392.0, 433.0, 487.0, 520.0, 550.0, 600.0, 650.0, 710.0, 760.0, 820.0, 870.0, 930.0, 990.0, 1040.0, 1100.0, 1150.0, 1210.0, 1475.0, 1527.0, 1584.0, 1644.0, 1702.0, 1758.0, 1845.0, 1904.0, 1967.0, 2026.0, 2261.0, 2320.0, 2383.0, 2443.0, 2640.0, 2708.0, 2870.0, 2941.0, 4888.0, 5013.0, 5156.0, 5307.0, 5452.0, 5594.0, 5846.0, 5994.0, 6156.0, 6305.0, 6724.0, 6854.0, 6997.0, 7130.0, 7760.0, 7910.0, 8210.0, 8360.0, 18040.0, 18400.0, 18790.0, 19150.0, 21470.0, 21920.0, 22500.0, 22868.1, 91515.82, 93254.3], "Electron affinity": 2.30861025}, "B": {"Atomic mass": 10.811, "Atomic no": 5, "Atomic orbitals": {"1s": -6.564347, "2p": -0.136603, "2s": -0.344701}, "Atomic radius": 0.85, "Atomic radius calculated": 0.87, "Boiling point": "4200 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "320 GPa", "Coefficient of linear thermal expansion": "6 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "2460 kg m-3", "Electrical resistivity": "> 101210-8 Ω m", "Electronic structure": "[He].2s2.2p1", "ICSD oxidation states": [3, -3], "Ionic radii": {"3": 0.41}, "Liquid range": "1851 K", "Melting point": "2349 K", "Mendeleev no": 86, "Mineral hardness": "9.3", "Molar volume": "4.39 cm3", "Name": "Boron", "Oxidation states": [1, 2, 3], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"III": {"": {"crystal_radius": 0.15, "ionic_radius": 0.01}}, "IV": {"": {"crystal_radius": 0.25, "ionic_radius": 0.11}}, "VI": {"": {"crystal_radius": 0.41, "ionic_radius": 0.27}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "27 W m-1 K-1", "Van der waals radius": 1.92, "Velocity of sound": "16200 m s-1", "Vickers hardness": "49000 MN m-2", "X": 2.04, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"B-10": 84.59, "B-11": 40.59}, "Metallic radius": "no data", "iupac_ordering": 81, "IUPAC ordering": 81, "Ground level": "2P\u00b01/2", "Ionization energies": [8.298019, 25.15483, 37.93059, 259.3715, 340.2260229], "Electron affinity": 0.27972325}, "Ba": {"Atomic mass": 137.327, "Atomic no": 56, "Atomic orbitals": {"1s": -1305.743258, "2p": -189.598483, "2s": -200.844444, "3d": -28.528933, "3p": -37.536931, "3s": -42.359434, "4d": -3.432441, "4p": -6.497622, "4s": -8.257061, "5p": -0.698605, "5s": -1.157159, "6s": -0.118967}, "Atomic radius": 2.15, "Atomic radius calculated": 2.53, "Boiling point": "2143 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "9.6 GPa", "Coefficient of linear thermal expansion": "20.6 x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "3510 kg m-3", "Electrical resistivity": "34 10-8 Ω m", "Electronic structure": "[Xe].6s2", "ICSD oxidation states": [2], "Ionic radii": {"2": 1.49}, "Liquid range": "1143 K", "Melting point": "1000 K", "Mendeleev no": 14, "Mineral hardness": "1.25", "Molar volume": "38.16 cm3", "Name": "Barium", "Oxidation states": [2], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "4.9 GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.49, "ionic_radius": 1.35}}, "VII": {"": {"crystal_radius": 1.52, "ionic_radius": 1.38}}, "VIII": {"": {"crystal_radius": 1.56, "ionic_radius": 1.42}}, "IX": {"": {"crystal_radius": 1.61, "ionic_radius": 1.47}}, "X": {"": {"crystal_radius": 1.66, "ionic_radius": 1.52}}, "XI": {"": {"crystal_radius": 1.71, "ionic_radius": 1.57}}, "XII": {"": {"crystal_radius": 1.75, "ionic_radius": 1.61}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "18 W m-1 K-1", "Van der waals radius": 2.68, "Velocity of sound": "1620 m s-1", "Vickers hardness": "no data MN m-2", "X": 0.89, "Youngs modulus": "13 GPa", "Metallic radius": 2.236, "iupac_ordering": 13, "IUPAC ordering": 13, "Ground level": "1S0", "Ionization energies": [5.2116646, 10.003826, 35.8438, 47.0, 58.0, 71.0, 86.0, 101.0, 130.5, 146.52, 241.0, 267.1, 296.0, 325.0, 354.0, 390.0, 422.0, 455.0, 488.0, 520.0, 646.0, 679.0, 717.0, 752.0, 809.0, 846.0, 935.0, 976.62, 1695.0, 1776.0, 1864.0, 1958.0, 2047.0, 2142.0, 2256.0, 2349.0, 2452.0, 2547.0, 2814.0, 2901.0, 2994.0, 3081.0, 3266.0, 3363.0, 3546.0, 3640.0, 8326.0, 8565.0, 8831.0, 9077.0, 9739.0, 10023.0, 10376.0, 10616.42, 43485.366, 44561.47], "Electron affinity": 0.144626}, "Be": {"Atomic mass": 9.012182, "Atomic no": 4, "Atomic orbitals": {"1s": -3.856411, "2s": -0.205744}, "Atomic radius": 1.05, "Atomic radius calculated": 1.12, "Boiling point": "2742 K", "Brinell hardness": "600 MN m-2", "Bulk modulus": "130 GPa", "Coefficient of linear thermal expansion": "11.3 x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "1848 kg m-3", "Electrical resistivity": "3.8 10-8 Ω m", "Electronic structure": "[He].2s2", "ICSD oxidation states": [2], "Ionic radii": {"2": 0.59}, "Liquid range": "1182 K", "Melting point": "1560 K", "Mendeleev no": 77, "Mineral hardness": "5.5", "Molar volume": "4.85 cm3", "Name": "Beryllium", "Oxidation states": [2], "Poissons ratio": "0.032", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "132 GPa", "Shannon radii": {"2": {"III": {"": {"crystal_radius": 0.3, "ionic_radius": 0.16}}, "IV": {"": {"crystal_radius": 0.41, "ionic_radius": 0.27}}, "VI": {"": {"crystal_radius": 0.59, "ionic_radius": 0.45}}}}, "Superconduction temperature": "0.026 K", "Thermal conductivity": "190 W m-1 K-1", "Van der waals radius": 1.53, "Velocity of sound": "13000 m s-1", "Vickers hardness": "1670 MN m-2", "X": 1.57, "Youngs modulus": "287 GPa", "NMR Quadrupole Moment": {"Be-9": 52.88}, "Metallic radius": 1.12, "iupac_ordering": 17, "IUPAC ordering": 17, "Ground level": "1S0", "Ionization energies": [9.322699, 18.21115, 153.896205, 217.7185861], "Electron affinity": -0.52}, "Bi": {"Atomic mass": 208.9804, "Atomic no": 83, "Atomic orbitals": {"1s": -2975.550959, "2p": -484.716359, "2s": -502.950758, "3d": -95.532476, "3p": -111.883393, "3s": -120.613998, "4d": -16.084817, "4f": -6.382744, "4p": -23.218641, "4s": -27.07034, "5d": -1.139408, "5p": -3.293637, "5s": -4.611934, "6p": -0.180198, "6s": -0.426129}, "Atomic radius": 1.6, "Atomic radius calculated": 1.43, "Boiling point": "1837 K", "Brinell hardness": "94.2 MN m-2", "Bulk modulus": "31 GPa", "Coefficient of linear thermal expansion": "13.4 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "9780 kg m-3", "Electrical resistivity": "130 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d10.6s2.6p3", "ICSD oxidation states": [1, 2, 3, 5], "Ionic radii": {"3": 1.17, "5": 0.9}, "Liquid range": "1292.6 K", "Melting point": "544.4 K", "Mendeleev no": 87, "Mineral hardness": "2.25", "Molar volume": "21.31 cm3", "Name": "Bismuth", "Oxidation states": [-3, 3, 5], "Poissons ratio": "0.33", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "12 GPa", "Shannon radii": {"3": {"V": {"": {"crystal_radius": 1.1, "ionic_radius": 0.96}}, "VI": {"": {"crystal_radius": 1.17, "ionic_radius": 1.03}}, "VIII": {"": {"crystal_radius": 1.31, "ionic_radius": 1.17}}}, "5": {"VI": {"": {"crystal_radius": 0.9, "ionic_radius": 0.76}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "8 W m-1 K-1", "Van der waals radius": 2.07, "Velocity of sound": "1790 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.02, "Youngs modulus": "32 GPa", "Metallic radius": 1.82, "iupac_ordering": 87, "IUPAC ordering": 87, "Ground level": "4S\u00b03/2", "Ionization energies": [7.285516, 16.703, 25.57075, 45.37, 54.856, 88.4, 103.0, 122.0, 143.0, 161.1, 183.0, 208.0, 229.0, 252.0, 272.6, 370.2, 409.0, 436.0, 464.0, 520.0, 550.0, 620.0, 660.0, 690.0, 750.0, 810.0, 870.0, 930.0, 990.0, 1060.0, 1120.0, 1180.0, 1250.0, 1310.0, 1380.0, 1440.0, 1500.0, 1784.0, 1840.0, 1902.0, 1967.0, 2029.0, 2090.0, 2190.0, 2253.0, 2321.0, 2385.0, 2641.0, 2703.0, 2771.0, 2835.0, 3078.0, 3151.0, 3329.0, 3401.8, 5599.0, 5740.0, 5892.0, 6054.0, 6208.0, 6358.0, 6648.0, 6804.0, 6977.0, 7137.0, 7580.0, 7720.0, 7870.0, 8010.0, 8780.0, 8950.0, 9270.0, 9430.0, 20130.0, 20500.0, 20920.0, 21300.0, 24150.0, 24640.0, 25260.0, 25656.9, 102251.76, 104132.8], "Electron affinity": 0.94236213}, "Bk": {"Atomic mass": 247.0, "Atomic no": 97, "Atomic orbitals": "no data", "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "14780 kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].5f9.7s2", "Ionic radii": {"3": 1.1, "4": 0.97}, "Liquid range": "no data K", "Melting point": "1259 K", "Mendeleev no": 40, "Mineral hardness": "no data", "Molar volume": "16.84 cm3", "Name": "Berkelium", "Oxidation states": [3, 4], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.1, "ionic_radius": 0.96}}}, "4": {"VI": {"": {"crystal_radius": 0.97, "ionic_radius": 0.83}}, "VIII": {"": {"crystal_radius": 1.07, "ionic_radius": 0.93}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "10 W m-1 K-1", "Van der waals radius": 2.44, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.3, "Youngs modulus": "no data GPa", "Metallic radius": 1.703, "iupac_ordering": 24, "IUPAC ordering": 24, "Ground level": "6H\u00b015/2", "Ionization energies": [6.19785, 11.9, 21.6, 36.0, 56.0, 70.1, 90.0, 114.0, 130.0, 147.0, 171.0, 195.0, 218.0, 240.0, 259.0, 279.0, 303.0, 339.0, 361.0, 497.0, 526.0, 557.0, 590.0, 621.0, 652.0, 700.0, 733.0, 768.0, 800.0, 960.0, 1000.0, 1040.0, 1080.0, 1200.0, 1240.0, 1360.0, 1410.0, 1550.0, 1630.0, 1720.0, 1800.0, 1890.0, 1970.0, 2050.0, 2140.0, 2240.0, 2320.0, 2410.0, 2490.0, 2580.0, 2670.0, 3080.0, 3154.0, 3232.0, 3315.0, 3393.0, 3469.0, 3630.0, 3709.0, 3797.0, 3877.0, 4202.0, 4281.0, 4365.0, 4445.0, 4940.0, 5040.0, 5270.0, 5360.0, 8500.0, 8670.0, 8850.0, 9050.0, 9240.0, 9420.0, 9880.0, 10070.0, 10280.0, 10480.0, 11020.0, 11190.0, 11380.0, 11550.0, 13090.0, 13300.0, 13720.0, 13910.0, 28380.0, 28800.0, 29300.0, 29800.0, 35500.0, 36200.0, 37000.0, 37457.6, 146904.7, 149398.0], "Electron affinity": -1.72}, "Br": {"Atomic mass": 79.904, "Atomic no": 35, "Atomic orbitals": {"1s": -480.182643, "2p": -55.67796, "2s": -61.710022, "3d": -2.52211, "3p": -6.298805, "3s": -8.409057, "4p": -0.295334, "4s": -0.720066}, "Atomic radius": 1.15, "Atomic radius calculated": 0.94, "Boiling point": "332 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "1.9 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-1, 1, 3, 5, 7], "Critical temperature": "586 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "> 101810-8 Ω m", "Electronic structure": "[Ar].3d10.4s2.4p5", "ICSD oxidation states": [5, -1], "Ionic radii": {"-1": 1.82, "3": 0.73, "5": 0.45, "7": 0.53}, "Liquid range": "66.2 K", "Melting point": "265.8 K", "Mendeleev no": 98, "Mineral hardness": "no data", "Molar volume": "19.78 cm3", "Name": "Bromine", "Oxidation states": [-1, 1, 3, 4, 5, 7], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.001132", "Rigidity modulus": "no data GPa", "Shannon radii": {"-1": {"VI": {"": {"crystal_radius": 1.82, "ionic_radius": 1.96}}}, "3": {"IVSQ": {"": {"crystal_radius": 0.73, "ionic_radius": 0.59}}}, "5": {"IIIPY": {"": {"crystal_radius": 0.45, "ionic_radius": 0.31}}}, "7": {"IV": {"": {"crystal_radius": 0.39, "ionic_radius": 0.25}}, "VI": {"": {"crystal_radius": 0.53, "ionic_radius": 0.39}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.12 W m-1 K-1", "Van der waals radius": 1.85, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 2.96, "Youngs modulus": "no data GPa", "Metallic radius": 1.14, "iupac_ordering": 100, "IUPAC ordering": 100, "Ground level": "2P\u00b03/2", "Ionization energies": [11.81381, 21.591, 34.871, 47.782, 59.595, 87.39, 103.03, 192.61, 224.0, 261.0, 301.0, 338.0, 393.0, 436.0, 481.0, 530.0, 577.0, 716.3, 761.0, 809.8, 870.0, 920.8, 963.0, 1070.6, 1119.17, 2731.4, 2869.0, 3021.0, 3169.0, 3361.0, 3523.1, 3735.0, 3868.986, 16317.011, 16937.127], "Electron affinity": 3.3635883}, "C": {"Atomic mass": 12.0107, "Atomic no": 6, "Atomic orbitals": {"1s": -9.947718, "2p": -0.199186, "2s": -0.500866}, "Atomic radius": 0.7, "Atomic radius calculated": 0.67, "Boiling point": "4300 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "33 GPa", "Coefficient of linear thermal expansion": "7.1 x10-6K-1", "Common oxidation states": [-4, 4], "Critical temperature": "no data K", "Density of solid": "2267 kg m-3", "Electrical resistivity": "about 1000 - direction dependent10-8 Ω m", "Electronic structure": "[He].2s2.2p2", "ICSD oxidation states": [2, 3, 4, -4, -3, -2], "Ionic radii": {"4": 0.3}, "Liquid range": "500 K", "Melting point": "3800 K", "Mendeleev no": 95, "Mineral hardness": "0.5 (graphite; diamond is 10.0)(no units)", "Molar volume": "5.29 cm3", "Name": "Carbon", "Oxidation states": [-4, -3, -2, -1, 1, 2, 3, 4], "Poissons ratio": "no data", "Reflectivity": "27 %", "Refractive index": "2.417 (diamond)(no units)", "Rigidity modulus": "no data GPa", "Shannon radii": {"4": {"III": {"": {"crystal_radius": 0.06, "ionic_radius": -0.08}}, "IV": {"": {"crystal_radius": 0.29, "ionic_radius": 0.15}}, "VI": {"": {"crystal_radius": 0.3, "ionic_radius": 0.16}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "140 W m-1 K-1", "Van der waals radius": 1.7, "Velocity of sound": "18350 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.55, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"C-11": 33.27}, "Metallic radius": "no data", "iupac_ordering": 86, "IUPAC ordering": 86, "Ground level": "3P0", "Ionization energies": [11.260288, 24.383154, 47.88778, 64.49352, 392.090518, 489.993198], "Electron affinity": 1.262113612}, "Ca": {"Atomic mass": 40.078, "Atomic no": 20, "Atomic orbitals": {"1s": -143.935181, "2p": -12.285376, "2s": -15.046905, "3p": -1.030572, "3s": -1.706331, "4s": -0.141411}, "Atomic radius": 1.8, "Atomic radius calculated": 1.94, "Boiling point": "1757 K", "Brinell hardness": "167 MN m-2", "Bulk modulus": "17 GPa", "Coefficient of linear thermal expansion": "22.3 x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "1550 kg m-3", "Electrical resistivity": "3.4 10-8 Ω m", "Electronic structure": "[Ar].4s2", "ICSD oxidation states": [2], "Ionic radii": {"2": 1.14}, "Liquid range": "642 K", "Melting point": "1115 K", "Mendeleev no": 16, "Mineral hardness": "1.75", "Molar volume": "26.20 cm3", "Name": "Calcium", "Oxidation states": [2], "Poissons ratio": "0.31", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "7.4 GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.14, "ionic_radius": 1.0}}, "VII": {"": {"crystal_radius": 1.2, "ionic_radius": 1.06}}, "VIII": {"": {"crystal_radius": 1.26, "ionic_radius": 1.12}}, "IX": {"": {"crystal_radius": 1.32, "ionic_radius": 1.18}}, "X": {"": {"crystal_radius": 1.37, "ionic_radius": 1.23}}, "XII": {"": {"crystal_radius": 1.48, "ionic_radius": 1.34}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "200 W m-1 K-1", "Van der waals radius": 2.31, "Velocity of sound": "3810 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.0, "Youngs modulus": "20 GPa", "NMR Quadrupole Moment": {"Ca-41": -66.5, "Ca-43": -40.8}, "Metallic radius": 1.976, "iupac_ordering": 15, "IUPAC ordering": 15, "Ground level": "1S0", "Ionization energies": [6.11315547, 11.871719, 50.91316, 67.2732, 84.34, 108.78, 127.21, 147.24, 188.54, 211.275, 591.6, 658.2, 728.6, 817.2, 894.0, 973.7, 1086.8, 1157.726, 5128.8578, 5469.8616], "Electron affinity": 0.024551}, "Cd": {"Atomic mass": 112.411, "Atomic no": 48, "Atomic orbitals": {"1s": -941.476646, "2p": -127.63512, "2s": -136.83249, "3d": -14.685252, "3p": -21.637522, "3s": -25.379908, "4d": -0.47053, "4p": -2.39526, "4s": -3.596069, "5s": -0.204228}, "Atomic radius": 1.55, "Atomic radius calculated": 1.61, "Boiling point": "1040 K", "Brinell hardness": "203 MN m-2", "Bulk modulus": "42 GPa", "Coefficient of linear thermal expansion": "30.8 x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "8650 kg m-3", "Electrical resistivity": "7 10-8 Ω m", "Electronic structure": "[Kr].4d10.5s2", "ICSD oxidation states": [2], "Ionic radii": {"2": 1.09}, "Liquid range": "445.78 K", "Melting point": "594.22 K", "Mendeleev no": 75, "Mineral hardness": "2.0", "Molar volume": "13.00 cm3", "Name": "Cadmium", "Oxidation states": [1, 2], "Poissons ratio": "0.30", "Reflectivity": "67 %", "Refractive index": "no data", "Rigidity modulus": "19 GPa", "Shannon radii": {"2": {"IV": {"": {"crystal_radius": 0.92, "ionic_radius": 0.78}}, "V": {"": {"crystal_radius": 1.01, "ionic_radius": 0.87}}, "VI": {"": {"crystal_radius": 1.09, "ionic_radius": 0.95}}, "VII": {"": {"crystal_radius": 1.17, "ionic_radius": 1.03}}, "VIII": {"": {"crystal_radius": 1.24, "ionic_radius": 1.1}}, "XII": {"": {"crystal_radius": 1.45, "ionic_radius": 1.31}}}}, "Superconduction temperature": "0.517 K", "Thermal conductivity": "97 W m-1 K-1", "Van der waals radius": 2.18, "Velocity of sound": "2310 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.69, "Youngs modulus": "50 GPa", "Metallic radius": 1.51, "iupac_ordering": 75, "IUPAC ordering": 75, "Ground level": "1S0", "Ionization energies": [8.99382, 16.908313, 37.468, 51.0, 67.9, 87.0, 105.0, 130.1, 150.0, 173.0, 195.0, 218.0, 305.0, 329.0, 358.0, 385.0, 421.0, 452.6, 513.0, 546.19, 963.0, 1026.0, 1095.0, 1167.0, 1237.0, 1320.0, 1401.0, 1477.0, 1558.0, 1635.0, 1852.0, 1917.9, 1998.0, 2091.0, 2195.0, 2250.0, 2427.0, 2498.62, 5839.0, 6039.0, 6257.0, 6460.0, 6869.0, 7109.0, 7414.0, 7607.95, 31451.062, 32341.49], "Electron affinity": -0.72}, "Ce": {"Atomic mass": 140.116, "Atomic no": 58, "Atomic orbitals": {"1s": -1406.148284, "2p": -206.925148, "2s": -218.684842, "3d": -32.412569, "3p": -41.938282, "3s": -47.035283, "4d": -4.192548, "4f": -0.337442, "4p": -7.532106, "4s": -9.432744, "5d": -0.14055, "5p": -0.85011, "5s": -1.369728, "6s": -0.133974}, "Atomic radius": 1.85, "Atomic radius calculated": "no data", "Boiling point": "3633 K", "Brinell hardness": "412 MN m-2", "Bulk modulus": "22 GPa", "Coefficient of linear thermal expansion": "6.3 x10-6K-1", "Common oxidation states": [3, 4], "Critical temperature": "no data K", "Density of solid": "6689 kg m-3", "Electrical resistivity": "74 10-8 Ω m", "Electronic structure": "[Xe].4f1.5d1.6s2", "ICSD oxidation states": [3, 4], "Ionic radii": {"3": 1.15, "4": 1.01}, "Liquid range": "2565 K", "Melting point": "1068 K", "Mendeleev no": 32, "Mineral hardness": "2.5", "Molar volume": "20.69 cm3", "Name": "Cerium", "Oxidation states": [2, 3, 4], "Poissons ratio": "0.24", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "14 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.15, "ionic_radius": 1.01}}, "VII": {"": {"crystal_radius": 1.21, "ionic_radius": 1.07}}, "VIII": {"": {"crystal_radius": 1.283, "ionic_radius": 1.143}}, "IX": {"": {"crystal_radius": 1.336, "ionic_radius": 1.196}}, "X": {"": {"crystal_radius": 1.39, "ionic_radius": 1.25}}, "XII": {"": {"crystal_radius": 1.48, "ionic_radius": 1.34}}}, "4": {"VI": {"": {"crystal_radius": 1.01, "ionic_radius": 0.87}}, "VIII": {"": {"crystal_radius": 1.11, "ionic_radius": 0.97}}, "X": {"": {"crystal_radius": 1.21, "ionic_radius": 1.07}}, "XII": {"": {"crystal_radius": 1.28, "ionic_radius": 1.14}}}}, "Superconduction temperature": "0.022 (under pressure)K", "Thermal conductivity": "11 W m-1 K-1", "Van der waals radius": 2.42, "Velocity of sound": "2100 m s-1", "Vickers hardness": "270 MN m-2", "X": 1.12, "Youngs modulus": "34 GPa", "Metallic radius": 1.707, "iupac_ordering": 46, "IUPAC ordering": 46, "Ground level": "1G\u00b04", "Ionization energies": [5.5386, 10.956, 20.1974, 36.906, 65.55, 77.6, 91.0, 106.0, 125.0, 140.0, 172.0, 192.24, 312.0, 340.0, 371.0, 403.0, 435.0, 472.0, 509.0, 543.0, 579.0, 613.0, 749.0, 785.0, 824.0, 862.0, 924.0, 965.0, 1060.0, 1103.5, 1908.0, 1994.0, 2087.0, 2185.0, 2280.0, 2378.0, 2500.0, 2600.0, 2706.0, 2806.0, 3087.0, 3176.0, 3274.0, 3366.0, 3570.0, 3672.0, 3865.0, 3963.0, 9020.0, 9269.0, 9545.0, 9803.0, 10542.0, 10840.0, 11210.0, 11459.85, 46840.306, 47965.72], "Electron affinity": 0.572}, "Cf": {"Atomic mass": 251.0, "Atomic no": 98, "Atomic orbitals": "no data", "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "15100 kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].5f10.7s2", "Ionic radii": {"3": 1.09, "4": 0.961}, "Liquid range": "no data K", "Melting point": "1173 K", "Mendeleev no": 39, "Mineral hardness": "no data", "Molar volume": "16.50 cm3", "Name": "Californium", "Oxidation states": [2, 3, 4], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.09, "ionic_radius": 0.95}}}, "4": {"VI": {"": {"crystal_radius": 0.961, "ionic_radius": 0.821}}, "VIII": {"": {"crystal_radius": 1.06, "ionic_radius": 0.92}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "no data W m-1 K-1", "Van der waals radius": 2.45, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.3, "Youngs modulus": "no data GPa", "Metallic radius": 1.86, "iupac_ordering": 23, "IUPAC ordering": 23, "Ground level": "5I8", "Ionization energies": [6.28166, 12.0, 22.4, 37.7, 51.9, 75.0, 91.0, 112.9, 133.0, 152.0, 178.0, 201.0, 225.0, 247.0, 265.0, 286.0, 310.0, 334.0, 368.0, 390.0, 536.0, 566.0, 597.0, 630.0, 662.0, 695.0, 744.0, 778.0, 814.0, 847.0, 1010.0, 1050.0, 1090.0, 1120.0, 1250.0, 1300.0, 1420.0, 1470.0, 1620.0, 1700.0, 1790.0, 1880.0, 1960.0, 2050.0, 2130.0, 2220.0, 2320.0, 2410.0, 2490.0, 2580.0, 2670.0, 2750.0, 3186.0, 3261.0, 3340.0, 3424.0, 3503.0, 3581.0, 3747.0, 3828.0, 3915.0, 3998.0, 4329.0, 4407.0, 4494.0, 4570.0, 5100.0, 5190.0, 5430.0, 5520.0, 8730.0, 8900.0, 9090.0, 9290.0, 9480.0, 9660.0, 10140.0, 10330.0, 10550.0, 10740.0, 11300.0, 11470.0, 11650.0, 11820.0, 13450.0, 13660.0, 14080.0, 14280.0, 29000.0, 29500.0, 30000.0, 30500.0, 36500.0, 37100.0, 37900.0, 38443.5, 150579.3, 153124.0], "Electron affinity": -1.01}, "Cl": {"Atomic mass": 35.453, "Atomic no": 17, "Atomic orbitals": {"1s": -100.369229, "2p": -7.039982, "2s": -9.187993, "3p": -0.32038, "3s": -0.754458}, "Atomic radius": 1.0, "Atomic radius calculated": 0.79, "Boiling point": "239.11 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "1.1 (liquid)GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-1, 1, 3, 5, 7], "Critical temperature": "417 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "> 101010-8 Ω m", "Electronic structure": "[Ne].3s2.3p5", "ICSD oxidation states": [-1], "Ionic radii": {"-1": 1.67, "5": 0.26, "7": 0.41}, "Liquid range": "67.51 K", "Melting point": "171.6 K", "Mendeleev no": 99, "Mineral hardness": "no data", "Molar volume": "17.39 cm3", "Name": "Chlorine", "Oxidation states": [-1, 1, 2, 3, 4, 5, 6, 7], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000773", "Rigidity modulus": "no data GPa", "Shannon radii": {"-1": {"VI": {"": {"crystal_radius": 1.67, "ionic_radius": 1.81}}}, "5": {"IIIPY": {"": {"crystal_radius": 0.26, "ionic_radius": 0.12}}}, "7": {"IV": {"": {"crystal_radius": 0.22, "ionic_radius": 0.08}}, "VI": {"": {"crystal_radius": 0.41, "ionic_radius": 0.27}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.0089 W m-1 K-1", "Van der waals radius": 1.75, "Velocity of sound": "206 m s-1", "Vickers hardness": "no data MN m-2", "X": 3.16, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"Cl-35": -81.65, "Cl-37": -64.35}, "Metallic radius": "no data", "iupac_ordering": 101, "IUPAC ordering": 101, "Ground level": "2P\u00b03/2", "Ionization energies": [12.967633, 23.81364, 39.8, 53.24, 67.68, 96.94, 114.2013, 348.306, 400.851, 456.7, 530.0, 591.58, 656.3, 750.23, 809.198, 3658.3438, 3946.2909], "Electron affinity": 3.61272528}, "Cm": {"Atomic mass": 247.0, "Atomic no": 96, "Atomic orbitals": "no data", "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "3383 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "13510 kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].5f7.6d1.7s2", "Ionic radii": {"3": 1.11, "4": 0.99}, "Liquid range": "1770 K", "Melting point": "1613 K", "Mendeleev no": 41, "Mineral hardness": "no data", "Molar volume": "18.05 cm3", "Name": "Curium", "Oxidation states": [3, 4], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.11, "ionic_radius": 0.97}}}, "4": {"VI": {"": {"crystal_radius": 0.99, "ionic_radius": 0.85}}, "VIII": {"": {"crystal_radius": 1.09, "ionic_radius": 0.95}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "8.8 W m-1 K-1", "Van der waals radius": 2.45, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.3, "Youngs modulus": "no data GPa", "Metallic radius": 1.743, "iupac_ordering": 25, "IUPAC ordering": 25, "Ground level": "9D\u00b02", "Ionization energies": [5.99141, 12.4, 20.1, 37.7, 51.0, 69.1, 97.0, 112.0, 128.0, 144.0, 167.0, 190.0, 213.0, 235.0, 253.0, 272.0, 311.0, 332.0, 460.0, 489.0, 518.0, 550.0, 580.0, 611.0, 657.0, 689.0, 723.0, 755.0, 910.0, 950.0, 990.0, 1030.0, 1140.0, 1180.0, 1300.0, 1340.0, 1480.0, 1560.0, 1650.0, 1730.0, 1810.0, 1890.0, 1980.0, 2060.0, 2160.0, 2240.0, 2320.0, 2410.0, 2490.0, 2580.0, 2976.0, 3050.0, 3125.0, 3207.0, 3284.0, 3360.0, 3515.0, 3593.0, 3679.0, 3758.0, 4078.0, 4156.0, 4239.0, 4317.0, 4791.0, 4880.0, 5110.0, 5200.0, 8270.0, 8440.0, 8620.0, 8820.0, 9000.0, 9180.0, 9630.0, 9820.0, 10020.0, 10220.0, 10760.0, 10920.0, 11100.0, 11270.0, 12740.0, 12950.0, 13350.0, 13550.0, 27740.0, 28180.0, 28700.0, 29100.0, 34600.0, 35200.0, 36000.0, 36493.0, 143299.6, 145743.0], "Electron affinity": 0.28}, "Co": {"Atomic mass": 58.933195, "Atomic no": 27, "Atomic orbitals": {"1s": -275.616639, "2p": -28.152095, "2s": -32.379758, "3d": -0.322368, "3p": -2.388285, "3s": -3.651812, "4s": -0.204497}, "Atomic radius": 1.35, "Atomic radius calculated": 1.52, "Boiling point": "3200 K", "Brinell hardness": "700 MN m-2", "Bulk modulus": "180 GPa", "Coefficient of linear thermal expansion": "13.0 x10-6K-1", "Common oxidation states": [2, 3], "Critical temperature": "no data K", "Density of solid": "8900 kg m-3", "Electrical resistivity": "6 10-8 Ω m", "Electronic structure": "[Ar].3d7.4s2", "ICSD oxidation states": [1, 2, 3, 4], "Ionic radii": {"2": 0.885, "3": 0.75, "4": 0.67}, "Ionic radii hs": {"2": 0.885, "3": 0.75, "4": 0.67}, "Ionic radii ls": {"2": 0.79, "3": 0.685}, "Liquid range": "1432 K", "Melting point": "1768 K", "Mendeleev no": 64, "Mineral hardness": "5.0", "Molar volume": "6.67 cm3", "Name": "Cobalt", "Oxidation states": [-1, 1, 2, 3, 4, 5], "Poissons ratio": "0.31", "Reflectivity": "67 %", "Refractive index": "no data", "Rigidity modulus": "75 GPa", "Shannon radii": {"2": {"IV": {"High Spin": {"crystal_radius": 0.72, "ionic_radius": 0.58}}, "V": {"": {"crystal_radius": 0.81, "ionic_radius": 0.67}}, "VI": {"Low Spin": {"crystal_radius": 0.79, "ionic_radius": 0.65}, "High Spin": {"crystal_radius": 0.885, "ionic_radius": 0.745}}, "VIII": {"": {"crystal_radius": 1.04, "ionic_radius": 0.9}}}, "3": {"VI": {"High Spin": {"crystal_radius": 0.75, "ionic_radius": 0.61}, "Low Spin": {"crystal_radius": 0.685, "ionic_radius": 0.545}}}, "4": {"IV": {"": {"crystal_radius": 0.54, "ionic_radius": 0.4}}, "VI": {"High Spin": {"crystal_radius": 0.67, "ionic_radius": 0.53}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "100 W m-1 K-1", "Van der waals radius": 2.0, "Velocity of sound": "4720 m s-1", "Vickers hardness": "1043 MN m-2", "X": 1.88, "Youngs modulus": "209 GPa", "NMR Quadrupole Moment": {"Co-59": 420.3}, "Metallic radius": 1.25, "iupac_ordering": 67, "IUPAC ordering": 67, "Ground level": "4F9/2", "Ionization energies": [7.88101, 17.0844, 33.5, 51.27, 79.5, 102.0, 128.9, 157.8, 186.14, 275.4, 305.32, 336.1, 378.5, 410.0, 441.1, 511.96, 546.588, 1397.2, 1504.5, 1606.0, 1724.0, 1844.0, 1960.8, 2119.4, 2218.876, 9544.1833, 10012.122], "Electron affinity": 0.662265}, "Cr": {"Atomic mass": 51.9961, "Atomic no": 24, "Atomic orbitals": {"1s": -213.881191, "2p": -20.526273, "2s": -24.113457, "3d": -0.118123, "3p": -1.65423, "3s": -2.649085, "4s": -0.150445}, "Atomic radius": 1.4, "Atomic radius calculated": 1.66, "Boiling point": "2944 K", "Brinell hardness": "1120 MN m-2", "Bulk modulus": "160 GPa", "Coefficient of linear thermal expansion": "4.9 x10-6K-1", "Common oxidation states": [3, 6], "Critical temperature": "no data K", "Density of solid": "7140 kg m-3", "Electrical resistivity": "12.7 10-8 Ω m", "Electronic structure": "[Ar].3d5.4s1", "ICSD oxidation states": [2, 3, 4, 5, 6], "Ionic radii": {"2": 0.94}, "Ionic radii hs": {"2": 0.94}, "Ionic radii ls": {"2": 0.87, "3": 0.755, "4": 0.69, "5": 0.63, "6": 0.58}, "Liquid range": "764 K", "Melting point": "2180 K", "Mendeleev no": 57, "Mineral hardness": "8.5", "Molar volume": "7.23 cm3", "Name": "Chromium", "Oxidation states": [-2, -1, 1, 2, 3, 4, 5, 6], "Poissons ratio": "0.21", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "115 GPa", "Shannon radii": {"2": {"VI": {"Low Spin": {"crystal_radius": 0.87, "ionic_radius": 0.73}, "High Spin": {"crystal_radius": 0.94, "ionic_radius": 0.8}}}, "3": {"VI": {"": {"crystal_radius": 0.755, "ionic_radius": 0.615}}}, "4": {"IV": {"": {"crystal_radius": 0.55, "ionic_radius": 0.41}}, "VI": {"": {"crystal_radius": 0.69, "ionic_radius": 0.55}}}, "5": {"IV": {"": {"crystal_radius": 0.485, "ionic_radius": 0.345}}, "VI": {"": {"crystal_radius": 0.63, "ionic_radius": 0.49}}, "VIII": {"": {"crystal_radius": 0.71, "ionic_radius": 0.57}}}, "6": {"IV": {"": {"crystal_radius": 0.4, "ionic_radius": 0.26}}, "VI": {"": {"crystal_radius": 0.58, "ionic_radius": 0.44}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "94 W m-1 K-1", "Van der waals radius": 2.06, "Velocity of sound": "5940 m s-1", "Vickers hardness": "1060 MN m-2", "X": 1.66, "Youngs modulus": "279 GPa", "NMR Quadrupole Moment": {"Cr-53": -150.5}, "Metallic radius": 1.285, "iupac_ordering": 58, "IUPAC ordering": 58, "Ground level": "7S3", "Ionization energies": [6.76651, 16.486305, 30.959, 49.16, 69.46, 90.6349, 160.29, 184.76, 209.5, 244.5, 270.8, 296.7, 354.7, 384.163, 1011.6, 1097.2, 1188.0, 1294.8, 1394.5, 1495.1, 1634.1, 1721.183, 7481.8628, 7894.7992], "Electron affinity": 0.6758412}, "Cs": {"Atomic mass": 132.9054519, "Atomic no": 55, "Atomic orbitals": {"1s": -1256.738791, "2p": -180.995344, "2s": -191.981873, "3d": -26.418398, "3p": -35.166423, "3s": -39.851584, "4d": -2.848386, "4p": -5.769326, "4s": -7.455966, "5p": -0.504903, "5s": -0.915819, "6s": -0.078699}, "Atomic radius": 2.6, "Atomic radius calculated": 2.98, "Boiling point": "944 K", "Brinell hardness": "0.14 MN m-2", "Bulk modulus": "1.6 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [1], "Critical temperature": "1938 K", "Density of solid": "1879 kg m-3", "Electrical resistivity": "21 10-8 Ω m", "Electronic structure": "[Xe].6s1", "ICSD oxidation states": [1], "Ionic radii": {"1": 1.81}, "Liquid range": "642.41 K", "Melting point": "301.59 K", "Mendeleev no": 8, "Mineral hardness": "0.2", "Molar volume": "70.94 cm3", "Name": "Cesium", "Oxidation states": [1], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"1": {"VI": {"": {"crystal_radius": 1.81, "ionic_radius": 1.67}}, "VIII": {"": {"crystal_radius": 1.88, "ionic_radius": 1.74}}, "IX": {"": {"crystal_radius": 1.92, "ionic_radius": 1.78}}, "X": {"": {"crystal_radius": 1.95, "ionic_radius": 1.81}}, "XI": {"": {"crystal_radius": 1.99, "ionic_radius": 1.85}}, "XII": {"": {"crystal_radius": 2.02, "ionic_radius": 1.88}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "36 W m-1 K-1", "Van der waals radius": 3.43, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 0.79, "Youngs modulus": "1.7 GPa", "Metallic radius": 2.719, "iupac_ordering": 7, "IUPAC ordering": 7, "Ground level": "2S1/2", "Ionization energies": [3.89390572743, 23.15745, 33.195, 43.0, 56.0, 69.1, 82.9, 110.1, 125.61, 213.3, 233.0, 261.0, 289.0, 316.0, 352.0, 382.0, 413.0, 445.0, 476.0, 597.0, 629.0, 666.0, 700.0, 753.0, 791.0, 875.0, 916.1, 1592.0, 1672.0, 1757.0, 1848.0, 1936.0, 2029.0, 2137.0, 2230.0, 2329.0, 2422.0, 2683.0, 2767.0, 2859.0, 2945.0, 3118.0, 3214.0, 3392.0, 3485.0, 7989.0, 8224.0, 8484.0, 8726.0, 9350.0, 9629.0, 9974.0, 10208.78, 41861.075, 42912.99], "Electron affinity": 0.47163025}, "Cu": {"Atomic mass": 63.546, "Atomic no": 29, "Atomic orbitals": {"1s": -320.78852, "2p": -33.481247, "2s": -38.14131, "3d": -0.202272, "3p": -2.609244, "3s": -4.057453, "4s": -0.172056}, "Atomic radius": 1.35, "Atomic radius calculated": 1.45, "Boiling point": "3200 K", "Brinell hardness": "874 MN m-2", "Bulk modulus": "140 GPa", "Coefficient of linear thermal expansion": "16.5 x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "8920 kg m-3", "Electrical resistivity": "1.72 10-8 Ω m", "Electronic structure": "[Ar].3d10.4s1", "ICSD oxidation states": [1, 2, 3], "Ionic radii": {"1": 0.91, "2": 0.87, "3": 0.68}, "Liquid range": "1842.23 K", "Melting point": "1357.77 K", "Mendeleev no": 72, "Mineral hardness": "3.0", "Molar volume": "7.11 cm3", "Name": "Copper", "Oxidation states": [1, 2, 3, 4], "Poissons ratio": "0.34", "Reflectivity": "90 %", "Refractive index": "no data", "Rigidity modulus": "48 GPa", "Shannon radii": {"1": {"II": {"": {"crystal_radius": 0.6, "ionic_radius": 0.46}}, "IV": {"": {"crystal_radius": 0.74, "ionic_radius": 0.6}}, "VI": {"": {"crystal_radius": 0.91, "ionic_radius": 0.77}}}, "2": {"IV": {"": {"crystal_radius": 0.71, "ionic_radius": 0.57}}, "IVSQ": {"": {"crystal_radius": 0.71, "ionic_radius": 0.57}}, "V": {"": {"crystal_radius": 0.79, "ionic_radius": 0.65}}, "VI": {"": {"crystal_radius": 0.87, "ionic_radius": 0.73}}}, "3": {"VI": {"Low Spin": {"crystal_radius": 0.68, "ionic_radius": 0.54}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "400 W m-1 K-1", "Van der waals radius": 1.96, "Velocity of sound": "3570 m s-1", "Vickers hardness": "369 MN m-2", "X": 1.9, "Youngs modulus": "130 GPa", "NMR Quadrupole Moment": {"Cu-63": -220.15, "Cu-65": -204.14}, "Metallic radius": 1.278, "iupac_ordering": 73, "IUPAC ordering": 73, "Ground level": "2S1/2", "Ionization energies": [7.72638, 20.29239, 36.841, 57.38, 79.8, 103.0, 139.0, 166.0, 198.0, 232.2, 265.33, 367.0, 401.0, 436.0, 483.1, 518.7, 552.8, 632.5, 670.608, 1690.5, 1800.0, 1918.0, 2044.0, 2179.4, 2307.3, 2479.1, 2586.954, 11062.4313, 11567.613], "Electron affinity": 1.235784}, "Dy": {"Atomic mass": 162.5, "Atomic no": 66, "Atomic orbitals": {"1s": -1843.229585, "2p": -281.558531, "2s": -295.342856, "3d": -47.4867, "3p": -59.091931, "3s": -65.299442, "4d": -5.686352, "4f": -0.265302, "4p": -10.094091, "4s": -12.551251, "5p": -0.90349, "5s": -1.547977, "6s": -0.132769}, "Atomic radius": 1.75, "Atomic radius calculated": 2.28, "Boiling point": "2840 K", "Brinell hardness": "500 MN m-2", "Bulk modulus": "41 GPa", "Coefficient of linear thermal expansion": "9.9 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "8551 kg m-3", "Electrical resistivity": "92.6 10-8 Ω m", "Electronic structure": "[Xe].4f10.6s2", "ICSD oxidation states": [3], "Ionic radii": {"2": 1.21, "3": 1.052}, "Liquid range": "1160 K", "Melting point": "1680 K", "Mendeleev no": 24, "Mineral hardness": "no data", "Molar volume": "19.01 cm3", "Name": "Dysprosium", "Oxidation states": [2, 3], "Poissons ratio": "0.25", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "25 GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.21, "ionic_radius": 1.07}}, "VII": {"": {"crystal_radius": 1.27, "ionic_radius": 1.13}}, "VIII": {"": {"crystal_radius": 1.33, "ionic_radius": 1.19}}}, "3": {"VI": {"": {"crystal_radius": 1.052, "ionic_radius": 0.912}}, "VII": {"": {"crystal_radius": 1.11, "ionic_radius": 0.97}}, "VIII": {"": {"crystal_radius": 1.167, "ionic_radius": 1.027}}, "IX": {"": {"crystal_radius": 1.223, "ionic_radius": 1.083}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "11 W m-1 K-1", "Van der waals radius": 2.31, "Velocity of sound": "2710 m s-1", "Vickers hardness": "540 MN m-2", "X": 1.22, "Youngs modulus": "61 GPa", "Metallic radius": 1.773, "iupac_ordering": 38, "IUPAC ordering": 38, "Ground level": "5I8", "Ionization energies": [5.93905, 11.647, 22.89, 41.23, 62.1, 93.0, 110.0, 127.0, 152.0, 170.0, 192.0, 224.0, 259.0, 279.0, 300.0, 332.0, 366.0, 399.0, 431.0, 464.9, 664.0, 702.0, 743.0, 786.0, 827.0, 872.0, 924.0, 969.0, 1014.0, 1059.0, 1232.0, 1275.0, 1325.0, 1371.0, 1468.0, 1520.0, 1638.0, 1691.7, 2882.0, 2987.0, 3098.0, 3217.0, 3331.0, 3445.0, 3607.0, 3725.0, 3852.0, 3970.0, 4303.0, 4407.0, 4523.0, 4629.0, 4945.0, 5066.0, 5296.0, 5412.0, 12081.0, 12370.0, 12690.0, 12986.0, 14144.0, 14495.0, 14936.0, 15228.06, 61736.56, 63073.5], "Electron affinity": 0.352}, "Er": {"Atomic mass": 167.259, "Atomic no": 68, "Atomic orbitals": {"1s": -1961.799176, "2p": -302.01827, "2s": -316.310631, "3d": -51.682149, "3p": -63.818655, "3s": -70.310142, "4d": -6.127443, "4f": -0.278577, "4p": -10.819574, "4s": -13.423547, "5p": -0.935202, "5s": -1.616073, "6s": -0.134905}, "Atomic radius": 1.75, "Atomic radius calculated": 2.26, "Boiling point": "3141 K", "Brinell hardness": "814 MN m-2", "Bulk modulus": "44 GPa", "Coefficient of linear thermal expansion": "12.2 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "9066 kg m-3", "Electrical resistivity": "86.0 10-8 Ω m", "Electronic structure": "[Xe].4f12.6s2", "ICSD oxidation states": [3], "Ionic radii": {"3": 1.03}, "Liquid range": "1371 K", "Melting point": "1802 K", "Mendeleev no": 22, "Mineral hardness": "no data", "Molar volume": "18.46 cm3", "Name": "Erbium", "Oxidation states": [3], "Poissons ratio": "0.24", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "28 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.03, "ionic_radius": 0.89}}, "VII": {"": {"crystal_radius": 1.085, "ionic_radius": 0.945}}, "VIII": {"": {"crystal_radius": 1.144, "ionic_radius": 1.004}}, "IX": {"": {"crystal_radius": 1.202, "ionic_radius": 1.062}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "15 W m-1 K-1", "Van der waals radius": 2.29, "Velocity of sound": "2830 m s-1", "Vickers hardness": "589 MN m-2", "X": 1.24, "Youngs modulus": "70 GPa", "Metallic radius": 1.756, "iupac_ordering": 36, "IUPAC ordering": 36, "Ground level": "3H6", "Ionization energies": [6.1077, 11.916, 22.7, 42.42, 65.1, 96.0, 114.0, 131.0, 158.0, 177.0, 201.0, 235.0, 268.0, 290.0, 311.0, 345.0, 381.0, 415.0, 450.0, 486.0, 520.0, 555.0, 770.0, 810.0, 853.0, 899.0, 943.0, 989.0, 1046.0, 1092.0, 1142.0, 1188.0, 1370.0, 1416.0, 1468.0, 1516.0, 1625.0, 1678.0, 1803.0, 1858.5, 3157.0, 3265.0, 3381.0, 3505.0, 3624.0, 3742.0, 3916.0, 4038.0, 4170.0, 4294.0, 4639.0, 4748.0, 4866.0, 4978.0, 5329.0, 5455.0, 5695.0, 5815.0, 12918.0, 13217.0, 13548.0, 13855.0, 15146.0, 15511.0, 15971.0, 16274.56, 65848.24, 67241.9], "Electron affinity": 0.312}, "Es": {"Atomic mass": 252.0, "Atomic no": 99, "Atomic orbitals": "no data", "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].5f11.7s2", "Liquid range": "no data K", "Melting point": "1133 K", "Mendeleev no": 38, "Mineral hardness": "no data", "Molar volume": "28.52 cm3", "Name": "Einsteinium", "Oxidation states": [2, 3], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Superconduction temperature": "no data K", "Thermal conductivity": "no data W m-1 K-1", "Van der waals radius": 2.45, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.3, "Youngs modulus": "no data GPa", "Metallic radius": 1.86, "iupac_ordering": 22, "IUPAC ordering": 22, "Ground level": "4I\u00b015/2", "Ionization energies": [6.36758, 12.2, 22.7, 38.8, 54.1, 71.0, 97.0, 112.9, 137.0, 157.0, 180.0, 206.0, 231.0, 252.0, 270.0, 294.0, 317.0, 342.0, 367.0, 398.0, 421.0, 576.0, 606.0, 638.0, 672.0, 705.0, 738.0, 790.0, 824.0, 861.0, 895.0, 1060.0, 1100.0, 1140.0, 1180.0, 1310.0, 1360.0, 1480.0, 1530.0, 1690.0, 1780.0, 1870.0, 1950.0, 2040.0, 2130.0, 2220.0, 2300.0, 2410.0, 2490.0, 2580.0, 2680.0, 2760.0, 2850.0, 3294.0, 3370.0, 3449.0, 3535.0, 3616.0, 3694.0, 3866.0, 3947.0, 4038.0, 4120.0, 4456.0, 4537.0, 4620.0, 4700.0, 5260.0, 5350.0, 5600.0, 5690.0, 8960.0, 9140.0, 9330.0, 9530.0, 9720.0, 9910.0, 10400.0, 10590.0, 10810.0, 11010.0, 11570.0, 11740.0, 11930.0, 12110.0, 13810.0, 14030.0, 14460.0, 14700.0, 29700.0, 30100.0, 30700.0, 31100.0, 37400.0, 38100.0, 38900.0, 39451.4, 154328.1, 156926.0], "Electron affinity": -0.3}, "Eu": {"Atomic mass": 151.964, "Atomic no": 63, "Atomic orbitals": {"1s": -1672.309322, "2p": -252.176697, "2s": -265.199534, "3d": -41.465518, "3p": -52.281987, "3s": -58.068128, "4d": -5.03242, "4f": -0.232773, "4p": -9.025455, "4s": -11.267747, "5p": -0.853575, "5s": -1.444087, "6s": -0.129426}, "Atomic radius": 1.85, "Atomic radius calculated": 2.31, "Boiling point": "1800 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "8.3 GPa", "Coefficient of linear thermal expansion": "35 x10-6K-1", "Common oxidation states": [2, 3], "Critical temperature": "no data K", "Density of solid": "5244 kg m-3", "Electrical resistivity": "90 10-8 Ω m", "Electronic structure": "[Xe].4f7.6s2", "ICSD oxidation states": [2, 3], "Ionic radii": {"2": 1.31, "3": 1.087}, "Liquid range": "701 K", "Melting point": "1099 K", "Mendeleev no": 18, "Mineral hardness": "no data", "Molar volume": "28.97 cm3", "Name": "Europium", "Oxidation states": [2, 3], "Poissons ratio": "0.15", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "7.9 GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.31, "ionic_radius": 1.17}}, "VII": {"": {"crystal_radius": 1.34, "ionic_radius": 1.2}}, "VIII": {"": {"crystal_radius": 1.39, "ionic_radius": 1.25}}, "IX": {"": {"crystal_radius": 1.44, "ionic_radius": 1.3}}, "X": {"": {"crystal_radius": 1.49, "ionic_radius": 1.35}}}, "3": {"VI": {"": {"crystal_radius": 1.087, "ionic_radius": 0.947}}, "VII": {"": {"crystal_radius": 1.15, "ionic_radius": 1.01}}, "VIII": {"": {"crystal_radius": 1.206, "ionic_radius": 1.066}}, "IX": {"": {"crystal_radius": 1.26, "ionic_radius": 1.12}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "14 W m-1 K-1", "Van der waals radius": 2.35, "Velocity of sound": "no data m s-1", "Vickers hardness": "167 MN m-2", "X": 1.2, "Youngs modulus": "18 GPa", "Metallic radius": 2.041, "iupac_ordering": 41, "IUPAC ordering": 41, "Ground level": "8S\u00b07/2", "Ionization energies": [5.670385, 11.24, 24.84, 42.94, 63.2, 89.0, 105.0, 120.0, 144.0, 161.0, 183.0, 213.0, 243.0, 263.0, 281.0, 311.0, 344.4, 518.0, 553.0, 590.0, 630.0, 667.0, 709.0, 755.0, 795.0, 838.0, 879.0, 1037.0, 1078.0, 1124.0, 1167.0, 1249.0, 1296.0, 1406.0, 1456.06, 2495.0, 2591.0, 2697.0, 2807.0, 2914.0, 3022.0, 3168.0, 3279.0, 3398.0, 3510.0, 3823.0, 3921.0, 4031.0, 4131.0, 4400.0, 4513.0, 4729.0, 4838.0, 10880.0, 11153.0, 11457.0, 11739.0, 12718.0, 13050.0, 13462.0, 13738.58, 55865.92, 57120.64], "Electron affinity": 0.11613}, "F": {"Atomic mass": 18.9984032, "Atomic no": 9, "Atomic orbitals": {"1s": -24.189391, "2p": -0.415606, "2s": -1.086859}, "Atomic radius": 0.5, "Atomic radius calculated": 0.42, "Boiling point": "85.03 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-1], "Critical temperature": "144 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[He].2s2.2p5", "ICSD oxidation states": [-1], "Ionic radii": {"-1": 1.19, "7": 0.22}, "Liquid range": "31.5 K", "Melting point": "53.53 K", "Mendeleev no": 102, "Mineral hardness": "no data", "Molar volume": "11.20 cm3", "Name": "Fluorine", "Oxidation states": [-1], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000195", "Rigidity modulus": "no data GPa", "Shannon radii": {"-1": {"II": {"": {"crystal_radius": 1.145, "ionic_radius": 1.285}}, "III": {"": {"crystal_radius": 1.16, "ionic_radius": 1.3}}, "IV": {"": {"crystal_radius": 1.17, "ionic_radius": 1.31}}, "VI": {"": {"crystal_radius": 1.19, "ionic_radius": 1.33}}}, "7": {"VI": {"": {"crystal_radius": 0.22, "ionic_radius": 0.08}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.0277 W m-1 K-1", "Van der waals radius": 1.47, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 3.98, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"F-19": -94.2}, "Metallic radius": "no data", "iupac_ordering": 102, "IUPAC ordering": 102, "Ground level": "2P\u00b03/2", "Ionization energies": [17.42282, 34.97081, 62.70798, 87.175, 114.249, 157.16311, 185.1868, 953.89805, 1103.11748], "Electron affinity": 3.401189824}, "Fe": {"Atomic mass": 55.845, "Atomic no": 26, "Atomic orbitals": {"1s": -254.225505, "2p": -25.551766, "2s": -29.56486, "3d": -0.295049, "3p": -2.187523, "3s": -3.360621, "4s": -0.197978}, "Atomic radius": 1.4, "Atomic radius calculated": 1.56, "Boiling point": "3134 K", "Brinell hardness": "490 MN m-2", "Bulk modulus": "170 GPa", "Coefficient of linear thermal expansion": "11.8 x10-6K-1", "Common oxidation states": [2, 3], "Critical temperature": "no data K", "Density of solid": "7874 kg m-3", "Electrical resistivity": "10 10-8 Ω m", "Electronic structure": "[Ar].3d6.4s2", "ICSD oxidation states": [2, 3], "Ionic radii": {"2": 0.92, "3": 0.785}, "Ionic radii hs": {"2": 0.92, "3": 0.785}, "Ionic radii ls": {"2": 0.75, "3": 0.69, "4": 0.725, "6": 0.39}, "Liquid range": "1323 K", "Melting point": "1811 K", "Mendeleev no": 61, "Mineral hardness": "4.0", "Molar volume": "7.09 cm3", "Name": "Iron", "Oxidation states": [-2, -1, 1, 2, 3, 4, 5, 6], "Poissons ratio": "0.29", "Reflectivity": "65 %", "Refractive index": "no data", "Rigidity modulus": "82 GPa", "Shannon radii": {"2": {"IV": {"High Spin": {"crystal_radius": 0.77, "ionic_radius": 0.63}}, "IVSQ": {"High Spin": {"crystal_radius": 0.78, "ionic_radius": 0.64}}, "VI": {"Low Spin": {"crystal_radius": 0.75, "ionic_radius": 0.61}, "High Spin": {"crystal_radius": 0.92, "ionic_radius": 0.78}}, "VIII": {"High Spin": {"crystal_radius": 1.06, "ionic_radius": 0.92}}}, "3": {"IV": {"High Spin": {"crystal_radius": 0.63, "ionic_radius": 0.49}}, "V": {"": {"crystal_radius": 0.72, "ionic_radius": 0.58}}, "VI": {"Low Spin": {"crystal_radius": 0.69, "ionic_radius": 0.55}, "High Spin": {"crystal_radius": 0.785, "ionic_radius": 0.645}}, "VIII": {"High Spin": {"crystal_radius": 0.92, "ionic_radius": 0.78}}}, "4": {"VI": {"": {"crystal_radius": 0.725, "ionic_radius": 0.585}}}, "6": {"IV": {"": {"crystal_radius": 0.39, "ionic_radius": 0.25}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "80 W m-1 K-1", "Van der waals radius": 2.04, "Velocity of sound": "4910 m s-1", "Vickers hardness": "608 MN m-2", "X": 1.83, "Youngs modulus": "211 GPa", "NMR Quadrupole Moment": {"Fe-57": 160.0}, "Metallic radius": 1.277, "iupac_ordering": 64, "IUPAC ordering": 64, "Ground level": "5D4", "Ionization energies": [7.9024681, 16.19921, 30.651, 54.91, 75.0, 98.985, 124.976, 151.06, 233.6, 262.1, 290.9, 330.8, 361.0, 392.2, 456.2, 489.312, 1262.7, 1357.8, 1460.0, 1575.6, 1687.0, 1798.4, 1950.4, 2045.759, 8828.1879, 9277.6818], "Electron affinity": 0.15323634}, "Fm": {"Atomic mass": 257.0, "Atomic no": 100, "Atomic orbitals": "no data", "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].5f12.7s2", "Liquid range": "no data K", "Melting point": "about 1800 K", "Mendeleev no": 37, "Mineral hardness": "no data", "Molar volume": "no data cm3", "Name": "Fermium", "Oxidation states": [2, 3], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Superconduction temperature": "no data K", "Thermal conductivity": "no data W m-1 K-1", "Van der waals radius": 2.45, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.3, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 21, "IUPAC ordering": 21, "Ground level": "3H6", "Ionization energies": [6.5, 12.4, 23.2, 39.3, 55.0, 74.0, 93.0, 120.0, 136.0, 162.0, 185.0, 209.0, 237.0, 257.0, 276.0, 300.0, 326.0, 351.0, 377.0, 402.0, 430.0, 453.0, 616.0, 647.0, 680.0, 716.0, 749.0, 782.0, 837.0, 871.0, 909.0, 944.0, 1110.0, 1150.0, 1190.0, 1230.0, 1370.0, 1420.0, 1550.0, 1600.0, 1770.0, 1850.0, 1940.0, 2030.0, 2120.0, 2210.0, 2300.0, 2390.0, 2490.0, 2590.0, 2680.0, 2760.0, 2850.0, 2950.0, 3403.0, 3480.0, 3561.0, 3647.0, 3730.0, 3810.0, 3986.0, 4070.0, 4160.0, 4245.0, 4586.0, 4670.0, 4760.0, 4840.0, 5420.0, 5510.0, 5760.0, 5860.0, 9200.0, 9370.0, 9570.0, 9770.0, 9970.0, 10160.0, 10660.0, 10860.0, 11080.0, 11280.0, 11850.0, 12020.0, 12220.0, 12390.0, 14180.0, 14400.0, 14800.0, 15000.0, 30300.0, 30800.0, 31300.0, 31800.0, 38400.0, 39100.0, 40000.0, 40482.2, 158152.5, 160804.0], "Electron affinity": 0.35}, "Fr": {"Atomic mass": 223.0, "Atomic no": 87, "Atomic orbitals": {"1s": -3283.263399, "2p": -542.41424, "2s": -561.73045, "3d": -111.085223, "3p": -128.607136, "3s": -137.959632, "4d": -20.812462, "4f": -10.050648, "4p": -28.648131, "4s": -32.861013, "5d": -2.360991, "5p": -4.97328, "5s": -6.509516, "6p": -0.466197, "6s": -0.841848, "7s": -0.076176}, "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [1], "Critical temperature": "no data K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].7s1", "Ionic radii": {"1": 1.94}, "Liquid range": "no data K", "Melting point": "maybe about 300 K", "Mendeleev no": 7, "Mineral hardness": "no data", "Molar volume": "no data cm3", "Name": "Francium", "Oxidation states": [1], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"1": {"VI": {"": {"crystal_radius": 1.94, "ionic_radius": 1.8}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "no data W m-1 K-1", "Van der waals radius": 3.48, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 0.7, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 6, "IUPAC ordering": 6, "Ground level": "2S1/2", "Ionization energies": [4.0727411, 22.4, 33.5, 39.1, 50.0, 67.0, 80.0, 106.0, 120.0, 179.0, 200.0, 222.1, 245.0, 269.0, 293.0, 324.0, 349.0, 375.0, 400.0, 530.0, 560.0, 590.0, 620.0, 690.0, 720.0, 810.0, 850.0, 910.0, 980.0, 1040.0, 1110.0, 1180.0, 1250.0, 1320.0, 1380.0, 1460.0, 1530.0, 1600.0, 1670.0, 1740.0, 1810.0, 2119.0, 2182.0, 2247.0, 2317.0, 2384.0, 2450.0, 2564.0, 2631.0, 2706.0, 2774.0, 3049.0, 3115.0, 3190.0, 3257.0, 3556.0, 3635.0, 3828.0, 3907.0, 6365.0, 6516.0, 6678.0, 6849.0, 7013.0, 7172.0, 7500.0, 7670.0, 7850.0, 8020.0, 8500.0, 8640.0, 8800.0, 8950.0, 9890.0, 10070.0, 10420.0, 10590.0, 22330.0, 22730.0, 23170.0, 23570.0, 27060.0, 27590.0, 28260.0, 28683.4, 113817.2, 115859.0], "Electron affinity": 0.486}, "Ga": {"Atomic mass": 69.723, "Atomic no": 31, "Atomic orbitals": {"1s": -370.170639, "2p": -40.093339, "2s": -45.200869, "3d": -0.736204, "3p": -3.584666, "3s": -5.241645, "4p": -0.101634, "4s": -0.328019}, "Atomic radius": 1.3, "Atomic radius calculated": 1.36, "Boiling point": "2477 K", "Brinell hardness": "60 MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "120 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "5904 kg m-3", "Electrical resistivity": "about 14 10-8 Ω m", "Electronic structure": "[Ar].3d10.4s2.4p1", "ICSD oxidation states": [2, 3], "Ionic radii": {"3": 0.76}, "Liquid range": "2174.09 K", "Melting point": "302.91 K", "Mendeleev no": 81, "Mineral hardness": "1.5", "Molar volume": "11.80 cm3", "Name": "Gallium", "Oxidation states": [1, 2, 3], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"IV": {"": {"crystal_radius": 0.61, "ionic_radius": 0.47}}, "V": {"": {"crystal_radius": 0.69, "ionic_radius": 0.55}}, "VI": {"": {"crystal_radius": 0.76, "ionic_radius": 0.62}}}}, "Superconduction temperature": "1.083 K", "Thermal conductivity": "29 W m-1 K-1", "Van der waals radius": 1.87, "Velocity of sound": "2740 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.81, "Youngs modulus": "no data GPa", "Metallic radius": 1.35, "iupac_ordering": 79, "IUPAC ordering": 79, "Ground level": "2P\u00b01/2", "Ionization energies": [5.999302, 20.51514, 30.72576, 63.241, 86.01, 112.7, 140.8, 169.9, 211.0, 244.0, 280.0, 319.0, 356.0, 471.2, 508.8, 548.3, 599.8, 640.0, 677.0, 765.7, 807.308, 2010.0, 2129.0, 2258.0, 2391.0, 2543.9, 2683.0, 2868.0, 2984.426, 12696.5575, 13239.489], "Electron affinity": 0.3012011}, "Gd": {"Atomic mass": 157.25, "Atomic no": 64, "Atomic orbitals": {"1s": -1728.625195, "2p": -262.081616, "2s": -275.36313, "3d": -43.754556, "3p": -54.836922, "3s": -60.764408, "4d": -5.531835, "4f": -0.489012, "4p": -9.669866, "4s": -11.986486, "5d": -0.12722, "5p": -0.978749, "5s": -1.608477, "6s": -0.143627}, "Atomic radius": 1.8, "Atomic radius calculated": 2.33, "Boiling point": "3523 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "38 GPa", "Coefficient of linear thermal expansion": "9.4 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "7901 kg m-3", "Electrical resistivity": "131 10-8 Ω m", "Electronic structure": "[Xe].4f7.5d1.6s2", "ICSD oxidation states": [3], "Ionic radii": {"3": 1.075}, "Liquid range": "1938 K", "Melting point": "1585 K", "Mendeleev no": 27, "Mineral hardness": "no data", "Molar volume": "19.90 cm3", "Name": "Gadolinium", "Oxidation states": [1, 2, 3], "Poissons ratio": "0.26", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "22 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.078, "ionic_radius": 0.938}}, "VII": {"": {"crystal_radius": 1.14, "ionic_radius": 1.0}}, "VIII": {"": {"crystal_radius": 1.193, "ionic_radius": 1.053}}, "IX": {"": {"crystal_radius": 1.247, "ionic_radius": 1.107}}}}, "Superconduction temperature": "1.083 K", "Thermal conductivity": "11 W m-1 K-1", "Van der waals radius": 2.34, "Velocity of sound": "2680 m s-1", "Vickers hardness": "570 MN m-2", "X": 1.2, "Youngs modulus": "55 GPa", "Metallic radius": 1.802, "iupac_ordering": 40, "IUPAC ordering": 40, "Ground level": "9D\u00b02", "Ionization energies": [6.1498, 12.076, 20.54, 44.44, 64.8, 89.0, 106.0, 123.0, 144.0, 165.0, 183.0, 213.0, 246.0, 268.0, 288.0, 319.0, 352.0, 384.4, 565.0, 601.0, 639.0, 680.0, 719.0, 761.0, 810.0, 851.0, 895.0, 937.0, 1100.0, 1142.0, 1189.0, 1233.0, 1321.0, 1368.0, 1481.0, 1532.3, 2621.0, 2720.0, 2827.0, 2941.0, 3050.0, 3160.0, 3312.0, 3424.0, 3546.0, 3660.0, 3980.0, 4080.0, 4191.0, 4294.0, 4578.0, 4693.0, 4914.0, 5025.0, 11273.0, 11552.0, 11861.0, 12147.0, 13183.0, 13521.0, 13943.0, 14224.57, 57783.9, 59065.53], "Electron affinity": 0.137}, "Ge": {"Atomic mass": 72.64, "Atomic no": 32, "Atomic orbitals": {"1s": -396.292991, "2p": -43.720129, "2s": -49.055282, "3d": -1.117316, "3p": -4.194822, "3s": -5.961472, "4p": -0.149882, "4s": -0.426523}, "Atomic radius": 1.25, "Atomic radius calculated": 1.25, "Boiling point": "3093 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "6 x10-6K-1", "Common oxidation states": [-4, 2, 4], "Critical temperature": "no data K", "Density of solid": "5323 kg m-3", "Electrical resistivity": "about 50000 10-8 Ω m", "Electronic structure": "[Ar].3d10.4s2.4p2", "ICSD oxidation states": [2, 3, 4], "Ionic radii": {"2": 0.87, "4": 0.67}, "Liquid range": "1881.6 K", "Melting point": "1211.4 K", "Mendeleev no": 84, "Mineral hardness": "6.0", "Molar volume": "13.63 cm3", "Name": "Germanium", "Oxidation states": [-4, 1, 2, 3, 4], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 0.87, "ionic_radius": 0.73}}}, "4": {"IV": {"": {"crystal_radius": 0.53, "ionic_radius": 0.39}}, "VI": {"": {"crystal_radius": 0.67, "ionic_radius": 0.53}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "60 W m-1 K-1", "Van der waals radius": 2.11, "Velocity of sound": "5400 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.01, "Youngs modulus": "no data GPa", "Metallic radius": 1.39, "iupac_ordering": 84, "IUPAC ordering": 84, "Ground level": "3P0", "Ionization energies": [7.899435, 15.93461, 34.0576, 45.7155, 90.5, 115.9, 144.9, 176.4, 212.5, 252.1, 286.0, 326.0, 367.0, 407.0, 527.9, 567.3, 609.1, 662.8, 706.7, 744.0, 837.1, 880.44, 2180.1, 2304.0, 2439.0, 2575.0, 2737.1, 2881.9, 3074.0, 3194.293, 13557.4208, 14119.43], "Electron affinity": 1.232676413}, "H": {"Atomic mass": 1.00794, "Atomic mass no": 1, "Atomic no": 1, "Atomic orbitals": {"1s": -0.233471}, "Atomic radius": 0.25, "Atomic radius calculated": 0.53, "Boiling point": "20.28 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-1, 1], "Critical temperature": "33 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "1s1", "ICSD oxidation states": [1, -1], "Is named isotope": false, "Liquid range": "6.27 K", "Melting point": "14.01 K", "Mendeleev no": 103, "Mineral hardness": "no data", "Molar volume": "11.42 cm3", "Name": "Hydrogen", "Oxidation states": [-1, 1], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000132 (gas; liquid 1.12)(no units)", "Rigidity modulus": "no data GPa", "Shannon radii": {"1": {"I": {"": {"crystal_radius": -0.24, "ionic_radius": -0.38}}, "II": {"": {"crystal_radius": -0.04, "ionic_radius": -0.18}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.1805 W m-1 K-1", "Van der waals radius": 1.1, "Velocity of sound": "1270 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.2, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"H-2": 2.86}, "Metallic radius": "no data", "iupac_ordering": 92, "IUPAC ordering": 92, "Ground level": "2S1/2", "Ionization energies": [13.598434599702], "Electron affinity": 0.754598}, "He": {"Atomic mass": 4.002602, "Atomic no": 2, "Atomic orbitals": {"1s": -0.570425}, "Atomic radius": "no data", "Atomic radius calculated": 0.31, "Boiling point": "4.22 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Critical temperature": "5.19 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "1s2", "Liquid range": "3.27 K", "Max oxidation state": 0.0, "Melting point": "0.95 K", "Mendeleev no": 1, "Min oxidation state": 0.0, "Mineral hardness": "no data", "Molar volume": "21.0 cm3", "Name": "Helium", "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000035 (gas; liquid 1.028)(no units)", "Rigidity modulus": "no data GPa", "Superconduction temperature": "no data K", "Thermal conductivity": "0.1513 W m-1 K-1", "Van der waals radius": 1.4, "Velocity of sound": "970 m s-1", "Vickers hardness": "no data MN m-2", "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 5, "IUPAC ordering": 5, "Ground level": "1S0", "Ionization energies": [24.587389011, 54.417765486], "Electron affinity": -0.52}, "Hf": {"Atomic mass": 178.49, "Atomic no": 72, "Atomic orbitals": {"1s": -2210.65199, "2p": -345.687023, "2s": -361.006527, "3d": -61.231443, "3p": -74.452656, "3s": -81.522812, "4d": -7.676638, "4f": -0.871574, "4p": -12.971211, "4s": -15.883625, "5d": -0.143805, "5p": -1.246441, "5s": -2.049828, "6s": -0.166465}, "Atomic radius": 1.55, "Atomic radius calculated": 2.08, "Boiling point": "4876 K", "Brinell hardness": "1700 MN m-2", "Bulk modulus": "110 GPa", "Coefficient of linear thermal expansion": "5.9 x10-6K-1", "Common oxidation states": [4], "Critical temperature": "no data K", "Density of solid": "13310 kg m-3", "Electrical resistivity": "34 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d2.6s2", "ICSD oxidation states": [4], "Ionic radii": {"4": 0.85}, "Liquid range": "2370 K", "Melting point": "2506 K", "Mendeleev no": 50, "Mineral hardness": "5.5", "Molar volume": "13.44 cm3", "Name": "Hafnium", "Oxidation states": [2, 3, 4], "Poissons ratio": "0.37", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "30 GPa", "Shannon radii": {"4": {"IV": {"": {"crystal_radius": 0.72, "ionic_radius": 0.58}}, "VI": {"": {"crystal_radius": 0.85, "ionic_radius": 0.71}}, "VII": {"": {"crystal_radius": 0.9, "ionic_radius": 0.76}}, "VIII": {"": {"crystal_radius": 0.97, "ionic_radius": 0.83}}}}, "Superconduction temperature": "0.128 K", "Thermal conductivity": "23 W m-1 K-1", "Van der waals radius": 2.23, "Velocity of sound": "3010 m s-1", "Vickers hardness": "1760 MN m-2", "X": 1.3, "Youngs modulus": "78 GPa", "Metallic radius": 1.58, "iupac_ordering": 50, "IUPAC ordering": 50, "Ground level": "3F2", "Ionization energies": [6.82507, 14.61, 22.55, 33.37, 68.37, 98.0, 118.0, 137.0, 157.0, 187.0, 209.0, 230.0, 270.0, 310.0, 334.0, 359.0, 399.0, 440.0, 481.0, 520.0, 570.0, 610.0, 650.0, 690.0, 730.0, 772.0, 1002.0, 1047.0, 1094.0, 1146.0, 1195.0, 1245.0, 1311.0, 1362.0, 1417.0, 1467.0, 1669.0, 1719.0, 1776.0, 1827.0, 1963.0, 2022.0, 2159.0, 2218.9, 3741.0, 3858.0, 3984.0, 4118.0, 4246.0, 4372.0, 4573.0, 4703.0, 4846.0, 4980.0, 5350.0, 5468.0, 5595.0, 5713.0, 6149.0, 6284.0, 6545.0, 6674.0, 14678.0, 14999.0, 15351.0, 15680.0, 17280.0, 17680.0, 18180.0, 18502.32, 74565.93, 76077.8], "Electron affinity": 0.17807}, "Hg": {"Atomic mass": 200.59, "Atomic no": 80, "Atomic orbitals": {"1s": -2755.022637, "2p": -443.848676, "2s": -461.27864, "3d": -84.845492, "3p": -100.328031, "3s": -108.597921, "4d": -13.019221, "4f": -4.110291, "4p": -19.636187, "4s": -23.222921, "5d": -0.452552, "5p": -2.261975, "5s": -3.423486, "6s": -0.205137}, "Atomic radius": 1.5, "Atomic radius calculated": 1.71, "Boiling point": "629.88 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "25 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [1, 2], "Critical temperature": "1750 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "96 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d10.6s2", "ICSD oxidation states": [1, 2], "Ionic radii": {"1": 1.33, "2": 1.16}, "Liquid range": "395.56 K", "Melting point": "234.32 K", "Mendeleev no": 74, "Mineral hardness": "1.5", "Molar volume": "14.09 cm3", "Name": "Mercury", "Oxidation states": [1, 2, 4], "Poissons ratio": "no data", "Reflectivity": "73 %", "Refractive index": "1.000933", "Rigidity modulus": "no data GPa", "Shannon radii": {"1": {"III": {"": {"crystal_radius": 1.11, "ionic_radius": 0.97}}, "VI": {"": {"crystal_radius": 1.33, "ionic_radius": 1.19}}}, "2": {"II": {"": {"crystal_radius": 0.83, "ionic_radius": 0.69}}, "IV": {"": {"crystal_radius": 1.1, "ionic_radius": 0.96}}, "VI": {"": {"crystal_radius": 1.16, "ionic_radius": 1.02}}, "VIII": {"": {"crystal_radius": 1.28, "ionic_radius": 1.14}}}}, "Superconduction temperature": "3.95 K", "Thermal conductivity": "8.3 W m-1 K-1", "Van der waals radius": 2.23, "Velocity of sound": "1407 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.0, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"Hg-201": 387.6}, "Metallic radius": 1.51, "iupac_ordering": 74, "IUPAC ordering": 74, "Ground level": "1S0", "Ionization energies": [10.437504, 18.75688, 34.49, 48.55, 61.2, 76.6, 93.0, 113.9, 134.0, 153.0, 173.0, 192.7, 276.9, 307.0, 332.0, 357.0, 402.0, 429.0, 477.0, 530.0, 560.0, 590.0, 650.0, 710.0, 760.0, 820.0, 880.0, 930.0, 990.0, 1050.0, 1110.0, 1160.0, 1220.0, 1280.0, 1549.0, 1603.0, 1661.0, 1723.0, 1780.0, 1839.0, 1928.0, 1989.0, 2052.0, 2113.0, 2354.0, 2412.0, 2478.0, 2539.0, 2745.0, 2815.0, 2981.0, 3049.9, 5055.0, 5191.0, 5335.0, 5490.0, 5636.0, 5780.0, 6041.0, 6192.0, 6356.0, 6508.0, 6933.0, 7066.0, 7211.0, 7350.0, 8010.0, 8160.0, 8470.0, 8620.0, 18550.0, 18910.0, 19310.0, 19680.0, 22120.0, 22580.0, 23170.0, 23544.1, 94124.7, 95897.7], "Electron affinity": -0.52}, "Ho": {"Atomic mass": 164.93032, "Atomic no": 67, "Atomic orbitals": {"1s": -1902.051908, "2p": -291.700994, "2s": -305.739294, "3d": -49.565996, "3p": -61.436304, "3s": -67.785492, "4d": -5.906195, "4f": -0.272677, "4p": -10.455303, "4s": -12.985498, "5p": -0.919463, "5s": -1.582088, "6s": -0.133845}, "Atomic radius": 1.75, "Atomic radius calculated": "no data", "Boiling point": "2993 K", "Brinell hardness": "746 MN m-2", "Bulk modulus": "40 GPa", "Coefficient of linear thermal expansion": "11.2 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "8795 kg m-3", "Electrical resistivity": "81.4 10-8 Ω m", "Electronic structure": "[Xe].4f11.6s2", "ICSD oxidation states": [3], "Ionic radii": {"3": 1.041}, "Liquid range": "1259 K", "Melting point": "1734 K", "Mendeleev no": 23, "Mineral hardness": "no data", "Molar volume": "18.74 cm3", "Name": "Holmium", "Oxidation states": [3], "Poissons ratio": "0.23", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "26 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.041, "ionic_radius": 0.901}}, "VIII": {"": {"crystal_radius": 1.155, "ionic_radius": 1.015}}, "IX": {"": {"crystal_radius": 1.212, "ionic_radius": 1.072}}, "X": {"": {"crystal_radius": 1.26, "ionic_radius": 1.12}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "16 W m-1 K-1", "Van der waals radius": 2.3, "Velocity of sound": "2760 m s-1", "Vickers hardness": "481 MN m-2", "X": 1.23, "Youngs modulus": "65 GPa", "Metallic radius": 1.765, "iupac_ordering": 37, "IUPAC ordering": 37, "Ground level": "4I\u00b015/2", "Ionization energies": [6.0215, 11.781, 22.79, 42.52, 63.9, 95.0, 112.0, 129.0, 155.0, 173.0, 197.0, 229.0, 263.0, 284.0, 305.0, 340.0, 373.0, 408.0, 441.0, 475.0, 510.0, 715.0, 755.0, 797.0, 842.0, 885.0, 929.0, 985.0, 1029.0, 1077.0, 1122.0, 1300.0, 1346.0, 1395.0, 1443.0, 1545.0, 1598.0, 1719.0, 1773.6, 3018.0, 3125.0, 3238.0, 3359.0, 3476.0, 3592.0, 3760.0, 3880.0, 4009.0, 4131.0, 4469.0, 4576.0, 4693.0, 4802.0, 5135.0, 5258.0, 5494.0, 5611.0, 12495.0, 12790.0, 13116.0, 13417.0, 14639.0, 14998.0, 15448.0, 15745.77, 63772.43, 65136.8], "Electron affinity": 0.338}, "I": {"Atomic mass": 126.90447, "Atomic no": 53, "Atomic orbitals": {"1s": -1161.787047, "2p": -164.603788, "2s": -175.073804, "3d": -22.600693, "3p": -30.831092, "3s": -35.243351, "4d": -1.938179, "4p": -4.572522, "4s": -6.115811, "5p": -0.267904, "5s": -0.596339}, "Atomic radius": 1.4, "Atomic radius calculated": 1.15, "Boiling point": "457.4 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "7.7 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-1, 1, 3, 5, 7], "Critical temperature": "819 K", "Density of solid": "4940 kg m-3", "Electrical resistivity": "> 101510-8 Ω m", "Electronic structure": "[Kr].4d10.5s2.5p5", "ICSD oxidation states": [5, -1], "Ionic radii": {"-1": 2.06, "5": 1.09, "7": 0.67}, "Liquid range": "70.55 K", "Melting point": "386.85 K", "Mendeleev no": 97, "Mineral hardness": "no data", "Molar volume": "25.72 cm3", "Name": "Iodine", "Oxidation states": [-1, 1, 3, 5, 7], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"-1": {"VI": {"": {"crystal_radius": 2.06, "ionic_radius": 2.2}}}, "5": {"IIIPY": {"": {"crystal_radius": 0.58, "ionic_radius": 0.44}}, "VI": {"": {"crystal_radius": 1.09, "ionic_radius": 0.95}}}, "7": {"IV": {"": {"crystal_radius": 0.56, "ionic_radius": 0.42}}, "VI": {"": {"crystal_radius": 0.67, "ionic_radius": 0.53}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.449 W m-1 K-1", "Van der waals radius": 1.98, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 2.66, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"I-127": -696.12, "I-129": -604.1}, "Metallic radius": "no data", "iupac_ordering": 99, "IUPAC ordering": 99, "Ground level": "2P\u00b03/2", "Ionization energies": [10.45126, 19.13126, 29.57, 40.357, 51.52, 74.4, 87.61, 150.81, 171.0, 197.0, 220.9, 247.0, 279.0, 307.0, 335.0, 365.0, 393.0, 505.0, 535.0, 569.0, 601.0, 649.0, 683.0, 762.0, 800.8, 1397.0, 1472.0, 1553.0, 1639.0, 1720.0, 1812.0, 1911.0, 1999.0, 2093.0, 2181.0, 2431.0, 2510.0, 2598.0, 2680.0, 2836.0, 2926.0, 3096.0, 3185.5, 7337.0, 7563.0, 7811.0, 8044.0, 8601.0, 8867.0, 9196.0, 9421.1, 38716.996, 39721.41], "Electron affinity": 3.05905238}, "In": {"Atomic mass": 114.818, "Atomic no": 49, "Atomic orbitals": {"1s": -983.647445, "2p": -134.628845, "2s": -144.078357, "3d": -16.139823, "3p": -23.345778, "3s": -27.2206, "4d": -0.730481, "4p": -2.795832, "4s": -4.062639, "5p": -0.101782, "5s": -0.290497}, "Atomic radius": 1.55, "Atomic radius calculated": 1.56, "Boiling point": "2345 K", "Brinell hardness": "8.83 MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "32.1 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "7310 kg m-3", "Electrical resistivity": "8 10-8 Ω m", "Electronic structure": "[Kr].4d10.5s2.5p1", "ICSD oxidation states": [1, 2, 3], "Ionic radii": {"3": 0.94}, "Liquid range": "1915.25 K", "Melting point": "429.75 K", "Mendeleev no": 79, "Mineral hardness": "1.2", "Molar volume": "15.76 cm3", "Name": "Indium", "Oxidation states": [1, 2, 3], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"IV": {"": {"crystal_radius": 0.76, "ionic_radius": 0.62}}, "VI": {"": {"crystal_radius": 0.94, "ionic_radius": 0.8}}, "VIII": {"": {"crystal_radius": 1.06, "ionic_radius": 0.92}}}}, "Superconduction temperature": "3.41 K", "Thermal conductivity": "82 W m-1 K-1", "Van der waals radius": 1.93, "Velocity of sound": "1215 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.78, "Youngs modulus": "11 GPa", "NMR Quadrupole Moment": {"In-113": 759.8, "In-115": 770.8}, "Metallic radius": 1.67, "iupac_ordering": 78, "IUPAC ordering": 78, "Ground level": "2P\u00b01/2", "Ionization energies": [5.7863557, 18.87041, 28.04415, 55.45, 69.3, 90.0, 109.0, 130.1, 156.0, 178.0, 201.0, 226.0, 249.0, 341.0, 368.0, 396.0, 425.0, 462.0, 497.1, 560.0, 593.38, 1043.0, 1109.0, 1181.0, 1255.0, 1328.0, 1413.0, 1496.0, 1575.0, 1659.0, 1738.0, 1961.0, 2028.5, 2111.0, 2207.0, 2317.0, 2373.0, 2555.0, 2628.77, 6126.0, 6331.0, 6554.0, 6770.0, 7196.0, 7442.0, 7754.0, 7953.14, 32837.592, 33750.31], "Electron affinity": 0.383926}, "Ir": {"Atomic mass": 192.217, "Atomic no": 77, "Atomic orbitals": {"1s": -2543.761342, "2p": -405.526834, "2s": -422.159424, "3d": -75.485027, "3p": -90.108427, "3s": -97.923081, "4d": -10.856593, "4f": -2.738339, "4p": -16.966578, "4s": -20.29429, "5d": -0.335189, "5p": -1.883349, "5s": -2.909174, "6s": -0.195511}, "Atomic radius": 1.35, "Atomic radius calculated": 1.8, "Boiling point": "4701 K", "Brinell hardness": "1670 MN m-2", "Bulk modulus": "320 GPa", "Coefficient of linear thermal expansion": "6.4 x10-6K-1", "Common oxidation states": [3, 4], "Critical temperature": "no data K", "Density of solid": "22650 kg m-3", "Electrical resistivity": "4.7 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d7.6s2", "ICSD oxidation states": [3, 4, 5], "Ionic radii": {"3": 0.82, "4": 0.765, "5": 0.71}, "Liquid range": "1962 K", "Melting point": "2739 K", "Mendeleev no": 66, "Mineral hardness": "6.5", "Molar volume": "8.52 cm3", "Name": "Iridium", "Oxidation states": [-3, -1, 1, 2, 3, 4, 5, 6], "Poissons ratio": "0.26", "Reflectivity": "78 %", "Refractive index": "no data", "Rigidity modulus": "210 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 0.82, "ionic_radius": 0.68}}}, "4": {"VI": {"": {"crystal_radius": 0.765, "ionic_radius": 0.625}}}, "5": {"VI": {"": {"crystal_radius": 0.71, "ionic_radius": 0.57}}}}, "Superconduction temperature": "0.11 K", "Thermal conductivity": "150 W m-1 K-1", "Van der waals radius": 2.13, "Velocity of sound": "4825 m s-1", "Vickers hardness": "1760 MN m-2", "X": 2.2, "Youngs modulus": "528 GPa", "Metallic radius": 1.357, "iupac_ordering": 65, "IUPAC ordering": 65, "Ground level": "4F9/2", "Ionization energies": [8.96702, 17.0, 28.0, 40.0, 57.0, 72.0, 89.0, 105.0, 122.7, 194.8, 217.0, 240.0, 264.0, 303.0, 329.0, 356.0, 407.0, 445.0, 472.0, 510.0, 560.0, 610.0, 670.0, 720.0, 770.0, 820.0, 870.0, 920.0, 980.0, 1030.0, 1080.0, 1331.0, 1381.0, 1436.0, 1493.0, 1548.0, 1603.0, 1684.0, 1739.0, 1801.0, 1857.0, 2083.0, 2139.0, 2201.0, 2258.0, 2435.0, 2500.0, 2656.0, 2720.4, 4540.0, 4668.0, 4806.0, 4952.0, 5092.0, 5229.0, 5466.0, 5609.0, 5765.0, 5910.0, 6315.0, 6441.0, 6580.0, 6708.0, 7274.0, 7421.0, 7710.0, 7850.0, 17040.0, 17390.0, 17770.0, 18120.0, 20210.0, 20650.0, 21200.0, 21556.6, 86438.9, 88113.3], "Electron affinity": 1.5643615}, "K": {"Atomic mass": 39.0983, "Atomic no": 19, "Atomic orbitals": {"1s": -128.414957, "2p": -10.283851, "2s": -12.839001, "3p": -0.693776, "3s": -1.281897, "4s": -0.088815}, "Atomic radius": 2.2, "Atomic radius calculated": 2.43, "Boiling point": "1032 K", "Brinell hardness": "0.363 MN m-2", "Bulk modulus": "3.1 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [1], "Critical temperature": "2223 K", "Density of solid": "856 kg m-3", "Electrical resistivity": "7.5 10-8 Ω m", "Electronic structure": "[Ar].4s1", "ICSD oxidation states": [1], "Ionic radii": {"1": 1.52}, "Liquid range": "695.47 K", "Melting point": "336.53 K", "Mendeleev no": 10, "Mineral hardness": "0.4", "Molar volume": "45.94 cm3", "Name": "Potassium", "Oxidation states": [-1, 1], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "1.3 GPa", "Shannon radii": {"1": {"IV": {"": {"crystal_radius": 1.51, "ionic_radius": 1.37}}, "VI": {"": {"crystal_radius": 1.52, "ionic_radius": 1.38}}, "VII": {"": {"crystal_radius": 1.6, "ionic_radius": 1.46}}, "VIII": {"": {"crystal_radius": 1.65, "ionic_radius": 1.51}}, "IX": {"": {"crystal_radius": 1.69, "ionic_radius": 1.55}}, "X": {"": {"crystal_radius": 1.73, "ionic_radius": 1.59}}, "XII": {"": {"crystal_radius": 1.78, "ionic_radius": 1.64}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "100 W m-1 K-1", "Van der waals radius": 2.75, "Velocity of sound": "2000 m s-1", "Vickers hardness": "no data MN m-2", "X": 0.82, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"K-39": 58.5, "K-40": -73.0, "K-41": 71.1}, "Metallic radius": 2.381, "iupac_ordering": 9, "IUPAC ordering": 9, "Ground level": "2S1/2", "Ionization energies": [4.34066373, 31.625, 45.8031, 60.917, 82.66, 99.44, 117.56, 154.87, 175.8174, 503.67, 565.6, 631.1, 714.7, 786.3, 860.92, 967.7, 1034.542, 4610.87018, 4934.0484], "Electron affinity": 0.50145913}, "Kr": {"Atomic mass": 83.798, "Atomic no": 36, "Atomic orbitals": {"1s": -509.982989, "2p": -60.017328, "2s": -66.285953, "3d": -3.074109, "3p": -7.086634, "3s": -9.315192, "4p": -0.34634, "4s": -0.820574}, "Atomic radius": "no data", "Atomic radius calculated": 0.88, "Boiling point": "119.93 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Critical temperature": "209.4 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Ar].3d10.4s2.4p6", "Liquid range": "4.14 K", "Max oxidation state": 0.0, "Melting point": "115.79 K", "Mendeleev no": 4, "Min oxidation state": 0.0, "Mineral hardness": "no data", "Molar volume": "27.99 cm3", "Name": "Krypton", "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000427", "Rigidity modulus": "no data GPa", "Superconduction temperature": "no data K", "Thermal conductivity": "0.00943 W m-1 K-1", "Van der waals radius": 2.02, "Velocity of sound": "1120 m s-1", "Vickers hardness": "no data MN m-2", "X": 3.0, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 2, "IUPAC ordering": 2, "Ground level": "1S0", "Ionization energies": [13.9996055, 24.35984, 35.838, 50.85, 64.69, 78.49, 109.13, 125.802, 233.0, 268.0, 308.0, 350.0, 391.0, 446.0, 492.0, 540.0, 591.0, 640.0, 785.0, 831.6, 882.8, 945.0, 999.0, 1042.0, 1155.0, 1205.23, 2928.9, 3072.0, 3228.0, 3380.0, 3584.0, 3752.0, 3971.0, 4109.083, 17296.421, 17936.209], "Electron affinity": -1.02}, "La": {"Atomic mass": 138.90547, "Atomic no": 57, "Atomic orbitals": {"1s": -1355.622446, "2p": -198.325243, "2s": -209.831151, "3d": -30.626696, "3p": -39.895838, "3s": -44.856283, "4d": -3.95801, "4p": -7.167724, "4s": -9.000543, "5d": -0.141085, "5p": -0.824498, "5s": -1.324936, "6s": -0.132233}, "Atomic radius": 1.95, "Atomic radius calculated": "no data", "Boiling point": "3743 K", "Brinell hardness": "363 MN m-2", "Bulk modulus": "28 GPa", "Coefficient of linear thermal expansion": "12.1 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "6146 kg m-3", "Electrical resistivity": "61.5 10-8 Ω m", "Electronic structure": "[Xe].5d1.6s2", "ICSD oxidation states": [2, 3], "Ionic radii": {"3": 1.172}, "Liquid range": "2550 K", "Melting point": "1193 K", "Mendeleev no": 33, "Mineral hardness": "2.5", "Molar volume": "22.39 cm3", "Name": "Lanthanum", "Oxidation states": [2, 3], "Poissons ratio": "0.28", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "14 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.172, "ionic_radius": 1.032}}, "VII": {"": {"crystal_radius": 1.24, "ionic_radius": 1.1}}, "VIII": {"": {"crystal_radius": 1.3, "ionic_radius": 1.16}}, "IX": {"": {"crystal_radius": 1.356, "ionic_radius": 1.216}}, "X": {"": {"crystal_radius": 1.41, "ionic_radius": 1.27}}, "XII": {"": {"crystal_radius": 1.5, "ionic_radius": 1.36}}}}, "Superconduction temperature": "6.00 K", "Thermal conductivity": "13 W m-1 K-1", "Van der waals radius": 2.43, "Velocity of sound": "2475 m s-1", "Vickers hardness": "491 MN m-2", "X": 1.1, "Youngs modulus": "37 GPa", "NMR Quadrupole Moment": {"La-139": 200.6}, "Metallic radius": 1.877, "iupac_ordering": 47, "IUPAC ordering": 47, "Ground level": "2D3/2", "Ionization energies": [5.5769, 11.18496, 19.1773, 49.95, 61.6, 74.0, 88.0, 105.0, 119.0, 151.4, 168.77, 275.0, 303.0, 332.0, 364.0, 393.0, 431.0, 464.0, 498.0, 533.0, 566.0, 696.0, 731.0, 770.0, 806.0, 865.0, 906.0, 995.0, 1039.09, 1800.0, 1884.0, 1974.0, 2069.0, 2162.0, 2259.0, 2377.0, 2473.0, 2577.0, 2674.0, 2950.0, 3036.0, 3133.0, 3222.0, 3416.0, 3515.0, 3704.0, 3800.0, 8669.0, 8914.0, 9184.0, 9437.0, 10136.0, 10426.0, 10789.0, 11033.4, 45144.996, 46245.6], "Electron affinity": 0.5575462}, "Li": {"Atomic mass": 6.941, "Atomic no": 3, "Atomic orbitals": {"1s": -1.878564, "2s": -0.10554}, "Atomic radius": 1.45, "Atomic radius calculated": 1.67, "Boiling point": "1615 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "11 GPa", "Coefficient of linear thermal expansion": "46 x10-6K-1", "Common oxidation states": [1], "Critical temperature": "3223 K", "Density of solid": "535 kg m-3", "Electrical resistivity": "9.5 10-8 Ω m", "Electronic structure": "[He].2s1", "ICSD oxidation states": [1], "Ionic radii": {"1": 0.9}, "Liquid range": "1161.31 K", "Melting point": "453.69 K", "Mendeleev no": 12, "Mineral hardness": "0.6", "Molar volume": "13.02 cm3", "Name": "Lithium", "Oxidation states": [1], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "4.2 GPa", "Shannon radii": {"1": {"IV": {"": {"crystal_radius": 0.73, "ionic_radius": 0.59}}, "VI": {"": {"crystal_radius": 0.9, "ionic_radius": 0.76}}, "VIII": {"": {"crystal_radius": 1.06, "ionic_radius": 0.92}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "85 W m-1 K-1", "Van der waals radius": 1.82, "Velocity of sound": "6000 m s-1", "Vickers hardness": "no data MN m-2", "X": 0.98, "Youngs modulus": "4.9 GPa", "NMR Quadrupole Moment": {"Li-6": -0.808, "Li-7": -40.1}, "Metallic radius": 1.52, "iupac_ordering": 11, "IUPAC ordering": 11, "Ground level": "2S1/2", "Ionization energies": [5.391714996, 75.640097, 122.45435914], "Electron affinity": 0.61804922}, "Lr": {"Atomic mass": 262.0, "Atomic no": 103, "Atomic orbitals": "no data", "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].5f14.7s2.7p1 (tentative)", "Liquid range": "no data K", "Melting point": "about 1900 K", "Mendeleev no": 34, "Mineral hardness": "no data", "Molar volume": "no data cm3", "Name": "Lawrencium", "Oxidation states": [3], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Superconduction temperature": "no data K", "Thermal conductivity": "no data W m-1 K-1", "Van der waals radius": "no data", "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.3, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 18, "IUPAC ordering": 18, "Ground level": "2P\u00b01/2", "Ionization energies": [4.96, 14.54, 21.8, 43.6, 56.0, 80.0, 96.0, 121.0, 143.0, 165.0, 197.0, 216.0, 244.0, 269.0, 290.0, 322.0, 344.0, 374.0, 403.0, 431.0, 459.0, 487.0, 510.0, 540.0, 560.0, 745.0, 779.0, 814.0, 852.0, 888.0, 922.0, 985.0, 1020.0, 1061.0, 1098.0, 1280.0, 1320.0, 1360.0, 1410.0, 1570.0, 1620.0, 1760.0, 1810.0, 2010.0, 2100.0, 2190.0, 2290.0, 2380.0, 2470.0, 2570.0, 2670.0, 2780.0, 2860.0, 2960.0, 3060.0, 3150.0, 3250.0, 3741.0, 3821.0, 3906.0, 3996.0, 4082.0, 4165.0, 4360.0, 4448.0, 4540.0, 4630.0, 4990.0, 5070.0, 5160.0, 5250.0, 5920.0, 6030.0, 6290.0, 6390.0, 9920.0, 10110.0, 10310.0, 10520.0, 10720.0, 10920.0, 11470.0, 11680.0, 11910.0, 12120.0, 12710.0, 12890.0, 13090.0, 13300.0, 15300.0, 15600.0, 16000.0, 16200.0, 32400.0, 32900.0, 33400.0, 33900.0, 41600.0, 42300.0, 43200.0, 43759.0, null, 172930.0], "Electron affinity": -0.31}, "Lu": {"Atomic mass": 174.967, "Atomic no": 71, "Atomic orbitals": {"1s": -2146.885351, "2p": -334.330902, "2s": -349.390492, "3d": -58.592982, "3p": -71.538779, "3s": -78.462398, "4d": -7.113364, "4f": -0.568096, "4p": -12.250904, "4s": -15.08337, "5d": -0.103686, "5p": -1.111991, "5s": -1.872086, "6s": -0.155112}, "Atomic radius": 1.75, "Atomic radius calculated": 2.17, "Boiling point": "3675 K", "Brinell hardness": "893 MN m-2", "Bulk modulus": "48 GPa", "Coefficient of linear thermal expansion": "9.9 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "9841 kg m-3", "Electrical resistivity": "58 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d1.6s2", "ICSD oxidation states": [3], "Ionic radii": {"3": 1.001}, "Liquid range": "1750 K", "Melting point": "1925 K", "Mendeleev no": 20, "Mineral hardness": "no data", "Molar volume": "17.78 cm3", "Name": "Lutetium", "Oxidation states": [3], "Poissons ratio": "0.26", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "27 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.001, "ionic_radius": 0.861}}, "VIII": {"": {"crystal_radius": 1.117, "ionic_radius": 0.977}}, "IX": {"": {"crystal_radius": 1.172, "ionic_radius": 1.032}}}}, "Superconduction temperature": "0.022 K", "Thermal conductivity": "16 W m-1 K-1", "Van der waals radius": 2.24, "Velocity of sound": "no data m s-1", "Vickers hardness": "1160 MN m-2", "X": 1.27, "Youngs modulus": "69 GPa", "Metallic radius": 1.735, "iupac_ordering": 33, "IUPAC ordering": 33, "Ground level": "2D3/2", "Ionization energies": [5.425871, 14.13, 20.9594, 45.249, 66.8, 98.0, 117.0, 136.0, 159.0, 185.0, 205.0, 238.0, 276.0, 305.0, 328.0, 361.0, 399.0, 438.0, 476.0, 520.0, 560.0, 600.0, 630.0, 670.0, 713.0, 941.0, 985.0, 1032.0, 1081.0, 1130.0, 1178.0, 1242.0, 1292.0, 1345.0, 1395.0, 1591.0, 1641.0, 1696.0, 1747.0, 1875.0, 1933.0, 2067.0, 2125.5, 3590.0, 3706.0, 3828.0, 3960.0, 4086.0, 4211.0, 4403.0, 4532.0, 4673.0, 4803.0, 5168.0, 5282.0, 5408.0, 5525.0, 5937.0, 6070.0, 6326.0, 6452.0, 14228.0, 14542.0, 14890.0, 15211.0, 16730.0, 17120.0, 17610.0, 17928.05, 72322.91, 73804.8], "Electron affinity": 0.23887}, "Md": {"Atomic mass": 258.0, "Atomic no": 101, "Atomic orbitals": "no data", "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].5f13.7s2", "Liquid range": "no data K", "Melting point": "about 1100 K", "Mendeleev no": 36, "Mineral hardness": "no data", "Molar volume": "no data cm3", "Name": "Mendelevium", "Oxidation states": [2, 3], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Superconduction temperature": "no data K", "Thermal conductivity": "no data W m-1 K-1", "Van der waals radius": 2.46, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.3, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 20, "IUPAC ordering": 20, "Ground level": "2F\u00b07/2", "Ionization energies": [6.58, 12.4, 24.3, 40.0, 54.1, 76.0, 96.0, 115.1, 143.9, 162.0, 187.0, 215.0, 240.0, 260.0, 282.0, 307.0, 334.0, 360.0, 386.0, 412.0, 438.0, 462.0, 486.0, 659.0, 690.0, 723.0, 760.0, 794.0, 828.0, 885.0, 920.0, 958.0, 994.0, 1160.0, 1210.0, 1250.0, 1290.0, 1430.0, 1480.0, 1620.0, 1660.0, 1840.0, 1930.0, 2020.0, 2110.0, 2200.0, 2290.0, 2390.0, 2480.0, 2580.0, 2680.0, 2760.0, 2860.0, 2950.0, 3050.0, 3513.0, 3592.0, 3675.0, 3762.0, 3845.0, 3926.0, 4109.0, 4194.0, 4286.0, 4371.0, 4720.0, 4800.0, 4890.0, 4970.0, 5580.0, 5680.0, 5930.0, 6030.0, 9430.0, 9620.0, 9810.0, 10020.0, 10220.0, 10410.0, 10930.0, 11130.0, 11350.0, 11560.0, 12130.0, 12310.0, 12500.0, 12680.0, 14560.0, 14800.0, 15200.0, 15400.0, 31000.0, 31500.0, 32000.0, 32500.0, 39500.0, 40100.0, 41000.0, 41548.0, null, 164764.0], "Electron affinity": 0.98}, "Mg": {"Atomic mass": 24.305, "Atomic no": 12, "Atomic orbitals": {"1s": -45.973167, "2p": -1.71897, "2s": -2.903746, "3s": -0.175427}, "Atomic radius": 1.5, "Atomic radius calculated": 1.45, "Boiling point": "1363 K", "Brinell hardness": "260 MN m-2", "Bulk modulus": "45 GPa", "Coefficient of linear thermal expansion": "8.2 x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "1738 kg m-3", "Electrical resistivity": "4.4 10-8 Ω m", "Electronic structure": "[Ne].3s2", "ICSD oxidation states": [2], "Ionic radii": {"2": 0.86}, "Liquid range": "440 K", "Melting point": "923 K", "Mendeleev no": 73, "Mineral hardness": "2.5", "Molar volume": "14.00 cm3", "Name": "Magnesium", "Oxidation states": [1, 2], "Poissons ratio": "0.29", "Reflectivity": "74 %", "Refractive index": "no data", "Rigidity modulus": "17 GPa", "Shannon radii": {"2": {"IV": {"": {"crystal_radius": 0.71, "ionic_radius": 0.57}}, "V": {"": {"crystal_radius": 0.8, "ionic_radius": 0.66}}, "VI": {"": {"crystal_radius": 0.86, "ionic_radius": 0.72}}, "VIII": {"": {"crystal_radius": 1.03, "ionic_radius": 0.89}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "160 W m-1 K-1", "Van der waals radius": 1.73, "Velocity of sound": "4602 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.31, "Youngs modulus": "45 GPa", "NMR Quadrupole Moment": {"Mg-25": 199.4}, "Metallic radius": 1.6, "iupac_ordering": 16, "IUPAC ordering": 16, "Ground level": "1S0", "Ionization energies": [7.646236, 15.035271, 80.1436, 109.2654, 141.33, 186.76, 225.02, 265.924, 327.99, 367.489, 1761.80488, 1962.66366], "Electron affinity": -0.42}, "Mn": {"Atomic mass": 54.938045, "Atomic no": 25, "Atomic orbitals": {"1s": -233.696912, "2p": -23.066297, "2s": -26.866646, "3d": -0.26654, "3p": -1.99145, "3s": -3.076637, "4s": -0.191136}, "Atomic radius": 1.4, "Atomic radius calculated": 1.61, "Boiling point": "2334 K", "Brinell hardness": "196 MN m-2", "Bulk modulus": "120 GPa", "Coefficient of linear thermal expansion": "21.7 x10-6K-1", "Common oxidation states": [2, 4, 7], "Critical temperature": "no data K", "Density of solid": "7470 kg m-3", "Electrical resistivity": "144 10-8 Ω m", "Electronic structure": "[Ar].3d5.4s2", "ICSD oxidation states": [2, 3, 4, 7], "Ionic radii": {"2": 0.97, "3": 0.785, "4": 0.67, "5": 0.47, "6": 0.395, "7": 0.6}, "Ionic radii hs": {"2": 0.97, "3": 0.785}, "Ionic radii ls": {"2": 0.81, "3": 0.72, "4": 0.67, "5": 0.47, "6": 0.395, "7": 0.6}, "Liquid range": "815 K", "Melting point": "1519 K", "Mendeleev no": 60, "Mineral hardness": "6.0", "Molar volume": "7.35 cm3", "Name": "Manganese", "Oxidation states": [-3, -2, -1, 1, 2, 3, 4, 5, 6, 7], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"2": {"IV": {"High Spin": {"crystal_radius": 0.8, "ionic_radius": 0.66}}, "V": {"High Spin": {"crystal_radius": 0.89, "ionic_radius": 0.75}}, "VI": {"Low Spin": {"crystal_radius": 0.81, "ionic_radius": 0.67}, "High Spin": {"crystal_radius": 0.97, "ionic_radius": 0.83}}, "VII": {"High Spin": {"crystal_radius": 1.04, "ionic_radius": 0.9}}, "VIII": {"": {"crystal_radius": 1.1, "ionic_radius": 0.96}}}, "3": {"V": {"": {"crystal_radius": 0.72, "ionic_radius": 0.58}}, "VI": {"Low Spin": {"crystal_radius": 0.72, "ionic_radius": 0.58}, "High Spin": {"crystal_radius": 0.785, "ionic_radius": 0.645}}}, "4": {"IV": {"": {"crystal_radius": 0.53, "ionic_radius": 0.39}}, "VI": {"": {"crystal_radius": 0.67, "ionic_radius": 0.53}}}, "5": {"IV": {"": {"crystal_radius": 0.47, "ionic_radius": 0.33}}}, "6": {"IV": {"": {"crystal_radius": 0.395, "ionic_radius": 0.255}}}, "7": {"IV": {"": {"crystal_radius": 0.39, "ionic_radius": 0.25}}, "VI": {"": {"crystal_radius": 0.6, "ionic_radius": 0.46}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "7.8 W m-1 K-1", "Van der waals radius": 2.05, "Velocity of sound": "5150 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.55, "Youngs modulus": "198 GPa", "NMR Quadrupole Moment": {"Mn-55": 330.1}, "Metallic radius": 1.292, "iupac_ordering": 61, "IUPAC ordering": 61, "Ground level": "6S5/2", "Ionization energies": [7.434038, 15.63999, 33.668, 51.21, 72.41, 95.604, 119.203, 195.5, 221.89, 248.6, 286.1, 314.4, 343.6, 402.95, 435.172, 1133.7, 1224.1, 1320.3, 1430.9, 1537.2, 1643.2, 1788.7, 1879.873, 8140.7872, 8571.9488], "Electron affinity": -0.52}, "Mo": {"Atomic mass": 95.94, "Atomic no": 42, "Atomic orbitals": {"1s": -709.232119, "2p": -90.791541, "2s": -98.503638, "3d": -8.257721, "3p": -13.71481, "3s": -16.681545, "4d": -0.153347, "4p": -1.39005, "4s": -2.234824, "5s": -0.14788}, "Atomic radius": 1.45, "Atomic radius calculated": 1.9, "Boiling point": "4912 K", "Brinell hardness": "1500 MN m-2", "Bulk modulus": "230 GPa", "Coefficient of linear thermal expansion": "4.8 x10-6K-1", "Common oxidation states": [4, 6], "Critical temperature": "no data K", "Density of solid": "10280 kg m-3", "Electrical resistivity": "5.5 10-8 Ω m", "Electronic structure": "[Kr].4d5.5s1", "ICSD oxidation states": [2, 3, 4, 5, 6], "Ionic radii": {"3": 0.83, "4": 0.79, "5": 0.75, "6": 0.73}, "Liquid range": "2016 K", "Melting point": "2896 K", "Mendeleev no": 56, "Mineral hardness": "5.5", "Molar volume": "9.38 cm3", "Name": "Molybdenum", "Oxidation states": [-2, -1, 1, 2, 3, 4, 5, 6], "Poissons ratio": "0.31", "Reflectivity": "58 %", "Refractive index": "no data", "Rigidity modulus": "20 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 0.83, "ionic_radius": 0.69}}}, "4": {"VI": {"": {"crystal_radius": 0.79, "ionic_radius": 0.65}}}, "5": {"IV": {"": {"crystal_radius": 0.6, "ionic_radius": 0.46}}, "VI": {"": {"crystal_radius": 0.75, "ionic_radius": 0.61}}}, "6": {"IV": {"": {"crystal_radius": 0.55, "ionic_radius": 0.41}}, "V": {"": {"crystal_radius": 0.64, "ionic_radius": 0.5}}, "VI": {"": {"crystal_radius": 0.73, "ionic_radius": 0.59}}, "VII": {"": {"crystal_radius": 0.87, "ionic_radius": 0.73}}}}, "Superconduction temperature": "0.915 K", "Thermal conductivity": "139 W m-1 K-1", "Van der waals radius": 2.17, "Velocity of sound": "6190 m s-1", "Vickers hardness": "1530 MN m-2", "X": 2.16, "Youngs modulus": "329 GPa", "Metallic radius": 1.402, "iupac_ordering": 57, "IUPAC ordering": 57, "Ground level": "7S3", "Ionization energies": [7.09243, 16.16, 27.13, 40.33, 54.417, 68.82704, 125.638, 143.6, 164.12, 186.3, 209.3, 230.28, 279.1, 302.6, 544.0, 591.0, 646.0, 702.0, 758.0, 829.0, 890.0, 953.0, 1019.0, 1082.0, 1263.0, 1319.6, 1385.1, 1462.0, 1537.0, 1587.0, 1730.1, 1790.93, 4259.0, 4430.0, 4618.0, 4800.0, 5084.0, 5287.0, 5548.0, 5713.194, 23810.654, 24572.156], "Electron affinity": 0.74733}, "N": {"Atomic mass": 14.0067, "Atomic no": 7, "Atomic orbitals": {"1s": -14.011501, "2p": -0.266297, "2s": -0.676151}, "Atomic radius": 0.65, "Atomic radius calculated": 0.56, "Boiling point": "77.36 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-3, 3, 5], "Critical temperature": "126.2 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[He].2s2.2p3", "ICSD oxidation states": [1, 3, 5, -1, -3, -2], "Ionic radii": {"-3": 1.32, "3": 0.3, "5": 0.27}, "Liquid range": "14.31 K", "Melting point": "63.05 K", "Mendeleev no": 100, "Mineral hardness": "no data", "Molar volume": "13.54 cm3", "Name": "Nitrogen", "Oxidation states": [-3, -2, -1, 1, 2, 3, 4, 5], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000298 (gas; liquid 1.197)(no units)", "Rigidity modulus": "no data GPa", "Shannon radii": {"-3": {"IV": {"": {"crystal_radius": 1.32, "ionic_radius": 1.46}}}, "3": {"VI": {"": {"crystal_radius": 0.3, "ionic_radius": 0.16}}}, "5": {"III": {"": {"crystal_radius": 0.044, "ionic_radius": -0.104}}, "VI": {"": {"crystal_radius": 0.27, "ionic_radius": 0.13}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.02583 W m-1 K-1", "Van der waals radius": 1.55, "Velocity of sound": "333.6 m s-1", "Vickers hardness": "no data MN m-2", "X": 3.04, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"N-14": 20.44}, "Metallic radius": "no data", "iupac_ordering": 91, "IUPAC ordering": 91, "Ground level": "4S\u00b03/2", "Ionization energies": [14.53413, 29.60125, 47.4453, 77.4735, 97.8901, 552.06733, 667.046121], "Electron affinity": -0.07}, "Na": {"Atomic mass": 22.98976928, "Atomic no": 11, "Atomic orbitals": {"1s": -37.719975, "2p": -1.060636, "2s": -2.063401, "3s": -0.103415}, "Atomic radius": 1.8, "Atomic radius calculated": 1.9, "Boiling point": "1156 K", "Brinell hardness": "0.69 MN m-2", "Bulk modulus": "6.3 GPa", "Coefficient of linear thermal expansion": "71 x10-6K-1", "Common oxidation states": [1], "Critical temperature": "2573 K", "Density of solid": "968 kg m-3", "Electrical resistivity": "4.9 10-8 Ω m", "Electronic structure": "[Ne].3s1", "ICSD oxidation states": [1], "Ionic radii": {"1": 1.16}, "Liquid range": "785.13 K", "Melting point": "370.87 K", "Mendeleev no": 11, "Mineral hardness": "0.5", "Molar volume": "23.78 cm3", "Name": "Sodium", "Oxidation states": [-1, 1], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "3.3 GPa", "Shannon radii": {"1": {"IV": {"": {"crystal_radius": 1.13, "ionic_radius": 0.99}}, "V": {"": {"crystal_radius": 1.14, "ionic_radius": 1.0}}, "VI": {"": {"crystal_radius": 1.16, "ionic_radius": 1.02}}, "VII": {"": {"crystal_radius": 1.26, "ionic_radius": 1.12}}, "VIII": {"": {"crystal_radius": 1.32, "ionic_radius": 1.18}}, "IX": {"": {"crystal_radius": 1.38, "ionic_radius": 1.24}}, "XII": {"": {"crystal_radius": 1.53, "ionic_radius": 1.39}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "140 W m-1 K-1", "Van der waals radius": 2.27, "Velocity of sound": "3200 m s-1", "Vickers hardness": "no data MN m-2", "X": 0.93, "Youngs modulus": "10 GPa", "NMR Quadrupole Moment": {"Na-23": 104.1}, "Metallic radius": 1.86, "iupac_ordering": 10, "IUPAC ordering": 10, "Ground level": "2S1/2", "Ionization energies": [5.13907696, 47.28636, 71.62, 98.936, 138.404, 172.23, 208.504, 264.192, 299.856, 1465.134502, 1648.7022], "Electron affinity": 0.54792625}, "Nb": {"Atomic mass": 92.90638, "Atomic no": 41, "Atomic orbitals": {"1s": -673.76253, "2p": -85.272175, "2s": -92.74086, "3d": -7.339839, "3p": -12.552855, "3s": -15.393727, "4d": -0.125252, "4p": -1.250049, "4s": -2.036693, "5s": -0.144272}, "Atomic radius": 1.45, "Atomic radius calculated": 1.98, "Boiling point": "5017 K", "Brinell hardness": "736 MN m-2", "Bulk modulus": "170 GPa", "Coefficient of linear thermal expansion": "7.3 x10-6K-1", "Common oxidation states": [5], "Critical temperature": "no data K", "Density of solid": "8570 kg m-3", "Electrical resistivity": "15.2 10-8 Ω m", "Electronic structure": "[Kr].4d4.5s1", "ICSD oxidation states": [2, 3, 4, 5], "Ionic radii": {"3": 0.86, "4": 0.82, "5": 0.78}, "Liquid range": "2267 K", "Melting point": "2750 K", "Mendeleev no": 53, "Mineral hardness": "6.0", "Molar volume": "10.83 cm3", "Name": "Niobium", "Oxidation states": [-1, 2, 3, 4, 5], "Poissons ratio": "0.40", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "38 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 0.86, "ionic_radius": 0.72}}}, "4": {"VI": {"": {"crystal_radius": 0.82, "ionic_radius": 0.68}}, "VIII": {"": {"crystal_radius": 0.93, "ionic_radius": 0.79}}}, "5": {"IV": {"": {"crystal_radius": 0.62, "ionic_radius": 0.48}}, "VI": {"": {"crystal_radius": 0.78, "ionic_radius": 0.64}}, "VII": {"": {"crystal_radius": 0.83, "ionic_radius": 0.69}}, "VIII": {"": {"crystal_radius": 0.88, "ionic_radius": 0.74}}}}, "Superconduction temperature": "9.25 K", "Thermal conductivity": "54 W m-1 K-1", "Van der waals radius": 2.18, "Velocity of sound": "3480 m s-1", "Vickers hardness": "1320 MN m-2", "X": 1.6, "Youngs modulus": "105 GPa", "Metallic radius": 1.473, "iupac_ordering": 54, "IUPAC ordering": 54, "Ground level": "6D1/2", "Ionization energies": [6.75885, 14.32, 25.04, 37.611, 50.5728, 102.069, 119.1, 136.0, 159.2, 180.0, 200.28, 246.1, 268.59, 482.5, 530.0, 581.0, 636.0, 688.0, 758.0, 816.0, 877.0, 940.0, 1000.0, 1176.0, 1230.6, 1293.7, 1368.0, 1439.0, 1488.0, 1625.9, 1684.97, 4020.1, 4187.0, 4369.0, 4540.0, 4815.0, 5011.0, 5265.0, 5426.066, 22648.046, 23388.801], "Electron affinity": 0.917407}, "Nd": {"Atomic mass": 144.242, "Atomic no": 60, "Atomic orbitals": {"1s": -1509.698955, "2p": -224.351816, "2s": -236.613572, "3d": -35.754515, "3p": -45.791219, "3s": -51.161263, "4d": -4.377027, "4f": -0.179508, "4p": -7.96782, "4s": -10.000891, "5p": -0.798503, "5s": -1.334934, "6s": -0.125796}, "Atomic radius": 1.85, "Atomic radius calculated": 2.06, "Boiling point": "3373 K", "Brinell hardness": "265 MN m-2", "Bulk modulus": "32 GPa", "Coefficient of linear thermal expansion": "9.6 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "6800 kg m-3", "Electrical resistivity": "64.3 10-8 Ω m", "Electronic structure": "[Xe].4f4.6s2", "ICSD oxidation states": [2, 3], "Ionic radii": {"2": 1.43, "3": 1.123}, "Liquid range": "2076 K", "Melting point": "1297 K", "Mendeleev no": 30, "Mineral hardness": "no data", "Molar volume": "20.59 cm3", "Name": "Neodymium", "Oxidation states": [2, 3], "Poissons ratio": "0.28", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "16 GPa", "Shannon radii": {"2": {"VIII": {"": {"crystal_radius": 1.43, "ionic_radius": 1.29}}, "IX": {"": {"crystal_radius": 1.49, "ionic_radius": 1.35}}}, "3": {"VI": {"": {"crystal_radius": 1.123, "ionic_radius": 0.983}}, "VIII": {"": {"crystal_radius": 1.249, "ionic_radius": 1.109}}, "IX": {"": {"crystal_radius": 1.303, "ionic_radius": 1.163}}, "XII": {"": {"crystal_radius": 1.41, "ionic_radius": 1.27}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "17 W m-1 K-1", "Van der waals radius": 2.39, "Velocity of sound": "2330 m s-1", "Vickers hardness": "343 MN m-2", "X": 1.14, "Youngs modulus": "41 GPa", "Metallic radius": 1.821, "iupac_ordering": 44, "IUPAC ordering": 44, "Ground level": "5I4", "Ionization energies": [5.525, 10.783, 22.09, 40.6, 60.0, 84.0, 99.0, 114.0, 136.0, 152.0, 168.0, 195.0, 221.0, 243.0, 389.0, 420.0, 453.0, 489.0, 522.0, 562.0, 602.0, 638.0, 678.0, 714.0, 859.0, 896.0, 939.0, 978.0, 1049.0, 1092.0, 1191.0, 1238.42, 2134.0, 2224.0, 2321.0, 2425.0, 2525.0, 2627.0, 2758.0, 2861.0, 2974.0, 3078.0, 3371.0, 3465.0, 3567.0, 3662.0, 3891.0, 3997.0, 4198.0, 4302.0, 9742.0, 10002.0, 10288.0, 10555.0, 11384.0, 11694.0, 12082.0, 12341.66, 50339.59, 51515.58], "Electron affinity": 0.0974933}, "Ne": {"Atomic mass": 20.1797, "Atomic no": 10, "Atomic orbitals": {"1s": -30.305855, "2p": -0.498034, "2s": -1.322809}, "Atomic radius": "no data", "Atomic radius calculated": 0.38, "Boiling point": "27.07 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Critical temperature": "44.4 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[He].2s2.2p6", "Liquid range": "2.51 K", "Max oxidation state": 0.0, "Melting point": "24.56 K", "Mendeleev no": 2, "Min oxidation state": 0.0, "Mineral hardness": "no data", "Molar volume": "13.23 cm3", "Name": "Neon", "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000067", "Rigidity modulus": "no data GPa", "Superconduction temperature": "no data K", "Thermal conductivity": "0.0491 W m-1 K-1", "Van der waals radius": 1.54, "Velocity of sound": "936 m s-1", "Vickers hardness": "no data MN m-2", "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"Ne-21": 101.55}, "Metallic radius": "no data", "iupac_ordering": 4, "IUPAC ordering": 4, "Ground level": "1S0", "Ionization energies": [21.564541, 40.96297, 63.4233, 97.19, 126.247, 157.934, 207.271, 239.097, 1195.80784, 1362.19916], "Electron affinity": -1.22}, "Ni": {"Atomic mass": 58.6934, "Atomic no": 28, "Atomic orbitals": {"1s": -297.870824, "2p": -30.868027, "2s": -35.312112, "3d": -0.348699, "3p": -2.594158, "3s": -3.950717, "4s": -0.210764}, "Atomic radius": 1.35, "Atomic radius calculated": 1.49, "Boiling point": "3186 K", "Brinell hardness": "700 MN m-2", "Bulk modulus": "180 GPa", "Coefficient of linear thermal expansion": "13.4 x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "8908 kg m-3", "Electrical resistivity": "7.2 10-8 Ω m", "Electronic structure": "[Ar].3d8.4s2", "ICSD oxidation states": [1, 2, 3, 4], "Ionic radii": {"3": 0.74}, "Ionic radii hs": {"3": 0.74}, "Ionic radii ls": {"2": 0.83, "3": 0.7, "4": 0.62}, "Liquid range": "1458 K", "Melting point": "1728 K", "Mendeleev no": 67, "Mineral hardness": "4.0", "Molar volume": "6.59 cm3", "Name": "Nickel", "Oxidation states": [-1, 1, 2, 3, 4], "Poissons ratio": "0.31", "Reflectivity": "72 %", "Refractive index": "no data", "Rigidity modulus": "76 GPa", "Shannon radii": {"2": {"IV": {"": {"crystal_radius": 0.69, "ionic_radius": 0.55}}, "IVSQ": {"": {"crystal_radius": 0.63, "ionic_radius": 0.49}}, "V": {"": {"crystal_radius": 0.77, "ionic_radius": 0.63}}, "VI": {"": {"crystal_radius": 0.83, "ionic_radius": 0.69}}}, "3": {"VI": {"Low Spin": {"crystal_radius": 0.7, "ionic_radius": 0.56}, "High Spin": {"crystal_radius": 0.74, "ionic_radius": 0.6}}}, "4": {"VI": {"Low Spin": {"crystal_radius": 0.62, "ionic_radius": 0.48}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "91 W m-1 K-1", "Van der waals radius": 1.97, "Velocity of sound": "4970 m s-1", "Vickers hardness": "638 MN m-2", "X": 1.91, "Youngs modulus": "200 GPa", "NMR Quadrupole Moment": {"Ni-61": 162.15}, "Metallic radius": 1.246, "iupac_ordering": 70, "IUPAC ordering": 70, "Ground level": "3F4", "Ionization energies": [7.639878, 18.168838, 35.187, 54.92, 76.06, 108.0, 132.0, 162.0, 193.2, 224.7, 319.5, 351.6, 384.5, 429.3, 462.8, 495.4, 571.07, 607.02, 1541.0, 1646.0, 1758.0, 1880.0, 2008.1, 2130.5, 2295.6, 2399.259, 10288.8862, 10775.386], "Electron affinity": 1.1571612}, "No": {"Atomic mass": 259.0, "Atomic no": 102, "Atomic orbitals": "no data", "Atomic radius": "no data", "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Rn].5f14.7s2", "Liquid range": "no data K", "Melting point": "about 1100 K", "Mendeleev no": 35, "Mineral hardness": "no data", "Molar volume": "no data cm3", "Name": "Nobelium", "Oxidation states": [2, 3], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.24, "ionic_radius": 1.1}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "no data W m-1 K-1", "Van der waals radius": 2.46, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.3, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 19, "IUPAC ordering": 19, "Ground level": "1S0", "Ionization energies": [6.62621, 12.93, 25.8, 41.5, 60.0, 74.0, 97.0, 119.0, 140.0, 170.0, 187.0, 216.0, 246.0, 267.0, 285.0, 312.0, 341.0, 367.0, 394.0, 422.0, 448.0, 475.0, 496.0, 520.0, 701.0, 734.0, 768.0, 805.0, 840.0, 875.0, 934.0, 969.0, 1010.0, 1045.0, 1220.0, 1260.0, 1300.0, 1350.0, 1500.0, 1550.0, 1680.0, 1730.0, 1920.0, 2010.0, 2110.0, 2200.0, 2290.0, 2380.0, 2470.0, 2570.0, 2680.0, 2760.0, 2860.0, 2950.0, 3050.0, 3140.0, 3627.0, 3705.0, 3790.0, 3878.0, 3962.0, 4045.0, 4234.0, 4320.0, 4413.0, 4500.0, 4850.0, 4930.0, 5030.0, 5110.0, 5750.0, 5850.0, 6110.0, 6210.0, 9680.0, 9860.0, 10060.0, 10270.0, 10470.0, 10660.0, 11200.0, 11410.0, 11630.0, 11840.0, 12420.0, 12600.0, 12800.0, 12980.0, 15000.0, 15200.0, 15600.0, 15800.0, 31700.0, 32200.0, 32700.0, 33200.0, 40500.0, 41200.0, 42100.0, 42632.0, null, 168806.0], "Electron affinity": -2.33}, "Np": {"Atomic mass": 237.0, "Atomic no": 93, "Atomic orbitals": "no data", "Atomic radius": 1.75, "Atomic radius calculated": "no data", "Boiling point": "4273 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [5], "Critical temperature": "no data K", "Density of solid": "20450 kg m-3", "Electrical resistivity": "120 10-8 Ω m", "Electronic structure": "[Rn].5f4.6d1.7s2", "Ionic radii": {"2": 1.24, "3": 1.15, "4": 1.01, "5": 0.89, "6": 0.86, "7": 0.85}, "Liquid range": "3363 K", "Melting point": "910 K", "Mendeleev no": 44, "Mineral hardness": "no data", "Molar volume": "11.59 cm3", "Name": "Neptunium", "Oxidation states": [3, 4, 5, 6, 7], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.24, "ionic_radius": 1.1}}}, "3": {"VI": {"": {"crystal_radius": 1.15, "ionic_radius": 1.01}}}, "4": {"VI": {"": {"crystal_radius": 1.01, "ionic_radius": 0.87}}, "VIII": {"": {"crystal_radius": 1.12, "ionic_radius": 0.98}}}, "5": {"VI": {"": {"crystal_radius": 0.89, "ionic_radius": 0.75}}}, "6": {"VI": {"": {"crystal_radius": 0.86, "ionic_radius": 0.72}}}, "7": {"VI": {"": {"crystal_radius": 0.85, "ionic_radius": 0.71}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "6 W m-1 K-1", "Van der waals radius": 2.39, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.36, "Youngs modulus": "no data GPa", "Metallic radius": 1.503, "iupac_ordering": 28, "IUPAC ordering": 28, "Ground level": "6L11/2", "Ionization energies": [6.26554, 11.5, 19.7, 33.8, 48.0, 65.0, 92.0, 107.0, 121.0, 136.0, 151.0, 179.0, 196.0, 233.0, 252.0, 355.0, 382.0, 408.0, 438.0, 466.0, 495.0, 535.0, 565.0, 596.0, 626.0, 770.0, 810.0, 850.0, 880.0, 980.0, 1020.0, 1130.0, 1170.0, 1280.0, 1360.0, 1430.0, 1510.0, 1590.0, 1670.0, 1740.0, 1820.0, 1910.0, 1990.0, 2070.0, 2140.0, 2230.0, 2310.0, 2675.0, 2745.0, 2817.0, 2894.0, 2969.0, 3041.0, 3181.0, 3255.0, 3338.0, 3413.0, 3718.0, 3792.0, 3872.0, 3947.0, 4353.0, 4441.0, 4658.0, 4744.0, 7610.0, 7770.0, 7950.0, 8130.0, 8310.0, 8480.0, 8890.0, 9070.0, 9270.0, 9450.0, 9970.0, 10130.0, 10300.0, 10470.0, 11730.0, 11930.0, 12320.0, 12500.0, 25870.0, 26300.0, 26770.0, 27210.0, 31910.0, 32500.0, 33300.0, 33722.2, 132901.8, 135202.0], "Electron affinity": 0.48}, "O": {"Atomic mass": 15.9994, "Atomic no": 8, "Atomic orbitals": {"1s": -18.758245, "2p": -0.338381, "2s": -0.871362}, "Atomic radius": 0.6, "Atomic radius calculated": 0.48, "Boiling point": "90.2 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-2], "Critical temperature": "154.6 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[He].2s2.2p4", "ICSD oxidation states": [-2], "Ionic radii": {"-2": 1.26}, "Liquid range": "35.4 K", "Melting point": "54.8 K", "Mendeleev no": 101, "Mineral hardness": "no data", "Molar volume": "17.36 cm3", "Name": "Oxygen", "Oxidation states": [-2, -1, 1, 2], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000271 (gas; liquid 1.221)(no units)", "Rigidity modulus": "no data GPa", "Shannon radii": {"-2": {"II": {"": {"crystal_radius": 1.21, "ionic_radius": 1.35}}, "III": {"": {"crystal_radius": 1.22, "ionic_radius": 1.36}}, "IV": {"": {"crystal_radius": 1.24, "ionic_radius": 1.38}}, "VI": {"": {"crystal_radius": 1.26, "ionic_radius": 1.4}}, "VIII": {"": {"crystal_radius": 1.28, "ionic_radius": 1.42}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.02658 W m-1 K-1", "Van der waals radius": 1.52, "Velocity of sound": "317.5 m s-1", "Vickers hardness": "no data MN m-2", "X": 3.44, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"O-17": -25.58}, "Metallic radius": "no data", "iupac_ordering": 97, "IUPAC ordering": 97, "Ground level": "3P2", "Ionization energies": [13.618055, 35.12112, 54.93554, 77.4135, 113.899, 138.1189, 739.32683, 871.409883], "Electron affinity": 1.4611053}, "Os": {"Atomic mass": 190.23, "Atomic no": 76, "Atomic orbitals": {"1s": -2475.238617, "2p": -393.15408, "2s": -409.522396, "3d": -72.497183, "3p": -86.837047, "3s": -94.501324, "4d": -10.176082, "4f": -2.321175, "4p": -16.119671, "4s": -19.362527, "5d": -0.296791, "5p": -1.757404, "5s": -2.738293, "6s": -0.191489}, "Atomic radius": 1.3, "Atomic radius calculated": 1.85, "Boiling point": "5285 K", "Brinell hardness": "3920 MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "5.1 x10-6K-1", "Common oxidation states": [4], "Critical temperature": "no data K", "Density of solid": "22610 kg m-3", "Electrical resistivity": "8.1 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d6.6s2", "Ionic radii": {"4": 0.77, "5": 0.715, "6": 0.685, "7": 0.665, "8": 0.53}, "Liquid range": "1979 K", "Melting point": "3306 K", "Mendeleev no": 63, "Mineral hardness": "7.0", "Molar volume": "8.42 cm3", "Name": "Osmium", "Oxidation states": [-2, -1, 1, 2, 3, 4, 5, 6, 7, 8], "Poissons ratio": "0.25", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "222 GPa", "Shannon radii": {"4": {"VI": {"": {"crystal_radius": 0.77, "ionic_radius": 0.63}}}, "5": {"VI": {"": {"crystal_radius": 0.715, "ionic_radius": 0.575}}}, "6": {"V": {"": {"crystal_radius": 0.63, "ionic_radius": 0.49}}, "VI": {"": {"crystal_radius": 0.685, "ionic_radius": 0.545}}}, "7": {"VI": {"": {"crystal_radius": 0.665, "ionic_radius": 0.525}}}, "8": {"IV": {"": {"crystal_radius": 0.53, "ionic_radius": 0.39}}}}, "Superconduction temperature": "0.66 K", "Thermal conductivity": "88 W m-1 K-1", "Van der waals radius": 2.16, "Velocity of sound": "4940 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.2, "Youngs modulus": "no data GPa", "Metallic radius": 1.352, "iupac_ordering": 62, "IUPAC ordering": 62, "Ground level": "5D4", "Ionization energies": [8.43823, 17.0, 25.0, 41.0, 55.0, 70.1, 85.1, 102.02, 168.7, 190.0, 213.0, 235.0, 269.0, 298.0, 322.0, 367.0, 410.0, 436.0, 470.0, 520.0, 570.0, 620.0, 670.0, 720.0, 770.0, 820.0, 870.0, 920.0, 970.0, 1015.0, 1262.0, 1311.0, 1364.0, 1420.0, 1474.0, 1528.0, 1606.0, 1660.0, 1720.0, 1776.0, 1996.0, 2052.0, 2112.0, 2168.0, 2336.0, 2400.0, 2552.0, 2615.5, 4374.0, 4501.0, 4635.0, 4779.0, 4917.0, 5052.0, 5280.0, 5421.0, 5575.0, 5717.0, 6115.0, 6240.0, 6376.0, 6503.0, 7039.0, 7185.0, 7468.0, 7610.0, 16560.0, 16900.0, 17270.0, 17620.0, 19600.0, 20030.0, 20570.0, 20920.6, 83976.21, 85614.4], "Electron affinity": 1.0778013}, "P": {"Atomic mass": 30.973762, "Atomic no": 15, "Atomic orbitals": {"1s": -76.061897, "2p": -4.576617, "2s": -6.329346, "3p": -0.20608, "3s": -0.512364}, "Atomic radius": 1.0, "Atomic radius calculated": 0.98, "Boiling point": "550 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "11 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-3, 3, 5], "Critical temperature": "994 K", "Density of solid": "1823 kg m-3", "Electrical resistivity": "about 10 10-8 Ω m", "Electronic structure": "[Ne].3s2.3p3", "ICSD oxidation states": [3, 4, 5, -2, -3, -1], "Ionic radii": {"3": 0.58, "5": 0.52}, "Liquid range": "232.7 K", "Melting point": "(white P) 317.3 K", "Mendeleev no": 90, "Mineral hardness": "no data", "Molar volume": "17.02 cm3", "Name": "Phosphorus", "Oxidation states": [-3, -2, -1, 1, 2, 3, 4, 5], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.001212", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 0.58, "ionic_radius": 0.44}}}, "5": {"IV": {"": {"crystal_radius": 0.31, "ionic_radius": 0.17}}, "V": {"": {"crystal_radius": 0.43, "ionic_radius": 0.29}}, "VI": {"": {"crystal_radius": 0.52, "ionic_radius": 0.38}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.236 W m-1 K-1", "Van der waals radius": 1.8, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 2.19, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 90, "IUPAC ordering": 90, "Ground level": "4S\u00b03/2", "Ionization energies": [10.486686, 19.76949, 30.20264, 51.44387, 65.02511, 220.43, 263.57, 309.6, 372.31, 424.4, 479.44, 560.62, 611.741, 2816.90879, 3069.8416], "Electron affinity": 0.7466071}, "Pa": {"Atomic mass": 231.03588, "Atomic no": 91, "Atomic orbitals": {"1s": -3606.333629, "2p": -603.470278, "2s": -623.870431, "3d": -127.781168, "3p": -146.485678, "3s": -156.466742, "4d": -25.933121, "4f": -14.105747, "4p": -34.48293, "4s": -39.064507, "5d": -3.659928, "5f": -0.316813, "5p": -6.709821, "5s": -8.463463, "6d": -0.142481, "6p": -0.799756, "6s": -1.287232, "7s": -0.129653}, "Atomic radius": 1.8, "Atomic radius calculated": "no data", "Boiling point": "no data K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [5], "Critical temperature": "no data K", "Density of solid": "15370 kg m-3", "Electrical resistivity": "18 10-8 Ω m", "Electronic structure": "[Rn].5f2.6d1.7s2", "Ionic radii": {"3": 1.16, "4": 1.04, "5": 0.92}, "Liquid range": "no data K", "Melting point": "1841 K", "Mendeleev no": 46, "Mineral hardness": "no data", "Molar volume": "15.18 cm3", "Name": "Protactinium", "Oxidation states": [3, 4, 5], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.18, "ionic_radius": 1.04}}}, "4": {"VI": {"": {"crystal_radius": 1.04, "ionic_radius": 0.9}}, "VIII": {"": {"crystal_radius": 1.15, "ionic_radius": 1.01}}}, "5": {"VI": {"": {"crystal_radius": 0.92, "ionic_radius": 0.78}}, "VIII": {"": {"crystal_radius": 1.05, "ionic_radius": 0.91}}, "IX": {"": {"crystal_radius": 1.09, "ionic_radius": 0.95}}}}, "Superconduction temperature": "1.4 K", "Thermal conductivity": "47 W m-1 K-1", "Van der waals radius": 2.1, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.5, "Youngs modulus": "no data GPa", "Metallic radius": 1.642, "iupac_ordering": 30, "IUPAC ordering": 30, "Ground level": "4K11/2", "Ionization energies": [5.89, 11.9, 18.6, 30.9, 44.3, 72.0, 85.1, 98.9, 111.0, 137.0, 153.0, 187.0, 203.0, 292.0, 316.0, 342.0, 369.0, 395.0, 423.0, 460.0, 488.0, 518.0, 546.0, 690.0, 720.0, 760.0, 790.0, 880.0, 920.0, 1020.0, 1060.0, 1150.0, 1220.0, 1300.0, 1370.0, 1450.0, 1520.0, 1600.0, 1670.0, 1760.0, 1830.0, 1910.0, 1980.0, 2060.0, 2130.0, 2483.0, 2550.0, 2620.0, 2696.0, 2766.0, 2837.0, 2968.0, 3040.0, 3119.0, 3193.0, 3488.0, 3558.0, 3637.0, 3709.0, 4077.0, 4161.0, 4370.0, 4454.0, 7181.0, 7341.0, 7510.0, 7690.0, 7870.0, 8040.0, 8410.0, 8590.0, 8780.0, 8960.0, 9460.0, 9620.0, 9790.0, 9950.0, 11100.0, 11290.0, 11660.0, 11840.0, 24660.0, 25080.0, 25540.0, 25970.0, 30230.0, 30800.0, 31520.0, 31971.6, 126296.6, 128507.1], "Electron affinity": 0.55}, "Pb": {"Atomic mass": 207.2, "Atomic no": 82, "Atomic orbitals": {"1s": -2901.078061, "2p": -470.877785, "2s": -488.843335, "3d": -91.889924, "3p": -107.950391, "3s": -116.526852, "4d": -15.030026, "4f": -5.592532, "4p": -21.990564, "4s": -25.75333, "5d": -0.902393, "5p": -2.941657, "5s": -4.206797, "6p": -0.141831, "6s": -0.357187}, "Atomic radius": 1.8, "Atomic radius calculated": 1.54, "Boiling point": "2022 K", "Brinell hardness": "38.3 MN m-2", "Bulk modulus": "46 GPa", "Coefficient of linear thermal expansion": "28.9 x10-6K-1", "Common oxidation states": [2, 4], "Critical temperature": "no data K", "Density of solid": "11340 kg m-3", "Electrical resistivity": "21 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d10.6s2.6p2", "ICSD oxidation states": [2, 4], "Ionic radii": {"2": 1.33, "4": 0.915}, "Liquid range": "1421.39 K", "Melting point": "600.61 K", "Mendeleev no": 82, "Mineral hardness": "1.5", "Molar volume": "18.26 cm3", "Name": "Lead", "Oxidation states": [-4, 2, 4], "Poissons ratio": "0.44", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "5.6 GPa", "Shannon radii": {"2": {"IVPY": {"": {"crystal_radius": 1.12, "ionic_radius": 0.98}}, "VI": {"": {"crystal_radius": 1.33, "ionic_radius": 1.19}}, "VII": {"": {"crystal_radius": 1.37, "ionic_radius": 1.23}}, "VIII": {"": {"crystal_radius": 1.43, "ionic_radius": 1.29}}, "IX": {"": {"crystal_radius": 1.49, "ionic_radius": 1.35}}, "X": {"": {"crystal_radius": 1.54, "ionic_radius": 1.4}}, "XI": {"": {"crystal_radius": 1.59, "ionic_radius": 1.45}}, "XII": {"": {"crystal_radius": 1.63, "ionic_radius": 1.49}}}, "4": {"IV": {"": {"crystal_radius": 0.79, "ionic_radius": 0.65}}, "V": {"": {"crystal_radius": 0.87, "ionic_radius": 0.73}}, "VI": {"": {"crystal_radius": 0.915, "ionic_radius": 0.775}}, "VIII": {"": {"crystal_radius": 1.08, "ionic_radius": 0.94}}}}, "Superconduction temperature": "7.2 K", "Thermal conductivity": "35 W m-1 K-1", "Van der waals radius": 2.02, "Velocity of sound": "1260 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.33, "Youngs modulus": "16 GPa", "Metallic radius": 1.75, "iupac_ordering": 82, "IUPAC ordering": 82, "Ground level": "1/2,1/2)0", "Ionization energies": [7.4166799, 15.032499, 31.9373, 42.33256, 68.8, 82.9, 100.1, 120.0, 138.0, 158.0, 182.0, 203.0, 224.0, 245.1, 338.1, 374.0, 401.0, 427.0, 478.0, 507.0, 570.0, 610.0, 650.0, 690.0, 750.0, 810.0, 870.0, 930.0, 990.0, 1050.0, 1120.0, 1180.0, 1240.0, 1300.0, 1360.0, 1430.0, 1704.0, 1760.0, 1819.0, 1884.0, 1945.0, 2004.0, 2101.0, 2163.0, 2230.0, 2292.0, 2543.0, 2605.0, 2671.0, 2735.0, 2965.0, 3036.0, 3211.0, 3282.1, 5414.0, 5555.0, 5703.0, 5862.0, 6015.0, 6162.0, 6442.0, 6597.0, 6767.0, 6924.0, 7362.0, 7500.0, 7650.0, 7790.0, 8520.0, 8680.0, 9000.0, 9150.0, 19590.0, 19970.0, 20380.0, 20750.0, 23460.0, 23940.0, 24550.0, 24938.2, 99491.85, 101336.4], "Electron affinity": 0.3567212}, "Pd": {"Atomic mass": 106.42, "Atomic no": 46, "Atomic orbitals": {"1s": -860.134909, "2p": -114.408286, "2s": -123.105078, "3d": -12.132197, "3p": -18.580798, "3s": -22.060898, "4d": -0.160771, "4p": -1.815215, "4s": -2.889173}, "Atomic radius": 1.4, "Atomic radius calculated": 1.69, "Boiling point": "3236 K", "Brinell hardness": "37.3 MN m-2", "Bulk modulus": "180 GPa", "Coefficient of linear thermal expansion": "11.8 x10-6K-1", "Common oxidation states": [2, 4], "Critical temperature": "no data K", "Density of solid": "12023 kg m-3", "Electrical resistivity": "10.8 10-8 Ω m", "Electronic structure": "[Kr].4d10", "ICSD oxidation states": [2, 4], "Ionic radii": {"1": 0.73, "2": 1.0, "3": 0.9, "4": 0.755}, "Liquid range": "1407.95 K", "Melting point": "1828.05 K", "Mendeleev no": 69, "Mineral hardness": "4.75", "Molar volume": "8.56 cm3", "Name": "Palladium", "Oxidation states": [2, 4], "Poissons ratio": "0.39", "Reflectivity": "72 %", "Refractive index": "no data", "Rigidity modulus": "44 GPa", "Shannon radii": {"1": {"II": {"": {"crystal_radius": 0.73, "ionic_radius": 0.59}}}, "2": {"IVSQ": {"": {"crystal_radius": 0.78, "ionic_radius": 0.64}}, "VI": {"": {"crystal_radius": 1.0, "ionic_radius": 0.86}}}, "3": {"VI": {"": {"crystal_radius": 0.9, "ionic_radius": 0.76}}}, "4": {"VI": {"": {"crystal_radius": 0.755, "ionic_radius": 0.615}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "72 W m-1 K-1", "Van der waals radius": 2.1, "Velocity of sound": "3070 m s-1", "Vickers hardness": "461 MN m-2", "X": 2.2, "Youngs modulus": "121 GPa", "Metallic radius": 1.376, "iupac_ordering": 69, "IUPAC ordering": 69, "Ground level": "1S0", "Ionization energies": [8.336839, 19.43, 32.93, 46.0, 61.0, 84.1, 101.0, 120.0, 141.0, 159.9, 238.57, 260.0, 286.0, 311.0, 342.0, 369.1, 427.0, 457.5, 810.0, 869.0, 933.0, 1000.0, 1065.0, 1145.0, 1218.0, 1290.0, 1366.0, 1438.0, 1644.0, 1706.2, 1781.3, 1869.0, 1962.0, 2016.0, 2181.0, 2248.87, 5284.0, 5475.0, 5683.0, 5880.0, 6242.0, 6469.0, 6759.0, 6943.097, 28776.034, 29622.6], "Electron affinity": 0.5621412}, "Pm": {"Atomic mass": 145.0, "Atomic no": 61, "Atomic orbitals": {"1s": -1562.980284, "2p": -233.455114, "2s": -245.970548, "3d": -37.625433, "3p": -47.921132, "3s": -53.429311, "4d": -4.596822, "4f": -0.200159, "4p": -8.320495, "4s": -10.422756, "5p": -0.817702, "5s": -1.372265, "6s": -0.127053}, "Atomic radius": 1.85, "Atomic radius calculated": 2.05, "Boiling point": "3273 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "33 GPa", "Coefficient of linear thermal expansion": "11 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "7264 kg m-3", "Electrical resistivity": "about 75 10-8 Ω m", "Electronic structure": "[Xe].4f5.6s2", "Ionic radii": {"3": 1.11}, "Liquid range": "1900 K", "Melting point": "1373 K", "Mendeleev no": 29, "Mineral hardness": "no data", "Molar volume": "20.23 cm3", "Name": "Promethium", "Oxidation states": [3], "Poissons ratio": "0.28", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "18 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.11, "ionic_radius": 0.97}}, "VIII": {"": {"crystal_radius": 1.233, "ionic_radius": 1.093}}, "IX": {"": {"crystal_radius": 1.284, "ionic_radius": 1.144}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "15 W m-1 K-1", "Van der waals radius": 2.38, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.13, "Youngs modulus": "46 GPa", "Metallic radius": 1.811, "iupac_ordering": 43, "IUPAC ordering": 43, "Ground level": "6H\u00b05/2", "Ionization energies": [5.58187, 10.938, 22.44, 41.17, 61.7, 85.0, 101.0, 116.0, 138.0, 155.0, 174.0, 202.0, 229.0, 248.0, 269.0, 430.0, 462.0, 497.0, 534.0, 569.0, 609.0, 651.0, 689.0, 730.0, 767.0, 916.0, 956.0, 998.0, 1040.0, 1113.0, 1158.0, 1261.0, 1308.7, 2251.0, 2344.0, 2443.0, 2549.0, 2652.0, 2755.0, 2892.0, 2997.0, 3112.0, 3219.0, 3519.0, 3613.0, 3718.0, 3816.0, 4056.0, 4166.0, 4371.0, 4476.0, 10115.0, 10378.0, 10671.0, 10942.0, 11819.0, 12136.0, 12532.0, 12797.26, 52144.29, 53346.1], "Electron affinity": 0.129}, "Po": {"Atomic mass": 210.0, "Atomic no": 84, "Atomic orbitals": {"1s": -3050.988417, "2p": -498.77192, "2s": -517.275843, "3d": -99.256068, "3p": -115.898384, "3s": -124.783683, "4d": -17.173307, "4f": -7.206499, "4p": -24.481337, "4s": -28.42254, "5d": -1.386458, "5p": -3.655382, "5s": -5.027447, "6p": -0.217889, "6s": -0.493528}, "Atomic radius": 1.9, "Atomic radius calculated": 1.35, "Boiling point": "1235 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-2, 2, 4], "Critical temperature": "no data K", "Density of solid": "9196 kg m-3", "Electrical resistivity": "40 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d10.6s2.6p4", "Ionic radii": {"4": 1.08, "6": 0.81}, "Liquid range": "708 K", "Melting point": "527 K", "Mendeleev no": 91, "Mineral hardness": "no data", "Molar volume": "22.97 cm3", "Name": "Polonium", "Oxidation states": [-2, 2, 4, 6], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"4": {"VI": {"": {"crystal_radius": 1.08, "ionic_radius": 0.94}}, "VIII": {"": {"crystal_radius": 1.22, "ionic_radius": 1.08}}}, "6": {"VI": {"": {"crystal_radius": 0.81, "ionic_radius": 0.67}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "20 W m-1 K-1", "Van der waals radius": 1.97, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 2.0, "Youngs modulus": "no data GPa", "Metallic radius": 1.53, "iupac_ordering": 93, "IUPAC ordering": 93, "Ground level": "3P2", "Ionization energies": [8.41807, 19.3, 27.3, 36.0, 57.0, 69.1, 108.0, 125.0, 146.1, 166.0, 186.0, 209.0, 235.0, 257.0, 281.0, 304.0, 416.0, 444.0, 473.0, 502.0, 560.0, 590.0, 670.0, 700.0, 740.0, 800.0, 870.0, 930.0, 990.0, 1060.0, 1120.0, 1180.0, 1250.0, 1320.0, 1380.0, 1440.0, 1510.0, 1570.0, 1865.0, 1923.0, 1986.0, 2052.0, 2115.0, 2177.0, 2281.0, 2345.0, 2414.0, 2480.0, 2740.0, 2803.0, 2873.0, 2938.0, 3194.0, 3268.0, 3450.0, 3524.2, 5785.0, 5930.0, 6084.0, 6248.0, 6405.0, 6557.0, 6856.0, 7015.0, 7191.0, 7350.0, 7810.0, 7950.0, 8100.0, 8240.0, 9050.0, 9220.0, 9550.0, 9710.0, 20670.0, 21050.0, 21470.0, 21860.0, 24860.0, 25360.0, 25990.0, 26390.4, 105064.3, 106982.7], "Electron affinity": 1.407}, "Pr": {"Atomic mass": 140.90765, "Atomic no": 59, "Atomic orbitals": {"1s": -1457.338067, "2p": -215.418313, "2s": -227.426363, "3d": -33.913996, "3p": -43.692548, "3s": -48.924994, "4d": -4.154228, "4f": -0.155138, "4p": -7.613108, "4s": -9.577447, "5p": -0.778046, "5s": -1.296106, "6s": -0.124465}, "Atomic radius": 1.85, "Atomic radius calculated": 2.47, "Boiling point": "3563 K", "Brinell hardness": "481 MN m-2", "Bulk modulus": "29 GPa", "Coefficient of linear thermal expansion": "6.7 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "6640 kg m-3", "Electrical resistivity": "70 10-8 Ω m", "Electronic structure": "[Xe].4f3.6s2", "ICSD oxidation states": [3, 4], "Ionic radii": {"3": 1.13, "4": 0.99}, "Liquid range": "2355 K", "Melting point": "1208 K", "Mendeleev no": 31, "Mineral hardness": "no data", "Molar volume": "20.80 cm3", "Name": "Praseodymium", "Oxidation states": [2, 3, 4], "Poissons ratio": "0.28", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "15 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.13, "ionic_radius": 0.99}}, "VIII": {"": {"crystal_radius": 1.266, "ionic_radius": 1.126}}, "IX": {"": {"crystal_radius": 1.319, "ionic_radius": 1.179}}}, "4": {"VI": {"": {"crystal_radius": 0.99, "ionic_radius": 0.85}}, "VIII": {"": {"crystal_radius": 1.1, "ionic_radius": 0.96}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "13 W m-1 K-1", "Van der waals radius": 2.4, "Velocity of sound": "2280 m s-1", "Vickers hardness": "400 MN m-2", "X": 1.13, "Youngs modulus": "37 GPa", "Metallic radius": 1.828, "iupac_ordering": 45, "IUPAC ordering": 45, "Ground level": "4I\u00b09/2", "Ionization energies": [5.4702, 10.631, 21.6237, 38.981, 57.53, 82.0, 97.0, 112.0, 131.0, 148.0, 162.0, 196.0, 217.02, 350.0, 378.0, 412.0, 445.0, 478.0, 516.0, 554.0, 590.0, 627.0, 663.0, 803.0, 840.0, 880.0, 920.0, 985.0, 1028.0, 1124.0, 1169.9, 2019.0, 2108.0, 2202.0, 2304.0, 2400.0, 2501.0, 2628.0, 2729.0, 2838.0, 2941.0, 3227.0, 3319.0, 3419.0, 3512.0, 3729.0, 3832.0, 4030.0, 4130.0, 9378.0, 9632.0, 9913.0, 10175.0, 10959.0, 11262.0, 11641.0, 11895.89, 48571.71, 49722.25], "Electron affinity": 0.1092346}, "Pt": {"Atomic mass": 195.084, "Atomic no": 78, "Atomic orbitals": {"1s": -2613.096532, "2p": -417.96053, "2s": -434.858003, "3d": -78.400271, "3p": -93.309108, "3s": -101.274869, "4d": -11.419476, "4f": -3.038049, "4p": -17.697297, "4s": -21.110651, "5d": -0.273634, "5p": -1.884256, "5s": -2.950526, "6s": -0.161308}, "Atomic radius": 1.35, "Atomic radius calculated": 1.77, "Boiling point": "4098 K", "Brinell hardness": "392 MN m-2", "Bulk modulus": "230 GPa", "Coefficient of linear thermal expansion": "8.8 x10-6K-1", "Common oxidation states": [2, 4], "Critical temperature": "no data K", "Density of solid": "21090 kg m-3", "Electrical resistivity": "10.6 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d9.6s1", "Ionic radii": {"2": 0.94, "4": 0.765, "5": 0.71}, "Liquid range": "2056.6 K", "Melting point": "2041.4 K", "Mendeleev no": 68, "Mineral hardness": "3.5", "Molar volume": "9.09 cm3", "Name": "Platinum", "Oxidation states": [-2, 2, 4, 5, 6], "Poissons ratio": "0.38", "Reflectivity": "73 %", "Refractive index": "no data", "Rigidity modulus": "61 GPa", "Shannon radii": {"2": {"IVSQ": {"": {"crystal_radius": 0.74, "ionic_radius": 0.6}}, "VI": {"": {"crystal_radius": 0.94, "ionic_radius": 0.8}}}, "4": {"VI": {"": {"crystal_radius": 0.765, "ionic_radius": 0.625}}}, "5": {"VI": {"": {"crystal_radius": 0.71, "ionic_radius": 0.57}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "72 W m-1 K-1", "Van der waals radius": 2.13, "Velocity of sound": "2680 m s-1", "Vickers hardness": "549 MN m-2", "X": 2.28, "Youngs modulus": "168 GPa", "Metallic radius": 1.387, "iupac_ordering": 68, "IUPAC ordering": 68, "Ground level": "3D3", "Ionization energies": [8.95883, 18.56, 29.0, 43.0, 56.0, 75.0, 91.0, 109.0, 126.0, 144.9, 220.4, 245.0, 269.0, 293.0, 332.0, 358.0, 392.0, 445.0, 479.0, 507.0, 550.0, 610.0, 660.0, 710.0, 760.0, 820.0, 870.0, 930.0, 980.0, 1040.0, 1090.0, 1140.0, 1402.0, 1454.0, 1509.0, 1567.0, 1624.0, 1680.0, 1763.0, 1821.0, 1883.0, 1941.0, 2171.0, 2228.0, 2291.0, 2350.0, 2536.0, 2603.0, 2762.0, 2827.8, 4715.0, 4839.0, 4980.0, 5128.0, 5270.0, 5410.0, 5654.0, 5800.0, 5959.0, 6106.0, 6517.0, 6646.0, 6787.0, 6918.0, 7512.0, 7660.0, 7960.0, 8100.0, 17540.0, 17890.0, 18280.0, 18630.0, 20840.0, 21280.0, 21840.0, 22205.7, 88955.18, 90659.7], "Electron affinity": 2.125105}, "Pu": {"Atomic mass": 244.0, "Atomic no": 94, "Atomic orbitals": "no data", "Atomic radius": 1.75, "Atomic radius calculated": "no data", "Boiling point": "3503 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [4], "Critical temperature": "no data K", "Density of solid": "19816 kg m-3", "Electrical resistivity": "150 10-8 Ω m", "Electronic structure": "[Rn].5f6.7s2", "Ionic radii": {"3": 1.14, "4": 1.0, "5": 0.88, "6": 0.85}, "Liquid range": "2590.5 K", "Melting point": "912.5 K", "Mendeleev no": 43, "Mineral hardness": "no data", "Molar volume": "12.29 cm3", "Name": "Plutonium", "Oxidation states": [3, 4, 5, 6, 7], "Poissons ratio": "0.21", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "43 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.14, "ionic_radius": 1.0}}}, "4": {"VI": {"": {"crystal_radius": 1.0, "ionic_radius": 0.86}}, "VIII": {"": {"crystal_radius": 1.1, "ionic_radius": 0.96}}}, "5": {"VI": {"": {"crystal_radius": 0.88, "ionic_radius": 0.74}}}, "6": {"VI": {"": {"crystal_radius": 0.85, "ionic_radius": 0.71}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "6 W m-1 K-1", "Van der waals radius": 2.43, "Velocity of sound": "2260 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.28, "Youngs modulus": "96 GPa", "Metallic radius": 1.523, "iupac_ordering": 27, "IUPAC ordering": 27, "Ground level": "7F0", "Ionization energies": [6.02576, 11.5, 21.1, 35.0, 49.0, 80.0, 95.0, 109.0, 124.0, 139.0, 159.0, 179.0, 200.0, 219.0, 258.0, 278.0, 389.0, 416.0, 444.0, 474.0, 503.0, 532.0, 575.0, 605.0, 637.0, 668.0, 820.0, 850.0, 890.0, 930.0, 1030.0, 1070.0, 1180.0, 1220.0, 1340.0, 1420.0, 1500.0, 1580.0, 1660.0, 1740.0, 1820.0, 1890.0, 1990.0, 2070.0, 2150.0, 2230.0, 2310.0, 2390.0, 2774.0, 2844.0, 2918.0, 2997.0, 3072.0, 3146.0, 3290.0, 3366.0, 3449.0, 3527.0, 3836.0, 3911.0, 3993.0, 4068.0, 4496.0, 4585.0, 4807.0, 4890.0, 7830.0, 7990.0, 8170.0, 8360.0, 8540.0, 8710.0, 9130.0, 9310.0, 9520.0, 9700.0, 10230.0, 10390.0, 10570.0, 10730.0, 12060.0, 12260.0, 12660.0, 12840.0, 26480.0, 26920.0, 27400.0, 27840.0, 32800.0, 33400.0, 34100.0, 34625.8, 136299.2, 138646.0], "Electron affinity": -0.5}, "Ra": {"Atomic mass": 226.0, "Atomic no": 88, "Atomic orbitals": {"1s": -3362.736563, "2p": -557.513214, "2s": -577.101208, "3d": -115.306476, "3p": -133.12325, "3s": -142.632426, "4d": -22.208125, "4f": -11.181066, "4p": -30.221208, "4s": -34.525628, "5d": -2.819853, "5p": -5.547203, "5s": -7.139137, "6p": -0.634674, "6s": -1.05135, "7s": -0.113732}, "Atomic radius": 2.15, "Atomic radius calculated": "no data", "Boiling point": "2010 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "5000 kg m-3", "Electrical resistivity": "100 10-8 Ω m", "Electronic structure": "[Rn].7s2", "Ionic radii": {"2": 1.62}, "Liquid range": "1037 K", "Melting point": "973 K", "Mendeleev no": 13, "Mineral hardness": "no data", "Molar volume": "41.09 cm3", "Name": "Radium", "Oxidation states": [2], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"2": {"VIII": {"": {"crystal_radius": 1.62, "ionic_radius": 1.48}}, "XII": {"": {"crystal_radius": 1.84, "ionic_radius": 1.7}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "19 W m-1 K-1", "Van der waals radius": 2.83, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 0.9, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"Ra-223": 1210.3}, "Metallic radius": 2.293, "iupac_ordering": 12, "IUPAC ordering": 12, "Ground level": "1S0", "Ionization energies": [5.2784239, 10.14718, 31.0, 41.0, 52.9, 64.0, 82.0, 97.0, 124.0, 140.0, 204.9, 227.0, 250.0, 274.0, 299.0, 324.0, 356.0, 382.0, 409.0, 435.0, 570.0, 600.0, 630.0, 660.0, 740.0, 770.0, 860.0, 900.0, 970.0, 1040.0, 1110.0, 1180.0, 1250.0, 1320.0, 1390.0, 1460.0, 1530.0, 1610.0, 1680.0, 1750.0, 1820.0, 1880.0, 2208.0, 2271.0, 2338.0, 2409.0, 2477.0, 2544.0, 2662.0, 2731.0, 2806.0, 2876.0, 3155.0, 3224.0, 3298.0, 3368.0, 3682.0, 3762.0, 3959.0, 4040.0, 6565.0, 6718.0, 6881.0, 7056.0, 7222.0, 7380.0, 7720.0, 7890.0, 8080.0, 8250.0, 8730.0, 8880.0, 9040.0, 9200.0, 10190.0, 10360.0, 10720.0, 10890.0, 22900.0, 23300.0, 23750.0, 24160.0, 27830.0, 28370.0, 29050.0, 29479.8, 116848.7, 118931.3], "Electron affinity": 0.1}, "Rb": {"Atomic mass": 85.4678, "Atomic no": 37, "Atomic orbitals": {"1s": -540.957115, "2p": -64.784678, "2s": -71.291202, "3d": -3.915508, "3p": -8.165416, "3s": -10.513861, "4p": -0.59217, "4s": -1.135051, "5s": -0.085375}, "Atomic radius": 2.35, "Atomic radius calculated": 2.65, "Boiling point": "961 K", "Brinell hardness": "0.216 MN m-2", "Bulk modulus": "2.5 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [1], "Critical temperature": "2093 K", "Density of solid": "1532 kg m-3", "Electrical resistivity": "13.3 10-8 Ω m", "Electronic structure": "[Kr].5s1", "ICSD oxidation states": [1], "Ionic radii": {"1": 1.66}, "Liquid range": "648.54 K", "Melting point": "312.46 K", "Mendeleev no": 9, "Mineral hardness": "0.3", "Molar volume": "55.76 cm3", "Name": "Rubidium", "Oxidation states": [1], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"1": {"VI": {"": {"crystal_radius": 1.66, "ionic_radius": 1.52}}, "VII": {"": {"crystal_radius": 1.7, "ionic_radius": 1.56}}, "VIII": {"": {"crystal_radius": 1.75, "ionic_radius": 1.61}}, "IX": {"": {"crystal_radius": 1.77, "ionic_radius": 1.63}}, "X": {"": {"crystal_radius": 1.8, "ionic_radius": 1.66}}, "XI": {"": {"crystal_radius": 1.83, "ionic_radius": 1.69}}, "XII": {"": {"crystal_radius": 1.86, "ionic_radius": 1.72}}, "XIV": {"": {"crystal_radius": 1.97, "ionic_radius": 1.83}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "58 W m-1 K-1", "Van der waals radius": 3.03, "Velocity of sound": "1300 m s-1", "Vickers hardness": "no data MN m-2", "X": 0.82, "Youngs modulus": "2.4 GPa", "Metallic radius": 2.537, "iupac_ordering": 8, "IUPAC ordering": 8, "Ground level": "2S1/2", "Ionization energies": [4.1771281, 27.28954, 39.247, 52.2, 68.44, 82.9, 98.67, 132.79, 150.628, 277.12, 313.1, 356.0, 400.0, 443.0, 502.0, 550.0, 601.0, 654.0, 706.0, 857.0, 905.3, 958.9, 1024.0, 1080.0, 1125.0, 1242.5, 1294.57, 3133.3, 3281.0, 3443.0, 3600.0, 3815.0, 3988.0, 4214.0, 4356.865, 18305.884, 18965.516], "Electron affinity": 0.48591621}, "Re": {"Atomic mass": 186.207, "Atomic no": 75, "Atomic orbitals": {"1s": -2407.665572, "2p": -380.982869, "2s": -397.087707, "3d": -69.57676, "3p": -83.634578, "3s": -91.149193, "4d": -9.516816, "4f": -1.92508, "4p": -15.295495, "4s": -18.454325, "5d": -0.258639, "5p": -1.631227, "5s": -2.567348, "6s": -0.186859}, "Atomic radius": 1.35, "Atomic radius calculated": 1.88, "Boiling point": "5869 K", "Brinell hardness": "1320 MN m-2", "Bulk modulus": "370 GPa", "Coefficient of linear thermal expansion": "6.2 x10-6K-1", "Common oxidation states": [4], "Critical temperature": "no data K", "Density of solid": "21020 kg m-3", "Electrical resistivity": "18 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d5.6s2", "ICSD oxidation states": [3, 4, 5, 6, 7], "Ionic radii": {"4": 0.77, "5": 0.72, "6": 0.69, "7": 0.67}, "Liquid range": "2410 K", "Melting point": "3459 K", "Mendeleev no": 58, "Mineral hardness": "7.0", "Molar volume": "8.86 cm3", "Name": "Rhenium", "Oxidation states": [-3, -1, 1, 2, 3, 4, 5, 6, 7], "Poissons ratio": "0.30", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "178 GPa", "Shannon radii": {"4": {"VI": {"": {"crystal_radius": 0.77, "ionic_radius": 0.63}}}, "5": {"VI": {"": {"crystal_radius": 0.72, "ionic_radius": 0.58}}}, "6": {"VI": {"": {"crystal_radius": 0.69, "ionic_radius": 0.55}}}, "7": {"IV": {"": {"crystal_radius": 0.52, "ionic_radius": 0.38}}, "VI": {"": {"crystal_radius": 0.67, "ionic_radius": 0.53}}}}, "Superconduction temperature": "1.70 K", "Thermal conductivity": "48 W m-1 K-1", "Van der waals radius": 2.16, "Velocity of sound": "4700 m s-1", "Vickers hardness": "2450 MN m-2", "X": 1.9, "Youngs modulus": "463 GPa", "Metallic radius": 1.375, "iupac_ordering": 59, "IUPAC ordering": 59, "Ground level": "6S5/2", "Ionization energies": [7.83352, 16.6, 27.0, 39.1, 51.9, 67.0, 82.71, 144.4, 165.0, 187.0, 208.0, 236.0, 268.0, 291.0, 330.0, 377.0, 403.0, 429.0, 476.0, 520.0, 570.0, 620.0, 670.0, 720.0, 760.0, 810.0, 860.0, 910.0, 953.0, 1194.0, 1242.0, 1294.0, 1349.0, 1402.0, 1454.0, 1530.0, 1583.0, 1641.0, 1696.0, 1912.0, 1966.0, 2025.0, 2080.0, 2240.0, 2302.0, 2450.0, 2514.5, 4214.0, 4335.0, 4468.0, 4609.0, 4745.0, 4877.0, 5099.0, 5236.0, 5388.0, 5528.0, 5919.0, 6042.0, 6176.0, 6300.0, 6810.0, 6952.0, 7230.0, 7366.0, 16080.0, 16410.0, 16780.0, 17120.0, 19000.0, 19420.0, 19950.0, 20297.4, 81556.9, 83162.3], "Electron affinity": 0.06039663}, "Rh": {"Atomic mass": 102.9055, "Atomic no": 45, "Atomic orbitals": {"1s": -821.136773, "2p": -108.357665, "2s": -116.80695, "3d": -11.21725, "3p": -17.415299, "3s": -20.765603, "4d": -0.239422, "4p": -1.806456, "4s": -2.825505, "5s": -0.154624}, "Atomic radius": 1.35, "Atomic radius calculated": 1.73, "Boiling point": "3968 K", "Brinell hardness": "1100 MN m-2", "Bulk modulus": "380 GPa", "Coefficient of linear thermal expansion": "8.2 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "12450 kg m-3", "Electrical resistivity": "4.3 10-8 Ω m", "Electronic structure": "[Kr].4d8.5s1", "ICSD oxidation states": [3, 4], "Ionic radii": {"3": 0.805, "4": 0.74, "5": 0.69}, "Liquid range": "1731 K", "Melting point": "2237 K", "Mendeleev no": 65, "Mineral hardness": "6.0", "Molar volume": "8.28 cm3", "Name": "Rhodium", "Oxidation states": [-1, 1, 2, 3, 4, 5, 6], "Poissons ratio": "0.26", "Reflectivity": "84 %", "Refractive index": "no data", "Rigidity modulus": "150 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 0.805, "ionic_radius": 0.665}}}, "4": {"VI": {"": {"crystal_radius": 0.74, "ionic_radius": 0.6}}}, "5": {"VI": {"": {"crystal_radius": 0.69, "ionic_radius": 0.55}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "150 W m-1 K-1", "Van der waals radius": 2.1, "Velocity of sound": "4700 m s-1", "Vickers hardness": "1246 MN m-2", "X": 2.28, "Youngs modulus": "275 GPa", "Metallic radius": 1.345, "iupac_ordering": 66, "IUPAC ordering": 66, "Ground level": "4F9/2", "Ionization energies": [7.4589, 18.08, 31.06, 42.0, 63.0, 80.0, 97.0, 115.1, 135.0, 207.51, 228.0, 252.1, 277.0, 306.0, 331.58, 389.3, 415.97, 739.0, 794.0, 857.0, 921.0, 984.0, 1061.0, 1131.0, 1202.0, 1274.0, 1344.0, 1544.0, 1604.9, 1677.6, 1763.0, 1851.0, 1903.0, 2063.0, 2129.22, 5018.0, 5203.0, 5406.0, 5600.0, 5940.0, 6161.0, 6444.0, 6623.262, 27486.983, 28311.965], "Electron affinity": 1.142892}, "Rn": {"Atomic mass": 220.0, "Atomic no": 86, "Atomic orbitals": {"1s": -3204.756288, "2p": -527.533025, "2s": -546.57796, "3d": -106.945006, "3p": -124.172862, "3s": -133.369144, "4d": -19.449994, "4f": -8.953318, "4p": -27.108985, "4s": -31.230804, "5d": -1.911329, "5p": -4.408702, "5s": -5.889683, "6p": -0.29318, "6s": -0.62657}, "Atomic radius": "no data", "Atomic radius calculated": 1.2, "Boiling point": "211.3 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Critical temperature": "377 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d10.6s2.6p6", "Liquid range": "9.3 K", "Max oxidation state": 0.0, "Melting point": "202 K", "Mendeleev no": 6, "Min oxidation state": 0.0, "Mineral hardness": "no data", "Molar volume": "50.50 cm3", "Name": "Radon", "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Superconduction temperature": "no data K", "Thermal conductivity": "0.00361 W m-1 K-1", "Van der waals radius": 2.2, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 2.2, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 0, "IUPAC ordering": 0, "Ground level": "1S0", "Ionization energies": [10.7485, 21.4, 29.4, 36.9, 52.9, 64.0, 88.0, 102.0, 154.0, 173.9, 195.0, 218.0, 240.0, 264.0, 293.0, 317.0, 342.0, 367.0, 488.0, 520.0, 550.0, 580.0, 640.0, 680.0, 760.0, 800.0, 850.0, 920.0, 980.0, 1050.0, 1110.0, 1180.0, 1250.0, 1310.0, 1390.0, 1460.0, 1520.0, 1590.0, 1660.0, 1720.0, 2033.0, 2094.0, 2158.0, 2227.0, 2293.0, 2357.0, 2467.0, 2535.0, 2606.0, 2674.0, 2944.0, 3010.0, 3082.0, 3149.0, 3433.0, 3510.0, 3699.0, 3777.0, 6169.0, 6318.0, 6476.0, 6646.0, 6807.0, 6964.0, 7283.0, 7450.0, 7630.0, 7800.0, 8260.0, 8410.0, 8570.0, 8710.0, 9610.0, 9780.0, 10120.0, 10290.0, 21770.0, 22160.0, 22600.0, 22990.0, 26310.0, 26830.0, 27490.0, 27903.1, 110842.0, 112843.7], "Electron affinity": -0.72}, "Ru": {"Atomic mass": 101.07, "Atomic no": 44, "Atomic orbitals": {"1s": -782.918621, "2p": -102.333649, "2s": -110.536054, "3d": -10.195668, "3p": -16.145217, "3s": -19.366692, "4d": -0.210375, "4p": -1.667549, "4s": -2.628363, "5s": -0.152834}, "Atomic radius": 1.3, "Atomic radius calculated": 1.78, "Boiling point": "4423 K", "Brinell hardness": "2160 MN m-2", "Bulk modulus": "220 GPa", "Coefficient of linear thermal expansion": "6.4 x10-6K-1", "Common oxidation states": [3, 4], "Critical temperature": "no data K", "Density of solid": "12370 kg m-3", "Electrical resistivity": "7.1 10-8 Ω m", "Electronic structure": "[Kr].4d7.5s1", "ICSD oxidation states": [2, 3, 4, 5, 6], "Ionic radii": {"3": 0.82, "4": 0.76, "5": 0.705, "7": 0.52, "8": 0.5}, "Liquid range": "1816 K", "Melting point": "2607 K", "Mendeleev no": 62, "Mineral hardness": "6.5", "Molar volume": "8.17 cm3", "Name": "Ruthenium", "Oxidation states": [-2, 1, 2, 3, 4, 5, 6, 7, 8], "Poissons ratio": "0.30", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "173 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 0.82, "ionic_radius": 0.68}}}, "4": {"VI": {"": {"crystal_radius": 0.76, "ionic_radius": 0.62}}}, "5": {"VI": {"": {"crystal_radius": 0.705, "ionic_radius": 0.565}}}, "7": {"IV": {"": {"crystal_radius": 0.52, "ionic_radius": 0.38}}}, "8": {"IV": {"": {"crystal_radius": 0.5, "ionic_radius": 0.36}}}}, "Superconduction temperature": "0.49 K", "Thermal conductivity": "120 W m-1 K-1", "Van der waals radius": 2.13, "Velocity of sound": "5970 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.2, "Youngs modulus": "447 GPa", "Metallic radius": 1.339, "iupac_ordering": 63, "IUPAC ordering": 63, "Ground level": "5F5", "Ionization energies": [7.3605, 16.76, 28.47, 45.0, 59.0, 76.0, 93.0, 110.0, 178.41, 198.0, 219.9, 245.0, 271.0, 295.9, 348.0, 376.25, 670.0, 723.0, 784.0, 845.0, 905.0, 981.0, 1048.0, 1115.0, 1187.0, 1253.0, 1447.0, 1506.7, 1577.0, 1659.0, 1743.0, 1794.0, 1949.0, 2013.04, 4758.0, 4939.0, 5136.0, 5330.0, 5647.0, 5861.0, 6137.0, 6311.721, 26229.895, 27033.502], "Electron affinity": 1.0463825}, "S": {"Atomic mass": 32.065, "Atomic no": 16, "Atomic orbitals": {"1s": -87.789937, "2p": -5.751257, "2s": -7.69994, "3p": -0.261676, "3s": -0.630912}, "Atomic radius": 1.0, "Atomic radius calculated": 0.88, "Boiling point": "717.87 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "7.7 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-2, 2, 4, 6], "Critical temperature": "1314 K", "Density of solid": "1960 kg m-3", "Electrical resistivity": "> 102310-8 Ω m", "Electronic structure": "[Ne].3s2.3p4", "ICSD oxidation states": [-1, 2, 4, -2, 6], "Ionic radii": {"-2": 1.7, "4": 0.51, "6": 0.43}, "Liquid range": "329.51 K", "Melting point": "388.36 K", "Mendeleev no": 94, "Mineral hardness": "2.0", "Molar volume": "15.53 cm3", "Name": "Sulfur", "Oxidation states": [-2, -1, 1, 2, 3, 4, 5, 6], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.001111", "Rigidity modulus": "no data GPa", "Shannon radii": {"-2": {"VI": {"": {"crystal_radius": 1.7, "ionic_radius": 1.84}}}, "4": {"VI": {"": {"crystal_radius": 0.51, "ionic_radius": 0.37}}}, "6": {"IV": {"": {"crystal_radius": 0.26, "ionic_radius": 0.12}}, "VI": {"": {"crystal_radius": 0.43, "ionic_radius": 0.29}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.205 W m-1 K-1", "Van der waals radius": 1.8, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 2.58, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"S-33": -67.8, "S-35": 47.1}, "Metallic radius": "no data", "iupac_ordering": 96, "IUPAC ordering": 96, "Ground level": "3P2", "Ionization energies": [10.36001, 23.33788, 34.86, 47.222, 72.5945, 88.0529, 280.954, 328.794, 379.84, 447.7, 504.55, 564.41, 651.96, 706.994, 3223.7807, 3494.1879], "Electron affinity": 2.077104512}, "Sb": {"Atomic mass": 121.76, "Atomic no": 51, "Atomic orbitals": {"1s": -1070.823495, "2p": -149.214271, "2s": -159.171745, "3d": -19.239895, "3p": -26.956184, "3s": -31.098242, "4d": -1.297338, "4p": -3.646579, "4s": -5.04964, "5p": -0.185623, "5s": -0.445605}, "Atomic radius": 1.45, "Atomic radius calculated": 1.33, "Boiling point": "1860 K", "Brinell hardness": "294 MN m-2", "Bulk modulus": "42 GPa", "Coefficient of linear thermal expansion": "11 x10-6K-1", "Common oxidation states": [-3, 3, 5], "Critical temperature": "no data K", "Density of solid": "6697 kg m-3", "Electrical resistivity": "40 10-8 Ω m", "Electronic structure": "[Kr].4d10.5s2.5p3", "ICSD oxidation states": [-2, 3, 5, -1, -3], "Ionic radii": {"3": 0.9, "5": 0.76}, "Liquid range": "956.22 K", "Melting point": "903.78 K", "Mendeleev no": 88, "Mineral hardness": "3.0", "Molar volume": "18.19 cm3", "Name": "Antimony", "Oxidation states": [-3, 3, 5], "Poissons ratio": "no data", "Reflectivity": "55 %", "Refractive index": "no data", "Rigidity modulus": "20 GPa", "Shannon radii": {"3": {"IVPY": {"": {"crystal_radius": 0.9, "ionic_radius": 0.76}}, "V": {"": {"crystal_radius": 0.94, "ionic_radius": 0.8}}, "VI": {"": {"crystal_radius": 0.9, "ionic_radius": 0.76}}}, "5": {"VI": {"": {"crystal_radius": 0.74, "ionic_radius": 0.6}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "24 W m-1 K-1", "Van der waals radius": 2.06, "Velocity of sound": "3420 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.05, "Youngs modulus": "55 GPa", "NMR Quadrupole Moment": {"Sb-121": -543.11, "Sb-123": -692.14}, "Metallic radius": 1.61, "iupac_ordering": 88, "IUPAC ordering": 88, "Ground level": "4S\u00b03/2", "Ionization energies": [8.608389, 16.626, 25.3235, 43.804, 55.0, 99.51, 117.0, 139.0, 162.0, 185.0, 214.0, 238.0, 265.0, 292.0, 317.0, 420.0, 447.0, 479.0, 510.0, 552.0, 584.0, 657.0, 693.26, 1214.0, 1285.0, 1360.0, 1441.0, 1518.0, 1606.0, 1698.0, 1781.0, 1869.0, 1954.0, 2190.0, 2266.0, 2349.0, 2428.0, 2567.0, 2654.0, 2815.0, 2900.0, 6714.0, 6929.0, 7167.0, 7390.0, 7887.0, 8140.0, 8455.0, 8669.48, 35710.028, 36668.05], "Electron affinity": 1.04740119}, "Sc": {"Atomic mass": 44.955912, "Atomic no": 21, "Atomic orbitals": {"1s": -160.184109, "2p": -14.240006, "2s": -17.206464, "3d": -0.13108, "3p": -1.233165, "3s": -1.988378, "4s": -0.156478}, "Atomic radius": 1.6, "Atomic radius calculated": 1.84, "Boiling point": "3103 K", "Brinell hardness": "750 MN m-2", "Bulk modulus": "57 GPa", "Coefficient of linear thermal expansion": "10.2 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "2985 kg m-3", "Electrical resistivity": "about 55 10-8 Ω m", "Electronic structure": "[Ar].3d1.4s2", "ICSD oxidation states": [2, 3], "Ionic radii": {"3": 0.885}, "Liquid range": "1289 K", "Melting point": "1814 K", "Mendeleev no": 19, "Mineral hardness": "no data", "Molar volume": "15.00 cm3", "Name": "Scandium", "Oxidation states": [1, 2, 3], "Poissons ratio": "0.28", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "29 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 0.885, "ionic_radius": 0.745}}, "VIII": {"": {"crystal_radius": 1.01, "ionic_radius": 0.87}}}}, "Superconduction temperature": "0.05 (under pressure)K", "Thermal conductivity": "16 W m-1 K-1", "Van der waals radius": 2.15, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.36, "Youngs modulus": "74 GPa", "NMR Quadrupole Moment": {"Sc-45": -220.2}, "Metallic radius": 1.641, "iupac_ordering": 49, "IUPAC ordering": 49, "Ground level": "2D3/2", "Ionization energies": [6.56149, 12.79977, 24.756839, 73.4894, 91.95, 110.68, 137.99, 158.08, 180.03, 225.18, 249.798, 687.36, 757.7, 833.2, 926.5, 1008.6, 1093.5, 1213.1, 1287.957, 5674.9037, 6033.7542], "Electron affinity": 0.1882}, "Se": {"Atomic mass": 78.96, "Atomic no": 34, "Atomic orbitals": {"1s": -451.300258, "2p": -51.514388, "2s": -57.311948, "3d": -2.011392, "3p": -5.553517, "3s": -7.547186, "4p": -0.245806, "4s": -0.621248}, "Atomic radius": 1.15, "Atomic radius calculated": 1.03, "Boiling point": "958 K", "Brinell hardness": "736 MN m-2", "Bulk modulus": "8.3 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-2, 2, 4, 6], "Critical temperature": "1766 K", "Density of solid": "4819 kg m-3", "Electrical resistivity": "high 10-8 Ω m", "Electronic structure": "[Ar].3d10.4s2.4p4", "ICSD oxidation states": [-1, 4, -2, 6], "Ionic radii": {"-2": 1.84, "4": 0.64, "6": 0.56}, "Liquid range": "464 K", "Melting point": "494 K", "Mendeleev no": 93, "Mineral hardness": "2.0", "Molar volume": "16.42 cm3", "Name": "Selenium", "Oxidation states": [-2, 2, 4, 6], "Poissons ratio": "0.33", "Reflectivity": "no data %", "Refractive index": "1.000895", "Rigidity modulus": "3.7 GPa", "Shannon radii": {"-2": {"VI": {"": {"crystal_radius": 1.84, "ionic_radius": 1.98}}}, "4": {"VI": {"": {"crystal_radius": 0.64, "ionic_radius": 0.5}}}, "6": {"IV": {"": {"crystal_radius": 0.42, "ionic_radius": 0.28}}, "VI": {"": {"crystal_radius": 0.56, "ionic_radius": 0.42}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.52 W m-1 K-1", "Van der waals radius": 1.9, "Velocity of sound": "3350 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.55, "Youngs modulus": "10 GPa", "Metallic radius": "no data", "iupac_ordering": 95, "IUPAC ordering": 95, "Ground level": "3P2", "Ionization energies": [9.752392, 21.196, 31.697, 42.947, 68.3, 81.83, 155.327, 184.0, 219.0, 255.0, 291.0, 342.9, 383.0, 426.0, 473.0, 517.0, 650.5, 693.4, 739.8, 798.0, 845.8, 887.0, 989.6, 1036.36, 2540.7, 2674.0, 2820.0, 2964.0, 3146.0, 3301.8, 3507.0, 3636.526, 15367.491, 15968.084], "Electron affinity": 2.020604712}, "Si": {"Atomic mass": 28.0855, "Atomic no": 14, "Atomic orbitals": {"1s": -65.184426, "2p": -3.514938, "2s": -5.075056, "3p": -0.153293, "3s": -0.398139}, "Atomic radius": 1.1, "Atomic radius calculated": 1.11, "Boiling point": "3173 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "100 GPa", "Coefficient of linear thermal expansion": "2.6 x10-6K-1", "Common oxidation states": [-4, 4], "Critical temperature": "no data K", "Density of solid": "2330 kg m-3", "Electrical resistivity": "about 100000 10-8 Ω m", "Electronic structure": "[Ne].3s2.3p2", "ICSD oxidation states": [-4, 4], "Ionic radii": {"4": 0.54}, "Liquid range": "1486 K", "Melting point": "1687 K", "Mendeleev no": 85, "Mineral hardness": "6.5", "Molar volume": "12.06 cm3", "Name": "Silicon", "Oxidation states": [-4, -3, -2, -1, 1, 2, 3, 4], "Poissons ratio": "no data", "Reflectivity": "28 %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"4": {"IV": {"": {"crystal_radius": 0.4, "ionic_radius": 0.26}}, "VI": {"": {"crystal_radius": 0.54, "ionic_radius": 0.4}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "150 W m-1 K-1", "Van der waals radius": 2.1, "Velocity of sound": "2200 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.9, "Youngs modulus": "47 GPa", "Metallic radius": "no data", "iupac_ordering": 85, "IUPAC ordering": 85, "Ground level": "3P0", "Ionization energies": [8.15168, 16.34585, 33.493, 45.14179, 166.767, 205.279, 246.57, 303.59, 351.28, 401.38, 476.273, 523.415, 2437.65815, 2673.17755], "Electron affinity": 1.38952128}, "Sm": {"Atomic mass": 150.36, "Atomic no": 62, "Atomic orbitals": {"1s": -1617.183426, "2p": -242.729726, "2s": -255.498846, "3d": -39.528656, "3p": -50.08426, "3s": -55.731133, "4d": -4.814978, "4f": -0.21776, "4p": -8.672685, "4s": -10.844667, "5p": -0.835987, "5s": -1.408552, "6s": -0.128259}, "Atomic radius": 1.85, "Atomic radius calculated": 2.38, "Boiling point": "2076 K", "Brinell hardness": "441 MN m-2", "Bulk modulus": "38 GPa", "Coefficient of linear thermal expansion": "12.7 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "7353 kg m-3", "Electrical resistivity": "94 10-8 Ω m", "Electronic structure": "[Xe].4f6.6s2", "ICSD oxidation states": [2, 3], "Ionic radii": {"2": 1.36, "3": 1.0979999999999999}, "Liquid range": "731 K", "Melting point": "1345 K", "Mendeleev no": 28, "Mineral hardness": "no data", "Molar volume": "19.98 cm3", "Name": "Samarium", "Oxidation states": [2, 3], "Poissons ratio": "0.27", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "20 GPa", "Shannon radii": {"2": {"VII": {"": {"crystal_radius": 1.36, "ionic_radius": 1.22}}, "VIII": {"": {"crystal_radius": 1.41, "ionic_radius": 1.27}}, "IX": {"": {"crystal_radius": 1.46, "ionic_radius": 1.32}}}, "3": {"VI": {"": {"crystal_radius": 1.098, "ionic_radius": 0.958}}, "VII": {"": {"crystal_radius": 1.16, "ionic_radius": 1.02}}, "VIII": {"": {"crystal_radius": 1.219, "ionic_radius": 1.079}}, "IX": {"": {"crystal_radius": 1.272, "ionic_radius": 1.132}}, "XII": {"": {"crystal_radius": 1.38, "ionic_radius": 1.24}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "13 W m-1 K-1", "Van der waals radius": 2.36, "Velocity of sound": "2130 m s-1", "Vickers hardness": "412 MN m-2", "X": 1.17, "Youngs modulus": "50 GPa", "Metallic radius": 1.804, "iupac_ordering": 42, "IUPAC ordering": 42, "Ground level": "7F0", "Ionization energies": [5.64371, 11.078, 23.55, 41.64, 62.7, 87.0, 103.0, 118.0, 141.0, 158.0, 179.0, 208.0, 237.0, 257.0, 276.0, 306.5, 474.0, 506.0, 543.0, 581.0, 617.0, 658.0, 702.0, 742.0, 782.0, 822.0, 976.0, 1016.0, 1060.0, 1103.0, 1180.0, 1226.0, 1332.0, 1381.56, 2371.0, 2466.0, 2569.0, 2676.0, 2782.0, 2887.0, 3028.0, 3137.0, 3253.0, 3363.0, 3669.0, 3766.0, 3873.0, 3971.0, 4227.0, 4337.0, 4548.0, 4655.0, 10494.0, 10762.0, 11060.0, 11337.0, 12264.0, 12588.0, 12992.0, 13262.85, 53986.12, 55214.23], "Electron affinity": 0.162}, "Sn": {"Atomic mass": 118.71, "Atomic no": 50, "Atomic orbitals": {"1s": -1026.762169, "2p": -141.821093, "2s": -151.523991, "3d": -17.657276, "3p": -25.117913, "3s": -29.125969, "4d": -1.004952, "4p": -3.211998, "4s": -4.546335, "5p": -0.14445, "5s": -0.369349}, "Atomic radius": 1.45, "Atomic radius calculated": 1.45, "Boiling point": "2875 K", "Brinell hardness": "51 MN m-2", "Bulk modulus": "58 GPa", "Coefficient of linear thermal expansion": "22 x10-6K-1", "Common oxidation states": [-4, 2, 4], "Critical temperature": "no data K", "Density of solid": "7310 kg m-3", "Electrical resistivity": "11.5 10-8 Ω m", "Electronic structure": "[Kr].4d10.5s2.5p2", "ICSD oxidation states": [2, 3, 4], "Ionic radii": {"4": 0.83}, "Liquid range": "2369.92 K", "Melting point": "505.08 K", "Mendeleev no": 83, "Mineral hardness": "1.5", "Molar volume": "16.29 cm3", "Name": "Tin", "Oxidation states": [-4, 2, 4], "Poissons ratio": "0.36", "Reflectivity": "54 %", "Refractive index": "no data", "Rigidity modulus": "18 GPa", "Shannon radii": {"4": {"IV": {"": {"crystal_radius": 0.69, "ionic_radius": 0.55}}, "V": {"": {"crystal_radius": 0.76, "ionic_radius": 0.62}}, "VI": {"": {"crystal_radius": 0.83, "ionic_radius": 0.69}}, "VII": {"": {"crystal_radius": 0.89, "ionic_radius": 0.75}}, "VIII": {"": {"crystal_radius": 0.95, "ionic_radius": 0.81}}}}, "Superconduction temperature": "3.72 K", "Thermal conductivity": "67 W m-1 K-1", "Van der waals radius": 2.17, "Velocity of sound": "2500 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.96, "Youngs modulus": "50 GPa", "NMR Quadrupole Moment": {"Sn-119": -132.1}, "Metallic radius": 1.58, "iupac_ordering": 83, "IUPAC ordering": 83, "Ground level": "3P0", "Ionization energies": [7.343918, 14.63307, 30.506, 40.74, 77.03, 94.0, 112.9, 135.0, 156.0, 184.0, 208.0, 232.0, 258.0, 282.0, 379.0, 407.0, 437.0, 466.0, 506.0, 537.0, 608.0, 642.35, 1127.0, 1195.0, 1269.0, 1347.0, 1421.0, 1508.0, 1596.0, 1676.0, 1763.0, 1844.0, 2074.0, 2142.1, 2227.0, 2326.0, 2443.0, 2499.0, 2687.0, 2762.49, 6421.0, 6631.0, 6859.0, 7080.0, 7531.0, 7790.0, 8103.0, 8306.95, 34257.143, 35192.39], "Electron affinity": 1.1120702}, "Sr": {"Atomic mass": 87.62, "Atomic no": 38, "Atomic orbitals": {"1s": -572.870169, "2p": -69.745941, "2s": -76.491823, "3d": -4.813498, "3p": -9.301863, "3s": -11.771585, "4p": -0.844489, "4s": -1.455317, "5s": -0.131793}, "Atomic radius": 2.0, "Atomic radius calculated": 2.19, "Boiling point": "1655 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "22.5 x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "2630 kg m-3", "Electrical resistivity": "13.5 10-8 Ω m", "Electronic structure": "[Kr].5s2", "ICSD oxidation states": [2], "Ionic radii": {"2": 1.32}, "Liquid range": "605 K", "Melting point": "1050 K", "Mendeleev no": 15, "Mineral hardness": "1.5", "Molar volume": "33.94 cm3", "Name": "Strontium", "Oxidation states": [2], "Poissons ratio": "0.28", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "6.1 GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.32, "ionic_radius": 1.18}}, "VII": {"": {"crystal_radius": 1.35, "ionic_radius": 1.21}}, "VIII": {"": {"crystal_radius": 1.4, "ionic_radius": 1.26}}, "IX": {"": {"crystal_radius": 1.45, "ionic_radius": 1.31}}, "X": {"": {"crystal_radius": 1.5, "ionic_radius": 1.36}}, "XII": {"": {"crystal_radius": 1.58, "ionic_radius": 1.44}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "35 W m-1 K-1", "Van der waals radius": 2.49, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 0.95, "Youngs modulus": "no data GPa", "NMR Quadrupole Moment": {"Sr-87": 305.2}, "Metallic radius": 2.151, "iupac_ordering": 14, "IUPAC ordering": 14, "Ground level": "1S0", "Ionization energies": [5.69486745, 11.0302765, 42.88353, 56.28, 70.7, 88.0, 104.0, 121.21, 158.33, 177.3, 324.07, 362.0, 408.0, 454.0, 499.0, 562.0, 612.0, 665.0, 722.0, 774.0, 932.0, 982.1, 1038.0, 1105.0, 1165.0, 1211.0, 1333.4, 1387.19, 3344.7, 3497.0, 3664.0, 3830.0, 4053.0, 4232.0, 4465.0, 4612.397, 19345.588, 20025.233], "Electron affinity": 0.052066}, "Ta": {"Atomic mass": 180.94788, "Atomic no": 73, "Atomic orbitals": {"1s": -2275.371387, "2p": -357.248334, "2s": -372.828724, "3d": -63.942521, "3p": -77.440942, "3s": -84.658467, "4d": -8.265848, "4f": -1.199347, "4p": -13.71981, "4s": -16.713337, "5d": -0.182464, "5p": -1.37653, "5s": -2.223807, "6s": -0.174814}, "Atomic radius": 1.45, "Atomic radius calculated": 2.0, "Boiling point": "5731 K", "Brinell hardness": "800 MN m-2", "Bulk modulus": "200 GPa", "Coefficient of linear thermal expansion": "6.3 x10-6K-1", "Common oxidation states": [5], "Critical temperature": "no data K", "Density of solid": "16650 kg m-3", "Electrical resistivity": "13.5 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d3.6s2", "ICSD oxidation states": [3, 4, 5], "Ionic radii": {"3": 0.86, "4": 0.82, "5": 0.78}, "Liquid range": "2441 K", "Melting point": "3290 K", "Mendeleev no": 52, "Mineral hardness": "6.5", "Molar volume": "10.85 cm3", "Name": "Tantalum", "Oxidation states": [-1, 2, 3, 4, 5], "Poissons ratio": "0.34", "Reflectivity": "78 %", "Refractive index": "no data", "Rigidity modulus": "69 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 0.86, "ionic_radius": 0.72}}}, "4": {"VI": {"": {"crystal_radius": 0.82, "ionic_radius": 0.68}}}, "5": {"VI": {"": {"crystal_radius": 0.78, "ionic_radius": 0.64}}, "VII": {"": {"crystal_radius": 0.83, "ionic_radius": 0.69}}, "VIII": {"": {"crystal_radius": 0.88, "ionic_radius": 0.74}}}}, "Superconduction temperature": "4.47 K", "Thermal conductivity": "57 W m-1 K-1", "Van der waals radius": 2.22, "Velocity of sound": "3400 m s-1", "Vickers hardness": "873 MN m-2", "X": 1.5, "Youngs modulus": "186 GPa", "Metallic radius": 1.47, "iupac_ordering": 53, "IUPAC ordering": 53, "Ground level": "4F3/2", "Ionization energies": [7.549571, 16.2, 23.1, 35.0, 48.272, 94.01, 119.0, 139.0, 159.0, 180.0, 213.0, 235.0, 262.0, 304.0, 338.0, 363.0, 396.0, 439.0, 482.0, 530.0, 570.0, 610.0, 660.0, 700.0, 750.0, 790.0, 832.0, 1064.0, 1110.0, 1160.0, 1211.0, 1262.0, 1313.0, 1382.0, 1434.0, 1490.0, 1542.0, 1748.0, 1799.0, 1857.0, 1910.0, 2053.0, 2113.0, 2254.0, 2314.7, 3898.7, 4014.0, 4143.0, 4278.0, 4410.0, 4537.0, 4745.0, 4877.0, 5024.0, 5159.0, 5537.0, 5655.0, 5785.0, 5907.0, 6364.0, 6502.0, 6769.0, 6900.0, 15137.0, 15461.0, 15820.0, 16150.0, 17840.0, 18250.0, 18760.0, 19088.51, 76852.03, 78394.7], "Electron affinity": 0.32312}, "Tb": {"Atomic mass": 158.92535, "Atomic no": 65, "Atomic orbitals": {"1s": -1785.331942, "2p": -271.590585, "2s": -285.121013, "3d": -45.443863, "3p": -56.785113, "3s": -62.851563, "4d": -5.467662, "4f": -0.256311, "4p": -9.735637, "4s": -12.120486, "5p": -0.88723, "5s": -1.513669, "6s": -0.131677}, "Atomic radius": 1.75, "Atomic radius calculated": 2.25, "Boiling point": "3503 K", "Brinell hardness": "677 MN m-2", "Bulk modulus": "38.7 GPa", "Coefficient of linear thermal expansion": "10.3 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "8219 kg m-3", "Electrical resistivity": "115 10-8 Ω m", "Electronic structure": "[Xe].4f9.6s2", "ICSD oxidation states": [3, 4], "Ionic radii": {"3": 1.063, "4": 0.9}, "Liquid range": "1874 K", "Melting point": "1629 K", "Mendeleev no": 26, "Mineral hardness": "no data", "Molar volume": "19.30 cm3", "Name": "Terbium", "Oxidation states": [1, 3, 4], "Poissons ratio": "0.26", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "22 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.063, "ionic_radius": 0.923}}, "VII": {"": {"crystal_radius": 1.12, "ionic_radius": 0.98}}, "VIII": {"": {"crystal_radius": 1.18, "ionic_radius": 1.04}}, "IX": {"": {"crystal_radius": 1.235, "ionic_radius": 1.095}}}, "4": {"VI": {"": {"crystal_radius": 0.9, "ionic_radius": 0.76}}, "VIII": {"": {"crystal_radius": 1.02, "ionic_radius": 0.88}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "11 W m-1 K-1", "Van der waals radius": 2.33, "Velocity of sound": "2620 m s-1", "Vickers hardness": "863 MN m-2", "X": 1.1, "Youngs modulus": "56 GPa", "Metallic radius": 1.781, "iupac_ordering": 39, "IUPAC ordering": 39, "Ground level": "6H\u00b015/2", "Ionization energies": [5.8638, 11.513, 21.82, 39.33, 66.5, 90.0, 108.0, 125.0, 143.0, 168.0, 186.0, 216.0, 250.0, 273.0, 294.0, 325.0, 358.0, 393.0, 426.6, 613.0, 651.0, 690.0, 732.0, 772.0, 816.0, 866.0, 909.0, 954.0, 997.0, 1165.0, 1208.0, 1256.0, 1301.0, 1393.0, 1443.0, 1559.0, 1610.4, 2750.0, 2852.0, 2961.0, 3078.0, 3189.0, 3300.0, 3458.0, 3573.0, 3698.0, 3814.0, 4139.0, 4242.0, 4355.0, 4460.0, 4760.0, 4877.0, 5103.0, 5217.0, 11673.0, 11957.0, 12272.0, 12563.0, 13658.0, 14003.0, 14434.0, 14721.02, 59739.3, 61049.65], "Electron affinity": 0.131318}, "Tc": {"Atomic mass": 98.0, "Atomic no": 43, "Atomic orbitals": {"1s": -745.742024, "2p": -96.61021, "2s": -104.567508, "3d": -9.33986, "3p": -15.041738, "3s": -18.135303, "4d": -0.270262, "4p": -1.64323, "4s": -2.550712, "5s": -0.183636}, "Atomic radius": 1.35, "Atomic radius calculated": 1.83, "Boiling point": "4538 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [4, 7], "Critical temperature": "no data K", "Density of solid": "11500 kg m-3", "Electrical resistivity": "about 22 10-8 Ω m", "Electronic structure": "[Kr].4d5.5s2", "Ionic radii": {"4": 0.785, "5": 0.74, "7": 0.7}, "Liquid range": "2108 K", "Melting point": "2430 K", "Mendeleev no": 59, "Mineral hardness": "no data", "Molar volume": "8.63 cm3", "Name": "Technetium", "Oxidation states": [-3, -1, 1, 2, 3, 4, 5, 6, 7], "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "no data GPa", "Shannon radii": {"4": {"VI": {"": {"crystal_radius": 0.785, "ionic_radius": 0.645}}}, "5": {"VI": {"": {"crystal_radius": 0.74, "ionic_radius": 0.6}}}, "7": {"IV": {"": {"crystal_radius": 0.51, "ionic_radius": 0.37}}, "VI": {"": {"crystal_radius": 0.7, "ionic_radius": 0.56}}}}, "Superconduction temperature": "7.8 K", "Thermal conductivity": "51 W m-1 K-1", "Van der waals radius": 2.16, "Velocity of sound": "no data m s-1", "Vickers hardness": "no data MN m-2", "X": 1.9, "Youngs modulus": "no data GPa", "Metallic radius": 1.363, "iupac_ordering": 60, "IUPAC ordering": 60, "Ground level": "6S5/2", "Ionization energies": [7.11938, 15.26, 29.55, 41.0, 57.0, 72.0, 88.0, 150.0, 169.0, 189.9, 214.0, 239.0, 262.08, 311.0, 338.55, 604.0, 655.0, 713.0, 773.0, 829.0, 904.0, 968.0, 1032.0, 1102.0, 1166.0, 1354.0, 1411.6, 1479.5, 1559.0, 1638.0, 1689.0, 1838.0, 1900.28, 4505.0, 4681.0, 4874.0, 5060.0, 5361.0, 5570.0, 5838.0, 6008.391, 25004.533, 25786.99], "Electron affinity": 0.552}, "Te": {"Atomic mass": 127.6, "Atomic no": 52, "Atomic orbitals": {"1s": -1115.831819, "2p": -156.808583, "2s": -167.021776, "3d": -20.887801, "3p": -28.860685, "3s": -33.137485, "4d": -1.608381, "4p": -4.100084, "4s": -5.572846, "5p": -0.226594, "5s": -0.520997}, "Atomic radius": 1.4, "Atomic radius calculated": 1.23, "Boiling point": "1261 K", "Brinell hardness": "180 MN m-2", "Bulk modulus": "65 GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Common oxidation states": [-2, 2, 4, 6], "Critical temperature": "no data K", "Density of solid": "6240 kg m-3", "Electrical resistivity": "about 10000 10-8 Ω m", "Electronic structure": "[Kr].4d10.5s2.5p4", "ICSD oxidation states": [-2, 4, -1, 6], "Ionic radii": {"-2": 2.07, "4": 1.11, "6": 0.7}, "Liquid range": "538.34 K", "Melting point": "722.66 K", "Mendeleev no": 92, "Mineral hardness": "2.25", "Molar volume": "20.46 cm3", "Name": "Tellurium", "Oxidation states": [-2, 2, 4, 5, 6], "Poissons ratio": "no data", "Reflectivity": "50 %", "Refractive index": "1.000991", "Rigidity modulus": "16 GPa", "Shannon radii": {"-2": {"VI": {"": {"crystal_radius": 2.07, "ionic_radius": 2.21}}}, "4": {"III": {"": {"crystal_radius": 0.66, "ionic_radius": 0.52}}, "IV": {"": {"crystal_radius": 0.8, "ionic_radius": 0.66}}, "VI": {"": {"crystal_radius": 1.11, "ionic_radius": 0.97}}}, "6": {"IV": {"": {"crystal_radius": 0.57, "ionic_radius": 0.43}}, "VI": {"": {"crystal_radius": 0.7, "ionic_radius": 0.56}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "3 W m-1 K-1", "Van der waals radius": 2.06, "Velocity of sound": "2610 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.1, "Youngs modulus": "43 GPa", "Metallic radius": "no data", "iupac_ordering": 94, "IUPAC ordering": 94, "Ground level": "3P2", "Ionization energies": [9.009808, 18.6, 27.84, 37.4155, 59.3, 69.1, 124.2, 143.0, 167.0, 191.1, 215.0, 245.0, 272.0, 299.0, 328.0, 354.0, 461.0, 491.0, 522.0, 555.0, 599.0, 633.0, 709.0, 746.12, 1304.0, 1377.0, 1455.0, 1538.0, 1618.0, 1707.0, 1803.0, 1889.0, 1979.0, 2066.0, 2309.0, 2386.0, 2472.0, 2552.0, 2700.0, 2788.0, 2954.0, 3041.0, 7022.0, 7243.0, 7485.0, 7714.0, 8240.0, 8499.0, 8821.0, 9040.83, 37196.522, 38177.56], "Electron affinity": 1.9708757}, "Th": {"Atomic mass": 232.03806, "Atomic no": 90, "Atomic orbitals": {"1s": -3524.439052, "2p": -588.218112, "2s": -608.350958, "3d": -123.846396, "3p": -142.25581, "3s": -152.079741, "4d": -24.955184, "4f": -13.397389, "4p": -33.325252, "4s": -37.814094, "5d": -3.625729, "5p": -6.58281, "5s": -8.287057, "6d": -0.172896, "6p": -0.846921, "6s": -1.333769, "7s": -0.135872}, "Atomic radius": 1.8, "Atomic radius calculated": "no data", "Boiling point": "5093 K", "Brinell hardness": "400 MN m-2", "Bulk modulus": "54 GPa", "Coefficient of linear thermal expansion": "11.0 x10-6K-1", "Common oxidation states": [4], "Critical temperature": "no data K", "Density of solid": "11724 kg m-3", "Electrical resistivity": "15 10-8 Ω m", "Electronic structure": "[Rn].6d2.7s2", "ICSD oxidation states": [4], "Ionic radii": {"4": 1.08}, "Liquid range": "2978 K", "Melting point": "2115 K", "Mendeleev no": 47, "Mineral hardness": "3.0", "Molar volume": "19.80 cm3", "Name": "Thorium", "Oxidation states": [2, 3, 4], "Poissons ratio": "0.27", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "31 GPa", "Shannon radii": {"4": {"VI": {"": {"crystal_radius": 1.08, "ionic_radius": 0.94}}, "VIII": {"": {"crystal_radius": 1.19, "ionic_radius": 1.05}}, "IX": {"": {"crystal_radius": 1.23, "ionic_radius": 1.09}}, "X": {"": {"crystal_radius": 1.27, "ionic_radius": 1.13}}, "XI": {"": {"crystal_radius": 1.32, "ionic_radius": 1.18}}, "XII": {"": {"crystal_radius": 1.35, "ionic_radius": 1.21}}}}, "Superconduction temperature": "1.38 K", "Thermal conductivity": "54 W m-1 K-1", "Van der waals radius": 2.45, "Velocity of sound": "2490 m s-1", "Vickers hardness": "350 MN m-2", "X": 1.3, "Youngs modulus": "79 GPa", "Metallic radius": 1.798, "iupac_ordering": 31, "IUPAC ordering": 31, "Ground level": "3F2", "Ionization energies": [6.3067, 12.1, 18.32, 28.648, 58.0, 69.1, 82.0, 95.0, 118.0, 133.0, 165.0, 181.0, 262.0, 285.0, 310.0, 336.0, 362.0, 389.0, 424.0, 451.0, 480.0, 508.0, 650.0, 680.0, 720.0, 750.0, 830.0, 870.0, 970.0, 1010.0, 1090.0, 1160.0, 1240.0, 1310.0, 1380.0, 1460.0, 1530.0, 1600.0, 1680.0, 1760.0, 1830.0, 1910.0, 1980.0, 2060.0, 2390.0, 2455.0, 2524.0, 2598.0, 2669.0, 2737.0, 2864.0, 2935.0, 3013.0, 3086.0, 3375.0, 3445.0, 3522.0, 3593.0, 3943.0, 4025.0, 4230.0, 4313.0, 6972.0, 7130.0, 7299.0, 7480.0, 7650.0, 7810.0, 8180.0, 8350.0, 8550.0, 8720.0, 9220.0, 9370.0, 9540.0, 9690.0, 10790.0, 10970.0, 11340.0, 11510.0, 24060.0, 24480.0, 24940.0, 25360.0, 29410.0, 29970.0, 30680.0, 31122.8, 123086.4, 125253.4], "Electron affinity": 1.17}, "Ti": {"Atomic mass": 47.867, "Atomic no": 22, "Atomic orbitals": {"1s": -177.276643, "2p": -16.285339, "2s": -19.457901, "3d": -0.17001, "3p": -1.422947, "3s": -2.258007, "4s": -0.167106}, "Atomic radius": 1.4, "Atomic radius calculated": 1.76, "Boiling point": "3560 K", "Brinell hardness": "716 MN m-2", "Bulk modulus": "110 GPa", "Coefficient of linear thermal expansion": "8.6 x10-6K-1", "Common oxidation states": [4], "Critical temperature": "no data K", "Density of solid": "4507 kg m-3", "Electrical resistivity": "about 40 10-8 Ω m", "Electronic structure": "[Ar].3d2.4s2", "ICSD oxidation states": [2, 3, 4], "Ionic radii": {"2": 1.0, "3": 0.81, "4": 0.745}, "Liquid range": "1619 K", "Melting point": "1941 K", "Mendeleev no": 51, "Mineral hardness": "6.0", "Molar volume": "10.64 cm3", "Name": "Titanium", "Oxidation states": [-1, 2, 3, 4], "Poissons ratio": "0.32", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "44 GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.0, "ionic_radius": 0.86}}}, "3": {"VI": {"": {"crystal_radius": 0.81, "ionic_radius": 0.67}}}, "4": {"IV": {"": {"crystal_radius": 0.56, "ionic_radius": 0.42}}, "V": {"": {"crystal_radius": 0.65, "ionic_radius": 0.51}}, "VI": {"": {"crystal_radius": 0.745, "ionic_radius": 0.605}}, "VIII": {"": {"crystal_radius": 0.88, "ionic_radius": 0.74}}}}, "Superconduction temperature": "0.40 K", "Thermal conductivity": "22 W m-1 K-1", "Van der waals radius": 2.11, "Velocity of sound": "4140 m s-1", "Vickers hardness": "970 MN m-2", "X": 1.54, "Youngs modulus": "116 GPa", "NMR Quadrupole Moment": {"Ti-47": 302.1, "Ti-49": 247.11}, "Metallic radius": 1.462, "iupac_ordering": 52, "IUPAC ordering": 52, "Ground level": "3F2", "Ionization energies": [6.82812, 13.5755, 27.49171, 43.26717, 99.299, 119.533, 140.68, 170.5, 192.1, 215.92, 265.07, 291.5, 787.67, 864.0, 944.5, 1042.5, 1130.2, 1220.3, 1346.3, 1425.257, 6249.0226, 6625.8073], "Electron affinity": 0.075545}, "Tl": {"Atomic mass": 204.3833, "Atomic no": 81, "Atomic orbitals": {"1s": -2827.569408, "2p": -457.255971, "2s": -474.953368, "3d": -88.328299, "3p": -104.099296, "3s": -112.52218, "4d": -14.008848, "4f": -4.835747, "4p": -20.797078, "4s": -24.471512, "5d": -0.674544, "5p": -2.59873, "5s": -3.811512, "6p": -0.101507, "6s": -0.28502}, "Atomic radius": 1.9, "Atomic radius calculated": 1.56, "Boiling point": "1746 K", "Brinell hardness": "26.4 MN m-2", "Bulk modulus": "43 GPa", "Coefficient of linear thermal expansion": "29.9 x10-6K-1", "Common oxidation states": [1, 3], "Critical temperature": "no data K", "Density of solid": "11850 kg m-3", "Electrical resistivity": "15 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d10.6s2.6p1", "ICSD oxidation states": [1, 3], "Ionic radii": {"1": 1.64, "3": 1.025}, "Liquid range": "1169 K", "Melting point": "577 K", "Mendeleev no": 78, "Mineral hardness": "1.2", "Molar volume": "17.22 cm3", "Name": "Thallium", "Oxidation states": [1, 3], "Poissons ratio": "0.45", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "2.8 GPa", "Shannon radii": {"1": {"VI": {"": {"crystal_radius": 1.64, "ionic_radius": 1.5}}, "VIII": {"": {"crystal_radius": 1.73, "ionic_radius": 1.59}}, "XII": {"": {"crystal_radius": 1.84, "ionic_radius": 1.7}}}, "3": {"IV": {"": {"crystal_radius": 0.89, "ionic_radius": 0.75}}, "VI": {"": {"crystal_radius": 1.025, "ionic_radius": 0.885}}, "VIII": {"": {"crystal_radius": 1.12, "ionic_radius": 0.98}}}}, "Superconduction temperature": "2.38 K", "Thermal conductivity": "46 W m-1 K-1", "Van der waals radius": 1.96, "Velocity of sound": "818 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.62, "Youngs modulus": "8 GPa", "Metallic radius": 1.7, "iupac_ordering": 77, "IUPAC ordering": 77, "Ground level": "2P\u00b01/2", "Ionization energies": [6.1082873, 20.4283, 29.852, 51.14, 62.6, 80.0, 97.9, 116.0, 135.0, 158.0, 177.0, 198.0, 218.3, 306.9, 340.0, 366.0, 392.0, 439.0, 467.0, 520.0, 570.0, 600.0, 640.0, 700.0, 760.0, 820.0, 880.0, 930.0, 990.0, 1060.0, 1110.0, 1170.0, 1230.0, 1290.0, 1350.0, 1625.0, 1681.0, 1740.0, 1802.0, 1862.0, 1920.0, 2014.0, 2075.0, 2140.0, 2202.0, 2447.0, 2508.0, 2574.0, 2635.0, 2854.0, 2925.0, 3094.0, 3164.7, 5234.0, 5371.0, 5518.0, 5674.0, 5824.0, 5969.0, 6241.0, 6392.0, 6560.0, 6714.0, 7146.0, 7281.0, 7430.0, 7570.0, 8260.0, 8420.0, 8730.0, 8880.0, 19070.0, 19440.0, 19840.0, 20210.0, 22780.0, 23250.0, 23850.0, 24234.1, 96783.21, 98591.6], "Electron affinity": 0.32005319}, "Tm": {"Atomic mass": 168.93421, "Atomic no": 69, "Atomic orbitals": {"1s": -2022.471608, "2p": -312.510608, "2s": -327.05712, "3d": -53.835494, "3p": -66.239338, "3s": -72.873753, "4d": -6.350307, "4f": -0.28312, "4p": -11.187151, "4s": -13.865665, "5p": -0.950748, "5s": -1.64999, "6s": -0.135953}, "Atomic radius": 1.75, "Atomic radius calculated": 2.22, "Boiling point": "2223 K", "Brinell hardness": "471 MN m-2", "Bulk modulus": "45 GPa", "Coefficient of linear thermal expansion": "13.3 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "9321 kg m-3", "Electrical resistivity": "67.6 10-8 Ω m", "Electronic structure": "[Xe].4f13.6s2", "ICSD oxidation states": [3], "Ionic radii": {"2": 1.17, "3": 1.02}, "Liquid range": "405 K", "Melting point": "1818 K", "Mendeleev no": 21, "Mineral hardness": "no data", "Molar volume": "19.1 cm3", "Name": "Thulium", "Oxidation states": [2, 3], "Poissons ratio": "0.21", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "31 GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.17, "ionic_radius": 1.03}}, "VII": {"": {"crystal_radius": 1.23, "ionic_radius": 1.09}}}, "3": {"VI": {"": {"crystal_radius": 1.02, "ionic_radius": 0.88}}, "VIII": {"": {"crystal_radius": 1.134, "ionic_radius": 0.994}}, "IX": {"": {"crystal_radius": 1.192, "ionic_radius": 1.052}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "17 W m-1 K-1", "Van der waals radius": 2.27, "Velocity of sound": "no data m s-1", "Vickers hardness": "520 MN m-2", "X": 1.25, "Youngs modulus": "74 GPa", "Metallic radius": 1.747, "iupac_ordering": 35, "IUPAC ordering": 35, "Ground level": "2F\u00b07/2", "Ionization energies": [6.18431, 12.065, 23.66, 42.41, 65.4, 98.0, 116.0, 133.0, 160.0, 180.0, 205.0, 239.0, 274.0, 295.0, 317.0, 352.0, 387.0, 424.0, 460.0, 496.0, 530.0, 570.0, 603.0, 825.0, 866.0, 911.0, 958.0, 1004.0, 1050.0, 1110.0, 1157.0, 1207.0, 1255.0, 1442.0, 1490.0, 1542.0, 1591.0, 1706.0, 1761.0, 1889.0, 1945.2, 3298.0, 3409.0, 3528.0, 3653.0, 3775.0, 3895.0, 4075.0, 4199.0, 4335.0, 4461.0, 4812.0, 4922.0, 5044.0, 5157.0, 5527.0, 5656.0, 5901.0, 6023.0, 13347.0, 13651.0, 13988.0, 14300.0, 15663.0, 16036.0, 16510.0, 16814.34, 67965.26, 69387.3], "Electron affinity": 1.02922}, "U": {"Atomic mass": 238.02891, "Atomic no": 92, "Atomic orbitals": {"1s": -3689.355141, "2p": -619.10855, "2s": -639.778728, "3d": -131.977358, "3p": -150.97898, "3s": -161.118073, "4d": -27.123212, "4f": -15.02746, "4p": -35.853321, "4s": -40.528084, "5d": -3.866175, "5f": -0.366543, "5p": -7.018092, "5s": -8.824089, "6d": -0.14319, "6p": -0.822538, "6s": -1.325976, "7s": -0.130948}, "Atomic radius": 1.75, "Atomic radius calculated": "no data", "Boiling point": "4200 K", "Brinell hardness": "2400 MN m-2", "Bulk modulus": "100 GPa", "Coefficient of linear thermal expansion": "13.9 x10-6K-1", "Common oxidation states": [6], "Critical temperature": "no data K", "Density of solid": "19050 kg m-3", "Electrical resistivity": "28 10-8 Ω m", "Electronic structure": "[Rn].5f3.6d1.7s2", "ICSD oxidation states": [3, 4, 5, 6], "Ionic radii": {"3": 1.165, "4": 1.03, "5": 0.9, "6": 0.87}, "Liquid range": "2794.7 K", "Melting point": "1405.3 K", "Mendeleev no": 45, "Mineral hardness": "6.0", "Molar volume": "12.49 cm3", "Name": "Uranium", "Oxidation states": [3, 4, 5, 6], "Poissons ratio": "0.23", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "111 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.165, "ionic_radius": 1.025}}}, "4": {"VI": {"": {"crystal_radius": 1.03, "ionic_radius": 0.89}}, "VII": {"": {"crystal_radius": 1.09, "ionic_radius": 0.95}}, "VIII": {"": {"crystal_radius": 1.14, "ionic_radius": 1.0}}, "IX": {"": {"crystal_radius": 1.19, "ionic_radius": 1.05}}, "XII": {"": {"crystal_radius": 1.31, "ionic_radius": 1.17}}}, "5": {"VI": {"": {"crystal_radius": 0.9, "ionic_radius": 0.76}}, "VII": {"": {"crystal_radius": 0.98, "ionic_radius": 0.84}}}, "6": {"II": {"": {"crystal_radius": 0.59, "ionic_radius": 0.45}}, "IV": {"": {"crystal_radius": 0.66, "ionic_radius": 0.52}}, "VI": {"": {"crystal_radius": 0.87, "ionic_radius": 0.73}}, "VII": {"": {"crystal_radius": 0.95, "ionic_radius": 0.81}}, "VIII": {"": {"crystal_radius": 1.0, "ionic_radius": 0.86}}}}, "Superconduction temperature": "0.2 K", "Thermal conductivity": "27 W m-1 K-1", "Van der waals radius": 2.41, "Velocity of sound": "3155 m s-1", "Vickers hardness": "1960 MN m-2", "X": 1.38, "Youngs modulus": "208 GPa", "Metallic radius": 1.542, "iupac_ordering": 29, "IUPAC ordering": 29, "Ground level": "5L\u00b06", "Ionization energies": [6.19405, 11.6, 19.8, 36.7, 46.0, 62.0, 89.0, 101.0, 116.0, 128.9, 158.0, 173.0, 210.0, 227.0, 323.0, 348.0, 375.0, 402.0, 431.0, 458.0, 497.0, 525.0, 557.0, 585.0, 730.0, 770.0, 800.0, 840.0, 930.0, 970.0, 1070.0, 1110.0, 1210.0, 1290.0, 1370.0, 1440.0, 1520.0, 1590.0, 1670.0, 1750.0, 1830.0, 1910.0, 1990.0, 2070.0, 2140.0, 2220.0, 2578.0, 2646.0, 2718.0, 2794.0, 2867.0, 2938.0, 3073.0, 3147.0, 3228.0, 3301.0, 3602.0, 3675.0, 3753.0, 3827.0, 4214.0, 4299.0, 4513.0, 4598.0, 7393.0, 7550.0, 7730.0, 7910.0, 8090.0, 8260.0, 8650.0, 8830.0, 9030.0, 9210.0, 9720.0, 9870.0, 10040.0, 10200.0, 11410.0, 11600.0, 11990.0, 12160.0, 25260.0, 25680.0, 26150.0, 26590.0, 31060.0, 31640.0, 32400.0, 32836.5, 129570.3, 131821.0], "Electron affinity": 0.53}, "V": {"Atomic mass": 50.9415, "Atomic no": 23, "Atomic orbitals": {"1s": -195.224014, "2p": -18.435189, "2s": -21.815346, "3d": -0.204634, "3p": -1.610516, "3s": -2.526904, "4s": -0.175968}, "Atomic radius": 1.35, "Atomic radius calculated": 1.71, "Boiling point": "3680 K", "Brinell hardness": "628 MN m-2", "Bulk modulus": "160 GPa", "Coefficient of linear thermal expansion": "8.4 x10-6K-1", "Common oxidation states": [5], "Critical temperature": "no data K", "Density of solid": "6110 kg m-3", "Electrical resistivity": "20 10-8 Ω m", "Electronic structure": "[Ar].3d3.4s2", "ICSD oxidation states": [2, 3, 4, 5], "Ionic radii": {"2": 0.93, "3": 0.78, "4": 0.72, "5": 0.68}, "Liquid range": "1497 K", "Melting point": "2183 K", "Mendeleev no": 54, "Mineral hardness": "7.0", "Molar volume": "8.32 cm3", "Name": "Vanadium", "Oxidation states": [-1, 1, 2, 3, 4, 5], "Poissons ratio": "0.37", "Reflectivity": "61 %", "Refractive index": "no data", "Rigidity modulus": "47 GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 0.93, "ionic_radius": 0.79}}}, "3": {"VI": {"": {"crystal_radius": 0.78, "ionic_radius": 0.64}}}, "4": {"V": {"": {"crystal_radius": 0.67, "ionic_radius": 0.53}}, "VI": {"": {"crystal_radius": 0.72, "ionic_radius": 0.58}}, "VIII": {"": {"crystal_radius": 0.86, "ionic_radius": 0.72}}}, "5": {"IV": {"": {"crystal_radius": 0.495, "ionic_radius": 0.355}}, "V": {"": {"crystal_radius": 0.6, "ionic_radius": 0.46}}, "VI": {"": {"crystal_radius": 0.68, "ionic_radius": 0.54}}}}, "Superconduction temperature": "5.40 K", "Thermal conductivity": "31 W m-1 K-1", "Van der waals radius": 2.07, "Velocity of sound": "4560 m s-1", "Vickers hardness": "628 MN m-2", "X": 1.63, "Youngs modulus": "128 GPa", "NMR Quadrupole Moment": {"V-50": 210.4, "V-51": -52.1}, "Metallic radius": 1.347, "iupac_ordering": 55, "IUPAC ordering": 55, "Ground level": "4F3/2", "Ionization energies": [6.746187, 14.634, 29.3111, 46.709, 65.28165, 128.125, 150.72, 173.55, 206.0, 230.5, 254.8, 308.5, 336.274, 896.0, 977.2, 1062.9, 1165.2, 1258.9, 1354.2, 1486.7, 1569.656, 6851.3109, 7246.1226], "Electron affinity": 0.527662}, "W": {"Atomic mass": 183.84, "Atomic no": 74, "Atomic orbitals": {"1s": -2341.042887, "2p": -369.013973, "2s": -384.856157, "3d": -66.724787, "3p": -80.502102, "3s": -87.867792, "4d": -8.879693, "4f": -1.550835, "4p": -14.495102, "4s": -17.570797, "5d": -0.220603, "5p": -1.504457, "5s": -2.396018, "6s": -0.181413}, "Atomic radius": 1.35, "Atomic radius calculated": 1.93, "Boiling point": "5828 K", "Brinell hardness": "2570 MN m-2", "Bulk modulus": "310 GPa", "Coefficient of linear thermal expansion": "4.5 x10-6K-1", "Common oxidation states": [4, 6], "Critical temperature": "no data K", "Density of solid": "19250 kg m-3", "Electrical resistivity": "5.4 10-8 Ω m", "Electronic structure": "[Xe].4f14.5d4.6s2", "ICSD oxidation states": [2, 3, 4, 5, 6], "Ionic radii": {"4": 0.8, "5": 0.76, "6": 0.74}, "Liquid range": "2133 K", "Melting point": "3695 K", "Mendeleev no": 55, "Mineral hardness": "7.5", "Molar volume": "9.47 cm3", "Name": "Tungsten", "Oxidation states": [-2, -1, 1, 2, 3, 4, 5, 6], "Poissons ratio": "0.28", "Reflectivity": "62 %", "Refractive index": "no data", "Rigidity modulus": "161 GPa", "Shannon radii": {"4": {"VI": {"": {"crystal_radius": 0.8, "ionic_radius": 0.66}}}, "5": {"VI": {"": {"crystal_radius": 0.76, "ionic_radius": 0.62}}}, "6": {"IV": {"": {"crystal_radius": 0.56, "ionic_radius": 0.42}}, "V": {"": {"crystal_radius": 0.65, "ionic_radius": 0.51}}, "VI": {"": {"crystal_radius": 0.74, "ionic_radius": 0.6}}}}, "Superconduction temperature": "0.015 K", "Thermal conductivity": "170 W m-1 K-1", "Van der waals radius": 2.18, "Velocity of sound": "5174 m s-1", "Vickers hardness": "3430 MN m-2", "X": 2.36, "Youngs modulus": "411 GPa", "Metallic radius": 1.41, "iupac_ordering": 56, "IUPAC ordering": 56, "Ground level": "5D0", "Ionization energies": [7.86403, 16.37, 26.0, 38.2, 51.6, 64.77, 122.01, 141.2, 160.2, 179.0, 208.9, 231.6, 258.3, 290.7, 325.3, 361.9, 387.9, 420.7, 462.1, 502.6, 543.4, 594.5, 640.6, 685.6, 734.1, 784.4, 833.4, 881.4, 1132.2, 1180.0, 1230.4, 1283.4, 1335.1, 1386.8, 1459.9, 1512.4, 1569.1, 1621.7, 1829.8, 1882.9, 1940.6, 1994.8, 2149.1, 2210.0, 2354.5, 2414.1, 4057.0, 4180.0, 4309.0, 4446.0, 4578.0, 4709.0, 4927.0, 5063.0, 5209.0, 5348.0, 5719.0, 5840.0, 5970.0, 6093.0, 6596.0, 6735.0, 7000.0, 7130.0, 15566.0, 15896.0, 16252.0, 16588.0, 18476.0, 18872.0, 19362.0, 19686.74, 79181.94, 80755.6], "Electron affinity": 0.816268}, "Xe": {"Atomic mass": 131.293, "Atomic no": 54, "Atomic orbitals": {"1s": -1208.688993, "2p": -172.599583, "2s": -183.327495, "3d": -24.37823, "3p": -32.867042, "3s": -37.415454, "4d": -2.286666, "4p": -5.063802, "4s": -6.67834, "5p": -0.309835, "5s": -0.672086}, "Atomic radius": "no data", "Atomic radius calculated": 1.08, "Boiling point": "165.1 K", "Brinell hardness": "no data MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "no data x10-6K-1", "Critical temperature": "289.7 K", "Density of solid": "no data kg m-3", "Electrical resistivity": "no data 10-8 Ω m", "Electronic structure": "[Kr].4d10.5s2.5p6", "Ionic radii": {"8": 0.62}, "Liquid range": "3.7 K", "Max oxidation state": 8.0, "Melting point": "161.4 K", "Mendeleev no": 5, "Min oxidation state": 2.0, "Mineral hardness": "no data", "Molar volume": "35.92 cm3", "Name": "Xenon", "Poissons ratio": "no data", "Reflectivity": "no data %", "Refractive index": "1.000702", "Rigidity modulus": "no data GPa", "Shannon radii": {"8": {"IV": {"": {"crystal_radius": 0.54, "ionic_radius": 0.4}}, "VI": {"": {"crystal_radius": 0.62, "ionic_radius": 0.48}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "0.00565 W m-1 K-1", "Van der waals radius": 2.16, "Velocity of sound": "1090 m s-1", "Vickers hardness": "no data MN m-2", "X": 2.6, "Youngs modulus": "no data GPa", "Metallic radius": "no data", "iupac_ordering": 1, "IUPAC ordering": 1, "Ground level": "1S0", "Ionization energies": [12.1298437, 20.975, 31.05, 42.2, 54.1, 66.703, 91.6, 105.9778, 179.84, 202.0, 229.02, 255.0, 281.0, 314.0, 343.0, 374.0, 404.0, 434.0, 549.0, 582.0, 616.0, 650.0, 700.0, 736.0, 818.0, 857.0, 1493.0, 1571.0, 1653.0, 1742.0, 1826.0, 1919.0, 2023.0, 2113.0, 2209.0, 2300.0, 2556.0, 2637.0, 2726.0, 2811.0, 2975.0, 3068.0, 3243.0, 3333.8, 7660.0, 7889.0, 8144.0, 8382.0, 8971.0, 9243.0, 9581.0, 9810.37, 40271.724, 41299.71], "Electron affinity": -0.82}, "Y": {"Atomic mass": 88.90585, "Atomic no": 39, "Atomic orbitals": {"1s": -605.631981, "2p": -74.803201, "2s": -81.789102, "3d": -5.671499, "3p": -10.399926, "3s": -12.992217, "4d": -0.108691, "4p": -1.02449, "4s": -1.697124, "5s": -0.150727}, "Atomic radius": 1.8, "Atomic radius calculated": 2.12, "Boiling point": "3609 K", "Brinell hardness": "589 MN m-2", "Bulk modulus": "41 GPa", "Coefficient of linear thermal expansion": "10.6 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "4472 kg m-3", "Electrical resistivity": "about 60 10-8 Ω m", "Electronic structure": "[Kr].4d1.5s2", "ICSD oxidation states": [3], "Ionic radii": {"3": 1.04}, "Liquid range": "1810 K", "Melting point": "1799 K", "Mendeleev no": 25, "Mineral hardness": "no data", "Molar volume": "19.88 cm3", "Name": "Yttrium", "Oxidation states": [1, 2, 3], "Poissons ratio": "0.24", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "26 GPa", "Shannon radii": {"3": {"VI": {"": {"crystal_radius": 1.04, "ionic_radius": 0.9}}, "VII": {"": {"crystal_radius": 1.1, "ionic_radius": 0.96}}, "VIII": {"": {"crystal_radius": 1.159, "ionic_radius": 1.019}}, "IX": {"": {"crystal_radius": 1.215, "ionic_radius": 1.075}}}}, "Superconduction temperature": "1.3 (under pressure)K", "Thermal conductivity": "17 W m-1 K-1", "Van der waals radius": 2.32, "Velocity of sound": "3300 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.22, "Youngs modulus": "64 GPa", "Metallic radius": 1.8, "iupac_ordering": 48, "IUPAC ordering": 48, "Ground level": "2D3/2", "Ionization energies": [6.21726, 12.2236, 20.52441, 60.6072, 75.35, 91.39, 110.02, 128.12, 145.64, 185.7, 205.814, 374.04, 414.0, 463.0, 512.0, 559.0, 624.0, 677.0, 733.0, 790.0, 847.0, 1010.0, 1061.9, 1120.2, 1190.0, 1253.0, 1300.0, 1427.6, 1483.12, 3562.9, 3720.0, 3892.0, 4060.0, 4299.0, 4484.0, 4724.0, 4875.731, 20415.717, 21115.55], "Electron affinity": 0.30712}, "Yb": {"Atomic mass": 173.04, "Atomic no": 70, "Atomic orbitals": {"1s": -2084.069389, "2p": -323.178219, "2s": -337.978976, "3d": -56.026315, "3p": -68.698655, "3s": -75.47663, "4d": -6.574963, "4f": -0.286408, "4p": -11.558246, "4s": -14.312076, "5p": -0.966137, "5s": -1.683886, "6s": -0.136989}, "Atomic radius": 1.75, "Atomic radius calculated": 2.22, "Boiling point": "1469 K", "Brinell hardness": "343 MN m-2", "Bulk modulus": "31 GPa", "Coefficient of linear thermal expansion": "26.3 x10-6K-1", "Common oxidation states": [3], "Critical temperature": "no data K", "Density of solid": "6570 kg m-3", "Electrical resistivity": "25.0 10-8 Ω m", "Electronic structure": "[Xe].4f14.6s2", "ICSD oxidation states": [2, 3], "Ionic radii": {"2": 1.16, "3": 1.008}, "Liquid range": "372 K", "Melting point": "1097 K", "Mendeleev no": 17, "Mineral hardness": "no data", "Molar volume": "24.84 cm3", "Name": "Ytterbium", "Oxidation states": [2, 3], "Poissons ratio": "0.21", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "9.9 GPa", "Shannon radii": {"2": {"VI": {"": {"crystal_radius": 1.16, "ionic_radius": 1.02}}, "VII": {"": {"crystal_radius": 1.22, "ionic_radius": 1.08}}, "VIII": {"": {"crystal_radius": 1.28, "ionic_radius": 1.14}}}, "3": {"VI": {"": {"crystal_radius": 1.008, "ionic_radius": 0.868}}, "VII": {"": {"crystal_radius": 1.065, "ionic_radius": 0.925}}, "VIII": {"": {"crystal_radius": 1.125, "ionic_radius": 0.985}}, "IX": {"": {"crystal_radius": 1.182, "ionic_radius": 1.042}}}}, "Superconduction temperature": "no data K", "Thermal conductivity": "39 W m-1 K-1", "Van der waals radius": 2.26, "Velocity of sound": "1590 m s-1", "Vickers hardness": "206 MN m-2", "X": 1.1, "Youngs modulus": "24 GPa", "Metallic radius": 1.94, "iupac_ordering": 34, "IUPAC ordering": 34, "Ground level": "1S0", "Ionization energies": [6.25416, 12.179185, 25.053, 43.61, 65.6, 99.0, 117.0, 135.0, 163.0, 182.0, 209.0, 244.0, 279.0, 301.0, 324.0, 360.0, 396.0, 431.0, 469.0, 505.0, 540.0, 580.0, 610.0, 651.0, 882.0, 924.0, 971.0, 1019.0, 1065.0, 1114.0, 1175.0, 1224.0, 1275.0, 1324.0, 1516.0, 1564.0, 1618.0, 1668.0, 1789.0, 1845.0, 1978.0, 2036.4, 3443.0, 3555.0, 3677.0, 3805.0, 3929.0, 4051.0, 4238.0, 4364.0, 4502.0, 4630.0, 4988.0, 5101.0, 5224.0, 5339.0, 5731.0, 5860.0, 6111.0, 6236.0, 13784.0, 14093.0, 14435.0, 14752.0, 16191.0, 16570.0, 17050.0, 17365.44, 70123.04, 71574.8], "Electron affinity": -0.02}, "Zn": {"Atomic mass": 65.409, "Atomic no": 30, "Atomic orbitals": {"1s": -344.969756, "2p": -36.648765, "2s": -41.531323, "3d": -0.398944, "3p": -3.022363, "3s": -4.573041, "4s": -0.222725}, "Atomic radius": 1.35, "Atomic radius calculated": 1.42, "Boiling point": "1180 K", "Brinell hardness": "412 MN m-2", "Bulk modulus": "70 GPa", "Coefficient of linear thermal expansion": "30.2 x10-6K-1", "Common oxidation states": [2], "Critical temperature": "no data K", "Density of solid": "7140 kg m-3", "Electrical resistivity": "6.0 10-8 Ω m", "Electronic structure": "[Ar].3d10.4s2", "ICSD oxidation states": [2], "Ionic radii": {"2": 0.88}, "Liquid range": "487.32 K", "Melting point": "692.68 K", "Mendeleev no": 76, "Mineral hardness": "2.5", "Molar volume": "9.16 cm3", "Name": "Zinc", "Oxidation states": [1, 2], "Poissons ratio": "0.25", "Reflectivity": "80 %", "Refractive index": "1.002050", "Rigidity modulus": "43 GPa", "Shannon radii": {"2": {"IV": {"": {"crystal_radius": 0.74, "ionic_radius": 0.6}}, "V": {"": {"crystal_radius": 0.82, "ionic_radius": 0.68}}, "VI": {"": {"crystal_radius": 0.88, "ionic_radius": 0.74}}, "VIII": {"": {"crystal_radius": 1.04, "ionic_radius": 0.9}}}}, "Superconduction temperature": "0.85 K", "Thermal conductivity": "120 W m-1 K-1", "Van der waals radius": 2.01, "Velocity of sound": "3700 m s-1", "Vickers hardness": "no data MN m-2", "X": 1.65, "Youngs modulus": "108 GPa", "NMR Quadrupole Moment": {"Zn-67": 150.15}, "Metallic radius": 1.34, "iupac_ordering": 76, "IUPAC ordering": 76, "Ground level": "1S0", "Ionization energies": [9.394197, 17.96439, 39.7233, 59.573, 82.6, 108.0, 133.9, 173.9, 203.0, 238.0, 274.4, 310.8, 417.6, 453.4, 490.6, 540.0, 577.8, 613.3, 697.5, 737.366, 1846.8, 1961.0, 2085.0, 2214.0, 2358.0, 2491.5, 2669.9, 2781.996, 11864.9399, 12388.929], "Electron affinity": -0.62}, "Zr": {"Atomic mass": 91.224, "Atomic no": 40, "Atomic orbitals": {"1s": -639.292236, "2p": -80.010043, "2s": -87.237062, "3d": -6.544643, "3p": -11.514415, "3s": -14.230432, "4d": -0.150673, "4p": -1.186597, "4s": -1.918971, "5s": -0.162391}, "Atomic radius": 1.55, "Atomic radius calculated": 2.06, "Boiling point": "4682 K", "Brinell hardness": "650 MN m-2", "Bulk modulus": "no data GPa", "Coefficient of linear thermal expansion": "5.7 x10-6K-1", "Common oxidation states": [4], "Critical temperature": "no data K", "Density of solid": "6511 kg m-3", "Electrical resistivity": "43.3 10-8 Ω m", "Electronic structure": "[Kr].4d2.5s2", "ICSD oxidation states": [2, 3, 4], "Ionic radii": {"4": 0.86}, "Liquid range": "2554 K", "Melting point": "2128 K", "Mendeleev no": 49, "Mineral hardness": "5.0", "Molar volume": "14.02 cm3", "Name": "Zirconium", "Oxidation states": [1, 2, 3, 4], "Poissons ratio": "0.34", "Reflectivity": "no data %", "Refractive index": "no data", "Rigidity modulus": "33 GPa", "Shannon radii": {"4": {"IV": {"": {"crystal_radius": 0.73, "ionic_radius": 0.59}}, "V": {"": {"crystal_radius": 0.8, "ionic_radius": 0.66}}, "VI": {"": {"crystal_radius": 0.86, "ionic_radius": 0.72}}, "VII": {"": {"crystal_radius": 0.92, "ionic_radius": 0.78}}, "VIII": {"": {"crystal_radius": 0.98, "ionic_radius": 0.84}}, "IX": {"": {"crystal_radius": 1.03, "ionic_radius": 0.89}}}}, "Superconduction temperature": "0.61 K", "Thermal conductivity": "23 W m-1 K-1", "Van der waals radius": 2.23, "Velocity of sound": "3800 m s-1", "Vickers hardness": "903 MN m-2", "X": 1.33, "Youngs modulus": "68 GPa", "Metallic radius": 1.602, "iupac_ordering": 51, "IUPAC ordering": 51, "Ground level": "3F2", "Ionization energies": [6.634126, 13.13, 23.17, 34.41836, 80.348, 96.38, 112.0, 133.7, 153.0, 172.02, 214.9, 236.252, 426.0, 470.0, 520.0, 573.0, 622.0, 690.0, 745.0, 803.0, 863.0, 922.0, 1092.0, 1144.7, 1205.4, 1277.0, 1344.0, 1392.0, 1525.1, 1582.37, 3788.0, 3950.0, 4127.0, 4300.0, 4553.0, 4744.0, 4991.0, 5146.935, 21516.469, 22236.678], "Electron affinity": 0.433289}, "Rf": {"Atomic mass": 267, "Atomic no": 104, "Name": "Rutherfordium", "Ground level": "3F2", "Ionization energies": [6.02, 14.35, 23.84, 31.87, 64.0, 77.0, 102.0, 119.0, 146.1, 169.0, 193.0, 225.0, 244.0, 275.0, null, 791.0, 825.0, 860.0, 899.0, 936.0, 972.0, 1036.0, 1073.0, 1114.0, 1151.0, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, 3857.0, 3938.0, 4025.0, 4116.0, 4203.0, 4287.0, 4489.0, 4580.0, 4670.0, 4760.0, 5130.0, 5210.0, 5300.0, 5390.0, 6100.0, 6200.0, 6470.0, 6570.0, 10170.0, 10360.0, 10560.0, 10780.0, 10980.0, 11180.0, 11750.0, 11960.0, 12200.0, 12410.0, 13010.0, 13190.0, 13400.0, 13600.0, 15800.0, 16000.0, 16400.0, 16700.0, 33100.0, 33600.0, 34100.0, 34600.0, 42700.0, 43400.0, 44300.0, null, null, 177148.0], "Electron affinity": null, "Van der waals radius": "no data"}, "Db": {"Atomic mass": 268, "Atomic no": 105, "Name": "Dubnium", "Ground level": "4F3/2", "Ionization energies": [6.8, 14.0, 23.1, 33.0, 43.0, 86.0, 98.9, 126.0, 145.1, 172.0, 196.0, 220.9, 254.0, 274.0, 307.0, null, 838.0, 872.0, 908.0, 948.0, 985.0, 1022.0, 1089.0, 1126.0, 1168.0, 1207.0, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, 3975.0, 4057.0, 4145.0, 4237.0, 4326.0, 4411.0, 4620.0, 4710.0, 4810.0, 4900.0, 5260.0, 5350.0, 5450.0, 5530.0, 6280.0, 6380.0, 6650.0, 6760.0, 10420.0, 10610.0, 10820.0, 11040.0, 11240.0, 11440.0, 12040.0, 12250.0, 12480.0, 12700.0, 13300.0, 13500.0, 13700.0, 13900.0, 16200.0, 16400.0, 16900.0, 17100.0, 33800.0, 34300.0, 34800.0, 35300.0, 43800.0, 44500.0, 45400.0, null, null, 181444.0], "Electron affinity": null, "Van der waals radius": "no data"}, "Sg": {"Atomic mass": 269, "Atomic no": 106, "Name": "Seaborgium", "Ground level": "0", "Ionization energies": [7.8, 17.1, 25.8, 35.5, 47.2, 59.3, 109.0, 122.0, 152.0, 170.0, 200.0, 224.0, 251.0, 285.0, 306.0, 339.0, null, 885.0, 921.0, 958.0, 998.0, 1036.0, 1073.0, 1143.0, 1181.0, 1223.0, 1263.0, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, 4095.0, 4178.0, 4267.0, 4360.0, 4450.0, 4540.0, 4750.0, 4840.0, 4940.0, 5030.0, 5410.0, 5490.0, 5590.0, 5680.0, 6460.0, 6570.0, 6840.0, 6950.0, 10680.0, 10870.0, 11080.0, 11300.0, 11510.0, 11710.0, 12320.0, 12540.0, 12780.0, 12990.0, 13600.0, 13800.0, 14000.0, 14200.0, 16600.0, 16800.0, 17300.0, 17500.0, 34500.0, 35000.0, 35600.0, 36100.0, 44900.0, 45700.0, 46600.0, null, null, 185839.0], "Electron affinity": null, "Van der waals radius": "no data"}, "Bh": {"Atomic mass": 270, "Atomic no": 107, "Name": "Bohrium", "Ground level": "5/2", "Ionization energies": [7.7, 17.5, 26.7, 37.3, 49.0, 62.1, 74.9, 134.0, 148.0, 178.0, 198.0, 228.0, 255.0, 281.0, 318.0, 337.0, 374.0, null, 934.0, 969.0, 1008.0, 1049.0, 1088.0, 1126.0, 1197.0, 1237.0, 1280.0, 1320.0, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, 4216.0, 4301.0, 4390.0, 4486.0, 4580.0, 4660.0, 4890.0, 4980.0, 5080.0, 5170.0, 5550.0, 5640.0, 5740.0, 5830.0, 6650.0, 6760.0, 7040.0, 7140.0, 10930.0, 11130.0, 11340.0, 11560.0, 11780.0, 11980.0, 12610.0, 12830.0, 13070.0, 13300.0, 13900.0, 14100.0, 14300.0, 14500.0, 17000.0, 17300.0, 17700.0, 18000.0, 35200.0, 35700.0, 36300.0, 36800.0, 46100.0, 46900.0, 47800.0, null, null, 190331.0], "Electron affinity": null, "Van der waals radius": "no data"}, "Hs": {"Atomic mass": 270, "Atomic no": 108, "Name": "Hassium", "Ground level": "4", "Ionization energies": [7.6, 18.2, 29.3, 37.7, 51.2, 64.0, 78.1, 91.7, 159.9, 173.9, 206.1, 227.0, 258.0, 285.0, 314.0, 351.0, 371.0, 409.0, null, 984.0, 1020.0, 1060.0, 1101.0, 1140.0, 1180.0, 1253.0, 1294.0, 1338.0, 1379.0, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, 4339.0, 4425.0, 4516.0, 4610.0, 4700.0, 4790.0, 5020.0, 5110.0, 5220.0, 5310.0, 5700.0, 5780.0, 5880.0, 5980.0, 6840.0, 6950.0, 7230.0, 7340.0, 11200.0, 11390.0, 11610.0, 11830.0, 12040.0, 12250.0, 12910.0, 13130.0, 13400.0, 13600.0, 14200.0, 14400.0, 14600.0, 14800.0, 17500.0, 17700.0, 18200.0, 18400.0, 35900.0, 36400.0, 37000.0, 37500.0, 47300.0, 48100.0, 49000.0, null, null, 194917.0], "Electron affinity": null, "Van der waals radius": "no data"}, "Mt": {"Atomic mass": 278, "Atomic no": 109, "Name": "Meitnerium", "Ground level": null, "Ionization energies": [50.0, null, null, 94.0, 109.0, 187.0, 202.0, 235.9, 257.0, 289.0, 318.0, 346.0, 386.0, 406.0, 445.0, null, 1035.0, 1072.0, 1112.0, 1154.0, 1195.0, 1234.0, 1311.0, 1352.0, 1397.0, 1439.0, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, 4464.0, 4551.0, 4640.0, 4740.0, 4830.0, 4920.0, 5160.0, 5250.0, 5360.0, 5450.0, 5840.0, 5930.0, 6030.0, 6130.0, 7030.0, 7150.0, 7430.0, 7550.0, 11460.0, 11660.0, 11870.0, 12100.0, 12320.0, 12530.0, 13200.0, 13400.0, 13700.0, 13900.0, 14500.0, 14700.0, 14900.0, 15100.0, 17900.0, 18200.0, 18700.0, 18900.0, 36700.0, 37200.0, 37800.0, 38300.0, 48500.0, 49400.0, 50300.0, null, null, 199606.0], "Electron affinity": null, "Van der waals radius": "no data"}, "Ds": {"Atomic mass": 281, "Atomic no": 110, "Name": "Darmstadtium", "Ground level": null, "Ionization energies": [65.0, null, null, 112.9, 128.0, 216.0, 231.0, 266.0, 288.0, 322.0, 352.0, 380.0, 422.0, 442.0, 483.0, null, 1087.0, 1125.0, 1165.0, 1208.0, 1250.0, 1290.0, 1369.0, 1412.0, 1457.0, 1500.0, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, 4590.0, 4680.0, 4770.0, 4870.0, 4960.0, 5060.0, 5300.0, 5400.0, 5500.0, 5600.0, 5990.0, 6080.0, 6190.0, 6280.0, 7230.0, 7350.0, 7640.0, 7750.0, 11730.0, 11930.0, 12140.0, 12380.0, 12600.0, 12810.0, 13500.0, 13700.0, 14000.0, 14200.0, 14800.0, 15000.0, 15300.0, 15500.0, 18400.0, 18600.0, 19100.0, 19400.0, 37400.0, 37900.0, 38500.0, 39100.0, 49800.0, 50700.0, 51600.0, null, null, 204400.0], "Electron affinity": null, "Van der waals radius": "no data"}, "Rg": {"Atomic mass": 282, "Atomic no": 111, "Name": "Roentgenium", "Ground level": null, "Ionization energies": [], "Electron affinity": 1.565, "Van der waals radius": "no data"}, "Cn": {"Atomic mass": 285, "Atomic no": 112, "Name": "Copernicium", "Ground level": null, "Ionization energies": [], "Electron affinity": null, "Van der waals radius": "no data"}, "Nh": {"Atomic mass": 286, "Atomic no": 113, "Name": "Nihonium", "Ground level": null, "Ionization energies": [], "Electron affinity": 0.69, "Van der waals radius": "no data"}, "Fl": {"Atomic mass": 289, "Atomic no": 114, "Name": "Flerovium", "Ground level": null, "Ionization energies": [], "Electron affinity": null, "Van der waals radius": "no data"}, "Mc": {"Atomic mass": 290, "Atomic no": 115, "Name": "Moscovium", "Ground level": null, "Ionization energies": [], "Electron affinity": 0.366, "Van der waals radius": "no data"}, "Lv": {"Atomic mass": 293, "Atomic no": 116, "Name": "Livermorium", "Ground level": null, "Ionization energies": [], "Electron affinity": 0.776, "Van der waals radius": "no data"}, "Ts": {"Atomic mass": 294, "Atomic no": 117, "Name": "Tennessine", "Ground level": null, "Ionization energies": [], "Electron affinity": 1.719, "Van der waals radius": "no data"}, "Og": {"Atomic mass": 294, "Atomic no": 118, "Name": "Oganesson", "Ground level": null, "Ionization energies": [], "Electron affinity": 0.0561, "Van der waals radius": "no data"}, "D": {"Atomic no": 1, "Atomic mass": 2.013553212712, "Atomic mass no": 2, "Common oxidation states": [-1, 1], "Is named isotope": true, "Name": "Deuterium", "Oxidation states": [-1, 1], "Shannon radii": {"1": {"II": {"": {"crystal_radius": 0.04, "ionic_radius": -0.1}}}}, "Electron affinity": 0.754674}, "T": {"Atomic no": 1, "Atomic mass": 3.0155007134, "Atomic mass no": 3, "Common oxidation states": [-1, 1], "Is named isotope": true, "Name": "Tritium", "Oxidation states": [-1, 1], "Electron affinity": null}} diff --git a/pymatgen/io/aims/sets/core.py b/pymatgen/io/aims/sets/core.py deleted file mode 100644 index db689c60701..00000000000 --- a/pymatgen/io/aims/sets/core.py +++ /dev/null @@ -1,99 +0,0 @@ -"""Module defining core FHI-aims input set generators.""" - -from __future__ import annotations - -from dataclasses import dataclass -from typing import TYPE_CHECKING - -from pymatgen.core import Structure -from pymatgen.io.aims.sets.base import AimsInputGenerator - -if TYPE_CHECKING: - from typing import Any - - from pymatgen.core import Molecule - - -@dataclass -class StaticSetGenerator(AimsInputGenerator): - """Common class for ground-state generators. - - Attributes: - calc_type (str): The type of calculation - """ - - calc_type: str = "static" - - def get_parameter_updates(self, structure: Structure | Molecule, prev_parameters: dict[str, Any]) -> dict[str, Any]: - """Get the parameter updates for the calculation. - - Args: - structure (Structure or Molecule): The structure to calculate the bands for - prev_parameters (Dict[str, Any]): The previous parameters - - Returns: - dict: The updated for the parameters for the output section of FHI-aims - """ - return prev_parameters - - -@dataclass -class RelaxSetGenerator(AimsInputGenerator): - """Generate FHI-aims relax sets for optimizing internal coordinates and lattice params. - - Attributes: - calc_type (str): The type of calculation - relax_cell (bool): If True then relax the unit cell from the structure - max_force (float): Maximum allowed force in the calculation - method (str): Method used for the geometry optimization - """ - - calc_type: str = "relaxation" - relax_cell: bool = True - max_force: float = 1e-3 - method: str = "trm" - - def get_parameter_updates(self, structure: Structure | Molecule, prev_parameters: dict[str, Any]) -> dict: - """Get the parameter updates for the calculation. - - Args: - structure (Structure or Molecule): The structure to calculate the bands for - prev_parameters (Dict[str, Any]): The previous parameters - - Returns: - dict: The updated for the parameters for the output section of FHI-aims - """ - updates = {"relax_geometry": f"{self.method} {self.max_force:e}"} - if isinstance(structure, Structure) and self.relax_cell: - updates["relax_unit_cell"] = "full" - elif isinstance(structure, Structure): - updates["relax_unit_cell"] = "none" - - return updates - - -@dataclass -class SocketIOSetGenerator(AimsInputGenerator): - """Generate FHI-aims input sets for running with the socket. - - Attributes: - calc_type (str): The type of calculation - host (str): The hostname for the server the socket is on - port (int): The port the socket server is listening on - """ - - calc_type: str = "multi_scf" - host: str = "localhost" - port: int = 12345 - - def get_parameter_updates(self, structure: Structure | Molecule, prev_parameters: dict[str, Any]) -> dict: - """Get the parameter updates for the calculation. - - Args: - structure (Structure or Molecule): The structure to calculate the bands for - prev_parameters (Dict[str, Any]): The previous parameters - - Returns: - dict: The updated for the parameters for the output section of FHI-aims - """ - return {"use_pimd_wrapper": (self.host, self.port)} diff --git a/pymatgen/symmetry/symm_data.json b/pymatgen/symmetry/symm_data.json deleted file mode 100644 index 067fcfe61fe..00000000000 --- a/pymatgen/symmetry/symm_data.json +++ /dev/null @@ -1 +0,0 @@ -{"abbreviated_spacegroup_symbols": {"C2": "C121", "C2/c": "C12/c1", "C2/m": "C12/m1", "Cc": "C1c1", "Cm": "C1m1", "P2": "P121", "P2/c": "P12/c1", "P2/m": "P12/m1", "P2_1": "P12_11", "P2_1/c": "P12_1/c1", "P2_1/m": "P12_1/m1", "Pc": "P1c1", "Pm": "P1m1"}, "generator_matrices": {"a": [[1, 0, 0], [0, 1, 0], [0, 0, 1]], "b": [[-1, 0, 0], [0, -1, 0], [0, 0, 1]], "c": [[-1, 0, 0], [0, 1, 0], [0, 0, -1]], "d": [[0, 0, 1], [1, 0, 0], [0, 1, 0]], "e": [[0, 1, 0], [1, 0, 0], [0, 0, -1]], "f": [[0, -1, 0], [-1, 0, 0], [0, 0, -1]], "g": [[0, -1, 0], [1, 0, 0], [0, 0, 1]], "h": [[-1, 0, 0], [0, -1, 0], [0, 0, -1]], "i": [[1, 0, 0], [0, 1, 0], [0, 0, -1]], "j": [[1, 0, 0], [0, -1, 0], [0, 0, 1]], "k": [[0, -1, 0], [-1, 0, 0], [0, 0, 1]], "l": [[0, 1, 0], [1, 0, 0], [0, 0, 1]], "m": [[0, 1, 0], [-1, 0, 0], [0, 0, -1]], "n": [[0, -1, 0], [1, -1, 0], [0, 0, 1]]}, "maximal_subgroups": {"1": [1], "2": [1, 2], "3": [1, 3, 4, 5], "4": [1, 4], "5": [1, 3, 4, 5], "6": [1, 6, 7, 8], "7": [1, 7, 9], "8": [1, 6, 7, 8, 9], "9": [1, 7, 9], "10": [2, 3, 6, 10, 11, 12, 13], "11": [2, 4, 6, 11, 14], "12": [2, 5, 8, 10, 11, 12, 13, 14, 15], "13": [2, 3, 7, 13, 14, 15], "14": [2, 4, 7, 14], "15": [2, 5, 9, 13, 14, 15], "16": [3, 16, 17, 21, 22], "17": [3, 4, 17, 18, 20], "18": [3, 4, 18, 19], "19": [4, 19], "20": [4, 5, 17, 18, 19, 20], "21": [3, 5, 16, 17, 18, 20, 21, 23, 24], "22": [5, 20, 21, 22], "23": [5, 16, 18, 23], "24": [5, 17, 19, 24], "25": [3, 6, 25, 26, 27, 28, 35, 38, 39, 42], "26": [4, 6, 7, 26, 29, 31, 36], "27": [3, 7, 27, 30, 37], "28": [3, 6, 7, 28, 29, 30, 31, 32, 40, 41], "29": [4, 7, 29, 33], "30": [3, 7, 30, 34], "31": [4, 6, 7, 31, 33], "32": [3, 7, 32, 33, 34], "33": [4, 7, 33], "34": [3, 7, 34, 43], "35": [3, 8, 25, 28, 32, 35, 36, 37, 44, 45, 46], "36": [4, 8, 9, 26, 29, 31, 33, 36], "37": [3, 9, 27, 30, 34, 37], "38": [5, 6, 8, 25, 26, 30, 31, 38, 40, 44, 46], "39": [5, 7, 8, 26, 27, 28, 29, 39, 41, 45, 46], "40": [5, 6, 9, 28, 31, 33, 34, 40], "41": [5, 7, 9, 29, 30, 32, 33, 41], "42": [5, 8, 35, 36, 37, 38, 39, 40, 41, 42], "43": [5, 9, 43], "44": [5, 8, 25, 31, 34, 44], "45": [5, 9, 27, 29, 32, 45], "46": [5, 8, 9, 26, 28, 30, 33, 46], "47": [10, 16, 25, 47, 49, 51, 65, 67, 69], "48": [13, 16, 34, 48, 70], "49": [10, 13, 16, 27, 28, 49, 50, 53, 54, 66, 68], "50": [13, 16, 30, 32, 48, 50, 52], "51": [10, 11, 13, 17, 25, 26, 28, 51, 53, 54, 55, 57, 59, 63, 64], "52": [13, 14, 17, 30, 33, 34, 52], "53": [10, 13, 14, 17, 28, 30, 31, 52, 53, 58, 60], "54": [13, 14, 17, 27, 29, 32, 52, 54, 56, 60], "55": [10, 14, 18, 26, 32, 55, 58, 62], "56": [13, 14, 18, 27, 33, 56], "57": [11, 13, 14, 18, 26, 28, 29, 57, 60, 61, 62], "58": [10, 14, 18, 31, 34, 58], "59": [11, 13, 18, 25, 31, 56, 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"patterson_symmetry": "R-3m", "point_group": "-3m"}, "R-3cH": {"enc": "13aECCnOOOeOOD0", "full_symbol": "R-32/c", "int_number": 167, "order": 36, "patterson_symmetry": "R-3m", "point_group": "-3m"}, "R-3m": {"enc": "12dOOOfOOO0", "full_symbol": "R-32/m", "int_number": 166, "order": 12, "patterson_symmetry": "R-3m", "point_group": "-3m"}, "R-3mH": {"enc": "13aECCnOOOeOOO0", "full_symbol": "R-32/m", "int_number": 166, "order": 36, "patterson_symmetry": "R-3m", "point_group": "-3m"}, "R3": {"enc": "01dOOO0", "full_symbol": "R3", "int_number": 146, "order": 3, "patterson_symmetry": "R-3", "point_group": "3"}, "R32": {"enc": "02dOOOfOOO0", "full_symbol": "R32", "int_number": 155, "order": 6, "patterson_symmetry": "R-3m", "point_group": "32"}, "R32H": {"enc": "03aECCnOOOeOOO0", "full_symbol": "R32", "int_number": 155, "order": 18, "patterson_symmetry": "R-3m", "point_group": "32"}, "R3H": {"enc": "02aECCnOOO0", "full_symbol": "R3", "int_number": 146, "order": 9, "patterson_symmetry": "R-3", "point_group": "3"}, "R3c": {"enc": "02dOOOlDDD0", "full_symbol": "R3c", "int_number": 161, "order": 6, "patterson_symmetry": "R-3m", "point_group": "3m"}, "R3cH": {"enc": "03aECCnOOOkOOD0", "full_symbol": "R3c", "int_number": 161, "order": 18, "patterson_symmetry": "R-3m", "point_group": "3m"}, "R3m": {"enc": "02dOOOlOOO0", "full_symbol": "R3m", "int_number": 160, "order": 6, "patterson_symmetry": "R-3m", "point_group": "3m"}, "R3mH": {"enc": "03aECCnOOOkOOO0", "full_symbol": "R3m", "int_number": 160, "order": 18, "patterson_symmetry": "R-3m", "point_group": "3m"}}, "translations": {"A": "1/6", "B": "1/4", "C": "1/3", "D": "1/2", "E": "2/3", "F": "3/4", "G": "5/6", "O": "0", "X": "-3/8", "Y": "-1/4", "Z": "-1/8"}} diff --git a/pymatgen/symmetry/symm_ops.json b/pymatgen/symmetry/symm_ops.json deleted file mode 100644 index 13927a5a1bd..00000000000 --- a/pymatgen/symmetry/symm_ops.json +++ /dev/null @@ -1 +0,0 @@ -[{"symops": ["x,y,z"], "universal_h_m": "P 1", "number": 1, "schoenflies": "C1^1", "hall": " P 1", "hermann_mauguin": "P 1", "crystal_class": "triclinic", "ncsym": ["x,y,z"]}, {"symops": ["x,y,z", "-x,-y,-z"], "universal_h_m": "P -1", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1", "hermann_mauguin": "P -1", "crystal_class": "triclinic", "ncsym": ["x,y,z", "-x,-y,-z"]}, {"symops": ["x,y,z", "-x,y,-z"], "universal_h_m": "P 1 2 1", "number": 3, "schoenflies": "C2^1", "hall": " P 2y", "hermann_mauguin": "P 1 2 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z"], "universal_h_m": "P 1 1 2", "number": 3, "schoenflies": "C2^1", "hall": " P 2", "hermann_mauguin": "P 1 1 2", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z"]}, {"symops": ["x,y,z", "x,-y,-z"], "universal_h_m": "P 2 1 1", "number": 3, "schoenflies": "C2^1", "hall": " P 2x", "hermann_mauguin": "P 2 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,-z"]}, {"symops": ["x,y,z", "-x,y+1/2,-z"], "universal_h_m": "P 1 21 1", "number": 4, "schoenflies": "C2^2", "hall": " P 2yb", "hermann_mauguin": "P 1 21 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2"], "universal_h_m": "P 1 1 21", "number": 4, "schoenflies": "C2^2", "hall": " P 2c", "hermann_mauguin": "P 1 1 21", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,-y,-z"], "universal_h_m": "P 21 1 1", "number": 4, "schoenflies": "C2^2", "hall": " P 2xa", "hermann_mauguin": "P 21 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,-z"]}, {"symops": ["x,y,z", "-x,y,-z", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "C 1 2 1", "number": 5, "schoenflies": "C2^3", "hall": " C 2y", "hermann_mauguin": "C 1 2 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,y,-z", "x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A 1 2 1", "number": 5, "schoenflies": "C2^3", "hall": " A 2y", "hermann_mauguin": "A 1 2 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I 1 2 1", "number": 5, "schoenflies": "C2^3", "hall": " I 2y", "hermann_mauguin": "I 1 2 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2"], "universal_h_m": "A 1 1 2", "number": 5, "schoenflies": "C2^3", "hall": " A 2", "hermann_mauguin": "A 1 1 2", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2"], "universal_h_m": "B 1 1 2", "number": 5, "schoenflies": "C2^3", "hall": " B 2", "hermann_mauguin": "B 1 1 2", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I 1 1 2", "number": 5, "schoenflies": "C2^3", "hall": " I 2", "hermann_mauguin": "I 1 1 2", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z"]}, {"symops": ["x,y,z", "x,-y,-z", "x+1/2,y,z+1/2", "x+1/2,-y,-z+1/2"], "universal_h_m": "B 2 1 1", "number": 5, "schoenflies": "C2^3", "hall": " B 2x", "hermann_mauguin": "B 2 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,-z"]}, {"symops": ["x,y,z", "x,-y,-z", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,-z"], "universal_h_m": "C 2 1 1", "number": 5, "schoenflies": "C2^3", "hall": " C 2x", "hermann_mauguin": "C 2 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,-z"]}, {"symops": ["x,y,z", "x,-y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2"], "universal_h_m": "I 2 1 1", "number": 5, "schoenflies": "C2^3", "hall": " I 2x", "hermann_mauguin": "I 2 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,-z"]}, {"symops": ["x,y,z", "x,-y,z"], "universal_h_m": "P 1 m 1", "number": 6, "schoenflies": "Cs^1", "hall": " P -2y", "hermann_mauguin": "P 1 m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z"], "universal_h_m": "P 1 1 m", "number": 6, "schoenflies": "Cs^1", "hall": " P -2", "hermann_mauguin": "P 1 1 m", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,y,-z"]}, {"symops": ["x,y,z", "-x,y,z"], "universal_h_m": "P m 1 1", "number": 6, "schoenflies": "Cs^1", "hall": " P -2x", "hermann_mauguin": "P m 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,z"]}, {"symops": ["x,y,z", "x,-y,z+1/2"], "universal_h_m": "P 1 c 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2yc", "hermann_mauguin": "P 1 c 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,-y,z+1/2"], "universal_h_m": "P 1 n 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2yac", "hermann_mauguin": "P 1 n 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,-y,z"], "universal_h_m": "P 1 a 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2ya", "hermann_mauguin": "P 1 a 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x+1/2,y,-z"], "universal_h_m": "P 1 1 a", "number": 7, "schoenflies": "Cs^2", "hall": " P -2a", "hermann_mauguin": "P 1 1 a", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,y,-z"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z"], "universal_h_m": "P 1 1 n", "number": 7, "schoenflies": "Cs^2", "hall": " P -2ab", "hermann_mauguin": "P 1 1 n", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "x,y+1/2,-z"], "universal_h_m": "P 1 1 b", "number": 7, "schoenflies": "Cs^2", "hall": " P -2b", "hermann_mauguin": "P 1 1 b", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,y+1/2,z"], "universal_h_m": "P b 1 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2xb", "hermann_mauguin": "P b 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,z"]}, {"symops": ["x,y,z", "-x,y+1/2,z+1/2"], "universal_h_m": "P n 1 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2xbc", "hermann_mauguin": "P n 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,z+1/2"]}, {"symops": ["x,y,z", "-x,y,z+1/2"], "universal_h_m": "P c 1 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2xc", "hermann_mauguin": "P c 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,z+1/2"]}, {"symops": ["x,y,z", "x,-y,z", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "C 1 m 1", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y", "hermann_mauguin": "C 1 m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,-y,z", "x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A 1 m 1", "number": 8, "schoenflies": "Cs^3", "hall": " A -2y", "hermann_mauguin": "A 1 m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I 1 m 1", "number": 8, "schoenflies": "Cs^3", "hall": " I -2y", "hermann_mauguin": "I 1 m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2"], "universal_h_m": "A 1 1 m", "number": 8, "schoenflies": "Cs^3", "hall": " A -2", "hermann_mauguin": "A 1 1 m", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,y,-z"]}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2"], "universal_h_m": "B 1 1 m", "number": 8, "schoenflies": "Cs^3", "hall": " B -2", "hermann_mauguin": "B 1 1 m", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,y,-z"]}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I 1 1 m", "number": 8, "schoenflies": "Cs^3", "hall": " I -2", "hermann_mauguin": "I 1 1 m", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,y,-z"]}, {"symops": ["x,y,z", "-x,y,z", "x+1/2,y,z+1/2", "-x+1/2,y,z+1/2"], "universal_h_m": "B m 1 1", "number": 8, "schoenflies": "Cs^3", "hall": " B -2x", "hermann_mauguin": "B m 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,z"]}, {"symops": ["x,y,z", "-x,y,z", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,z"], "universal_h_m": "C m 1 1", "number": 8, "schoenflies": "Cs^3", "hall": " C -2x", "hermann_mauguin": "C m 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,z"]}, {"symops": ["x,y,z", "-x,y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "I m 1 1", "number": 8, "schoenflies": "Cs^3", "hall": " I -2x", "hermann_mauguin": "I m 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,z"]}, {"symops": ["x,y,z", "x,-y,z+1/2", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C 1 c 1", "number": 9, "schoenflies": "Cs^4", "hall": " C -2yc", "hermann_mauguin": "C 1 c 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "x+1/2,-y+1,z+1/2"], "universal_h_m": "A 1 n 1", "number": 9, "schoenflies": "Cs^4", "hall": " A -2yab", "hermann_mauguin": "A 1 n 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y+1/2,z"]}, {"symops": ["x,y,z", "x+1/2,-y,z", "x+1/2,y+1/2,z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "I 1 a 1", "number": 9, "schoenflies": "Cs^4", "hall": " I -2ya", "hermann_mauguin": "I 1 a 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A 1 a 1", "number": 9, "schoenflies": "Cs^4", "hall": " A -2ya", "hermann_mauguin": "A 1 a 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "x+1,-y+1/2,z+1/2"], "universal_h_m": "C 1 n 1", "number": 9, "schoenflies": "Cs^4", "hall": " C -2yac", "hermann_mauguin": "C 1 n 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "x,-y,z+1/2", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1"], "universal_h_m": "I 1 c 1", "number": 9, "schoenflies": "Cs^4", "hall": " I -2yc", "hermann_mauguin": "I 1 c 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "A 1 1 a", "number": 9, "schoenflies": "Cs^4", "hall": " A -2a", "hermann_mauguin": "A 1 1 a", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,y,-z"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x+1/2,y,z+1/2", "x+1,y+1/2,-z+1/2"], "universal_h_m": "B 1 1 n", "number": 9, "schoenflies": "Cs^4", "hall": " B -2ab", "hermann_mauguin": "B 1 1 n", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2"], "universal_h_m": "I 1 1 b", "number": 9, "schoenflies": "Cs^4", "hall": " I -2b", "hermann_mauguin": "I 1 1 b", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,y+1/2,-z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "x+1/2,y,z+1/2", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "B 1 1 b", "number": 9, "schoenflies": "Cs^4", "hall": " B -2b", "hermann_mauguin": "B 1 1 b", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,y+1/2,-z"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2"], "universal_h_m": "A 1 1 n", "number": 9, "schoenflies": "Cs^4", "hall": " A -2ab", "hermann_mauguin": "A 1 1 n", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x+1/2,y+1/2,z+1/2", "x+1,y+1/2,-z+1/2"], "universal_h_m": "I 1 1 a", "number": 9, "schoenflies": "Cs^4", "hall": " I -2a", "hermann_mauguin": "I 1 1 a", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,y,-z"]}, {"symops": ["x,y,z", "-x,y+1/2,z", "x+1/2,y,z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "B b 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " B -2xb", "hermann_mauguin": "B b 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,z"]}, {"symops": ["x,y,z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x+1,y+1/2,z+1/2"], "universal_h_m": "C n 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " C -2xac", "hermann_mauguin": "C n 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x+1/2,y,z+1/2"]}, {"symops": ["x,y,z", "-x,y,z+1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,z+1"], "universal_h_m": "I c 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " I -2xc", "hermann_mauguin": "I c 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,z+1/2"]}, {"symops": ["x,y,z", "-x,y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "C c 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " C -2xc", "hermann_mauguin": "C c 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x+1,y+1/2,z+1/2"], "universal_h_m": "B n 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " B -2xab", "hermann_mauguin": "B n 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x+1/2,y+1/2,z"]}, {"symops": ["x,y,z", "-x,y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1,z+1/2"], "universal_h_m": "I b 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " I -2xb", "hermann_mauguin": "I b 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,z"]}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"], "universal_h_m": "P 1 2/m 1", "number": 10, "schoenflies": "C2h^1", "hall": "-P 2y", "hermann_mauguin": "P 1 2/m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z"], "universal_h_m": "P 1 1 2/m", "number": 10, "schoenflies": "C2h^1", "hall": "-P 2", "hermann_mauguin": "P 1 1 2/m", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z"]}, {"symops": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z"], "universal_h_m": "P 2/m 1 1", "number": 10, "schoenflies": "C2h^1", "hall": "-P 2x", "hermann_mauguin": "P 2/m 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z"]}, {"symops": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y-1/2,z"], "universal_h_m": "P 1 21/m 1", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2yb", "hermann_mauguin": "P 1 21/m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y-1/2,z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z-1/2"], "universal_h_m": "P 1 1 21/m", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2c", "hermann_mauguin": "P 1 1 21/m", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z-1/2"]}, {"symops": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x-1/2,y,z"], "universal_h_m": "P 21/m 1 1", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2xa", "hermann_mauguin": "P 21/m 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x-1/2,y,z"]}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "C 1 2/m 1", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y", "hermann_mauguin": "C 1 2/m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z", "x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A 1 2/m 1", "number": 12, "schoenflies": "C2h^3", "hall": "-A 2y", "hermann_mauguin": "A 1 2/m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I 1 2/m 1", "number": 12, "schoenflies": "C2h^3", "hall": "-I 2y", "hermann_mauguin": "I 1 2/m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z", "x,y+1/2,z+1/2", 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{"symops": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z-1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "I 1 2/c 1", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2yc", "hermann_mauguin": "I 1 2/c 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z-1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z", "x,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,y+1/2,-z+1/2"], "universal_h_m": "A 1 1 2/a", "number": 15, "schoenflies": "C2h^6", "hall": "-A 2a", "hermann_mauguin": "A 1 1 2/a", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z", "x+1/2,y,z+1/2", "-x+1,-y+1/2,z+1/2", "-x+1/2,-y,-z+1/2", "x,y-1/2,-z+1/2"], "universal_h_m": "B 1 1 2/n", "number": 15, "schoenflies": "C2h^6", "hall": "-B 2ab", "hermann_mauguin": "B 1 1 2/n", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z"]}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y,-z+1/2"], "universal_h_m": "I 1 1 2/b", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2b", "hermann_mauguin": "I 1 1 2/b", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z"]}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z", "x+1/2,y,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y-1/2,-z+1/2"], "universal_h_m": "B 1 1 2/b", "number": 15, "schoenflies": "C2h^6", "hall": "-B 2b", "hermann_mauguin": "B 1 1 2/b", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z", "x,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,y,-z+1/2"], "universal_h_m": "A 1 1 2/n", "number": 15, "schoenflies": "C2h^6", "hall": "-A 2ab", "hermann_mauguin": "A 1 1 2/n", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z", "x+1/2,y+1/2,z+1/2", "-x+1,-y+1/2,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2"], "universal_h_m": "I 1 1 2/a", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2a", "hermann_mauguin": "I 1 1 2/a", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z"]}, {"symops": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z", "x+1/2,y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "-x+1/2,y-1/2,z+1/2"], "universal_h_m": "B 2/b 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-B 2xb", "hermann_mauguin": "B 2/b 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z"]}, {"symops": ["x,y,z", "x+1/2,-y,-z+1/2", "-x,-y,-z", "-x-1/2,y,z-1/2", "x+1/2,y+1/2,z", "x+1,-y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "-x,y+1/2,z-1/2"], "universal_h_m": "C 2/n 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-C 2xac", "hermann_mauguin": "C 2/n 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,-z+1/2", "-x,-y,-z", "-x-1/2,y,z-1/2"]}, {"symops": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1", "-x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,z"], "universal_h_m": "I 2/c 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2xc", "hermann_mauguin": "I 2/c 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2"]}, {"symops": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,z-1/2"], "universal_h_m": "C 2/c 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-C 2xc", "hermann_mauguin": "C 2/c 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2"]}, {"symops": ["x,y,z", "x+1/2,-y+1/2,-z", "-x,-y,-z", "-x-1/2,y-1/2,z", "x+1/2,y,z+1/2", "x+1,-y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "-x,y-1/2,z+1/2"], "universal_h_m": "B 2/n 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-B 2xab", "hermann_mauguin": "B 2/n 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y+1/2,-z", "-x,-y,-z", "-x-1/2,y-1/2,z"]}, {"symops": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "-x+1/2,y,z+1/2"], "universal_h_m": "I 2/b 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2xb", "hermann_mauguin": "I 2/b 1 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"], "universal_h_m": "P 2 2 2", "number": 16, "schoenflies": "D2^1", "hall": " P 2 2", "hermann_mauguin": "P 2 2 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2"], "universal_h_m": "P 2 2 21", "number": 17, "schoenflies": "D2^2", "hall": " P 2c 2", "hermann_mauguin": "P 2 2 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z"], "universal_h_m": "P 21 2 2", "number": 17, "schoenflies": "D2^2", "hall": " P 2a 2a", "hermann_mauguin": "P 21 2 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z"], "universal_h_m": "P 2 21 2", "number": 17, "schoenflies": "D2^2", "hall": " P 2 2b", "hermann_mauguin": "P 2 21 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z"], "universal_h_m": "P 21 21 2", "number": 18, "schoenflies": "D2^3", "hall": " P 2 2ab", "hermann_mauguin": "P 21 21 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z", "-x,y+1/2,-z+1/2"], "universal_h_m": "P 2 21 21", "number": 18, "schoenflies": "D2^3", "hall": " P 2bc 2", "hermann_mauguin": "P 2 21 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z", "-x,y+1/2,-z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z"], "universal_h_m": "P 21 2 21", "number": 18, "schoenflies": "D2^3", "hall": " P 2ac 2ac", "hermann_mauguin": "P 21 2 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z"]}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z", "-x,y+1/2,-z+1/2"], "universal_h_m": "P 21 21 21", "number": 19, "schoenflies": "D2^4", "hall": " P 2ac 2ab", "hermann_mauguin": "P 21 21 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z", "-x,y+1/2,-z+1/2"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "C 2 2 21", "number": 20, "schoenflies": "D2^5", "hall": " C 2c 2", "hermann_mauguin": "C 2 2 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "x,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A 21 2 2", "number": 20, "schoenflies": "D2^5", "hall": " A 2a 2a", "hermann_mauguin": "A 21 2 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "B 2 21 2", "number": 20, "schoenflies": "D2^5", "hall": " B 2 2b", "hermann_mauguin": "B 2 21 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z"], "universal_h_m": "C 2 2 2", "number": 21, "schoenflies": "D2^6", "hall": " C 2 2", "hermann_mauguin": "C 2 2 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A 2 2 2", "number": 21, "schoenflies": "D2^6", "hall": " A 2 2", "hermann_mauguin": "A 2 2 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2"], "universal_h_m": "B 2 2 2", "number": 21, "schoenflies": "D2^6", "hall": " B 2 2", "hermann_mauguin": "B 2 2 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z"], "universal_h_m": "F 2 2 2", "number": 22, "schoenflies": "D2^7", "hall": " F 2 2", "hermann_mauguin": "F 2 2 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I 2 2 2", "number": 23, "schoenflies": "D2^8", "hall": " I 2 2", "hermann_mauguin": "I 2 2 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "x+1/2,-y+1/2,-z+1", "-x+1/2,y+1,-z+1"], "universal_h_m": "I 21 21 21", "number": 24, "schoenflies": "D2^9", "hall": " I 2b 2c", "hermann_mauguin": "I 21 21 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z+1/2", "-x,y+1/2,-z+1/2"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"], "universal_h_m": "P m m 2", "number": 25, "schoenflies": "C2v^1", "hall": " P 2 -2", "hermann_mauguin": "P m m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"], "universal_h_m": "P 2 m m", "number": 25, "schoenflies": "C2v^1", "hall": " P -2 2", "hermann_mauguin": "P 2 m m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"], "universal_h_m": "P m 2 m", "number": 25, "schoenflies": "C2v^1", "hall": " P -2 -2", "hermann_mauguin": "P m 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"], "universal_h_m": "P m c 21", "number": 26, "schoenflies": "C2v^2", "hall": " P 2c -2", "hermann_mauguin": "P m c 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"], "universal_h_m": "P c m 21", "number": 26, "schoenflies": "C2v^2", "hall": " P 2c -2c", "hermann_mauguin": "P c m 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x,-y,z"], "universal_h_m": "P 21 m a", "number": 26, "schoenflies": "C2v^2", "hall": " P -2a 2a", "hermann_mauguin": "P 21 m a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,-y,-z", "x+1/2,-y,z"], "universal_h_m": "P 21 a m", "number": 26, "schoenflies": "C2v^2", "hall": " P -2 2a", "hermann_mauguin": "P 21 a m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "x+1/2,-y,-z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"], "universal_h_m": "P b 21 m", "number": 26, "schoenflies": "C2v^2", "hall": " P -2 -2b", "hermann_mauguin": "P b 21 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"], "universal_h_m": "P m 21 b", "number": 26, "schoenflies": "C2v^2", "hall": " P -2b -2", "hermann_mauguin": "P m 21 b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"], "universal_h_m": "P c c 2", "number": 27, "schoenflies": "C2v^3", "hall": " P 2 -2c", "hermann_mauguin": "P c c 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"], "universal_h_m": "P 2 a a", "number": 27, "schoenflies": "C2v^3", "hall": " P -2a 2", "hermann_mauguin": "P 2 a a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"], "universal_h_m": "P b 2 b", "number": 27, "schoenflies": "C2v^3", "hall": " P -2b -2b", "hermann_mauguin": "P b 2 b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"], "universal_h_m": "P m a 2", "number": 28, "schoenflies": "C2v^4", "hall": " P 2 -2a", "hermann_mauguin": "P m a 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"], "universal_h_m": "P b m 2", "number": 28, "schoenflies": "C2v^4", "hall": " P 2 -2b", "hermann_mauguin": "P b m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z"], "universal_h_m": "P 2 m b", "number": 28, "schoenflies": "C2v^4", "hall": " P -2b 2", "hermann_mauguin": "P 2 m b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z"]}, {"symops": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2"], "universal_h_m": "P 2 c m", "number": 28, "schoenflies": "C2v^4", "hall": " P -2c 2", "hermann_mauguin": "P 2 c m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"], "universal_h_m": "P c 2 m", "number": 28, "schoenflies": "C2v^4", "hall": " P -2c -2c", "hermann_mauguin": "P c 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"], "universal_h_m": "P m 2 a", "number": 28, "schoenflies": "C2v^4", "hall": " P -2a -2a", "hermann_mauguin": "P m 2 a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"], "universal_h_m": "P c a 21", "number": 29, "schoenflies": "C2v^5", "hall": " P 2c -2ac", "hermann_mauguin": "P c a 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x,-y+1/2,z+1/2"], "universal_h_m": "P b c 21", "number": 29, "schoenflies": "C2v^5", "hall": " P 2c -2b", "hermann_mauguin": "P b c 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "x+1/2,-y,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "P 21 a b", "number": 29, "schoenflies": "C2v^5", "hall": " P -2b 2a", "hermann_mauguin": "P 21 a b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "x+1/2,-y,-z", "x+1/2,-y+1/2,z"]}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "x+1/2,-y,-z", "x,-y,z+1/2"], "universal_h_m": "P 21 c a", "number": 29, "schoenflies": "C2v^5", "hall": " P -2ac 2a", "hermann_mauguin": "P 21 c a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "x+1/2,-y,-z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "P c 21 b", "number": 29, "schoenflies": "C2v^5", "hall": " P -2bc -2c", "hermann_mauguin": "P c 21 b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y+1/2,z", "-x,y+1/2,-z"], "universal_h_m": "P b 21 a", "number": 29, "schoenflies": "C2v^5", "hall": " P -2a -2ab", "hermann_mauguin": "P b 21 a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y+1/2,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "P n c 2", "number": 30, "schoenflies": "C2v^6", "hall": " P 2 -2bc", "hermann_mauguin": "P n c 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "P c n 2", "number": 30, "schoenflies": "C2v^6", "hall": " P 2 -2ac", "hermann_mauguin": "P c n 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "x,-y,-z", "x+1/2,-y,z+1/2"], "universal_h_m": "P 2 n a", "number": 30, "schoenflies": "C2v^6", "hall": " P -2ac 2", "hermann_mauguin": "P 2 n a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "x,-y,-z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x,-y,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "P 2 a n", "number": 30, "schoenflies": "C2v^6", "hall": " P -2ab 2", "hermann_mauguin": "P 2 a n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "x,-y,-z", "x+1/2,-y+1/2,z"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z"], "universal_h_m": "P b 2 n", "number": 30, "schoenflies": "C2v^6", "hall": " P -2ab -2ab", "hermann_mauguin": "P b 2 n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z"]}, {"symops": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "-x,y,-z"], "universal_h_m": "P n 2 b", "number": 30, "schoenflies": "C2v^6", "hall": " P -2bc -2bc", "hermann_mauguin": "P n 2 b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "-x,y,-z"]}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"], "universal_h_m": "P m n 21", "number": 31, "schoenflies": "C2v^7", "hall": " P 2ac -2", "hermann_mauguin": "P m n 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"], "universal_h_m": "P n m 21", "number": 31, "schoenflies": "C2v^7", "hall": " P 2bc -2bc", "hermann_mauguin": "P n m 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x+1/2,-y+1/2,-z", "x,-y,z"], "universal_h_m": "P 21 m n", "number": 31, "schoenflies": "C2v^7", "hall": " P -2ab 2ab", "hermann_mauguin": "P 21 m n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "x+1/2,-y+1/2,-z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "P 21 n m", "number": 31, "schoenflies": "C2v^7", "hall": " P -2 2ac", "hermann_mauguin": "P 21 n m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "P n 21 m", "number": 31, "schoenflies": "C2v^7", "hall": " P -2 -2bc", "hermann_mauguin": "P n 21 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "P m 21 n", "number": 31, "schoenflies": "C2v^7", "hall": " P -2ab -2", "hermann_mauguin": "P m 21 n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "P b a 2", "number": 32, "schoenflies": "C2v^8", "hall": " P 2 -2ab", "hermann_mauguin": "P b a 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"]}, {"symops": ["x,y,z", "x,y+1/2,-z+1/2", "x,-y,-z", "x,-y+1/2,z+1/2"], "universal_h_m": "P 2 c b", "number": 32, "schoenflies": "C2v^8", "hall": " P -2bc 2", "hermann_mauguin": "P 2 c b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "x,-y,-z", "x,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x,y,-z"], "universal_h_m": "P c 2 a", "number": 32, "schoenflies": "C2v^8", "hall": " P -2ac -2ac", "hermann_mauguin": "P c 2 a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "P n a 21", "number": 33, "schoenflies": "C2v^9", "hall": " P 2c -2n", "hermann_mauguin": "P n a 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P b n 21", "number": 33, "schoenflies": "C2v^9", "hall": " P 2c -2ab", "hermann_mauguin": "P b n 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "x,y+1/2,-z+1/2", "x+1/2,-y,-z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P 21 n b", "number": 33, "schoenflies": "C2v^9", "hall": " P -2bc 2a", "hermann_mauguin": "P 21 n b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "x+1/2,-y,-z", "x+1/2,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y,-z", "x,-y+1/2,z+1/2"], "universal_h_m": "P 21 c n", "number": 33, "schoenflies": "C2v^9", "hall": " P -2n 2a", "hermann_mauguin": "P 21 c n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y,-z", "x,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "P c 21 n", "number": 33, "schoenflies": "C2v^9", "hall": " P -2n -2ac", "hermann_mauguin": "P c 21 n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "P n 21 a", "number": 33, "schoenflies": "C2v^9", "hall": " P -2ac -2n", "hermann_mauguin": "P n 21 a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P n n 2", "number": 34, "schoenflies": "C2v^10", "hall": " P 2 -2n", "hermann_mauguin": "P n n 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "x,-y,-z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P 2 n n", "number": 34, "schoenflies": "C2v^10", "hall": " P -2n 2", "hermann_mauguin": "P 2 n n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "x,-y,-z", "x+1/2,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y,-z"], "universal_h_m": "P n 2 n", "number": 34, "schoenflies": "C2v^10", "hall": " P -2n -2n", "hermann_mauguin": "P n 2 n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "C m m 2", "number": 35, "schoenflies": "C2v^11", "hall": " C 2 -2", "hermann_mauguin": "C m m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "x,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A 2 m m", "number": 35, "schoenflies": "C2v^11", "hall": " A -2 2", "hermann_mauguin": "A 2 m m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2"], "universal_h_m": "B m 2 m", "number": 35, "schoenflies": "C2v^11", "hall": " B -2 -2", "hermann_mauguin": "B m 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C m c 21", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2", "hermann_mauguin": "C m c 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "C c m 21", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2c", "hermann_mauguin": "C c m 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x,-y,z", "x,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A 21 m a", "number": 36, "schoenflies": "C2v^12", "hall": " A -2a 2a", "hermann_mauguin": "A 21 m a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,-y,-z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A 21 a m", "number": 36, "schoenflies": "C2v^12", "hall": " A -2 2a", "hermann_mauguin": "A 21 a m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "x+1/2,-y,-z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "B b 21 m", "number": 36, "schoenflies": "C2v^12", "hall": " B -2 -2b", "hermann_mauguin": "B b 21 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z", "x+1/2,y,z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "B m 21 b", "number": 36, "schoenflies": "C2v^12", "hall": " B -2b -2", "hermann_mauguin": "B m 21 b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C c c 2", "number": 37, "schoenflies": "C2v^13", "hall": " C 2 -2c", "hermann_mauguin": "C c c 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "x,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A 2 a a", "number": 37, "schoenflies": "C2v^13", "hall": " A -2a 2", "hermann_mauguin": "A 2 a a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z", "x+1/2,y,z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x+1/2,y,-z+1/2"], "universal_h_m": "B b 2 b", "number": 37, "schoenflies": "C2v^13", "hall": " B -2b -2b", "hermann_mauguin": "B b 2 b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A m m 2", "number": 38, "schoenflies": "C2v^14", "hall": " A 2 -2", "hermann_mauguin": "A m m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "B m m 2", "number": 38, "schoenflies": "C2v^14", "hall": " B 2 -2", "hermann_mauguin": "B m m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "B 2 m m", "number": 38, "schoenflies": "C2v^14", "hall": " B -2 2", "hermann_mauguin": "B 2 m m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z", "x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "C 2 m m", "number": 38, "schoenflies": "C2v^14", "hall": " C -2 2", "hermann_mauguin": "C 2 m m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "C m 2 m", "number": 38, "schoenflies": "C2v^14", "hall": " C -2 -2", "hermann_mauguin": "C m 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A m 2 m", "number": 38, "schoenflies": "C2v^14", "hall": " A -2 -2", "hermann_mauguin": "A m 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,y+1,z+1/2", "x,-y+1,z+1/2"], "universal_h_m": "A e m 2", "number": 39, "schoenflies": "C2v^15", "hall": " A 2 -2b", "hermann_mauguin": "A e m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1,y,z+1/2", "x+1,-y,z+1/2"], "universal_h_m": "B m e 2", "number": 39, "schoenflies": "C2v^15", "hall": " B 2 -2a", "hermann_mauguin": "B m e 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z", "x+1/2,y,z+1/2", "x+1,y,-z+1/2", "x+1/2,-y,-z+1/2", "x+1,-y,z+1/2"], "universal_h_m": "B 2 e m", "number": 39, "schoenflies": "C2v^15", "hall": " B -2a 2", "hermann_mauguin": "B 2 e m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z", "x+1/2,y+1/2,z", "x+1,y+1/2,-z", "x+1/2,-y+1/2,-z", "x+1,-y+1/2,z"], "universal_h_m": "C 2 m e", "number": 39, "schoenflies": "C2v^15", "hall": " C -2a 2", "hermann_mauguin": "C 2 m e", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z", "x+1/2,y+1/2,z", "x+1,y+1/2,-z", "-x+1,y+1/2,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "C m 2 e", "number": 39, "schoenflies": "C2v^15", "hall": " C -2a -2a", "hermann_mauguin": "C m 2 e", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z", "x,y+1/2,z+1/2", "x,y+1,-z+1/2", "-x,y+1,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A e 2 m", "number": 39, "schoenflies": "C2v^15", "hall": " A -2b -2b", "hermann_mauguin": "A e 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A m a 2", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a", "hermann_mauguin": "A m a 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "B b m 2", "number": 40, "schoenflies": "C2v^16", "hall": " B 2 -2b", "hermann_mauguin": "B b m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z", "x+1/2,y,z+1/2", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "B 2 m b", "number": 40, "schoenflies": "C2v^16", "hall": " B -2b 2", "hermann_mauguin": "B 2 m b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z"]}, {"symops": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C 2 c m", "number": 40, "schoenflies": "C2v^16", "hall": " C -2c 2", "hermann_mauguin": "C 2 c m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z"], "universal_h_m": "C c 2 m", "number": 40, "schoenflies": "C2v^16", "hall": " C -2c -2c", "hermann_mauguin": "C c 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z", "x,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A m 2 a", "number": 40, "schoenflies": "C2v^16", "hall": " A -2a -2a", "hermann_mauguin": "A m 2 a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x+1/2,y+1,z+1/2", "x+1/2,-y+1,z+1/2"], "universal_h_m": "A e a 2", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab", "hermann_mauguin": "A e a 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1,y+1/2,z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "B b e 2", "number": 41, "schoenflies": "C2v^17", "hall": " B 2 -2ab", "hermann_mauguin": "B b e 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x,-y,-z", "x+1/2,-y+1/2,z", "x+1/2,y,z+1/2", "x+1,y+1/2,-z+1/2", "x+1/2,-y,-z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "B 2 e b", "number": 41, "schoenflies": "C2v^17", "hall": " B -2ab 2", "hermann_mauguin": "B 2 e b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "x,-y,-z", "x+1/2,-y+1/2,z"]}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "x,-y,-z", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "x+1,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z", "x+1,-y+1/2,z+1/2"], "universal_h_m": "C 2 e b", "number": 41, "schoenflies": "C2v^17", "hall": " C -2ac 2", "hermann_mauguin": "C 2 e b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "x,-y,-z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x,y,-z", "x+1/2,y+1/2,z", "x+1,y+1/2,-z+1/2", "-x+1,y+1/2,z+1/2", "-x+1/2,y+1/2,-z"], "universal_h_m": "C c 2 e", "number": 41, "schoenflies": "C2v^17", "hall": " C -2ac -2ac", "hermann_mauguin": "C c 2 e", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x,y,-z"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z", "x,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2", "-x+1/2,y+1,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A e 2 a", "number": 41, "schoenflies": "C2v^17", "hall": " A -2ab -2ab", "hermann_mauguin": "A e 2 a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "F m m 2", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2", "hermann_mauguin": "F m m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "x,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z", "x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "F 2 m m", "number": 42, "schoenflies": "C2v^18", "hall": " F -2 2", "hermann_mauguin": "F 2 m m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "F m 2 m", "number": 42, "schoenflies": "C2v^18", "hall": " F -2 -2", "hermann_mauguin": "F m 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/4,y+1/4,z+1/4", "x+3/4,-y+3/4,z+1/4", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x+1/4,y+3/4,z+3/4", "x+3/4,-y+5/4,z+3/4", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+3/4,y+1/4,z+3/4", "x+5/4,-y+3/4,z+3/4", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+3/4,y+3/4,z+1/4", "x+5/4,-y+5/4,z+1/4"], "universal_h_m": "F d d 2", "number": 43, "schoenflies": "C2v^19", "hall": " F 2 -2d", "hermann_mauguin": "F d d 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/4,y+1/4,z+1/4", "x+3/4,-y+3/4,z+1/4"]}, {"symops": ["x,y,z", "x+1/4,y+1/4,-z+1/4", "x,-y,-z", "x+1/4,-y+1/4,z+1/4", "x,y+1/2,z+1/2", "x+1/4,y+3/4,-z+3/4", "x,-y+1/2,-z+1/2", "x+1/4,-y+3/4,z+3/4", "x+1/2,y,z+1/2", "x+3/4,y+1/4,-z+3/4", "x+1/2,-y,-z+1/2", "x+3/4,-y+1/4,z+3/4", "x+1/2,y+1/2,z", "x+3/4,y+3/4,-z+1/4", "x+1/2,-y+1/2,-z", "x+3/4,-y+3/4,z+1/4"], "universal_h_m": "F 2 d d", "number": 43, "schoenflies": "C2v^19", "hall": " F -2d 2", "hermann_mauguin": "F 2 d d", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/4,y+1/4,-z+1/4", "x,-y,-z", "x+1/4,-y+1/4,z+1/4"]}, {"symops": ["x,y,z", "x+1/4,y+1/4,-z+1/4", "-x+1/4,y+1/4,z+1/4", "-x+1/2,y+1/2,-z", "x,y+1/2,z+1/2", "x+1/4,y+3/4,-z+3/4", "-x+1/4,y+3/4,z+3/4", "-x+1/2,y+1,-z+1/2", "x+1/2,y,z+1/2", "x+3/4,y+1/4,-z+3/4", "-x+3/4,y+1/4,z+3/4", "-x+1,y+1/2,-z+1/2", "x+1/2,y+1/2,z", "x+3/4,y+3/4,-z+1/4", "-x+3/4,y+3/4,z+1/4", "-x+1,y+1,-z"], "universal_h_m": "F d 2 d", "number": 43, "schoenflies": "C2v^19", "hall": " F -2d -2d", "hermann_mauguin": "F d 2 d", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/4,y+1/4,-z+1/4", "-x+1/4,y+1/4,z+1/4", "-x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I m m 2", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2", "hermann_mauguin": "I m m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I 2 m m", "number": 44, "schoenflies": "C2v^20", "hall": " I -2 2", "hermann_mauguin": "I 2 m m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I m 2 m", "number": 44, "schoenflies": "C2v^20", "hall": " I -2 -2", "hermann_mauguin": "I m 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1", "x+1/2,-y+1/2,z+1"], "universal_h_m": "I b a 2", "number": 45, "schoenflies": "C2v^21", "hall": " I 2 -2c", "hermann_mauguin": "I b a 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z", "x+1/2,y+1/2,z+1/2", "x+1,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "I 2 c b", "number": 45, "schoenflies": "C2v^21", "hall": " I -2a 2", "hermann_mauguin": "I 2 c b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2", "-x+1/2,y+1,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I c 2 a", "number": 45, "schoenflies": "C2v^21", "hall": " I -2b -2b", "hermann_mauguin": "I c 2 a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1,y+1/2,z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "I m a 2", "number": 46, "schoenflies": "C2v^22", "hall": " I 2 -2a", "hermann_mauguin": "I m a 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1,z+1/2", "x+1/2,-y+1,z+1/2"], "universal_h_m": "I b m 2", "number": 46, "schoenflies": "C2v^22", "hall": " I 2 -2b", "hermann_mauguin": "I b m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"]}, {"symops": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1,z+1/2"], "universal_h_m": "I 2 m b", "number": 46, "schoenflies": "C2v^22", "hall": " I -2b 2", "hermann_mauguin": "I 2 m b", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z"]}, {"symops": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1", "x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1"], "universal_h_m": "I 2 c m", "number": 46, "schoenflies": "C2v^22", "hall": " I -2c 2", "hermann_mauguin": "I 2 c m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1", "-x+1/2,y+1/2,z+1", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I c 2 m", "number": 46, "schoenflies": "C2v^22", "hall": " I -2c -2c", "hermann_mauguin": "I c 2 m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1,y+1/2,-z+1/2", "-x+1,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I m 2 a", "number": 46, "schoenflies": "C2v^22", "hall": " I -2a -2a", "hermann_mauguin": "I m 2 a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z"], "universal_h_m": "P m m m", "number": 47, "schoenflies": "D2h^1", "hall": "-P 2 2", "hermann_mauguin": "P m m m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P n n n :1", "number": 48, "schoenflies": "D2h^2", "hall": " P 2 2 -1n", "hermann_mauguin": "P n n n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z-1/2", "x-1/2,-y,z-1/2"], "universal_h_m": "P n n n :2", "number": 48, "schoenflies": "D2h^2", "hall": "-P 2ab 2bc", "hermann_mauguin": "P n n n", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z-1/2", "x-1/2,-y,z-1/2"]}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y,z-1/2", "x,-y,z-1/2"], "universal_h_m": "P c c m", "number": 49, "schoenflies": "D2h^3", "hall": "-P 2 2c", "hermann_mauguin": "P c c m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y,z-1/2", "x,-y,z-1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z"], "universal_h_m": "P m a a", "number": 49, "schoenflies": "D2h^3", "hall": "-P 2a 2", "hermann_mauguin": "P m a a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z"]}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z", "x,-y,z"], "universal_h_m": "P b m b", "number": 49, "schoenflies": "D2h^3", "hall": 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"-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,y,-z", "-x,y+1/2,z+1/2", "x,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y-1/2,z-1/2", "x,-y-1/2,z"], "universal_h_m": "P n m m :2", "number": 59, "schoenflies": "D2h^13", "hall": "-P 2c 2bc", "hermann_mauguin": "P n m m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y-1/2,z-1/2", "x,-y-1/2,z"]}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z", "-x+1/2,-y,-z+1/2", "x,y,-z", "-x,y,z", "x+1/2,-y,z+1/2"], "universal_h_m": "P m n m :1", "number": 59, "schoenflies": "D2h^13", "hall": " P 2ac 2ac -1ac", "hermann_mauguin": "P m n m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z", "-x+1/2,-y,-z+1/2", "x,y,-z", "-x,y,z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x+1/2,-y,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", 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"z+3/4,y+1/4,-x+1/4", "-y,z+1/2,-x+1/2", "-z+1/4,-y+1/4,-x+1/4", "-y+1/2,-z,x+1/2", "z+3/4,-y+3/4,x+1/4", "-z+3/4,y+1/4,x+3/4", "-x,-y,-z", "y-1/4,-x-3/4,-z-1/4", "x-1/2,y,-z-1/2", "-y-1/4,x-1/4,-z-3/4", "-x,y,z-1/2", "-y-1/4,-x-3/4,z-3/4", "x-1/2,-y,z", "y-1/4,x-1/4,z-1/4", "-z,-x,-y", "x-1/4,-z-3/4,-y-1/4", "z-1/2,x,-y-1/2", "-x-1/4,z-1/4,-y-3/4", "-z,x,y-1/2", "-x-1/4,-z-3/4,y-3/4", "z-1/2,-x,y", "x-1/4,z-1/4,y-1/4", "-y,-z,-x", "-y-1/2,z-1/2,x", "-z-3/4,-y-1/4,x-1/4", "y,-z-1/2,x-1/2", "z-1/4,y-1/4,x-1/4", "y-1/2,z,-x-1/2", "-z-3/4,y-3/4,-x-1/4", "z-3/4,-y-1/4,-x-3/4"]}, {"symops": ["x,y,z", "1/2+x,1/2+y,z"], "universal_h_m": "C 1", "number": 1, "schoenflies": "C1^1", "hall": "P 1 (1/2*x+1/2*y,1/2*x-1/2*y,-z)", "hermann_mauguin": "C 1", "crystal_class": "triclinic", "ncsym": ["x, y, z"]}, {"symops": ["x,y,z", "-x,-y,-z", "x,1/2+y,1/2+z", "-x,1/2-y,1/2-z"], "universal_h_m": "A -1", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1 (-x,-1/2*y+1/2*z,1/2*y+1/2*z)", "hermann_mauguin": "A -1", "crystal_class": "triclinic", "ncsym": ["x, y, z", "-x, -y, -z"]}, {"symops": ["x, y, z", "x+1/2, y, z+1/2", "-x, -y, -z", "-x+1/2, -y, -z+1/2"], "universal_h_m": "B -1", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1 (-1/2*x+1/2*z,-y,1/2*x+1/2*z)", "hermann_mauguin": "B -1", "crystal_class": "triclinic", "ncsym": ["x, y, z", "-x, -y, -z"]}, {"symops": ["x,y,z", "1/2-x,1/2-y,1/2-z", "1/2+x,1/2+y,1/2+z", "-x,-y,-z"], "universal_h_m": "I -1", "number": 2, "schoenflies": "D2^4", "hall": "-P 1 (-1/2*x+1/2*y+1/2*z,1/2*x-1/2*y+1/2*z,1/2*x+1/2*y-1/2*z)", "hermann_mauguin": "I -1", "crystal_class": "triclinic", "ncsym": ["x,y,z", "-x,-y,-z"]}, {"symops": ["x, y, z", "y, x, -z+1/2", "x+2/3, y+1/3, z+1/3", "y+2/3, x+1/3, -z+5/6", "x+1/3, y+2/3, z+2/3", "y+1/3, x+2/3, -z+7/6", "-x, -y, -z", "-y, -x, z-1/2", "-x+2/3, -y+1/3, -z+1/3", "-y+2/3, -x+1/3, z-1/6", "-x+1/3, -y+2/3, -z+2/3", "-y+1/3, -x+2/3, z+1/6"], "universal_h_m": "R 1 2/c 1", "number": 15, "schoenflies": "C2h^6", "hall": "-C 2yc (x+y-16/3*z,-x+y+16/3*z,1/3*z)", "hermann_mauguin": "R 1 2/c 1 (\"rhombohedral\" setting)", "crystal_class": "rhombohedral", "ncsym": ["x, y, z", "y, x, -z+1/2", "-x, -y, -z", "-y, -x, z-1/2"]}, {"symops": ["x,y,z", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x+1/2,-y,z+1/2"], "universal_h_m": "P 21 21 21 (origin shift x,y,z+1/4)", "number": 19, "schoenflies": "D2^4", "hall": " P 2ac 2ab (x,y,z+1/4)", "hermann_mauguin": "P 21 21 21 (origin shift x,y,z+1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x+1/2,-y,z+1/2"]}, {"symops": ["x, y, z", "-x, y+1/2, -z", "x+1/2, y, z+1/2", "-x+1/2, y+1/2, -z+1/2"], "universal_h_m": "B 1 21 1", "number": 4, "schoenflies": "C2^2", "hall": "P 2yb (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "B 1 21 1", "crystal_class": "monoclinic", "ncsym": ["x, y, z", "-x, y+1/2, -z"]}, {"symops": ["x, y, z", "x+1/2, y+1/2, z", "-x, -y, -z", "-x+1/2, -y+1/2, -z"], "universal_h_m": "C -1", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1 (1/2*x+1/2*y,1/2*x-1/2*y,-z)", "hermann_mauguin": "C -1", "crystal_class": "triclinic", "ncsym": ["x, y, z", "-x, -y, -z"]}, {"symops": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y-1/2,z", "x+1/2,y,z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,-y-1/2,z+1/2"], "universal_h_m": "B 1 21/m 1", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2yb (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "B 1 21/m 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y-1/2,z", "x+1/2,y,z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,-y-1/2,z+1/2"]}, {"symops": ["x,y,z", "x,y+1/2,z+1/2"], "universal_h_m": "P 1 (-a,-b+c,b+c)", "number": 1, "schoenflies": "C1^1", "hall": " P 1 (-x,-1/2*y+1/2*z,1/2*y+1/2*z)", "hermann_mauguin": "P 1 (-a,-b+c,b+c)", "crystal_class": "triclinic", "ncsym": ["x,y,z"]}, {"symops": ["x,y,z", "x+1/2,y,z+1/2"], "universal_h_m": "P 1 (-a+c,-b,a+c)", "number": 1, "schoenflies": "C1^1", "hall": " P 1 (-1/2*x+1/2*z,-y,1/2*x+1/2*z)", "hermann_mauguin": "P 1 (-a+c,-b,a+c)", "crystal_class": "triclinic", "ncsym": ["x,y,z"]}, {"symops": ["x,y,z", "x+1/2,y+1/2,z+1/2"], "universal_h_m": "P 1 (b+c,a+c,a+b)", "number": 1, "schoenflies": "C1^1", "hall": " P 1 (-1/2*x+1/2*y+1/2*z,1/2*x-1/2*y+1/2*z,1/2*x+1/2*y-1/2*z)", "hermann_mauguin": "P 1 (b+c,a+c,a+b)", "crystal_class": "triclinic", "ncsym": ["x,y,z"]}, {"symops": ["x,y,z", "x,y+1/2,z+1/2", "x+1/2,y,z+1/2", "x+1/2,y+1/2,z"], "universal_h_m": "P 1 (-a+b+c,a-b+c,a+b-c)", "number": 1, "schoenflies": "C1^1", "hall": " P 1 (1/2*y+1/2*z,1/2*x+1/2*z,1/2*x+1/2*y)", "hermann_mauguin": "P 1 (-a+b+c,a-b+c,a+b-c)", "crystal_class": "triclinic", "ncsym": ["x,y,z"]}, {"symops": ["x,y,z", "-x,-y,-z", "x,y+1/2,z+1/2", "-x,-y+1/2,-z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,-z"], "universal_h_m": "P -1 (-a+b+c,a-b+c,a+b-c)", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1 (1/2*y+1/2*z,1/2*x+1/2*z,1/2*x+1/2*y)", "hermann_mauguin": "P -1 (-a+b+c,a-b+c,a+b-c)", "crystal_class": "triclinic", "ncsym": ["x,y,z", "-x,-y,-z"]}, {"symops": ["x,y,z", "-x,y,-z", "x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2"], "universal_h_m": "P 1 2 1 (2*a+c,b,c)", "number": 3, "schoenflies": "C2^1", "hall": " P 2y (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "P 1 2 1 (2*a+c,b,c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,y,-z", "x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z", "x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "C 1 2 1 (a,b,a+2*c)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (x-1/2*z,y,1/2*z)", "hermann_mauguin": "C 1 2 1 (a,b,a+2*c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z"], "universal_h_m": "P 1 2 1 (c,2*a+c,b)", "number": 3, "schoenflies": "C2^1", "hall": " P 2y (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 2 1 (c,2*a+c,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z"]}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2"], "universal_h_m": "C 1 2 1 (a+2*c,a,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (1/2*z,x-1/2*z,y)", "hermann_mauguin": "C 1 2 1 (a+2*c,a,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z"]}, {"symops": ["x,y,z", "-x,y,-z+1/2", "x,y+1/2,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "C 1 2 1 (c-1/4,b-1/4,-a)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (z,y+1/4,-x-1/4)", "hermann_mauguin": "C 1 2 1 (c-1/4,b-1/4,-a)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x+1/2,y+1/2,z", "-x,y+1/2,-z"], "universal_h_m": "C 1 2 1 (a-1/4,b-1/4,c)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (x+1/4,y+1/4,z)", "hermann_mauguin": "C 1 2 1 (a-1/4,b-1/4,c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "C 1 2 1 (a+c-1/4,b-1/4,c)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (x+1/4,y+1/4,-x+z-1/4)", "hermann_mauguin": "C 1 2 1 (a+c-1/4,b-1/4,c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x+1/2,y,z+1/2", "-x,y,-z+1/2", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "C 1 2 1 (a-1/4,b-1/4,a+2*c)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (x-1/2*z+1/4,y+1/4,1/2*z)", "hermann_mauguin": "C 1 2 1 (a-1/4,b-1/4,a+2*c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2"], "universal_h_m": "C 1 2 1 (c-1/4,a-1/4,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (z,x+1/4,y+1/4)", "hermann_mauguin": "C 1 2 1 (c-1/4,a-1/4,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,y,z+1/2", "-x,-y,z+1/2"], "universal_h_m": "C 1 2 1 (-a-1/4,c-1/4,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (-x-1/4,z,y+1/4)", "hermann_mauguin": "C 1 2 1 (-a-1/4,c-1/4,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z+1/2"]}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P 1 21 1 (c,2*a+c,b)", "number": 4, "schoenflies": "C2^2", "hall": " P 2yb (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 21 1 (c,2*a+c,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x,-y,z+1/2"], "universal_h_m": "C 1 2 1 (c-1/4,a+c-1/4,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (-x+z-1/4,x+1/4,y+1/4)", "hermann_mauguin": "C 1 2 1 (c-1/4,a+c-1/4,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z+1/2"]}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x+1/2,y+1/2,z", "-x+1/2,-y,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C 1 2 1 (a+2*c-1/4,a-1/4,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (1/2*z,x-1/2*z+1/4,y+1/4)", "hermann_mauguin": "C 1 2 1 (a+2*c-1/4,a-1/4,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,-y,z+1/2"]}, {"symops": ["x,y,z", "x,-y,z", "x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "P 1 m 1 (2*a+c,b,c)", "number": 6, "schoenflies": "Cs^1", "hall": " P -2y (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "P 1 m 1 (2*a+c,b,c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,-y,z", "x+1/2,y,z+1/2", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "C 1 m 1 (a,b,a+2*c)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (x-1/2*z,y,1/2*z)", "hermann_mauguin": "C 1 m 1 (a,b,a+2*c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z"]}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z"], "universal_h_m": "P 1 m 1 (c,2*a+c,b)", "number": 6, "schoenflies": "Cs^1", "hall": " P -2y (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 m 1 (c,2*a+c,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,y,-z"]}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2"], "universal_h_m": "C 1 m 1 (a+2*c,a,b)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (1/2*z,x-1/2*z,y)", "hermann_mauguin": "C 1 m 1 (a+2*c,a,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,y,-z"]}, {"symops": ["x,y,z", "-x,y,z", "x,y+1/2,z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "P 1 m 1 (b,c,2*a+c)", "number": 6, "schoenflies": "Cs^1", "hall": " P -2y (y,-1/2*x+z,1/2*x)", "hermann_mauguin": "P 1 m 1 (b,c,2*a+c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,z"]}, {"symops": ["x,y,z", "-x,y,z", "x,y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,z"], "universal_h_m": "C 1 m 1 (b,a+2*c,a)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (y,1/2*z,x-1/2*z)", "hermann_mauguin": "C 1 m 1 (b,a+2*c,a)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,z"]}, {"symops": ["x,y,z", "x,-y+1/2,z", "x,y+1/2,z+1/2", "x,-y,z+1/2"], "universal_h_m": "C 1 m 1 (c-1/4,b-1/4,-a)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (z,y+1/4,-x-1/4)", "hermann_mauguin": "C 1 m 1 (c-1/4,b-1/4,-a)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x,-y,z+1/2", "x+1/2,y,z+1/2", "x+1/2,-y,z"], "universal_h_m": "P 1 c 1 (2*a+c,b,c)", "number": 7, "schoenflies": "Cs^2", "hall": " P -2yc (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "P 1 c 1 (2*a+c,b,c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x,-y+1/2,z", "x+1/2,y,z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "x,-y,z+1/2"], "universal_h_m": "C 1 m 1 (a-1/4,b-1/4,a+2*c)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (x-1/2*z+1/4,y+1/4,1/2*z)", "hermann_mauguin": "C 1 m 1 (a-1/4,b-1/4,a+2*c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "x,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "C 1 m 1 (a+c-1/4,b-1/4,c)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (x+1/4,y+1/4,-x+z-1/4)", "hermann_mauguin": "C 1 m 1 (a+c-1/4,b-1/4,c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "x,-y+1/2,z", "x+1/2,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "C 1 m 1 (a-1/4,b-1/4,c)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (x+1/4,y+1/4,z)", "hermann_mauguin": "C 1 m 1 (a-1/4,b-1/4,c)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "x,y,-z+1/2", "x+1/2,y,z+1/2", "x+1/2,y,-z"], "universal_h_m": "C 1 m 1 (-a-1/4,c-1/4,b)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (-x-1/4,z,y+1/4)", "hermann_mauguin": "C 1 m 1 (-a-1/4,c-1/4,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,y,-z"]}, {"symops": ["x,y,z", "x+1/2,y,-z", "x+1/2,y+1/2,z", "x,y+1/2,-z"], "universal_h_m": "P 1 c 1 (c,2*a+c,b)", "number": 7, "schoenflies": "Cs^2", "hall": " P -2yc (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 c 1 (c,2*a+c,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,y,-z"]}, {"symops": ["x,y,z", "x,y,-z+1/2", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z+1/2", "x,y+1/2,z+1/2", "x,y+1/2,-z", "x+1/2,y,z+1/2", "x+1/2,y,-z"], "universal_h_m": "C 1 m 1 (a+2*c-1/4,a-1/4,b)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (1/2*z,x-1/2*z+1/4,y+1/4)", "hermann_mauguin": "C 1 m 1 (a+2*c-1/4,a-1/4,b)", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x+1/2,y,-z"]}, {"symops": ["x,y,z", "x,y,-z+1/2", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "C 1 m 1 (c-1/4,a+c-1/4,b)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (-x+z-1/4,x+1/4,y+1/4)", 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"-x,y,z+1/2"], "universal_h_m": "F m m 2 (b,c-1/4,a-1/4)", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2 (y+1/4,z+1/4,x)", "hermann_mauguin": "F m m 2 (b,c-1/4,a-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x,y,z", "x,y,-z+1/2", "x,y+1/2,z+1/2", "-x,y+1/2,-z", "-x,y+1/2,z+1/2", "x,y+1/2,-z"], "universal_h_m": "A m m 2 (-a,c+1/4,b-1/4)", "number": 38, "schoenflies": "C2v^14", "hall": " A 2 -2 (-x,z+1/4,y-1/4)", "hermann_mauguin": "A m m 2 (-a,c+1/4,b-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x+1/2,y,-z", "-x,y,z", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x,y+1/2,-z", "-x+1/2,y+1/2,z"], "universal_h_m": "A e m 2 (b,c+1/4,a-1/4)", "number": 39, "schoenflies": "C2v^15", "hall": " A 2 -2b (y-1/4,z+1/4,x)", "hermann_mauguin": "A e m 2 (b,c+1/4,a-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", 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["x,y,z", "-x+1/2,-y+1/2,z", "-x+1/2,y,z", "x,-y+1/2,z", "x,y+1/2,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x,-y,z+1/2", "x+1/2,y,z+1/2", "-x,-y+1/2,z+1/2", "-x,y,z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x,-y,z", "-x,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "F m m 2 (a+1/4,b+1/4,c+1/2)", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2 (x-1/4,y-1/4,z+1/2)", "hermann_mauguin": "F m m 2 (a+1/4,b+1/4,c+1/2)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y,-z+1/2", "-x+1/2,y,z", "x+1/2,y+1/2,z", "-x,y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x,y+1/2,z", "x,y+1/2,z+1/2", "-x+1/2,y+1/2,-z", "x,y+1/2,-z", "-x+1/2,y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x,y,-z", "x+1/2,y,-z", "-x,y,z+1/2"], "universal_h_m": "F m m 2 (b+1/4,c+1/4,a+1/2)", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2 (y-1/4,z+1/2,x-1/4)", "hermann_mauguin": "F m m 2 (b+1/4,c+1/4,a+1/2)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x+1/2,y,z", "x,-y+1/2,z", "x+1/2,y+1/2,z", "-x,-y,z", "-x,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "C m m 2 (a-1/4,b-1/4,c)", "number": 35, "schoenflies": "C2v^11", "hall": " C 2 -2 (x+1/4,y+1/4,z)", "hermann_mauguin": "C m m 2 (a-1/4,b-1/4,c)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y,-z+1/2", "-x+1/2,y,z", "x+1/2,y,z+1/2", "-x,y,-z", "x+1/2,y,-z", "-x,y,z+1/2"], "universal_h_m": "C m m 2 (b-1/4,c-1/4,a)", "number": 35, "schoenflies": "C2v^11", "hall": " C 2 -2 (y+1/4,z,x+1/4)", "hermann_mauguin": "C m m 2 (b-1/4,c-1/4,a)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"]}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A e a 2 (a,b+1/4,c-1/4)", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab (x,y-1/4,z+1/4)", "hermann_mauguin": "A e a 2 (a,b+1/4,c-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y+1/2,z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x,-y,z+1/2", "x+1/2,-y,z", "-x,y+1/2,z+1/2"], "universal_h_m": "C m c 21 (b-1/4,-a-1/4,c)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (y+1/4,-x-1/4,z)", "hermann_mauguin": "C m c 21 (b-1/4,-a-1/4,c)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x+1/2,y,z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y+1/2,z+1/2", "-x,-y,z+1/2", "-x,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "I b a 2 (a-1/4,b-1/4,c+1/4)", "number": 45, "schoenflies": "C2v^21", "hall": " I 2 -2c (x+1/4,y+1/4,z-1/4)", "hermann_mauguin": "I b a 2 (a-1/4,b-1/4,c+1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y+1/2,z", "-x,y+1/2,z", "x+1/2,y,z+1/2", "-x,-y,z+1/2", "x,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "A e a 2 (b,-a+1/4,c-1/4)", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab (y-1/4,-x,z+1/4)", "hermann_mauguin": "A e a 2 (b,-a+1/4,c-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y,z", "x,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x+1/2,-y,z+1/2"], "universal_h_m": "C m c 21 (a-1/4,b-1/4,c)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (x+1/4,y+1/4,z)", "hermann_mauguin": "C m c 21 (a-1/4,b-1/4,c)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z", "x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "-x,y+1/2,-z", "-x,y,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "C m c 21 (-a-1/4,c-1/4,b)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (-x-1/4,z,y+1/4)", "hermann_mauguin": "C m c 21 (-a-1/4,c-1/4,b)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x+1/2,y,-z+1/2", "-x,y,z+1/2", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "A e a 2 (b,c+1/4,a-1/4)", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab (y-1/4,z+1/4,x)", "hermann_mauguin": "A e a 2 (b,c+1/4,a-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y+1/2,-z+1/2", "-x+1/2,y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z", "x+1/2,y,-z", "-x,y,z+1/2"], "universal_h_m": "I b a 2 (b-1/4,c-1/4,a+1/4)", "number": 45, "schoenflies": "C2v^21", "hall": " I 2 -2c (y+1/4,z-1/4,x+1/4)", "hermann_mauguin": "I b a 2 (b-1/4,c-1/4,a+1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,y,-z", "x,y+1/2,z+1/2", "-x,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "A e a 2 (-a,c+1/4,b-1/4)", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab (-x,z+1/4,y-1/4)", "hermann_mauguin": "A e a 2 (-a,c+1/4,b-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y+1/2,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z+1/2", "x,y,-z+1/2", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,y+1/2,-z", "x+1/2,y,-z", "-x,y+1/2,z+1/2"], "universal_h_m": "C m c 21 (b-1/4,c-1/4,a)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (y+1/4,z,x+1/4)", "hermann_mauguin": "C m c 21 (b-1/4,c-1/4,a)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y+1/2,z", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x+1/2,y,z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x,-y,z", "-x,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "C c c 2 (a-1/4,b-1/4,c)", "number": 37, "schoenflies": "C2v^13", "hall": " C 2 -2c (x+1/4,y+1/4,z)", "hermann_mauguin": "C c c 2 (a-1/4,b-1/4,c)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y+1/2,-z+1/2", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,y,-z", "x+1/2,y+1/2,-z", "-x,y+1/2,z+1/2"], "universal_h_m": "C c c 2 (b-1/4,c-1/4,a)", "number": 37, "schoenflies": "C2v^13", "hall": " C 2 -2c (y+1/4,z,x+1/4)", "hermann_mauguin": "C c c 2 (b-1/4,c-1/4,a)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,y,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x+1/2,-y,z+1/2", "-x,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "A m a 2 (a+1/4,b+1/4,c-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (x-1/4,y-1/4,z+1/4)", "hermann_mauguin": "A m a 2 (a+1/4,b+1/4,c-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y,z", "x,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y,z+1/2"], "universal_h_m": "C m c 21 (a,b+1/4,c)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (x,y-1/4,z)", "hermann_mauguin": "C m c 21 (a,b+1/4,c)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,y,z", "x,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "I m m 2 (a,b-1/4,c)", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2 (x,y+1/4,z)", "hermann_mauguin": "I m m 2 (a,b-1/4,c)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,-y+1/2,z+1/2", "x+1/2,-y,z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "A m a 2 (b+1/4,-a+1/4,c-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (y-1/4,-x+1/4,z+1/4)", "hermann_mauguin": "A m a 2 (b+1/4,-a+1/4,c-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"]}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y,z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x,-y+1/2,z+1/2", "x+1/2,-y+1/2,z", "-x,y+1/2,z+1/2"], "universal_h_m": "C m c 21 (b,-a+1/4,c)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (y-1/4,-x,z)", "hermann_mauguin": "C m c 21 (b,-a+1/4,c)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"]}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x+1/2,y,z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I m m 2 (a-1/4,b,c+1/4)", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2 (x+1/4,y,z-1/4)", "hermann_mauguin": "I m m 2 (a-1/4,b,c+1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"]}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z", "x,y,-z", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y,-z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "C m c 21 (b,c+1/4,a)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (y-1/4,z,x)", "hermann_mauguin": "C m c 21 (b,c+1/4,a)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y,-z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x,y+1/2,-z+1/2", "x+1/2,y+1/2,-z", "-x,y+1/2,z+1/2"], "universal_h_m": "A m a 2 (b+1/4,c+1/4,a-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (y-1/4,z+1/4,x-1/4)", "hermann_mauguin": "A m a 2 (b+1/4,c+1/4,a-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x,y,-z", "-x+1/2,y,z", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "I m m 2 (b,c-1/4,a)", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2 (y+1/4,z,x)", "hermann_mauguin": "I m m 2 (b,c-1/4,a)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "-x,y,z", "x+1/2,y,-z+1/2", "x,y+1/2,z+1/2", "-x+1/2,y+1/2,-z", "-x,y+1/2,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "A m a 2 (-a+1/4,c+1/4,b-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (-x+1/4,z+1/4,y-1/4)", "hermann_mauguin": "A m a 2 (-a+1/4,c+1/4,b-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,y+1/2,-z+1/2", "-x,y,z", "x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "-x+1/2,y+1/2,-z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "C m c 21 (-a,c+1/4,b)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (-x,z,y-1/4)", "hermann_mauguin": "C m c 21 (-a,c+1/4,b)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,y,-z+1/2", "x,y,-z+1/2", "-x,y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "I m m 2 (b-1/4,c,a+1/4)", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2 (y,z-1/4,x+1/4)", "hermann_mauguin": "I m m 2 (b-1/4,c,a+1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x+1/2,y,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "A m a 2 (a,b+1/4,c-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (x,y-1/4,z+1/4)", "hermann_mauguin": "A m a 2 (a,b+1/4,c-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z"]}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,-y,z+1/2", "x+1/2,-y+1/2,z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "A m a 2 (b,-a+1/4,c-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (y-1/4,-x,z+1/4)", "hermann_mauguin": "A m a 2 (b,-a+1/4,c-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"]}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x+1/2,y+1/2,-z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "A m a 2 (b,c+1/4,a-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (y-1/4,z+1/4,x)", "hermann_mauguin": "A m a 2 (b,c+1/4,a-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x+1/2,y,z", "x+1/2,y,-z+1/2", "x,y+1/2,z+1/2", "-x,y+1/2,-z", "-x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "A m a 2 (-a,c+1/4,b-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (-x,z+1/4,y-1/4)", "hermann_mauguin": "A m a 2 (-a,c+1/4,b-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z"]}, {"symops": ["x,y,z", "x,-y,-z", "-x,y,-z", "-x,-y,z", "-x+1/2,-y,-z", "-x+1/2,y,z", "x+1/2,-y,z", "x+1/2,y,-z", "x,y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "C c c m (c,a,b-1/4)", "number": 66, "schoenflies": "D2h^20", "hall": "-C 2 2c (z+1/4,x,y)", "hermann_mauguin": "C c c m (c,a,b-1/4)", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"]}, {"symops": 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"z,-x,-y", "x+1/2,z+1/2,-y+1/2", "-z,x,-y", "-x+1/2,-z+1/2,-y+1/2", "y,z,x", "y,-z,-x", "z+1/2,y+1/2,-x+1/2", "-y,z,-x", "-z+1/2,-y+1/2,-x+1/2", "-y,-z,x", "z+1/2,-y+1/2,x+1/2", "-z+1/2,y+1/2,x+1/2", "-x+1/2,-y+1/2,-z+1/2", "y,-x,-z", "x+1/2,y+1/2,-z+1/2", "-y,x,-z", "-x+1/2,y+1/2,z+1/2", "-y,-x,z", "x+1/2,-y+1/2,z+1/2", "y,x,z", "-z+1/2,-x+1/2,-y+1/2", "x,-z,-y", "z+1/2,x+1/2,-y+1/2", "-x,z,-y", "-z+1/2,x+1/2,y+1/2", "-x,-z,y", "z+1/2,-x+1/2,y+1/2", "x,z,y", "-y+1/2,-z+1/2,-x+1/2", "-y+1/2,z+1/2,x+1/2", "-z,-y,x", "y+1/2,-z+1/2,x+1/2", "z,y,x", "y+1/2,z+1/2,-x+1/2", "-z,y,-x", "z,-y,-x"]}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z", "x,y,z+1/2", "-y,x,z+1/2", "-x,-y,z+1/2", "y,-x,z+1/2", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "y+1/2,x+1/2,z+1/2"], "universal_h_m": "P 4 b m (a,b,2*c)", "number": 100, "schoenflies": "C4v^2", "hall": " P 4 -2ab (x,y,1/2*z)", "hermann_mauguin": "P 4 b m", "crystal_class": "tetragonal", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z", "x,y,z+1/2", "-y,x,z+1/2", "-x,-y,z+1/2", "y,-x,z+1/2", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "y+1/2,x+1/2,z+1/2"]}, {"symops": ["x,y,z", "x,-y,z+1/2", "x+1/2,y,z+1/2", "x+1/2,-y,z", "x+1/4,y+1/2,z+3/4", "x+1/4,-y+1/2,z+1/4", "x+3/4,y+1/2,z+1/4", "x+3/4,-y+1/2,z+3/4"], "universal_h_m": "C 1 c 1 (2*a+c,b,c)", "number": 9, "schoenflies": "Cs^4", "hall": " C -2yc (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "C 1 c 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "x,-y,z+1/2", "x+1/2,y,z+1/2", "x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x,y,z", "x,-y,z+1/2", "-x,-y,z+1/2", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,-y,z+1/2", "-x+1/2,-y,z+1/2"], "universal_h_m": "P m c 21 (2*a,b,c)", "number": 26, "schoenflies": "C2v^2", "hall": " P 2c -2 (1/2*x,y,z)", "hermann_mauguin": "P m c 21", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,y,z", "x,-y,z+1/2", "-x,-y,z+1/2"]}, {"symops": ["x,y,z", "x,-y,z", "x,y,-z", "x,-y,-z", "x,y+1/2,z+1/2", "x,-y+1/2,z+1/2", "x,y+1/2,-z+1/2", "x,-y+1/2,-z+1/2", "x+1/2,y,z", "x+1/2,-y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2"], "universal_h_m": "C m m 2 (2*c,a,b)", "number": 35, "schoenflies": "C2v^11", "hall": " C 2 -2 (1/2*z,x,y)", "hermann_mauguin": "C m m 2", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "x,-y,z", "x,y,-z", "x,-y,-z"]}, {"symops": ["x,y,z", "-x+1/4,-y,z+1/2", "-x,-y,-z", "x-1/4,y,-z-1/2", "x+3/4,y+1/2,z", "-x+1,-y+1/2,z+1/2", "-x+3/4,-y+1/2,-z", "x+1/2,y+1/2,-z-1/2", "x+1/4,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "-x+1/4,-y+1/2,-z", "x,y+1/2,-z-1/2", "x+1/2,y,z", "-x+3/4,-y,z+1/2", "-x+1/2,-y,-z", "x+1/4,y,-z-1/2"], "universal_h_m": "P 1 21/c 1 (2*c,2*a+c,b)", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2ybc (-1/4*x+1/2*z,1/2*x,y)", "hermann_mauguin": "P 1 21/c 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x+1/4,-y,z+1/2", "-x,-y,-z", "x-1/4,y,-z-1/2"]}, {"symops": ["x,y,z", "-x,y,z", "x,y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,-z", "-x,-y,z-1/2", "x,-y,z-1/2", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,-z+1/2", "-x+1/2,-y,-z", "x+1/2,-y,-z", "-x+1/2,-y,z-1/2", "x+1/2,-y,z-1/2"], "universal_h_m": "P m m a (2*b,c,a)", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2a 2a (1/2*y,z,x)", "hermann_mauguin": "P m m a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,y,z", "x,y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,-z", "-x,-y,z-1/2", "x,-y,z-1/2"]}, {"symops": ["x,y,z", "-x,y,z", "x,y,-z", "-x,y,-z", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,y,-z", "-x+1/2,y,-z", "-x,-y+2/3,-z+1/2", "x,-y+2/3,-z+1/2", "-x,-y+2/3,z+1/2", "x,-y+2/3,z+1/2", "-x+1/2,-y+2/3,-z+1/2", "x+1/2,-y+2/3,-z+1/2", "-x+1/2,-y+2/3,z+1/2", "x+1/2,-y+2/3,z+1/2"], "universal_h_m": "P m m a (2*b+1/4,c,a-1/3)", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2a 2a (1/2*y,z+1/3,x-1/4)", "hermann_mauguin": "P m m a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,y,z", "x,y,-z", "-x,y,-z", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,y,-z", "-x+1/2,y,-z"]}, {"symops": ["x,y,z", "-x,y,-z+1/2", "x,y+1/2,z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,-y,z+1/2", "-x,-y+1/2,-z", "x,-y+1/2,z+1/2"], "universal_h_m": "P 1 2/c 1 (a,2*b,c)", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2yc (x,1/2*y,z)", "hermann_mauguin": "P 1 2/c 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x,y,-z+1/2", "x,y+1/2,z", "-x,y+1/2,-z+1/2"]}, {"symops": ["x,y,z", "-x,y,z", "x,-y,z", "-x,-y,z", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,-y,z", "-x+1/2,-y,z", "x,y+1/2,z", "-x,y+1/2,z", "x,-y+1/2,z", "-x,-y+1/2,z", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x,-y,-z", "-x,y,-z", "x,y,-z", "-x+1/2,-y,-z", "x+1/2,-y,-z", "-x+1/2,y,-z", "x+1/2,y,-z", "-x,-y+1/2,-z", "x,-y+1/2,-z", "-x,y+1/2,-z", "x,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "x+1/2,y+1/2,-z"], "universal_h_m": "P m m m (2*a,2*b,c)", "number": 47, "schoenflies": "D2h^1", "hall": "-P 2 2 (1/2*x,1/2*y,z)", "hermann_mauguin": "P m m m", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x,y,z", "x,-y,z", "-x,-y,z", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,-y,z", "-x+1/2,-y,z"]}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "P 1 21 1 (a-1/4,b,c)", "number": 4, "schoenflies": "C2^2", "hall": " P 2yb (x+1/4,y,z)", "hermann_mauguin": "P 1 21 1", "crystal_class": "monoclinic", "ncsym": ["x,y,z", "-x+1/2,y+1/2,-z"]}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z", "-x,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,-y,-z+1/2", "x+1/2,-y+1/2,z+1/2", "x,y,-z", "-x+1/2,y+1/2,z"], "universal_h_m": "P n m a (c,a-1/4,b)", "number": 62, "schoenflies": "D2h^16", "hall": "-P 2ac 2n (z,x,y+1/4)", "hermann_mauguin": "P n m a", "crystal_class": "orthorhombic", "ncsym": ["x,y,z", "-x+1/2,y+1/2,-z", "-x,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,-y,-z+1/2", "x+1/2,-y+1/2,z+1/2", "x,y,-z", "-x+1/2,y+1/2,z"]}] diff --git a/pymatgen/vis/ElementColorSchemes.yaml b/pymatgen/vis/ElementColorSchemes.yaml deleted file mode 100644 index 1480a741d64..00000000000 --- a/pymatgen/vis/ElementColorSchemes.yaml +++ /dev/null @@ -1,220 +0,0 @@ -Jmol: - Ac: [112, 171, 250] - Ag: [192, 192, 192] - Al: [191, 166, 166] - Am: [84, 92, 242] - Ar: [128, 209, 227] - As: [189, 128, 227] - At: [117, 79, 69] - Au: [255, 209, 35] - B: [255, 181, 181] - Ba: [0, 201, 0] - Be: [194, 255, 0] - Bh: [224, 0, 56] - Bi: [158, 79, 181] - Bk: [138, 79, 227] - Br: [166, 41, 41] - C: [144, 144, 144] - Ca: [61, 255, 0] - Cd: [255, 217, 143] - Ce: [255, 255, 199] - Cf: [161, 54, 212] - Cl: [31, 240, 31] - Cm: [120, 92, 227] - Co: [240, 144, 160] - Cr: [138, 153, 199] - Cs: [87, 23, 143] - Cu: [200, 128, 51] - Db: [209, 0, 79] - Dy: [31, 255, 199] - Er: [0, 230, 117] - Es: [179, 31, 212] - Eu: [97, 255, 199] - F: [144, 224, 80] - Fe: [224, 102, 51] - Fm: [179, 31, 186] - Fr: [66, 0, 102] - Ga: [194, 143, 143] - Gd: [69, 255, 199] - Ge: [102, 143, 143] - H: [255, 255, 255] - He: [217, 255, 255] - Hf: [77, 194, 255] - Hg: [184, 184, 208] - Ho: [0, 255, 156] - Hs: [230, 0, 46] - I: [148, 0, 148] - In: [166, 117, 115] - Ir: [23, 84, 135] - K: [143, 64, 212] - Kr: [92, 184, 209] - La: [112, 212, 255] - Li: [204, 128, 255] - Lr: [199, 0, 102] - Lu: [0, 171, 36] - Md: [179, 13, 166] - Mg: [138, 255, 0] - Mn: [156, 122, 199] - Mo: [84, 181, 181] - Mt: [235, 0, 38] - N: [48, 80, 248] - Na: [171, 92, 242] - Nb: [115, 194, 201] - Nd: [199, 255, 199] - Ne: [179, 227, 245] - Ni: [80, 208, 80] - 'No': [189, 13, 135] - Np: [0, 128, 255] - O: [255, 13, 13] - Os: [38, 102, 150] - P: [255, 128, 0] - Pa: [0, 161, 255] - Pb: [87, 89, 97] - Pd: [0, 105, 133] - Pm: [163, 255, 199] - Po: [171, 92, 0] - Pr: [217, 255, 199] - Pt: [208, 208, 224] - Pu: [0, 107, 255] - Ra: [0, 125, 0] - Rb: [112, 46, 176] - Re: [38, 125, 171] - Rf: [204, 0, 89] - Rh: [10, 125, 140] - Rn: [66, 130, 150] - Ru: [36, 143, 143] - S: [255, 255, 48] - Sb: [158, 99, 181] - Sc: [230, 230, 230] - Se: [255, 161, 0] - Sg: [217, 0, 69] - Si: [240, 200, 160] - Sm: [143, 255, 199] - Sn: [102, 128, 128] - Sr: [0, 255, 0] - Ta: [77, 166, 255] - Tb: [48, 255, 199] - Tc: [59, 158, 158] - Te: [212, 122, 0] - Th: [0, 186, 255] - Ti: [191, 194, 199] - Tl: [166, 84, 77] - Tm: [0, 212, 82] - U: [0, 143, 255] - V: [166, 166, 171] - W: [33, 148, 214] - Xe: [66, 158, 176] - Y: [148, 255, 255] - Yb: [0, 191, 56] - Zn: [125, 128, 176] - Zr: [148, 224, 224] -VESTA: - Ac: [112, 171, 250] - Ag: [192, 192, 192] - Al: [129, 178, 214] - Am: [84, 92, 242] - Ar: [207, 254, 196] - As: [116, 208, 87] - At: [117, 79, 69] - Au: [255, 209, 35] - B: [31, 162, 15] - Ba: [0, 201, 0] - Be: [94, 215, 123] - Bh: [224, 0, 56] - Bi: [158, 79, 181] - Bk: [138, 79, 227] - Br: [126, 49, 2] - C: [76, 76, 76] - Ca: [90, 150, 189] - Cd: [255, 217, 143] - Ce: [255, 255, 199] - Cf: [161, 54, 212] - Cl: [49, 252, 2] - Cm: [120, 92, 227] - Co: [0, 0, 175] - Cr: [0, 0, 158] - Cs: [87, 23, 143] - Cu: [34, 71, 220] - Db: [209, 0, 79] - Dy: [31, 255, 199] - Er: [0, 230, 117] - Es: [179, 31, 212] - Eu: [97, 255, 199] - F: [176, 185, 230] - Fe: [181, 113, 0] - Fm: [179, 31, 186] - Fr: [66, 0, 102] - Ga: [158, 227, 115] - Gd: [69, 255, 199] - Ge: [126, 110, 166] - H: [255, 204, 204] - He: [252, 232, 206] - Hf: [77, 194, 255] - Hg: [184, 184, 208] - Ho: [0, 255, 156] - Hs: [230, 0, 46] - I: [148, 0, 148] - In: [166, 117, 115] - Ir: [23, 84, 135] - K: [161, 33, 246] - Kr: [250, 193, 243] - La: [90, 196, 73] - Li: [134, 223, 115] - Lr: [199, 0, 102] - Lu: [0, 171, 36] - Md: [179, 13, 166] - Mg: [251, 123, 21] - Mn: [167, 8, 157] - Mo: [84, 181, 181] - Mt: [235, 0, 38] - N: [176, 185, 230] - Na: [249, 220, 60] - Nb: [115, 194, 201] - Nd: [199, 255, 199] - Ne: [254, 55, 181] - Ni: [183, 187, 189] - 'No': [189, 13, 135] - Np: [0, 128, 255] - O: [254, 3, 0] - Os: [38, 102, 150] - P: [192, 156, 194] - Pa: [0, 161, 255] - Pb: [87, 89, 97] - Pd: [0, 105, 133] - Pm: [163, 255, 199] - Po: [171, 92, 0] - Pr: [217, 255, 199] - Pt: [208, 208, 224] - Pu: [0, 107, 255] - Ra: [0, 125, 0] - Rb: [112, 46, 176] - Re: [38, 125, 171] - Rf: [204, 0, 89] - Rh: [10, 125, 140] - Rn: [66, 130, 150] - Ru: [36, 143, 143] - S: [255, 250, 0] - Sb: [158, 99, 181] - Sc: [181, 99, 171] - Se: [154, 239, 15] - Sg: [217, 0, 69] - Si: [27, 59, 250] - Sm: [143, 255, 199] - Sn: [154, 142, 185] - Sr: [0, 255, 0] - Ta: [77, 166, 255] - Tb: [48, 255, 199] - Tc: [59, 158, 158] - Te: [212, 122, 0] - Th: [0, 186, 255] - Ti: [120, 202, 255] - Tl: [166, 84, 77] - Tm: [0, 212, 82] - U: [0, 143, 255] - V: [229, 25, 0] - W: [33, 148, 214] - Xe: [66, 158, 176] - Y: [148, 255, 255] - Yb: [0, 191, 56] - Zn: [143, 143, 129] - Zr: [0, 255, 0] diff --git a/pyproject.toml b/pyproject.toml index 22da05a9b2a..0546b4b7ac0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,12 +1,179 @@ [build-system] requires = [ - "Cython>=0.29.23", - # pin NumPy version used in the build - "oldest-supported-numpy", - "setuptools>=65.0.0", + "Cython>=0.29.23", + # pin NumPy version used in the build + "oldest-supported-numpy", + "setuptools>=65.0.0", ] build-backend = "setuptools.build_meta" + +[project] +name = "pymatgen" +authors = [ + { name = "Pymatgen Development Team", email = "ongsp@ucsd.edu" }, +] +maintainers = [ + { name = "Shyue Ping Ong", email = "ongsp@ucsd.edu" }, + { name = "Matthew Horton", email = "m.k.horton@gmail.com" }, + { name = "Janosh Riebesell", email = "janosh.riebesell@gmail.com" }, +] +description = """ +Python Materials Genomics is a robust materials analysis code that defines core object representations for structures +and molecules with support for many electronic structure codes. It is currently the core analysis code powering the +Materials Project (https://materialsproject.org).""" +readme = "README.md" +requires-python = ">=3.9" +keywords = [ + "ABINIT", + "analysis", + "crystal", + "diagrams", + "electronic", + "gaussian", + "materials", + "nwchem", + "phase", + "project", + "qchem", + "science", + "structure", + "VASP", +] +license = { text = "MIT" } +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering :: Chemistry", + "Topic :: Scientific/Engineering :: Information Analysis", + "Topic :: Scientific/Engineering :: Physics", + "Topic :: Software Development :: Libraries :: Python Modules", +] +dependencies = [ + "matplotlib>=3.8", + "monty>=2024.5.24", + "networkx>=2.2", + 'numpy>=1.25.0,<2.0 ; platform_system == "Windows"', + 'numpy>=1.25.0 ; platform_system != "Windows"', + "palettable>=3.1.1", + "pandas>=2", + "plotly>=4.5.0", + "pybtex>=0.24.0", + "requests>=2.32", + "ruamel.yaml>=0.17.0", + "scipy>=1.13.0", + "spglib>=2.5.0", + "sympy>=1.2", + "tabulate>=0.9", + "tqdm>=4.60", + "uncertainties>=3.1.4", + "joblib>=1", +] +version = "2024.7.18" + +[project.urls] +Homepage = "https://pymatgen.org" +Documentation = "https://pymatgen.org" +Repository = "https://github.com/materialsproject/pymatgen" +Issues = "https://github.com/materialsproject/pymatgen/issues" +Pypi = "https://pypi.org/project/pymatgen" + +[project.optional-dependencies] +ase = ["ase>=3.23.0"] +# don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175 +tblite = ["tblite[ase]>=0.3.0; python_version<'3.12'"] +vis = ["vtk>=6.0.0"] +abinit = ["netcdf4>=1.6.5"] +mlp = ["matgl>=1.1.1", "chgnet>=0.3.8"] +electronic_structure = ["fdint>=2.0.2"] +ci = [ + "pytest>=8", + "pytest-cov>=4", + "pytest-split>=0.8", +] +docs = [ + "sphinx", + "sphinx_rtd_theme", +] +optional = [ + "ase>=3.23.0", + # TODO restore BoltzTraP2 when install fixed, hopefully following merge of + # https://gitlab.com/sousaw/BoltzTraP2/-/merge_requests/18 + # caused CI failure due to ModuleNotFoundError: No module named 'packaging' + # "BoltzTraP2>=22.3.2; platform_system!='Windows'", + "chemview>=0.6", + "chgnet>=0.3.8", + "f90nml>=1.1.2", + "galore>=0.6.1", + "h5py>=3.11.0", + "jarvis-tools>=2020.7.14", + "matgl>=1.1.1", + "netCDF4>=1.6.5", + "phonopy>=2.23", + "seekpath>=2.0.1", + # don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175 + "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'", + # "hiphive>=0.6", + # "openbabel>=3.1.1; platform_system=='Linux'", +] +numba = ["numba>=0.55"] + +[project.scripts] +pmg = "pymatgen.cli.pmg:main" +feff_plot_cross_section = "pymatgen.cli.feff_plot_cross_section:main" +feff_plot_dos = "pymatgen.cli.feff_plot_dos:main" +get_environment = "pymatgen.cli.get_environment:main" + +[tool.setuptools] +include-package-data = false + +[tool.setuptools.packages.find] +where = ["src"] +include = ["pymatgen", "pymatgen.*"] + +[tool.setuptools.package-data] +"pymatgen.analysis" = ["*.yaml", "*.json", "*.csv"] +"pymatgen.analysis.chemenv" = [ + "coordination_environments/coordination_geometries_files/*.json", + "coordination_environments/coordination_geometries_files/*.txt", + "coordination_environments/strategy_files/ImprovedConfidenceCutoffDefaultParameters.json", +] +"pymatgen.analysis.structure_prediction" = ["*.yaml", "data/*.json"] +"pymatgen.analysis.diffraction" = ["*.json"] +"pymatgen.analysis.magnetism" = ["default_magmoms.yaml"] +"pymatgen.analysis.solar" = ["am1.5G.dat"] +"pymatgen.entries" = ["*.json.gz", "*.yaml", "data/*.json"] +"pymatgen.core" = ["*.json"] +"pymatgen" = ["py.typed"] +"pymatgen.io.vasp" = ["*.yaml", "*.json", "*.json.gz", "*.json.bz2"] +"pymatgen.io.feff" = ["*.yaml"] +"pymatgen.io.cp2k" = ["*.yaml"] +"pymatgen.io.lobster" = ["lobster_basis/*.yaml"] +"pymatgen.command_line" = ["*"] +"pymatgen.util" = ["structures/*.json", "*.json"] +"pymatgen.vis" = ["*.yaml"] +"pymatgen.io.lammps" = ["CoeffsDataType.yaml", "templates/*.template"] +"pymatgen.symmetry" = ["*.yaml", "*.json", "*.sqlite"] + +[tool.pdm.dev-dependencies] +lint = [ + "mypy>=1.10.0", + "ruff>=0.4.9", + "pre-commit>=3.7.1", +] +test = [ + "pytest>=8.2.2", + "pytest-cov>=5.0.0", + "pytest-split>=0.9.0", +] + [tool.versioningit.vcs] method = "git" default-tag = "0.0.1" @@ -24,41 +191,30 @@ target-version = "py39" line-length = 120 [tool.ruff.lint] -select = [ - "B", # flake8-bugbear - "C4", # flake8-comprehensions - "D", # pydocstyle - "E", # pycodestyle error - "EXE", # flake8-executable - "F", # pyflakes - "FA", # flake8-future-annotations - "FBT003", # boolean-positional-value-in-call - "FLY", # flynt - "I", # isort - "ICN", # flake8-import-conventions - "ISC", # flake8-implicit-str-concat - "PD", # pandas-vet - "PERF", # perflint - "PIE", # flake8-pie - "PL", # pylint - "PLR0402", - "PLR1714", - "PLR5501", - "PT", # flake8-pytest-style - "PYI", # flakes8-pyi - "Q", # flake8-quotes - "RET", # flake8-return - "RSE", # flake8-raise - "RUF", # Ruff-specific rules - "SIM", # flake8-simplify - "SLOT", # flake8-slots - "TCH", # flake8-type-checking - "TID", # flake8-tidy-imports - "UP", # pyupgrade - "W", # pycodestyle warning - "YTT", # flake8-2020 -] +select = ["ALL"] ignore = [ + # Rule families + "ANN", # flake8-annotations (not ready, require types for ALL args) + "ARG", # Check for unused function arguments + "BLE", # General catch of Exception + "C90", # Check for functions with a high McCabe complexity + "COM", # flake8-commas (conflict with line wrapper) + "CPY", # Missing copyright notice at top of file (need preview mode) + "EM", # Format nice error messages + "ERA", # Check for commented-out code + "FIX", # Check for FIXME, TODO and other developer notes + "FURB", # refurb (need preview mode, too many preview errors) + "G", # validate logging format strings + "INP", # Ban PEP-420 implicit namespace packages + "N", # pep8-naming (many var/arg names are intended) + "NPY", # NumPy-specific rules (TODO: enable this) + "PTH", # Prefer pathlib over os.path + "S", # flake8-bandit (TODO: enable this) + "SLF", # Access "private" class members + "T20", # Check for print/pprint + "TD", # TODO tags related + + # Single rules "B023", # Function definition does not bind loop variable "B028", # No explicit stacklevel keyword argument found "B904", # Within an except clause, raise exceptions with ... @@ -66,14 +222,23 @@ ignore = [ "D105", # Missing docstring in magic method "D205", # 1 blank line required between summary line and description "D212", # Multi-line docstring summary should start at the first line + "DTZ003", # TODO: fix this (issue #3791) + "FBT001", # Boolean-typed positional argument in function definition + "FBT002", # Boolean default positional argument in function "PD901", # pandas-df-variable-name "PERF203", # try-except-in-loop "PERF401", # manual-list-comprehension - "PLR", # pylint refactor + "PLR0911", # too many return statements + "PLR0912", # too many branches + "PLR0913", # too many arguments + "PLR0915", # too many statements + "PLR2004", # magic values in comparison "PLW2901", # Outer for loop variable overwritten by inner assignment target "PT013", # pytest-incorrect-pytest-import - "PTH", # prefer pathlib to os.path "SIM105", # Use contextlib.suppress() instead of try-except-pass + "TRY003", # Avoid specifying long messages outside the exception class + "TRY300", # Checks for return statements in try blocks + "TRY301", # Checks for raise statements within try blocks ] pydocstyle.convention = "google" isort.required-imports = ["from __future__ import annotations"] @@ -84,11 +249,9 @@ docstring-code-format = true [tool.ruff.lint.per-file-ignores] "__init__.py" = ["F401"] -"tests/**" = ["ANN201", "D", "S101"] -"tasks.py" = ["D"] -"pymatgen/analysis/*" = ["D"] -"pymatgen/vis/*" = ["D"] -"pymatgen/io/*" = ["D"] +"tests/**" = ["ANN201", "D", "PLR0124"] +"src/pymatgen/analysis/*" = ["D"] +"src/pymatgen/io/*" = ["D"] "dev_scripts/*" = ["D"] [tool.pytest.ini_options] @@ -97,31 +260,31 @@ addopts = "--durations=30 --quiet -r xXs --color=yes -p no:warnings --import-mod [tool.coverage.run] parallel = true omit = [ - "pymatgen/cli/feff_plot_cross_section.py", - "pymatgen/cli/feff_plot_dos.py", - "pymatgen/cli/pmg_config.py", - "pymatgen/cli/pmg_plot.py", - "pymatgen/cli/pmg_potcar.py", - "pymatgen/cli/pmg_query.py", - "pymatgen/dao.py", + "pymatgen/cli/feff_plot_cross_section.py", + "pymatgen/cli/feff_plot_dos.py", + "pymatgen/cli/pmg_config.py", + "pymatgen/cli/pmg_plot.py", + "pymatgen/cli/pmg_potcar.py", + "pymatgen/cli/pmg_query.py", + "pymatgen/dao.py", ] [tool.coverage.report] exclude_also = [ - "@deprecated", - "@np.deprecate", - "def __repr__", - "except ImportError:", - "if 0:", - "if TYPE_CHECKING:", - "if __name__ == .__main__.:", - "if self.debug:", - "if settings.DEBUG", - "if typing.TYPE_CHECKING:", - "pragma: no cover", - "raise AssertionError", - "raise NotImplementedError", - "show_plot", + "@deprecated", + "@np.deprecate", + "def __repr__", + "except ImportError:", + "if 0:", + "if TYPE_CHECKING:", + "if __name__ == .__main__.:", + "if self.debug:", + "if settings.DEBUG", + "if typing.TYPE_CHECKING:", + "pragma: no cover", + "raise AssertionError", + "raise NotImplementedError", + "show_plot", ] [tool.mypy] diff --git a/requirements-optional.txt b/requirements-optional.txt deleted file mode 100644 index 11220380cb6..00000000000 --- a/requirements-optional.txt +++ /dev/null @@ -1,15 +0,0 @@ -ase>=3.23.0 -beautifulsoup4==4.12.2 -BoltzTraP2>=22.3.2 -chemview>=0.6 -f90nml>=1.4.3 -fdint>=2.0.2 -galore>=0.7.0 -h5py==3.11.0 -# hiphive>=0.6 -icet>=2.2 -jarvis-tools>=2022.9.16 -matgl==1.1.1 -netCDF4>=1.5.8 -phonopy==2.23.1 -seekpath>=2.0.1 diff --git a/requirements.txt b/requirements.txt index b50daba5ea2..aecf3fc2b4d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,18 +1,88 @@ -numpy==1.26.4 -sympy==1.12 -requests==2.32.0 +# This file was autogenerated by uv via the following command: +# uv pip compile pyproject.toml -o requirements.txt +certifi==2024.7.4 + # via requests +charset-normalizer==3.3.2 + # via requests +contourpy==1.2.1 + # via matplotlib +cycler==0.12.1 + # via matplotlib +fonttools==4.53.0 + # via matplotlib +idna==3.7 + # via requests +joblib==1.4.2 + # via pymatgen (pyproject.toml) +kiwisolver==1.4.5 + # via matplotlib +latexcodec==3.0.0 + # via pybtex +matplotlib==3.9.0 + # via pymatgen (pyproject.toml) monty==2024.5.24 -ruamel.yaml==0.18.6 -scipy==1.11.3 -tabulate==0.9.0 -matplotlib==3.8.0 -palettable==3.3.3 -spglib==2.1.0 -pandas==2.1.1 + # via pymatgen (pyproject.toml) +mpmath==1.3.0 + # via sympy networkx==3.3 -plotly==5.17.0 -uncertainties==3.1.7 -Cython==3.0.2 + # via pymatgen (pyproject.toml) +numpy==2.0.0 + # via + # pymatgen (pyproject.toml) + # contourpy + # matplotlib + # pandas + # scipy + # spglib +packaging==24.1 + # via + # matplotlib + # plotly +palettable==3.3.3 + # via pymatgen (pyproject.toml) +pandas==2.2.2 + # via pymatgen (pyproject.toml) +pillow==10.3.0 + # via matplotlib +plotly==5.22.0 + # via pymatgen (pyproject.toml) pybtex==0.24.0 + # via pymatgen (pyproject.toml) +pyparsing==3.1.2 + # via matplotlib +python-dateutil==2.9.0.post0 + # via + # matplotlib + # pandas +pytz==2024.1 + # via pandas +pyyaml==6.0.1 + # via pybtex +requests==2.32.3 + # via pymatgen (pyproject.toml) +ruamel-yaml==0.18.6 + # via pymatgen (pyproject.toml) +ruamel-yaml-clib==0.2.8 + # via ruamel-yaml +scipy==1.13.1 + # via pymatgen (pyproject.toml) +six==1.16.0 + # via + # pybtex + # python-dateutil +spglib==2.4.0 + # via pymatgen (pyproject.toml) +sympy==1.12.1 + # via pymatgen (pyproject.toml) +tabulate==0.9.0 + # via pymatgen (pyproject.toml) +tenacity==8.4.1 + # via plotly tqdm==4.66.4 -joblib==1.3.2 + # via pymatgen (pyproject.toml) +tzdata==2024.1 + # via pandas +uncertainties==3.2.1 + # via pymatgen (pyproject.toml) +urllib3==2.2.2 + # via requests diff --git a/setup.py b/setup.py index ad5656dd6b2..c07456e18cc 100644 --- a/setup.py +++ b/setup.py @@ -6,195 +6,28 @@ import sys import numpy as np -from setuptools import Extension, find_namespace_packages, setup +from setuptools import Extension, setup is_win_64 = sys.platform.startswith("win") and platform.machine().endswith("64") extra_link_args = ["-Wl,--allow-multiple-definition"] if is_win_64 else [] -with open("README.md") as file: - long_description = file.read() - -# unlike GitHub readmes, PyPI doesn't support tags used for responsive images -# (i.e. adaptive to OS light/dark mode) -# NOTE this manual fix won't work once we migrate to pyproject.toml -logo_url = "https://raw.githubusercontent.com/materialsproject/pymatgen/master/docs/_images/pymatgen.svg" -long_description = ( - f"

                                                                                        Logo

                                                                                        " + long_description.split("                                                                                        ")[-1] -) - setup( - name="pymatgen", - packages=find_namespace_packages(include=["pymatgen.*", "pymatgen.**.*"]), - version="2024.6.10", - python_requires=">=3.9", - install_requires=[ - "matplotlib>=3.8", - "monty>=2024.5.24", - "networkx>=2.2", - "numpy>=1.25.0", - "palettable>=3.1.1", - "pandas>=2", - "plotly>=4.5.0", - "pybtex>=0.24.0", - "requests>=2.32", - "ruamel.yaml>=0.17.0", - "scipy>=1.13.0", - "spglib>=2.0.2", - "sympy>=1.2", - "tabulate>=0.9", - "tqdm>=4.60", - "uncertainties>=3.1.4", - "joblib>=1", - ], - extras_require={ - "ase": ["ase>=3.23.0"], - # don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175 - "tblite": ["tblite[ase]>=0.3.0; python_version<'3.12'"], - "vis": ["vtk>=6.0.0"], - "abinit": ["netcdf4>=1.6.5"], - "relaxation": ["matgl>=1.1.1", "chgnet>=0.3.8"], - "electronic_structure": ["fdint>=2.0.2"], - "dev": [ - "mypy>=1.10.0", - "pre-commit>=3", - "pytest-cov>=4", - "pytest-split>=0.8", - "pytest>8", - "ruff>=0.4", - ], - "ci": [ - "pytest>=8", - "pytest-cov>=4", - "pytest-split>=0.8", - ], - "docs": [ - "sphinx", - "sphinx_rtd_theme", - "doc2dash", - ], - "optional": [ - "ase>=3.23.0", - # TODO restore BoltzTraP2 when install fixed, hopefully following merge of - # https://gitlab.com/sousaw/BoltzTraP2/-/merge_requests/18 - # caused CI failure due to ModuleNotFoundError: No module named 'packaging' - # "BoltzTraP2>=22.3.2; platform_system!='Windows'", - "chemview>=0.6", - "chgnet>=0.3.8", - "f90nml>=1.1.2", - "galore>=0.6.1", - "h5py>=3.11.0", - "jarvis-tools>=2020.7.14", - "matgl>=1.1.1", - "netCDF4>=1.6.5", - "phonopy>=2.23", - "seekpath>=2.0.1", - # don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175 - "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'", - # "hiphive>=0.6", - # "openbabel>=3.1.1; platform_system=='Linux'", - ], - "numba": ["numba>=0.55"], - }, - # All package data has to be explicitly defined. Do not use automated codes like last time. It adds - # all sorts of useless files like test files and is prone to path errors. - package_data={ - "pymatgen.analysis": ["*.yaml", "*.json", "*.csv"], - "pymatgen.analysis.chemenv": [ - "coordination_environments/coordination_geometries_files/*.json", - "coordination_environments/coordination_geometries_files/*.txt", - "coordination_environments/strategy_files/ImprovedConfidenceCutoffDefaultParameters.json", - ], - "pymatgen.analysis.structure_prediction": ["*.yaml", "data/*.json"], - "pymatgen.analysis.diffraction": ["*.json"], - "pymatgen.analysis.magnetism": ["default_magmoms.yaml"], - "pymatgen.analysis.solar": ["am1.5G.dat"], - "pymatgen.entries": ["*.json.gz", "*.yaml", "data/*.json"], - "pymatgen.core": ["*.json"], - "pymatgen": ["py.typed"], - "pymatgen.io.vasp": ["*.yaml", "*.json", "*.json.gz", "*.json.bz2"], - "pymatgen.io.feff": ["*.yaml"], - "pymatgen.io.cp2k": ["*.yaml"], - "pymatgen.io.lobster": ["lobster_basis/*.yaml"], - "pymatgen.command_line": ["*"], - "pymatgen.util": ["structures/*.json", "*.json"], - "pymatgen.vis": ["*.yaml"], - "pymatgen.io.lammps": ["CoeffsDataType.yaml", "templates/*.template"], - "pymatgen.symmetry": ["*.yaml", "*.json", "*.sqlite"], - }, - author="Pymatgen Development Team", - author_email="ongsp@ucsd.edu", - maintainer="Shyue Ping Ong, Matthew Horton, Janosh Riebesell", - maintainer_email="ongsp@ucsd.edu, mkhorton@lbl.gov, janosh.riebesell@gmail.com", - url="https://pymatgen.org", - license="MIT", - project_urls={ - "Docs": "https://pymatgen.org", - "Package": "https://pypi.org/project/pymatgen", - "Repo": "https://github.com/materialsproject/pymatgen", - }, - description="Python Materials Genomics is a robust materials " - "analysis code that defines core object representations for " - "structures and molecules with support for many electronic " - "structure codes. It is currently the core analysis code " - "powering the Materials Project " - "(https://materialsproject.org).", - long_description=long_description, - long_description_content_type="text/markdown", - keywords=[ - "ABINIT", - "analysis", - "crystal", - "diagrams", - "electronic", - "gaussian", - "materials", - "nwchem", - "phase", - "project", - "qchem", - "science", - "structure", - "VASP", - ], - classifiers=[ - "Development Status :: 4 - Beta", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "Programming Language :: Python :: 3", - "Topic :: Scientific/Engineering :: Chemistry", - "Topic :: Scientific/Engineering :: Information Analysis", - "Topic :: Scientific/Engineering :: Physics", - "Topic :: Software Development :: Libraries :: Python Modules", - ], ext_modules=[ Extension( "pymatgen.optimization.linear_assignment", - ["pymatgen/optimization/linear_assignment.pyx"], + ["src/pymatgen/optimization/linear_assignment.pyx"], extra_link_args=extra_link_args, ), Extension( "pymatgen.util.coord_cython", - ["pymatgen/util/coord_cython.pyx"], + ["src/pymatgen/util/coord_cython.pyx"], extra_link_args=extra_link_args, ), Extension( "pymatgen.optimization.neighbors", - ["pymatgen/optimization/neighbors.pyx"], + ["src/pymatgen/optimization/neighbors.pyx"], extra_link_args=extra_link_args, ), ], - entry_points={ - "console_scripts": [ - "pmg = pymatgen.cli.pmg:main", - "feff_plot_cross_section = pymatgen.cli.feff_plot_cross_section:main", - "feff_plot_dos = pymatgen.cli.feff_plot_dos:main", - "get_environment = pymatgen.cli.get_environment:main", - ] - }, include_dirs=[np.get_include()], ) diff --git a/pymatgen/alchemy/__init__.py b/src/pymatgen/alchemy/__init__.py similarity index 100% rename from pymatgen/alchemy/__init__.py rename to src/pymatgen/alchemy/__init__.py diff --git a/pymatgen/alchemy/filters.py b/src/pymatgen/alchemy/filters.py similarity index 99% rename from pymatgen/alchemy/filters.py rename to src/pymatgen/alchemy/filters.py index 97dedf80919..c16c05bf634 100644 --- a/pymatgen/alchemy/filters.py +++ b/src/pymatgen/alchemy/filters.py @@ -7,15 +7,13 @@ from typing import TYPE_CHECKING from monty.json import MSONable - from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher from pymatgen.core import get_el_sp from pymatgen.symmetry.analyzer import SpacegroupAnalyzer if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.core import Structure + from typing_extensions import Self class AbstractStructureFilter(MSONable, abc.ABC): @@ -179,7 +177,7 @@ def __init__(self, structure_matcher: dict | StructureMatcher | None = None, sym self.symprec = symprec self.structure_list: dict[str, list[Structure]] = defaultdict(list) if not isinstance(structure_matcher, (dict, StructureMatcher, type(None))): - raise ValueError(f"{structure_matcher=} must be a dict, StructureMatcher or None") + raise TypeError(f"{structure_matcher=} must be a dict, StructureMatcher or None") if isinstance(structure_matcher, dict): self.structure_matcher = StructureMatcher.from_dict(structure_matcher) else: diff --git a/pymatgen/alchemy/materials.py b/src/pymatgen/alchemy/materials.py similarity index 98% rename from pymatgen/alchemy/materials.py rename to src/pymatgen/alchemy/materials.py index de3338e183f..701133215e3 100644 --- a/pymatgen/alchemy/materials.py +++ b/src/pymatgen/alchemy/materials.py @@ -12,7 +12,6 @@ from warnings import warn from monty.json import MSONable, jsanitize - from pymatgen.core.structure import Structure from pymatgen.io.cif import CifParser from pymatgen.io.vasp.inputs import Poscar @@ -24,9 +23,8 @@ from collections.abc import Sequence from typing import Any - from typing_extensions import Self - from pymatgen.alchemy.filters import AbstractStructureFilter + from typing_extensions import Self class TransformedStructure(MSONable): @@ -270,10 +268,10 @@ def from_cif_str( primitive: bool = True, occupancy_tolerance: float = 1.0, ) -> Self: - """Generate TransformedStructure from a cif string. + """Generate TransformedStructure from a CIF string. Args: - cif_string (str): Input cif string. Should contain only one + cif_string (str): Input CIF string. Should contain only one structure. For CIFs containing multiple structures, please use CifTransmuter. transformations (list[Transformation]): Sequence of transformations @@ -302,7 +300,7 @@ def from_cif_str( source = "uploaded cif" source_info = { "source": source, - "datetime": str(datetime.datetime.now()), + "datetime": str(datetime.datetime.now(tz=datetime.timezone.utc)), "original_file": raw_str, "cif_data": cif_dict[cif_keys[0]], } @@ -330,7 +328,7 @@ def from_poscar_str( struct = poscar.structure source_info = { "source": "POSCAR", - "datetime": str(datetime.datetime.now()), + "datetime": str(datetime.datetime.now(tz=datetime.timezone.utc)), "original_file": raw_str, } return cls(struct, transformations, history=[source_info]) diff --git a/pymatgen/alchemy/transmuters.py b/src/pymatgen/alchemy/transmuters.py similarity index 97% rename from pymatgen/alchemy/transmuters.py rename to src/pymatgen/alchemy/transmuters.py index 545876d53e1..d51ea47c247 100644 --- a/pymatgen/alchemy/transmuters.py +++ b/src/pymatgen/alchemy/transmuters.py @@ -21,9 +21,8 @@ from collections.abc import Sequence from typing import Callable - from typing_extensions import Self - from pymatgen.alchemy.filters import AbstractStructureFilter + from typing_extensions import Self __author__ = "Shyue Ping Ong, Will Richards" __copyright__ = "Copyright 2012, The Materials Project" @@ -121,10 +120,10 @@ def append_transformation(self, transformation, extend_collection=False, clear_r describes whether the transformation altered the structure """ if self.ncores and transformation.use_multiprocessing: - with Pool(self.ncores) as p: + with Pool(self.ncores) as pool: # need to condense arguments into single tuple to use map z = ((ts, transformation, extend_collection, clear_redo) for ts in self.transformed_structures) - trafo_new_structs = p.map(_apply_transformation, z, 1) + trafo_new_structs = pool.map(_apply_transformation, z, 1) self.transformed_structures = [] for ts in trafo_new_structs: self.transformed_structures.extend(ts) @@ -223,19 +222,17 @@ def from_structures(cls, structures, transformations=None, extend_collection=0) class CifTransmuter(StandardTransmuter): - """Generate a Transmuter from a cif string, possibly containing multiple - structures. - """ + """Generate a Transmuter from a CIF string, possibly containing multiple structures.""" def __init__(self, cif_string, transformations=None, primitive=True, extend_collection=False): - """Generate a Transmuter from a cif string, possibly + """Generate a Transmuter from a CIF string, possibly containing multiple structures. Args: - cif_string: A string containing a cif or a series of CIFs + cif_string: A string containing a CIF or a series of CIFs transformations: New transformations to be applied to all structures - primitive: Whether to generate the primitive cell from the cif. + primitive: Whether to generate the primitive cell from the CIF. extend_collection: Whether to use more than one output structure from one-to-many transformations. extend_collection can be a number, which determines the maximum branching for each @@ -262,7 +259,7 @@ def from_filenames(cls, filenames, transformations=None, primitive=True, extend_ containing multiple structures. Args: - filenames: List of strings of the cif files + filenames: List of strings of the CIF files transformations: New transformations to be applied to all structures primitive: Same meaning as in __init__. diff --git a/pymatgen/analysis/adsorption.py b/src/pymatgen/analysis/adsorption.py similarity index 99% rename from pymatgen/analysis/adsorption.py rename to src/pymatgen/analysis/adsorption.py index 5fe6b7a3742..88f9f98dc3e 100644 --- a/pymatgen/analysis/adsorption.py +++ b/src/pymatgen/analysis/adsorption.py @@ -12,8 +12,6 @@ from matplotlib import patches from matplotlib.path import Path from monty.serialization import loadfn -from scipy.spatial import Delaunay - from pymatgen import vis from pymatgen.analysis.local_env import VoronoiNN from pymatgen.analysis.structure_matcher import StructureMatcher @@ -22,13 +20,13 @@ from pymatgen.core.surface import generate_all_slabs from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.coord import in_coord_list_pbc +from scipy.spatial import Delaunay if TYPE_CHECKING: import matplotlib.pyplot as plt from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.core.surface import Slab + from typing_extensions import Self __author__ = "Joseph Montoya" __copyright__ = "Copyright 2016, The Materials Project" diff --git a/src/pymatgen/analysis/aflow_prototypes.json b/src/pymatgen/analysis/aflow_prototypes.json new file mode 100644 index 00000000000..a80e1621420 --- /dev/null +++ b/src/pymatgen/analysis/aflow_prototypes.json @@ -0,0 +1,82528 @@ +[ + { + "snl": { + "@module": "pymatgen.util.provenance", + "@class": "StructureNL", + "charge": null, + "lattice": { + "matrix": [ + [ + -2.0725000000000007, + -3.5896752986864984, + -5.076160982465778e-16 + ], + [ + -2.072499999999999, + 3.5896752986864984, + 2.538080491232889e-16 + ], + [ + 0.0, + 0.0, + -9.496 + ] + ], + "a": 4.1450000000000005, + "b": 4.145, + "c": 9.496, + "alpha": 90.0, + "beta": 90.0, + "gamma": 120.00000000000001, + "volume": 141.29292225757536 + }, + "sites": [ + { + "species": [ + { + "element": "Hg", + "occu": 1.0 + } + ], + "abc": [ + 0.2802000000000002, + 0.2801999999999999, + 0.33333 + ], + "xyz": [ + -1.1614290000000003, + -1.1019124286649907e-15, + -3.1653016800000002 + ], + "label": "Hg" + }, + { + "species": [ + { + "element": "Hg", + "occu": 1.0 + } + ], + "abc": [ + 0.9999999999999999, + 0.7198000000000001, + 0.6666633333333334 + ], + "xyz": [ + -3.5642854999999996, + -1.005827018691956, + -6.3306350133333344 + ], + "label": "Hg" + }, + { + "species": [ + { + "element": "Hg", + "occu": 1.0 + } + ], + "abc": [ + 0.7198, + 1.9537414457130542e-18, + 0.9999966666666666 + ], + "xyz": [ + -1.4917855000000004, + -2.5838482799945415, + -9.495968346666666 + ], + "label": "Hg" + }, + { + "species": [ + { + "element": "S", + "occu": 1.0 + } + ], + "abc": [ + 0.5111000000000001, + 0.5110999999999999, + 0.83333 + ], + "xyz": [ + -2.1185094999999996, + -8.4113601217869895e-16, + -7.913301680000001 + ], + "label": "S" + }, + { + "species": [ + { + "element": "S", + "occu": 1.0 + } + ], + "abc": [ + 0.9999999999999999, + 0.4889000000000001, + 0.16666333333333339 + ], + "xyz": [ + -3.08574525, + -1.8346830451586684, + -1.5826350133333342 + ], + "label": "S" + }, + { + "species": [ + { + "element": "S", + "occu": 1.0 + } + ], + "abc": [ + 0.4889, + 1.0, + 0.49999666666666664 + ], + "xyz": [ + -3.0857452499999996, + 1.8346830451586693, + -4.747968346666667 + ], + "label": "S" + } + ], + "about": { + "authors": [ + { + "name": "AFLOW Library of Crystallographic Prototypes", + "email": "" + } + ], + "projects": [], + "references": "@article{reference0,\n author = \"P. Auvray and F. Genet\",\n title = \" Affinement de la structure cristalline du cinabre $\\alpha$-HgS\",\n journal = \" Bulletin de la Societe Francaise de Mineralogie et de Cristallographie\",\n volume = \"96\",\n year = \"1973\",\n page_first = \"218\",\n page_last = \"219\",\n pages = \"218--219\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", + "remarks": [ + "Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication." + ], + "history": [], + "created_at": { + "@module": "datetime", + "@class": "datetime", + "string": "2018-01-17 19:44:09.074386" + } + } + }, + "tags": { + "pearson": "hP6", + "aflow": "AB_hP6_154_a_b", + "strukturbericht": "B9", + "mineral": "Cinnabar" + } + }, + { + "snl": { + "@module": "pymatgen.util.provenance", + "@class": "StructureNL", + "charge": null, + "lattice": { + "matrix": [ + [ + 3.2064, + -0.0, + -0.0 + ], + [ + -1.9633537483930366e-16, + 3.2064, + 1.9633537483930366e-16 + ], + [ + -1.6031999999999997, + -1.6032, + 3.9239 + ] + ], + "a": 3.2064, + "b": 3.2064, + "c": 4.531830942345489, + "alpha": 110.71773016459983, + "beta": 110.71773016459983, + "gamma": 90.0, + "volume": 40.341619666944005 + }, + "sites": [ + { + "species": [ + { + "element": "Mo", + "occu": 1.0 + } + ], + "abc": [ + 0.0, + 0.0, + 0.0 + ], + "xyz": [ + 0.0, + 0.0, + 0.0 + ], + "label": "Mo" + }, + { + "species": [ + { + "element": "Si", + "occu": 1.0 + } + ], + "abc": [ + 0.33529999999999993, + 0.33529999999999993, + 0.6705999999999999 + ], + "xyz": [ + 1.117631143188191e-16, + -3.7139997743906866e-17, + 2.6313673399999997 + ], + "label": "Si" + }, + { + "species": [ + { + "element": "Si", + "occu": 1.0 + } + ], + "abc": [ + 0.6647000000000001, + 0.6647000000000001, + 0.32940000000000014 + ], + "xyz": [ + 1.6031999999999997, + 1.6031999999999997, + 1.2925326600000007 + ], + "label": "Si" + } + ], + "about": { + "authors": [ + { + "name": "AFLOW Library of Crystallographic Prototypes", + "email": "" + } + ], + "projects": [], + "references": "@article{reference0,\n author = \"Y. Harada and M. Morinaga and D. Saso and M. Takata and M. Sakata\",\n title = \" Refinement of crystal structure in MoSi$_2$\",\n journal = \" Intermetallics\",\n volume = \"6\",\n year = \"1998\",\n page_first = \"523\",\n page_last = \"527\",\n pages = \"523--527\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", + "remarks": [ + "Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication." + ], + "history": [], + "created_at": { + "@module": "datetime", + "@class": "datetime", + "string": "2018-01-17 19:44:09.091941" + } + } + }, + "tags": { + "pearson": "tI6", + "aflow": "AB2_tI6_139_a_e", + "strukturbericht": "C11_b", + "mineral": "" + } + }, + { + "snl": { + "@module": "pymatgen.util.provenance", + "@class": "StructureNL", + "charge": null, + "lattice": { + "matrix": [ + [ + 5.74, + 0.0, + 3.514736313552904e-16 + ], + [ + -3.514736313552904e-16, + 5.74, + 3.514736313552904e-16 + ], + [ + 0.0, + 0.0, + 5.74 + ] + ], + "a": 5.74, + "b": 5.74, + "c": 5.74, + "alpha": 90.0, + "beta": 90.0, + "gamma": 90.0, + "volume": 189.119224 + }, + "sites": [ + { + "species": [ + { + "element": "Cr", + "occu": 1.0 + } + ], + "abc": [ + 0.0, + 0.0, + 0.0 + ], + "xyz": [ + 0.0, + 0.0, + 0.0 + ], + "label": "Cr" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.5, + 0.0, + 0.0 + ], + "xyz": [ + 2.87, + 0.0, + 1.757368156776452e-16 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.0, + 0.0, + 0.5 + ], + "xyz": [ + 0.0, + 0.0, + 2.87 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.0, + 0.5, + 0.0 + ], + "xyz": [ + -1.757368156776452e-16, + 2.87, + 1.757368156776452e-16 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.245, + 0.245, + 0.245 + ], + "xyz": [ + 1.4063, + 1.4063, + 1.4063 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.245, + 0.755, + 0.755 + ], + "xyz": [ + 1.4062999999999999, + 4.3337, + 4.3337 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.755, + 0.245, + 0.755 + ], + "xyz": [ + 4.3337, + 1.4063, + 4.3337 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.755, + 0.755, + 0.245 + ], + "xyz": [ + 4.3337, + 4.3337, + 1.4063000000000005 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.755, + 0.755, + 0.755 + ], + "xyz": [ + 4.3337, + 4.3337, + 4.3337 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.755, + 0.245, + 0.245 + ], + "xyz": [ + 4.3337, + 1.4063, + 1.4063000000000003 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.245, + 0.755, + 0.245 + ], + "xyz": [ + 1.4062999999999999, + 4.3337, + 1.4063000000000003 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Fe", + "occu": 1.0 + } + ], + "abc": [ + 0.245, + 0.245, + 0.755 + ], + "xyz": [ + 1.4063, + 1.4063, + 4.3337 + ], + "label": "Fe" + }, + { + "species": [ + { + "element": "Ni", + "occu": 1.0 + } + ], + "abc": [ + 0.0, + 0.5, + 0.5 + ], + "xyz": [ + -1.757368156776452e-16, + 2.87, + 2.87 + ], + "label": "Ni" + }, + { + "species": [ + { + "element": "Ni", + "occu": 1.0 + } + ], + "abc": [ + 0.5, + 0.5, + 0.0 + ], + "xyz": [ + 2.87, + 2.87, + 3.514736313552904e-16 + ], + "label": "Ni" + }, + { + "species": [ + { + "element": "Ni", + "occu": 1.0 + } + ], + "abc": [ + 0.5, + 0.0, + 0.5 + ], + "xyz": [ + 2.87, + 0.0, + 2.87 + ], + "label": "Ni" + }, + { + "species": [ + { + "element": "Mo", + "occu": 1.0 + } + ], + "abc": [ + 0.5, + 0.5, + 0.5 + ], + "xyz": [ + 2.87, + 2.87, + 2.8700000000000006 + ], + "label": "Mo" + } + ], + "about": { + "authors": [ + { + "name": "AFLOW Library of Crystallographic Prototypes", + "email": "" + } + ], + "projects": [], + "references": "@article{reference0,\n author = \"Michael J. Mehl\",\n title = \" Hypothetical cP16 Austenite Structure\",\n journal = \" None\",\n volume = \"0\",\n year = \"2008\",\n page_first = \"0\",\n page_last = \"0\",\n pages = \"0--0\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", + "remarks": [ + "Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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A. Yurko and J. W. Barton and J. Gordon Parr\",\n title = \" The crystal structure of Ti$_2$Ni\",\n journal = \" Acta Crystallographica\",\n volume = \"12\",\n year = \"1959\",\n page_first = \"909\",\n page_last = \"911\",\n pages = \"909--911\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", + "remarks": [ + "Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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Petrillo and O. Moze and R. M. Ibberson\",\n title = \" High resolution neutron powder diffraction investigation of the low temperature crystal structure of molecular iodine (I$_2$)\",\n journal = \" Physica B\",\n volume = \"180-181\",\n year = \"1992\",\n page_first = \"639\",\n page_last = \"641\",\n pages = \"639--641\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", + "remarks": [ + "Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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author = \"Gary B. Adams and Michael O'Keeffe and Alexander A. Demkov and Otto F. Sankey and Yin-Min Huang\",\n title = \" Wide-band-gap Si in open fourfold-coordinated clathrate structures\",\n journal = \" Physical Review B\",\n volume = \"49\",\n year = \"1994\",\n page_first = \"8048\",\n page_last = \"8053\",\n pages = \"8048--8053\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", + "remarks": [ + "Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. 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B. Pearson\",\n title = \" The Cu$_2$Sb and related structures\",\n journal = { Zeitschrift f\\\"{u}r Kristallographie},\n volume = \"171\",\n year = \"1985\",\n page_first = \"23\",\n page_last = \"39\",\n pages = \"23--39\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", + "remarks": [ + "Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication." + ], + "history": [], + "created_at": { + "@module": "datetime", + "@class": "datetime", + "string": "2018-01-17 19:44:15.337757" + } + } + }, + "tags": { + "pearson": "tP6", + "aflow": "A2B_tP6_129_ac_c", + "strukturbericht": "C38", + "mineral": "" + } + }, + { + "snl": { + "@module": "pymatgen.util.provenance", + "@class": "StructureNL", + "charge": null, + "lattice": { + "matrix": [ + [ + 0.0, + 0.0, + 3.772 + ], + [ + -5.082, + 5.082, + 1.886 + ], + [ + -5.081999999999999, + -5.082, + 1.8859999999999992 + ] + ], + "a": 3.772, + "b": 7.430373072733293, + "c": 7.430373072733292, + "alpha": 86.3060954640227, + "beta": 75.2961431175098, + "gamma": 75.29614311750977, + "volume": 194.83680585599996 + }, + "sites": [ + { + "species": [ + { + "element": "Te", + "occu": 1.0 + } + ], + "abc": [ + 0.27970000000000006, + 0.6614, + 0.7791999999999999 + ], + "xyz": [ + -7.321129199999998, + -0.5986595999999997, + 3.7719999999999994 + ], + "label": "Te" + }, + { + "species": [ + { + "element": "Te", + "occu": 1.0 + } + ], + "abc": [ + 0.7202999999999999, + 0.3385999999999998, + 0.2208000000000002 + ], + "xyz": [ + -2.8428707999999996, + 0.598659599999998, + 3.7719999999999994 + ], + "label": "Te" + }, + { + "species": [ + { + "element": "Te", + "occu": 1.0 + } + ], + "abc": [ + 0.05889999999999995, + 0.22080000000000008, + 0.6614 + ], + "xyz": [ + -4.4833403999999994, + -2.2391291999999994, + 1.8859999999999995 + ], + "label": "Te" + }, + { + "species": [ + { + "element": "Te", + "occu": 1.0 + } + ], + "abc": [ + 0.9411, + 0.7791999999999999, + 0.3386 + ], + "xyz": [ + -5.6806595999999985, + 2.239129199999999, + 5.6579999999999995 + ], + "label": "Te" + }, + { + "species": [ + { + "element": "Ti", + "occu": 1.0 + } + ], + "abc": [ + 0.0, + 0.0, + 0.0 + ], + "xyz": [ + 0.0, + 0.0, + 0.0 + ], + "label": "Ti" + }, + { + "species": [ + { + "element": "Ti", + "occu": 1.0 + } + ], + "abc": [ + 0.3752, + 0.31039999999999995, + 0.9391999999999999 + ], + "xyz": [ + -6.350467199999998, + -3.1955616, + 3.771999999999999 + ], + "label": "Ti" + }, + { + "species": [ + { + "element": "Ti", + "occu": 1.0 + } + ], + "abc": [ + 0.6248, + 0.6896, + 0.06079999999999996 + ], + "xyz": [ + -3.8135327999999995, + 3.1955616, + 3.772 + ], + "label": "Ti" + }, + { + "species": [ + { + "element": "Ti", + "occu": 1.0 + } + ], + "abc": [ + 0.3143999999999999, + 0.060799999999999944, + 0.3104000000000001 + ], + "xyz": [ + -1.8864384, + -1.2684672000000008, + 1.8859999999999992 + ], + "label": "Ti" + }, + { + "species": [ + { + "element": "Ti", + "occu": 1.0 + } + ], + "abc": [ + 0.6856, + 0.9391999999999999, + 0.6895999999999999 + ], + "xyz": [ + -8.277561599999999, + 1.2684672, + 5.657999999999999 + ], + "label": "Ti" + } + ], + "about": { + "authors": [ + { + "name": "AFLOW Library of Crystallographic Prototypes", + "email": "" + } + ], + "projects": [], + "references": "@article{reference0,\n author = \"F. Gr\\onvold and A. Kjekshus and F. Raaum\",\n title = \" The crystal structure of Ti$_5$Te$_4$\",\n journal = \" Acta Crystallographica\",\n volume = \"14\",\n year = \"1961\",\n page_first = \"930\",\n page_last = \"934\",\n pages = \"930--934\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", + "remarks": [ + "Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication." + ], + "history": [], + "created_at": { + "@module": "datetime", + "@class": "datetime", + "string": "2018-01-17 19:44:15.353613" + } + } + }, + "tags": { + "pearson": "tI18", + "aflow": "A4B5_tI18_87_h_ah", + "strukturbericht": "None", + "mineral": "Titanium telluride" + } + }, + { + "snl": { + "@module": "pymatgen.util.provenance", + "@class": "StructureNL", + "charge": null, + "lattice": { + "matrix": [ + [ + -2.300099999999999, + -2.3001, + 2.4731499999999995 + ], + [ + -2.3001, + 2.3001, + -2.47315 + ], + [ + 2.3001, + -2.3001, + -2.47315 + ] + ], + "a": 4.086244111956601, + "b": 4.086244111956602, + "c": 4.086244111956602, + "alpha": 105.50806729351963, + "beta": 111.48840768130603, + "gamma": 111.48840768130606, + "volume": 52.33640469492599 + }, + "sites": [ + { + "species": [ + { + "element": "In", + "occu": 1.0 + } + ], + "abc": [ + 0.0, + 0.0, + 0.0 + ], + "xyz": [ + 0.0, + 0.0, + 0.0 + ], + "label": "In" + } + ], + "about": { + "authors": [ + { + "name": "AFLOW Library of Crystallographic Prototypes", + "email": "" + } + ], + "projects": [], + "references": "@article{reference0,\n author = \"V. T. Deshpande and R. R. Pawar\",\n title = \" Anisotropic Thermal Expansion of Indium\",\n journal = \" Acta Crystallographica A\",\n volume = \"25\",\n year = \"1969\",\n page_first = \"415\",\n page_last = \"416\",\n pages = \"415--416\"\n}\n\n\n@article{Mehl2017,\n doi = {10.1016/j.commatsci.2017.01.017},\n url = {https://doi.org/10.1016/j.commatsci.2017.01.017},\n year = {2017},\n month = {aug},\n publisher = {Elsevier {BV}},\n volume = {136},\n pages = {S1--S828},\n author = {Michael J. Mehl and David Hicks and Cormac Toher and Ohad Levy and Robert M. Hanson and Gus Hart and Stefano Curtarolo},\n title = {The {AFLOW} Library of Crystallographic Prototypes: Part 1},\n journal = {Computational Materials Science}\n}\n\n", + "remarks": [ + "Parsed from AFLOW Library of Crystallographic Prototypes for purposes of structure matching. Please cite appropriate AFLOW publication." + ], + "history": [], + "created_at": { + "@module": "datetime", + "@class": "datetime", + "string": "2018-01-17 19:44:15.363933" + } + } + }, + "tags": { + "pearson": "tI2", + "aflow": "A_tI2_139_a", + "strukturbericht": "A6", + "mineral": "Indium" + } + } +] diff --git a/pymatgen/analysis/atomic_subshell_photoionization_cross_sections.csv b/src/pymatgen/analysis/atomic_subshell_photoionization_cross_sections.csv similarity index 100% rename from pymatgen/analysis/atomic_subshell_photoionization_cross_sections.csv rename to src/pymatgen/analysis/atomic_subshell_photoionization_cross_sections.csv diff --git a/pymatgen/analysis/bond_dissociation.py b/src/pymatgen/analysis/bond_dissociation.py similarity index 99% rename from pymatgen/analysis/bond_dissociation.py rename to src/pymatgen/analysis/bond_dissociation.py index 73b9f2d4fe2..cbf6ed83845 100644 --- a/pymatgen/analysis/bond_dissociation.py +++ b/src/pymatgen/analysis/bond_dissociation.py @@ -8,7 +8,6 @@ import networkx as nx from monty.json import MSONable - from pymatgen.analysis.fragmenter import open_ring from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError from pymatgen.analysis.local_env import OpenBabelNN diff --git a/pymatgen/analysis/bond_valence.py b/src/pymatgen/analysis/bond_valence.py similarity index 99% rename from pymatgen/analysis/bond_valence.py rename to src/pymatgen/analysis/bond_valence.py index e9cbe1fc47b..a81a71f5462 100644 --- a/pymatgen/analysis/bond_valence.py +++ b/src/pymatgen/analysis/bond_valence.py @@ -11,7 +11,6 @@ import numpy as np from monty.serialization import loadfn - from pymatgen.core import Element, Species, get_el_sp from pymatgen.symmetry.analyzer import SpacegroupAnalyzer diff --git a/pymatgen/analysis/bonds_jmol_ob.yaml b/src/pymatgen/analysis/bonds_jmol_ob.yaml similarity index 100% rename from pymatgen/analysis/bonds_jmol_ob.yaml rename to src/pymatgen/analysis/bonds_jmol_ob.yaml diff --git a/pymatgen/analysis/bvparam_1991.yaml b/src/pymatgen/analysis/bvparam_1991.yaml similarity index 100% rename from pymatgen/analysis/bvparam_1991.yaml rename to src/pymatgen/analysis/bvparam_1991.yaml diff --git a/pymatgen/analysis/chemenv/__init__.py b/src/pymatgen/analysis/chemenv/__init__.py similarity index 100% rename from pymatgen/analysis/chemenv/__init__.py rename to src/pymatgen/analysis/chemenv/__init__.py diff --git a/pymatgen/analysis/chemenv/connectivity/__init__.py b/src/pymatgen/analysis/chemenv/connectivity/__init__.py similarity index 100% rename from pymatgen/analysis/chemenv/connectivity/__init__.py rename to src/pymatgen/analysis/chemenv/connectivity/__init__.py diff --git a/pymatgen/analysis/chemenv/connectivity/connected_components.py b/src/pymatgen/analysis/chemenv/connectivity/connected_components.py similarity index 99% rename from pymatgen/analysis/chemenv/connectivity/connected_components.py rename to src/pymatgen/analysis/chemenv/connectivity/connected_components.py index d05fd6cfc29..a7b361eda31 100644 --- a/pymatgen/analysis/chemenv/connectivity/connected_components.py +++ b/src/pymatgen/analysis/chemenv/connectivity/connected_components.py @@ -13,7 +13,6 @@ from monty.json import MSONable, jsanitize from networkx.algorithms.components import is_connected from networkx.algorithms.traversal import bfs_tree - from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode from pymatgen.analysis.chemenv.utils.chemenv_errors import ChemenvError from pymatgen.analysis.chemenv.utils.graph_utils import get_delta @@ -483,7 +482,7 @@ def compute_periodicity_cycle_basis(self) -> None: for current_delta in this_cycle_deltas: this_cycle_deltas_new.append(current_delta + delta) this_cycle_deltas = this_cycle_deltas_new - all_deltas.extend(this_cycle_deltas) # type: ignore + all_deltas.extend(this_cycle_deltas) all_deltas = get_linearly_independent_vectors(all_deltas) if len(all_deltas) == 3: return @@ -501,7 +500,7 @@ def compute_periodicity_cycle_basis(self) -> None: current_delta = get_delta(n1, n2, e1data) delta = get_delta(n2, n1, e2data) current_delta += delta - all_deltas.append(current_delta) # type: ignore + all_deltas.append(current_delta) else: raise ValueError("Should not be here ...") all_deltas = get_linearly_independent_vectors(all_deltas) @@ -532,7 +531,6 @@ def show_graph( If not provided, the graph is not saved. drawing_type (str): The type of drawing to use. Can be "internal" or "external". """ - shown_graph = self._connected_subgraph if graph is None else graph plt.figure() @@ -770,7 +768,7 @@ def _edgedictkey_to_edgekey(key): except ValueError: return key else: - raise ValueError("Edge key in a dict of dicts representation of a graph should be either a str or an int.") + raise TypeError("Edge key in a dict of dicts representation of a graph should be either a str or an int.") @staticmethod def _retuplify_edgedata(edata): diff --git a/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py b/src/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py similarity index 99% rename from pymatgen/analysis/chemenv/connectivity/connectivity_finder.py rename to src/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py index 99cb354f89c..26495f4a437 100644 --- a/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py +++ b/src/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py @@ -5,7 +5,6 @@ import logging import numpy as np - from pymatgen.analysis.chemenv.connectivity.structure_connectivity import StructureConnectivity __author__ = "David Waroquiers" diff --git a/pymatgen/analysis/chemenv/connectivity/environment_nodes.py b/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py similarity index 100% rename from pymatgen/analysis/chemenv/connectivity/environment_nodes.py rename to src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py diff --git a/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py b/src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py similarity index 99% rename from pymatgen/analysis/chemenv/connectivity/structure_connectivity.py rename to src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py index 7258be9baf4..4fb4c54cc50 100644 --- a/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py +++ b/src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py @@ -9,7 +9,6 @@ import networkx as nx import numpy as np from monty.json import MSONable, jsanitize - from pymatgen.analysis.chemenv.connectivity.connected_components import ConnectedComponent from pymatgen.analysis.chemenv.connectivity.environment_nodes import get_environment_node from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments diff --git a/pymatgen/analysis/chemenv/coordination_environments/__init__.py b/src/pymatgen/analysis/chemenv/coordination_environments/__init__.py similarity index 100% rename from pymatgen/analysis/chemenv/coordination_environments/__init__.py rename to src/pymatgen/analysis/chemenv/coordination_environments/__init__.py diff --git a/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py b/src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py similarity index 97% rename from pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py rename to src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py index 55438d3c56c..abc7c2b4778 100644 --- a/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py +++ b/src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py @@ -13,8 +13,6 @@ import numpy as np from monty.json import MSONable -from scipy.stats import gmean - from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer from pymatgen.analysis.chemenv.utils.chemenv_errors import EquivalentSiteSearchError @@ -29,6 +27,7 @@ from pymatgen.core.operations import SymmOp from pymatgen.core.sites import PeriodicSite from pymatgen.symmetry.analyzer import SpacegroupAnalyzer +from scipy.stats import gmean if TYPE_CHECKING: from typing import ClassVar @@ -236,7 +235,7 @@ def set_structure_environments(self, structure_environments): """ self.structure_environments = structure_environments if not isinstance(self.structure_environments.voronoi, DetailedVoronoiContainer): - raise ValueError('Voronoi Container not of type "DetailedVoronoiContainer"') + raise TypeError('Voronoi Container not of type "DetailedVoronoiContainer"') self.prepare_symmetries() def prepare_symmetries(self): @@ -403,7 +402,7 @@ def get_site_coordination_environments_fractions( def get_site_ce_fractions_and_neighbors(self, site, full_ce_info=False, strategy_info=False): """ Applies the strategy to the structure_environments object in order to get coordination environments, their - fraction, csm, geometry_info, and neighbors + fraction, csm, geometry_info, and neighbors. Args: site: Site for which the above information is sought @@ -458,7 +457,7 @@ def setup_options(self, all_options_dict): @abc.abstractmethod def __eq__(self, other: object) -> bool: """ - Equality method that should be implemented for any strategy + Equality method that should be implemented for any strategy. Args: other: strategy to be compared with the current one @@ -512,28 +511,28 @@ class SimplestChemenvStrategy(AbstractChemenvStrategy): DEFAULT_ANGLE_CUTOFF = 0.3 DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF = 10 DEFAULT_ADDITIONAL_CONDITION = AbstractChemenvStrategy.AC.ONLY_ACB - STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = dict( # type: ignore - distance_cutoff=dict( - type=DistanceCutoffFloat, - internal="_distance_cutoff", - default=DEFAULT_DISTANCE_CUTOFF, - ), - angle_cutoff=dict( - type=AngleCutoffFloat, - internal="_angle_cutoff", - default=DEFAULT_ANGLE_CUTOFF, - ), - additional_condition=dict( - type=AdditionalConditionInt, - internal="_additional_condition", - default=DEFAULT_ADDITIONAL_CONDITION, - ), - continuous_symmetry_measure_cutoff=dict( - type=CSMFloat, - internal="_continuous_symmetry_measure_cutoff", - default=DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF, - ), - ) + STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = { + "distance_cutoff": { + "type": DistanceCutoffFloat, + "internal": "_distance_cutoff", + "default": DEFAULT_DISTANCE_CUTOFF, + }, + "angle_cutoff": { + "type": AngleCutoffFloat, + "internal": "_angle_cutoff", + "default": DEFAULT_ANGLE_CUTOFF, + }, + "additional_condition": { + "type": AdditionalConditionInt, + "internal": "_additional_condition", + "default": DEFAULT_ADDITIONAL_CONDITION, + }, + "continuous_symmetry_measure_cutoff": { + "type": CSMFloat, + "internal": "_continuous_symmetry_measure_cutoff", + "default": DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF, + }, + } STRATEGY_DESCRIPTION = ( "Simplest ChemenvStrategy using fixed angle and distance parameters \n" @@ -598,7 +597,7 @@ def angle_cutoff(self, angle_cutoff): self._angle_cutoff = AngleCutoffFloat(angle_cutoff) @property - def additional_condition(self): + def additional_condition(self) -> AdditionalConditionInt: """Additional condition for this strategy.""" return self._additional_condition @@ -897,14 +896,14 @@ class SimpleAbundanceChemenvStrategy(AbstractChemenvStrategy): DEFAULT_MAX_DIST = 2.0 DEFAULT_ADDITIONAL_CONDITION = AbstractChemenvStrategy.AC.ONLY_ACB - STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = dict( # type: ignore - surface_calculation_type={}, - additional_condition=dict( - type=AdditionalConditionInt, - internal="_additional_condition", - default=DEFAULT_ADDITIONAL_CONDITION, - ), - ) + STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = { + "surface_calculation_type": {}, + "additional_condition": { + "type": AdditionalConditionInt, + "internal": "_additional_condition", + "default": DEFAULT_ADDITIONAL_CONDITION, + }, + } STRATEGY_DESCRIPTION = ( 'Simple Abundance ChemenvStrategy using the most "abundant" neighbors map \n' "for the definition of neighbors in the Voronoi approach. \n" @@ -1057,7 +1056,7 @@ def __eq__(self, other: object) -> bool: if not isinstance(other, type(self)): return NotImplemented - return self._additional_condition == other.additional_condition # type: ignore + return self._additional_condition == other.additional_condition # type: ignore[has-type] def as_dict(self): """ @@ -1122,7 +1121,6 @@ def __init__( max_csm: symmetry_measure_type: """ - raise NotImplementedError("TargetedPenaltiedAbundanceChemenvStrategy not yet implemented") super().__init__( @@ -1347,7 +1345,7 @@ def angle_sumn(self, nb_set): def __eq__(self, other: object) -> bool: if not hasattr(other, "aa"): return NotImplemented - return self.aa == other.aa # type: ignore + return self.aa == other.aa def as_dict(self): """MSONable dict.""" @@ -1587,6 +1585,7 @@ def get_effective_csm( symmetry_measure_type: Type of symmetry measure to be used in the effective CSM. max_effective_csm: Max CSM to use for the effective CSM calculation. effective_csm_estimator_ratio_function: Ratio function to use to compute effective CSM. + Returns: Effective CSM of a given Neighbors set. """ @@ -1644,14 +1643,14 @@ class SelfCSMNbSetWeight(NbSetWeight): SHORT_NAME = "SelfCSMWeight" - DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = dict( - function="power2_inverse_decreasing", - options={"max_csm": 8.0}, - ) - DEFAULT_WEIGHT_ESTIMATOR: ClassVar = dict( - function="power2_decreasing_exp", - options={"max_csm": 8.0, "alpha": 1}, - ) + DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = { + "function": "power2_inverse_decreasing", + "options": {"max_csm": 8.0}, + } + DEFAULT_WEIGHT_ESTIMATOR: ClassVar = { + "function": "power2_decreasing_exp", + "options": {"max_csm": 8.0, "alpha": 1}, + } DEFAULT_SYMMETRY_MEASURE_TYPE = "csm_wcs_ctwcc" def __init__( @@ -1747,15 +1746,15 @@ class DeltaCSMNbSetWeight(NbSetWeight): SHORT_NAME = "DeltaCSMWeight" - DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = dict( - function="power2_inverse_decreasing", - options={"max_csm": 8.0}, - ) + DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = { + "function": "power2_inverse_decreasing", + "options": {"max_csm": 8.0}, + } DEFAULT_SYMMETRY_MEASURE_TYPE = "csm_wcs_ctwcc" - DEFAULT_WEIGHT_ESTIMATOR: ClassVar = dict( - function="smootherstep", - options={"delta_csm_min": 0.5, "delta_csm_max": 3.0}, - ) + DEFAULT_WEIGHT_ESTIMATOR: ClassVar = { + "function": "smootherstep", + "options": {"delta_csm_min": 0.5, "delta_csm_max": 3.0}, + } def __init__( self, @@ -1951,9 +1950,7 @@ def delta_cn_specifics( ) def as_dict(self): - """ - MSONable dict. - """ + """MSONable dict.""" return { "@module": type(self).__module__, "@class": type(self).__name__, @@ -2125,11 +2122,11 @@ class DistanceAngleAreaNbSetWeight(NbSetWeight): SHORT_NAME = "DistAngleAreaWeight" AC = AdditionalConditions() - DEFAULT_SURFACE_DEFINITION: ClassVar = dict( - type="standard_elliptic", - distance_bounds={"lower": 1.2, "upper": 1.8}, - angle_bounds={"lower": 0.1, "upper": 0.8}, - ) + DEFAULT_SURFACE_DEFINITION: ClassVar = { + "type": "standard_elliptic", + "distance_bounds": {"lower": 1.2, "upper": 1.8}, + "angle_bounds": {"lower": 0.1, "upper": 0.8}, + } def __init__( self, @@ -2648,10 +2645,10 @@ class WeightedNbSetChemenvStrategy(AbstractChemenvStrategy): """WeightedNbSetChemenvStrategy.""" STRATEGY_DESCRIPTION = " WeightedNbSetChemenvStrategy" - DEFAULT_CE_ESTIMATOR: ClassVar = dict( - function="power2_inverse_power2_decreasing", - options={"max_csm": 8.0}, - ) + DEFAULT_CE_ESTIMATOR: ClassVar = { + "function": "power2_inverse_power2_decreasing", + "options": {"max_csm": 8.0}, + } def __init__( self, @@ -2952,10 +2949,10 @@ class MultiWeightsChemenvStrategy(WeightedNbSetChemenvStrategy): # 'cn_map_delta_csm', 'cn_map_delta_csms_cn_map2', 'cn_map_delta_csm_weight', # 'cn_map_cn_weight', # 'cn_map_fraction', 'cn_map_ce_fraction', 'ce_fraction'] - DEFAULT_CE_ESTIMATOR: ClassVar = dict( - function="power2_inverse_power2_decreasing", - options={"max_csm": 8.0}, - ) + DEFAULT_CE_ESTIMATOR: ClassVar = { + "function": "power2_inverse_power2_decreasing", + "options": {"max_csm": 8.0}, + } def __init__( self, diff --git a/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py b/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py similarity index 99% rename from pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py rename to src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py index 142fe838f7e..3e9df3df9cf 100644 --- a/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py +++ b/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py @@ -101,9 +101,7 @@ def as_dict(self): @classmethod def from_dict(cls, dct: dict) -> Self: - """ - Reconstruct ExplicitPermutationsAlgorithm from its JSON-serializable dict representation. - """ + """Reconstruct ExplicitPermutationsAlgorithm from its JSON-serializable dict representation.""" return cls(dct["permutations"]) @@ -767,7 +765,7 @@ def faces(self, sites, permutation=None): coords = [site.coords for site in sites] if permutation is None else [sites[ii].coords for ii in permutation] return [[coords[ii] for ii in face] for face in self._faces] - def edges(self, sites, permutation=None, input="sites"): + def edges(self, sites, permutation=None, input="sites"): # noqa: A002 """Get the list of edges of this coordination geometry. Each edge is given as a list of its end vertices coordinates. """ @@ -1144,7 +1142,7 @@ def is_a_valid_coordination_geometry( # TODO give a more helpful error message that suggests possible reasons and solutions raise RuntimeError("Should not be here!") - def pretty_print(self, type="implemented_geometries", maxcn=8, additional_info=None): + def pretty_print(self, type="implemented_geometries", maxcn=8, additional_info=None): # noqa: A002 """Get a string with a list of the Coordination Geometries. Args: diff --git a/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/A#2.json b/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/A#2.json similarity index 100% rename from pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/A#2.json rename to src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/A#2.json diff --git a/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/AC#12.json b/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/AC#12.json similarity index 100% rename from pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/AC#12.json rename to src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/AC#12.json diff --git a/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_1#8.json 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pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py rename to src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py index f202bec079a..523448b5bde 100644 --- a/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py +++ b/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py @@ -23,7 +23,6 @@ import numpy as np from numpy.linalg import norm, svd - from pymatgen.analysis.bond_valence import BVAnalyzer from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import MultiWeightsChemenvStrategy from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import ( @@ -86,7 +85,7 @@ def __init__( optimization=None, ): """ - Constructor for the abstract geometry + Constructor for the abstract geometry. Args: central_site: Coordinates of the central site @@ -159,7 +158,7 @@ def __init__( self.bare_coords = self._bare_coords def __str__(self): - """String representation of the AbstractGeometry + """String representation of the AbstractGeometry. Returns: str: String representation of the AbstractGeometry. @@ -277,12 +276,12 @@ def points_wocs_ctwocc(self, permutation=None): @property def cn(self): - """Coordination number""" + """Coordination number.""" return len(self.coords) @property def coordination_number(self): - """Coordination number""" + """Coordination number.""" return len(self.coords) @@ -364,12 +363,12 @@ class LocalGeometryFinder: """Main class used to find the local environments in a structure.""" DEFAULT_BVA_DISTANCE_SCALE_FACTOR = 1.0 - BVA_DISTANCE_SCALE_FACTORS: ClassVar = dict( - experimental=1.0, - GGA_relaxed=1.015, - LDA_relaxed=0.995, - ) - DEFAULT_SPG_ANALYZER_OPTIONS: ClassVar = dict(symprec=1e-3, angle_tolerance=5) + BVA_DISTANCE_SCALE_FACTORS: ClassVar = { + "experimental": 1.0, + "GGA_relaxed": 1.015, + "LDA_relaxed": 0.995, + } + DEFAULT_SPG_ANALYZER_OPTIONS: ClassVar = {"symprec": 1e-3, "angle_tolerance": 5} STRUCTURE_REFINEMENT_NONE = "none" STRUCTURE_REFINEMENT_REFINED = "refined" STRUCTURE_REFINEMENT_SYMMETRIZED = "symmetrized" @@ -453,7 +452,7 @@ def setup_parameters( def setup_parameter(self, parameter, value): """Setup of one specific parameter to the given value. The other parameters are unchanged. See setup_parameters - method for the list of possible parameters + method for the list of possible parameters. Args: parameter: Parameter to setup/update @@ -463,7 +462,7 @@ def setup_parameter(self, parameter, value): def setup_structure(self, structure: Structure): """Set up the structure for which the coordination geometries have to be identified. The structure is analyzed - with the space group analyzer and a refined structure is used + with the space group analyzer and a refined structure is used. Args: structure: A pymatgen Structure. @@ -502,7 +501,7 @@ def get_structure(self): def set_structure(self, lattice: Lattice, species, coords, coords_are_cartesian): """Set up the pymatgen structure for which the coordination geometries have to be identified starting from the - lattice, the species and the coordinates + lattice, the species and the coordinates. Args: lattice: The lattice of the structure @@ -580,7 +579,7 @@ def compute_structure_environments( optimization=PRESETS["DEFAULT"]["optimization"], ): """Compute and returns the StructureEnvironments object containing all the information - about the coordination environments in the structure + about the coordination environments in the structure. Args: excluded_atoms: Atoms for which the coordination geometries does not have to be identified @@ -1123,7 +1122,7 @@ def setup_random_structure(self, coordination): self.setup_random_indices_local_geometry(coordination) def setup_random_indices_local_geometry(self, coordination): - """Set up random indices for the local geometry, for testing purposes + """Set up random indices for the local geometry, for testing purposes. Args: coordination: coordination of the local geometry. @@ -1133,7 +1132,7 @@ def setup_random_indices_local_geometry(self, coordination): np.random.shuffle(self.indices) def setup_ordered_indices_local_geometry(self, coordination): - """Set up ordered indices for the local geometry, for testing purposes + """Set up ordered indices for the local geometry, for testing purposes. Args: coordination: coordination of the local geometry. @@ -1142,7 +1141,7 @@ def setup_ordered_indices_local_geometry(self, coordination): self.indices = list(range(1, coordination + 1)) def setup_explicit_indices_local_geometry(self, explicit_indices): - """Set up explicit indices for the local geometry, for testing purposes + """Set up explicit indices for the local geometry, for testing purposes. Args: explicit_indices: explicit indices for the neighbors (set of numbers @@ -1428,7 +1427,7 @@ def coordination_geometry_symmetry_measures_standard( ): """Get the symmetry measures for a set of permutations (whose setup depends on the coordination geometry) for the coordination geometry "coordination_geometry". Standard implementation looking for the symmetry - measures of each permutation + measures of each permutation. Args: coordination_geometry: The coordination geometry to be investigated @@ -2032,7 +2031,7 @@ def coordination_geometry_symmetry_measures_fallback_random( ): """Get the symmetry measures for a random set of permutations for the coordination geometry "coordination_geometry". Fallback implementation for the plane separation algorithms measures - of each permutation + of each permutation. Args: coordination_geometry: The coordination geometry to be investigated diff --git a/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py b/src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py similarity index 99% rename from pymatgen/analysis/chemenv/coordination_environments/structure_environments.py rename to src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py index 5d03166f83f..5b81229ced8 100644 --- a/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py +++ b/src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py @@ -17,7 +17,6 @@ from matplotlib.gridspec import GridSpec from matplotlib.patches import Polygon from monty.json import MontyDecoder, MSONable, jsanitize - from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer from pymatgen.analysis.chemenv.utils.chemenv_errors import ChemenvError diff --git a/pymatgen/analysis/chemenv/coordination_environments/voronoi.py b/src/pymatgen/analysis/chemenv/coordination_environments/voronoi.py similarity index 99% rename from pymatgen/analysis/chemenv/coordination_environments/voronoi.py rename to src/pymatgen/analysis/chemenv/coordination_environments/voronoi.py index 77fc1ffcbd4..08f257d3ae2 100644 --- a/pymatgen/analysis/chemenv/coordination_environments/voronoi.py +++ b/src/pymatgen/analysis/chemenv/coordination_environments/voronoi.py @@ -9,8 +9,6 @@ import matplotlib.pyplot as plt import numpy as np from monty.json import MSONable -from scipy.spatial import Voronoi - from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import ( get_lower_and_upper_f, rectangle_surface_intersection, @@ -20,6 +18,7 @@ from pymatgen.analysis.chemenv.utils.math_utils import normal_cdf_step from pymatgen.core.sites import PeriodicSite from pymatgen.core.structure import Structure +from scipy.spatial import Voronoi if TYPE_CHECKING: from typing_extensions import Self diff --git a/pymatgen/analysis/chemenv/utils/__init__.py b/src/pymatgen/analysis/chemenv/utils/__init__.py similarity index 100% rename from pymatgen/analysis/chemenv/utils/__init__.py rename to src/pymatgen/analysis/chemenv/utils/__init__.py diff --git a/pymatgen/analysis/chemenv/utils/chemenv_config.py b/src/pymatgen/analysis/chemenv/utils/chemenv_config.py similarity index 98% rename from pymatgen/analysis/chemenv/utils/chemenv_config.py rename to src/pymatgen/analysis/chemenv/utils/chemenv_config.py index 4e9ee6e8e1a..ae75a351d3d 100644 --- a/pymatgen/analysis/chemenv/utils/chemenv_config.py +++ b/src/pymatgen/analysis/chemenv/utils/chemenv_config.py @@ -29,8 +29,8 @@ class ChemEnvConfig: - Default options (strategies, ...). """ - DEFAULT_PACKAGE_OPTIONS: ClassVar = dict( - default_strategy={ + DEFAULT_PACKAGE_OPTIONS: ClassVar = { + "default_strategy": { "strategy": "SimplestChemenvStrategy", "strategy_options": { "distance_cutoff": strategies_class_lookup["SimplestChemenvStrategy"].DEFAULT_DISTANCE_CUTOFF, @@ -41,8 +41,8 @@ class ChemEnvConfig: ].DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF, }, }, - default_max_distance_factor=1.5, - ) + "default_max_distance_factor": 1.5, + } def __init__(self, package_options=None): """ diff --git a/pymatgen/analysis/chemenv/utils/chemenv_errors.py b/src/pymatgen/analysis/chemenv/utils/chemenv_errors.py similarity index 100% rename from pymatgen/analysis/chemenv/utils/chemenv_errors.py rename to src/pymatgen/analysis/chemenv/utils/chemenv_errors.py diff --git a/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py b/src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py similarity index 98% rename from pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py rename to src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py index 788cd1a5942..358d03d39a0 100644 --- a/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py +++ b/src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py @@ -7,12 +7,11 @@ import numpy as np from numpy.linalg import norm +from pymatgen.analysis.chemenv.utils.chemenv_errors import SolidAngleError from scipy.integrate import quad from scipy.interpolate import UnivariateSpline from scipy.spatial import ConvexHull -from pymatgen.analysis.chemenv.utils.chemenv_errors import SolidAngleError - if TYPE_CHECKING: from typing import Callable @@ -415,7 +414,7 @@ def matrixTimesVector(MM, aa): """ Args: MM: A matrix of size 3x3 - aa: A vector of size 3 + aa: A vector of size 3. Returns: A vector of size 3 which is the product of the matrix by the vector @@ -428,7 +427,7 @@ def matrixTimesVector(MM, aa): def rotateCoords(coords, R): """ - Rotate the list of points using rotation matrix R + Rotate the list of points using rotation matrix R. Args: coords: List of points to be rotated @@ -446,7 +445,7 @@ def rotateCoords(coords, R): def rotateCoordsOpt(coords, R): """ - Rotate the list of points using rotation matrix R + Rotate the list of points using rotation matrix R. Args: coords: List of points to be rotated @@ -467,6 +466,7 @@ def changebasis(uu, vv, nn, pps): vv: Second vector of the basis nn: Third vector of the basis pps: List of points in basis (e1, e2, e3) + Returns: List of points in basis (uu, vv, nn). """ @@ -488,7 +488,7 @@ def collinear(p1, p2, p3=None, tolerance=0.25): checked by computing the area of the triangle defined by the three points p1, p2 and p3. If the area of this triangle is less than (tolerance x largest_triangle), then the three points are considered collinear. The largest_triangle is defined as the right triangle whose legs are the two smallest distances between the three - points ie, its area is : 0.5 x (min(|p2-p1|,|p3-p1|,|p3-p2|) x second_min(|p2-p1|,|p3-p1|,|p3-p2|)) + points ie, its area is : 0.5 x (min(|p2-p1|,|p3-p1|,|p3-p2|) x second_min(|p2-p1|,|p3-p1|,|p3-p2|)). Args: p1: First point @@ -511,7 +511,7 @@ def collinear(p1, p2, p3=None, tolerance=0.25): def anticlockwise_sort(pps): """ - Sort a list of 2D points in anticlockwise order + Sort a list of 2D points in anticlockwise order. Args: pps: List of points to be sorted @@ -530,7 +530,7 @@ def anticlockwise_sort(pps): def anticlockwise_sort_indices(pps): - """Get the indices that would sort a list of 2D points in anticlockwise order + """Get the indices that would sort a list of 2D points in anticlockwise order. Args: pps: List of points to be sorted @@ -582,7 +582,7 @@ def sort_separation_tuple(separation): def separation_in_list(separation_indices, separation_indices_list): """ - Checks if the separation indices of a plane are already in the list + Checks if the separation indices of a plane are already in the list. Args: separation_indices: list of separation indices (three arrays of integers) @@ -645,7 +645,7 @@ class Plane: ) def __init__(self, coefficients, p1=None, p2=None, p3=None): - """Initialize a plane from the 4 coefficients a, b, c and d of ax + by + cz + d = 0 + """Initialize a plane from the 4 coefficients a, b, c and d of ax + by + cz + d = 0. Args: coefficients: abcd coefficients of the plane. @@ -714,7 +714,7 @@ def __str__(self): def is_in_plane(self, pp, dist_tolerance) -> bool: """ - Determines if point pp is in the plane within the tolerance dist_tolerance + Determines if point pp is in the plane within the tolerance dist_tolerance. Args: pp: point to be tested @@ -727,7 +727,7 @@ def is_in_plane(self, pp, dist_tolerance) -> bool: def is_same_plane_as(self, plane) -> bool: """ - Checks whether the plane is identical to another Plane "plane" + Checks whether the plane is identical to another Plane "plane". Args: plane: Plane to be compared to @@ -739,7 +739,7 @@ def is_same_plane_as(self, plane) -> bool: def is_in_list(self, plane_list) -> bool: """ - Checks whether the plane is identical to one of the Planes in the plane_list list of Planes + Checks whether the plane is identical to one of the Planes in the plane_list list of Planes. Args: plane_list: List of Planes to be compared to @@ -752,7 +752,7 @@ def is_in_list(self, plane_list) -> bool: def indices_separate(self, points, dist_tolerance): """Get three lists containing the indices of the points lying on one side of the plane, on the plane and on the other side of the plane. The dist_tolerance parameter controls the tolerance to which a point - is considered to lie on the plane or not (distance to the plane) + is considered to lie on the plane or not (distance to the plane). Args: points: list of points @@ -776,7 +776,7 @@ def indices_separate(self, points, dist_tolerance): return [side1, inplane, side2] def distance_to_point(self, point): - """Compute the absolute distance from the plane to the point + """Compute the absolute distance from the plane to the point. Args: point: Point for which distance is computed @@ -854,7 +854,7 @@ def distances_indices_groups(self, points, delta=None, delta_factor=0.05, sign=F def projectionpoints(self, pps): """ - Projects each points in the point list pps on plane and returns the list of projected points + Projects each points in the point list pps on plane and returns the list of projected points. Args: pps: List of points to project on plane @@ -866,7 +866,7 @@ def projectionpoints(self, pps): def orthonormal_vectors(self): """Get a list of three orthogonal vectors, the two first being parallel to the plane and the - third one is the normal vector of the plane + third one is the normal vector of the plane. Returns: List of orthogonal vectors @@ -881,7 +881,7 @@ def orthonormal_vectors(self): def project_and_to2dim_ordered_indices(self, pps, plane_center="mean"): """ Projects each points in the point list pps on plane and returns the indices that would sort the - list of projected points in anticlockwise order + list of projected points in anticlockwise order. Args: pps: List of points to project on plane @@ -894,7 +894,7 @@ def project_and_to2dim_ordered_indices(self, pps, plane_center="mean"): def project_and_to2dim(self, pps, plane_center): """ - Projects the list of points pps to the plane and changes the basis from 3D to the 2D basis of the plane + Projects the list of points pps to the plane and changes the basis from 3D to the 2D basis of the plane. Args: pps: List of points to be projected diff --git a/pymatgen/analysis/chemenv/utils/defs_utils.py b/src/pymatgen/analysis/chemenv/utils/defs_utils.py similarity index 100% rename from pymatgen/analysis/chemenv/utils/defs_utils.py rename to src/pymatgen/analysis/chemenv/utils/defs_utils.py diff --git a/pymatgen/analysis/chemenv/utils/func_utils.py b/src/pymatgen/analysis/chemenv/utils/func_utils.py similarity index 94% rename from pymatgen/analysis/chemenv/utils/func_utils.py rename to src/pymatgen/analysis/chemenv/utils/func_utils.py index 3d227c62a6e..d8437cde208 100644 --- a/pymatgen/analysis/chemenv/utils/func_utils.py +++ b/src/pymatgen/analysis/chemenv/utils/func_utils.py @@ -5,7 +5,6 @@ from typing import TYPE_CHECKING import numpy as np - from pymatgen.analysis.chemenv.utils.math_utils import ( power2_decreasing_exp, power2_inverse_decreasing, @@ -116,15 +115,15 @@ def from_dict(cls, dct: dict) -> Self: class RatioFunction(AbstractRatioFunction): """Concrete implementation of a series of ratio functions.""" - ALLOWED_FUNCTIONS: ClassVar = dict( - power2_decreasing_exp=["max", "alpha"], - smoothstep=["lower", "upper"], - smootherstep=["lower", "upper"], - inverse_smoothstep=["lower", "upper"], - inverse_smootherstep=["lower", "upper"], - power2_inverse_decreasing=["max"], - power2_inverse_power2_decreasing=["max"], - ) + ALLOWED_FUNCTIONS: ClassVar = { + "power2_decreasing_exp": ["max", "alpha"], + "smoothstep": ["lower", "upper"], + "smootherstep": ["lower", "upper"], + "inverse_smoothstep": ["lower", "upper"], + "inverse_smootherstep": ["lower", "upper"], + "power2_inverse_decreasing": ["max"], + "power2_inverse_power2_decreasing": ["max"], + } def power2_decreasing_exp(self, vals): """Get the evaluation of the ratio function f(x)=exp(-a*x)*(x-1)^2. @@ -229,11 +228,11 @@ class CSMFiniteRatioFunction(AbstractRatioFunction): D. Waroquiers et al., Acta Cryst. B 76, 683 (2020). """ - ALLOWED_FUNCTIONS: ClassVar = dict( - power2_decreasing_exp=["max_csm", "alpha"], - smoothstep=["lower_csm", "upper_csm"], - smootherstep=["lower_csm", "upper_csm"], - ) + ALLOWED_FUNCTIONS: ClassVar = { + "power2_decreasing_exp": ["max_csm", "alpha"], + "smoothstep": ["lower_csm", "upper_csm"], + "smootherstep": ["lower_csm", "upper_csm"], + } def power2_decreasing_exp(self, vals): """Get the evaluation of the ratio function f(x)=exp(-a*x)*(x-1)^2. @@ -330,10 +329,10 @@ class CSMInfiniteRatioFunction(AbstractRatioFunction): D. Waroquiers et al., Acta Cryst. B 76, 683 (2020). """ - ALLOWED_FUNCTIONS: ClassVar = dict( - power2_inverse_decreasing=["max_csm"], - power2_inverse_power2_decreasing=["max_csm"], - ) + ALLOWED_FUNCTIONS: ClassVar = { + "power2_inverse_decreasing": ["max_csm"], + "power2_inverse_power2_decreasing": ["max_csm"], + } def power2_inverse_decreasing(self, vals): """Get the evaluation of the ratio function f(x)=(x-1)^2 / x. @@ -421,7 +420,7 @@ class DeltaCSMRatioFunction(AbstractRatioFunction): D. Waroquiers et al., Acta Cryst. B 76, 683 (2020). """ - ALLOWED_FUNCTIONS: ClassVar = dict(smootherstep=["delta_csm_min", "delta_csm_max"]) + ALLOWED_FUNCTIONS: ClassVar = {"smootherstep": ["delta_csm_min", "delta_csm_max"]} def smootherstep(self, vals): """Get the evaluation of the smootherstep ratio function: f(x)=6*x^5-15*x^4+10*x^3. diff --git a/pymatgen/analysis/chemenv/utils/graph_utils.py b/src/pymatgen/analysis/chemenv/utils/graph_utils.py similarity index 99% rename from pymatgen/analysis/chemenv/utils/graph_utils.py rename to src/pymatgen/analysis/chemenv/utils/graph_utils.py index cceaa3622a3..6f57f1132a9 100644 --- a/pymatgen/analysis/chemenv/utils/graph_utils.py +++ b/src/pymatgen/analysis/chemenv/utils/graph_utils.py @@ -290,7 +290,7 @@ def from_edges(cls, edges, edges_are_ordered: bool = True) -> Self: return cls(nodes) def as_dict(self) -> dict: - """MSONable dict""" + """MSONable dict.""" dct = MSONable.as_dict(self) # Transforming tuple object to a list to allow BSON and MongoDB dct["nodes"] = list(dct["nodes"]) diff --git a/pymatgen/analysis/chemenv/utils/math_utils.py b/src/pymatgen/analysis/chemenv/utils/math_utils.py similarity index 98% rename from pymatgen/analysis/chemenv/utils/math_utils.py rename to src/pymatgen/analysis/chemenv/utils/math_utils.py index 78ea88f1df1..4422e98f5ba 100644 --- a/pymatgen/analysis/chemenv/utils/math_utils.py +++ b/src/pymatgen/analysis/chemenv/utils/math_utils.py @@ -47,7 +47,7 @@ def _cartesian_product(lists): def prime_factors(n: int) -> list[int]: - """Lists prime factors of a given natural integer, from greatest to smallest + """Lists prime factors of a given natural integer, from greatest to smallest. Args: n: Natural integer @@ -66,7 +66,7 @@ def prime_factors(n: int) -> list[int]: def _factor_generator(n: int) -> dict[int, int]: - """From a given natural integer, returns the prime factors and their multiplicity + """From a given natural integer, returns the prime factors and their multiplicity. Args: n: Natural integer @@ -82,7 +82,7 @@ def _factor_generator(n: int) -> dict[int, int]: def divisors(n): - """From a given natural integer, returns the list of divisors in ascending order + """From a given natural integer, returns the list of divisors in ascending order. Args: n: Natural integer @@ -122,7 +122,7 @@ def get_center_of_arc(p1, p2, radius): def get_linearly_independent_vectors(vectors: list[ArrayLike]) -> list[np.ndarray]: """ Args: - vectors (list[ArrayLike]): List of vectors + vectors (list[ArrayLike]): List of vectors. """ independent_vectors: list[np.ndarray] = [] for vector in vectors: diff --git a/pymatgen/analysis/chemenv/utils/scripts_utils.py b/src/pymatgen/analysis/chemenv/utils/scripts_utils.py similarity index 98% rename from pymatgen/analysis/chemenv/utils/scripts_utils.py rename to src/pymatgen/analysis/chemenv/utils/scripts_utils.py index 087a42b2402..e153a7fcb63 100644 --- a/pymatgen/analysis/chemenv/utils/scripts_utils.py +++ b/src/pymatgen/analysis/chemenv/utils/scripts_utils.py @@ -3,11 +3,10 @@ from __future__ import annotations import re +from typing import TYPE_CHECKING import numpy as np - from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import ( - AbstractChemenvStrategy, SimpleAbundanceChemenvStrategy, SimplestChemenvStrategy, TargetedPenaltiedAbundanceChemenvStrategy, @@ -32,6 +31,9 @@ except ImportError: StructureVis = None # type: ignore[misc] +if TYPE_CHECKING: + from typing import Any + __author__ = "David Waroquiers" __copyright__ = "Copyright 2012, The Materials Project" __credits__ = "Geoffroy Hautier" @@ -40,10 +42,10 @@ __email__ = "david.waroquiers@gmail.com" __date__ = "Feb 20, 2016" -strategies_class_lookup: dict[str, AbstractChemenvStrategy] = { - "SimplestChemenvStrategy": SimplestChemenvStrategy, # type: ignore - "SimpleAbundanceChemenvStrategy": SimpleAbundanceChemenvStrategy, # type: ignore - "TargetedPenaltiedAbundanceChemenvStrategy": TargetedPenaltiedAbundanceChemenvStrategy, # type: ignore +strategies_class_lookup: dict[str, Any] = { + "SimplestChemenvStrategy": SimplestChemenvStrategy, + "SimpleAbundanceChemenvStrategy": SimpleAbundanceChemenvStrategy, + "TargetedPenaltiedAbundanceChemenvStrategy": TargetedPenaltiedAbundanceChemenvStrategy, } diff --git a/pymatgen/analysis/chempot_diagram.py b/src/pymatgen/analysis/chempot_diagram.py similarity index 99% rename from pymatgen/analysis/chempot_diagram.py rename to src/pymatgen/analysis/chempot_diagram.py index 2890ca9db28..769c3a69b8f 100644 --- a/pymatgen/analysis/chempot_diagram.py +++ b/src/pymatgen/analysis/chempot_diagram.py @@ -33,13 +33,12 @@ import plotly.express as px from monty.json import MSONable from plotly.graph_objects import Figure, Mesh3d, Scatter, Scatter3d -from scipy.spatial import ConvexHull, HalfspaceIntersection - from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram from pymatgen.core.composition import Composition, Element from pymatgen.util.coord import Simplex from pymatgen.util.due import Doi, due from pymatgen.util.string import htmlify +from scipy.spatial import ConvexHull, HalfspaceIntersection if TYPE_CHECKING: from pymatgen.entries.computed_entries import ComputedEntry @@ -187,7 +186,7 @@ def get_plot( default_min_limit=self.default_min_limit, formal_chempots=self.formal_chempots, ) - fig = cpd.get_plot(elements=elems, label_stable=label_stable) # type: ignore + fig = cpd.get_plot(elements=elems, label_stable=label_stable) # type: ignore[arg-type] else: fig = self._get_3d_plot( elements=elems, @@ -211,7 +210,7 @@ def _get_domains(self) -> dict[str, np.ndarray]: interior_point = np.min(self.lims, axis=1) + 1e-1 hs_int = HalfspaceIntersection(hs_hyperplanes, interior_point) - domains = {entry.reduced_formula: [] for entry in entries} # type: ignore + domains: dict[str, list] = {entry.reduced_formula: [] for entry in entries} for intersection, facet in zip(hs_int.intersections, hs_int.dual_facets): for v in facet: @@ -585,7 +584,7 @@ def get_chempot_axis_title(element) -> str: return axes_layout - @property # type: ignore + @property @lru_cache(maxsize=1) # noqa: B019 def domains(self) -> dict[str, np.ndarray]: """Mapping of formulas to array of domain boundary points.""" diff --git a/pymatgen/analysis/cn_opt_params.yaml b/src/pymatgen/analysis/cn_opt_params.yaml similarity index 100% rename from pymatgen/analysis/cn_opt_params.yaml rename to src/pymatgen/analysis/cn_opt_params.yaml diff --git a/pymatgen/analysis/cost.py b/src/pymatgen/analysis/cost.py similarity index 99% rename from pymatgen/analysis/cost.py rename to src/pymatgen/analysis/cost.py index 458fea711e6..8ed4689301c 100644 --- a/pymatgen/analysis/cost.py +++ b/src/pymatgen/analysis/cost.py @@ -17,7 +17,6 @@ import scipy.constants as const from monty.design_patterns import singleton - from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram from pymatgen.core import Composition, Element from pymatgen.util.provenance import is_valid_bibtex diff --git a/pymatgen/analysis/costdb_elements.csv b/src/pymatgen/analysis/costdb_elements.csv similarity index 100% rename from pymatgen/analysis/costdb_elements.csv rename to src/pymatgen/analysis/costdb_elements.csv diff --git a/pymatgen/analysis/diffraction/__init__.py b/src/pymatgen/analysis/diffraction/__init__.py similarity index 100% rename from pymatgen/analysis/diffraction/__init__.py rename to src/pymatgen/analysis/diffraction/__init__.py diff --git a/pymatgen/analysis/diffraction/atomic_scattering_params.json b/src/pymatgen/analysis/diffraction/atomic_scattering_params.json similarity index 100% rename from pymatgen/analysis/diffraction/atomic_scattering_params.json rename to src/pymatgen/analysis/diffraction/atomic_scattering_params.json diff --git a/pymatgen/analysis/diffraction/core.py b/src/pymatgen/analysis/diffraction/core.py similarity index 99% rename from pymatgen/analysis/diffraction/core.py rename to src/pymatgen/analysis/diffraction/core.py index 7b80d318709..4a4dce2623a 100644 --- a/pymatgen/analysis/diffraction/core.py +++ b/src/pymatgen/analysis/diffraction/core.py @@ -8,7 +8,6 @@ import matplotlib.pyplot as plt import numpy as np - from pymatgen.core.spectrum import Spectrum from pymatgen.util.plotting import add_fig_kwargs, pretty_plot @@ -166,7 +165,7 @@ def show_plot(self, structure: Structure, **kwargs): version (oriented vertically), e.g. 100. If 'full', show long version, e.g. (1, 0, 0). If None, do not show anything. """ - self.get_plot(structure, **kwargs).show() + self.get_plot(structure, **kwargs).get_figure().show() @add_fig_kwargs def plot_structures(self, structures, fontsize=6, **kwargs): @@ -185,7 +184,6 @@ def plot_structures(self, structures, fontsize=6, **kwargs): long version, e.g. (1, 0, 0). If None, do not show anything. fontsize: (int) fontsize for peak labels. """ - n_rows = len(structures) fig, axes = plt.subplots(nrows=n_rows, ncols=1, sharex=True, squeeze=False) diff --git a/pymatgen/analysis/diffraction/neutron.py b/src/pymatgen/analysis/diffraction/neutron.py similarity index 95% rename from pymatgen/analysis/diffraction/neutron.py rename to src/pymatgen/analysis/diffraction/neutron.py index 694182dc960..d9ef7328935 100644 --- a/pymatgen/analysis/diffraction/neutron.py +++ b/src/pymatgen/analysis/diffraction/neutron.py @@ -8,7 +8,6 @@ from typing import TYPE_CHECKING import numpy as np - from pymatgen.analysis.diffraction.core import ( AbstractDiffractionPatternCalculator, DiffractionPattern, @@ -26,8 +25,8 @@ __email__ = "resnant@outlook.jp" __date__ = "4/19/18" -with open(os.path.join(os.path.dirname(__file__), "neutron_scattering_length.json")) as file: - # This table was cited from "Neutron Data Booklet" 2nd ed (Old City 2003). +# This table was cited from "Neutron Data Booklet" 2nd ed (Old City 2003). +with open(os.path.join(os.path.dirname(__file__), "neutron_scattering_length.json"), encoding="utf-8") as file: ATOMIC_SCATTERING_LEN = json.load(file) @@ -133,7 +132,7 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90) two_thetas: list[float] = [] for hkl, g_hkl, ind, _ in sorted(recip_pts, key=lambda i: (i[1], -i[0][0], -i[0][1], -i[0][2])): - # Force miller indices to be integers. + # Force miller indices to be integers hkl = [int(round(i)) for i in hkl] if g_hkl != 0: d_hkl = 1 / g_hkl @@ -149,7 +148,7 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90) dw_correction = np.exp(-dw_factors * (s**2)) # Vectorized computation of g.r for all fractional coords and - # hkl. + # hkl g_dot_r = np.dot(frac_coords, np.transpose([hkl])).T[0] # Structure factor = sum of atomic scattering factors (with @@ -160,24 +159,24 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90) # Lorentz polarization correction for hkl lorentz_factor = 1 / (sin(theta) ** 2 * cos(theta)) - # Intensity for hkl is modulus square of structure factor. + # Intensity for hkl is modulus square of structure factor i_hkl = (f_hkl * f_hkl.conjugate()).real two_theta = degrees(2 * theta) if is_hex: - # Use Miller-Bravais indices for hexagonal lattices. + # Use Miller-Bravais indices for hexagonal lattices hkl = (hkl[0], hkl[1], -hkl[0] - hkl[1], hkl[2]) - # Deal with floating point precision issues. + # Deal with floating point precision issues ind = np.where(np.abs(np.subtract(two_thetas, two_theta)) < self.TWO_THETA_TOL) if len(ind[0]) > 0: peaks[two_thetas[ind[0][0]]][0] += i_hkl * lorentz_factor - peaks[two_thetas[ind[0][0]]][1].append(tuple(hkl)) # type: ignore + peaks[two_thetas[ind[0][0]]][1].append(tuple(hkl)) # type: ignore[union-attr] else: peaks[two_theta] = [i_hkl * lorentz_factor, [tuple(hkl)], d_hkl] two_thetas.append(two_theta) - # Scale intensities so that the max intensity is 100. + # Scale intensities so that the max intensity is 100 max_intensity = max(v[0] for v in peaks.values()) x = [] y = [] @@ -186,7 +185,7 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90) for key in sorted(peaks): v = peaks[key] fam = get_unique_families(v[1]) - if v[0] / max_intensity * 100 > self.SCALED_INTENSITY_TOL: # type: ignore + if v[0] / max_intensity * 100 > self.SCALED_INTENSITY_TOL: # type: ignore[operator] x.append(key) y.append(v[0]) hkls.append([{"hkl": hkl, "multiplicity": mult} for hkl, mult in fam.items()]) diff --git a/pymatgen/analysis/diffraction/neutron_scattering_length.json b/src/pymatgen/analysis/diffraction/neutron_scattering_length.json similarity index 100% rename from pymatgen/analysis/diffraction/neutron_scattering_length.json rename to src/pymatgen/analysis/diffraction/neutron_scattering_length.json diff --git a/pymatgen/analysis/diffraction/tem.py b/src/pymatgen/analysis/diffraction/tem.py similarity index 99% rename from pymatgen/analysis/diffraction/tem.py rename to src/pymatgen/analysis/diffraction/tem.py index 7c7a7584102..98103a22945 100644 --- a/pymatgen/analysis/diffraction/tem.py +++ b/src/pymatgen/analysis/diffraction/tem.py @@ -11,7 +11,6 @@ import pandas as pd import plotly.graph_objects as go import scipy.constants as sc - from pymatgen.analysis.diffraction.core import AbstractDiffractionPatternCalculator from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.string import latexify_spacegroup, unicodeify_spacegroup @@ -19,7 +18,6 @@ if TYPE_CHECKING: from numpy.typing import NDArray - from pymatgen.core import Structure __author__ = "Frank Wan, Jason Liang" @@ -101,7 +99,7 @@ def generate_points(coord_left: int = -10, coord_right: int = 10) -> np.ndarray: """ points = [0, 0, 0] coord_values = np.arange(coord_left, coord_right + 1) - points[0], points[1], points[2] = np.meshgrid(coord_values, coord_values, coord_values) # type: ignore + points[0], points[1], points[2] = np.meshgrid(coord_values, coord_values, coord_values) points_matrix = (np.ravel(points[i]) for i in range(3)) return np.vstack(list(points_matrix)).transpose() @@ -120,7 +118,7 @@ def zone_axis_filter(self, points: list[Tuple3Ints] | np.ndarray, laue_zone: int if len(points) == 0: return [] filtered = np.where(np.dot(np.array(self.beam_direction), np.transpose(points)) == laue_zone) - result = points[filtered] # type: ignore + result = points[filtered] return cast(list[Tuple3Ints], [tuple(x) for x in result.tolist()]) def get_interplanar_spacings( @@ -194,7 +192,7 @@ def x_ray_factors( for plane in bragg_angles: scattering_factor_curr = atom.Z - 41.78214 * s2[plane] * np.sum( coeffs[:, 0] * np.exp(-coeffs[:, 1] * s2[plane]), - axis=None, # type: ignore + axis=None, ) scattering_factors_for_atom[plane] = scattering_factor_curr x_ray_factors[atom.symbol] = scattering_factors_for_atom diff --git a/pymatgen/analysis/diffraction/xrd.py b/src/pymatgen/analysis/diffraction/xrd.py similarity index 96% rename from pymatgen/analysis/diffraction/xrd.py rename to src/pymatgen/analysis/diffraction/xrd.py index 8a15d24fc9c..654cab6d3fe 100644 --- a/pymatgen/analysis/diffraction/xrd.py +++ b/src/pymatgen/analysis/diffraction/xrd.py @@ -8,7 +8,6 @@ from typing import TYPE_CHECKING import numpy as np - from pymatgen.analysis.diffraction.core import ( AbstractDiffractionPatternCalculator, DiffractionPattern, @@ -47,7 +46,7 @@ "AgKb1": 0.497082, } -with open(os.path.join(os.path.dirname(__file__), "atomic_scattering_params.json")) as file: +with open(os.path.join(os.path.dirname(__file__), "atomic_scattering_params.json"), encoding="utf-8") as file: ATOMIC_SCATTERING_PARAMS = json.load(file) @@ -196,7 +195,7 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90) two_thetas: list[float] = [] for hkl, g_hkl, ind, _ in sorted(recip_pts, key=lambda i: (i[1], -i[0][0], -i[0][1], -i[0][2])): - # Force miller indices to be integers. + # Force miller indices to be integers hkl = [int(round(i)) for i in hkl] if g_hkl != 0: # Bragg condition @@ -206,11 +205,11 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90) # 1/|ghkl|) s = g_hkl / 2 - # Store s^2 since we are using it a few times. + # Store s^2 since we are using it a few times s2 = s**2 # Vectorized computation of g.r for all fractional coords and - # hkl. + # hkl g_dot_r = np.dot(frac_coords, np.transpose([hkl])).T[0] # Highly vectorized computation of atomic scattering factors. @@ -223,7 +222,7 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90) # [d[0] * exp(-d[1] * s2) for d in coeff]) fs = zs - 41.78214 * s2 * np.sum( coeffs[:, :, 0] * np.exp(-coeffs[:, :, 1] * s2), - axis=1, # type: ignore + axis=1, ) dw_correction = np.exp(-dw_factors * s2) @@ -236,27 +235,27 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90) # Lorentz polarization correction for hkl lorentz_factor = (1 + cos(2 * theta) ** 2) / (sin(theta) ** 2 * cos(theta)) - # Intensity for hkl is modulus square of structure factor. + # Intensity for hkl is modulus square of structure factor i_hkl = (f_hkl * f_hkl.conjugate()).real two_theta = degrees(2 * theta) if is_hex: - # Use Miller-Bravais indices for hexagonal lattices. + # Use Miller-Bravais indices for hexagonal lattices hkl = (hkl[0], hkl[1], -hkl[0] - hkl[1], hkl[2]) - # Deal with floating point precision issues. + # Deal with floating point precision issues ind = np.where( np.abs(np.subtract(two_thetas, two_theta)) < AbstractDiffractionPatternCalculator.TWO_THETA_TOL ) if len(ind[0]) > 0: peaks[two_thetas[ind[0][0]]][0] += i_hkl * lorentz_factor - peaks[two_thetas[ind[0][0]]][1].append(tuple(hkl)) # type: ignore + peaks[two_thetas[ind[0][0]]][1].append(tuple(hkl)) # type: ignore[union-attr] else: d_hkl = 1 / g_hkl peaks[two_theta] = [i_hkl * lorentz_factor, [tuple(hkl)], d_hkl] two_thetas.append(two_theta) - # Scale intensities so that the max intensity is 100. + # Scale intensities so that the max intensity is 100 max_intensity = max(v[0] for v in peaks.values()) x = [] y = [] @@ -265,7 +264,7 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90) for k in sorted(peaks): v = peaks[k] fam = get_unique_families(v[1]) - if v[0] / max_intensity * 100 > AbstractDiffractionPatternCalculator.SCALED_INTENSITY_TOL: # type: ignore + if v[0] / max_intensity * 100 > AbstractDiffractionPatternCalculator.SCALED_INTENSITY_TOL: # type: ignore[operator] x.append(k) y.append(v[0]) hkls.append([{"hkl": hkl, "multiplicity": mult} for hkl, mult in fam.items()]) diff --git a/pymatgen/analysis/dimensionality.py b/src/pymatgen/analysis/dimensionality.py similarity index 99% rename from pymatgen/analysis/dimensionality.py rename to src/pymatgen/analysis/dimensionality.py index 7ce19444e03..93746d4f5db 100644 --- a/pymatgen/analysis/dimensionality.py +++ b/src/pymatgen/analysis/dimensionality.py @@ -29,7 +29,6 @@ import networkx as nx import numpy as np from networkx.readwrite import json_graph - from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph from pymatgen.analysis.local_env import JmolNN from pymatgen.analysis.structure_analyzer import get_max_bond_lengths diff --git a/pymatgen/analysis/disorder.py b/src/pymatgen/analysis/disorder.py similarity index 86% rename from pymatgen/analysis/disorder.py rename to src/pymatgen/analysis/disorder.py index a47221add8c..538c9863228 100644 --- a/pymatgen/analysis/disorder.py +++ b/src/pymatgen/analysis/disorder.py @@ -24,17 +24,17 @@ def get_warren_cowley_parameters(structure: Structure, r: float, dr: float) -> d """ comp = structure.composition - n_ij = defaultdict(int) # type: ignore - n_neighbors = defaultdict(int) # type: ignore + n_ij: defaultdict = defaultdict(int) + n_neighbors: defaultdict = defaultdict(int) for site in structure: for nn in structure.get_neighbors_in_shell(site.coords, r, dr): n_ij[(site.specie, nn.specie)] += 1 n_neighbors[site.specie] += 1 - alpha_ij = {} # type: ignore + alpha_ij = {} for sp1, sp2 in itertools.product(comp, comp): pij = n_ij.get((sp1, sp2), 0) / n_neighbors[sp1] conc2 = comp.get_atomic_fraction(sp2) alpha_ij[(sp1, sp2)] = (pij - conc2) / ((1 if sp1 == sp2 else 0) - conc2) - return alpha_ij # type: ignore + return alpha_ij diff --git a/pymatgen/analysis/elasticity/__init__.py b/src/pymatgen/analysis/elasticity/__init__.py similarity index 100% rename from pymatgen/analysis/elasticity/__init__.py rename to src/pymatgen/analysis/elasticity/__init__.py diff --git a/pymatgen/analysis/elasticity/elastic.py b/src/pymatgen/analysis/elasticity/elastic.py similarity index 99% rename from pymatgen/analysis/elasticity/elastic.py rename to src/pymatgen/analysis/elasticity/elastic.py index fc9809de459..805b6017013 100644 --- a/pymatgen/analysis/elasticity/elastic.py +++ b/src/pymatgen/analysis/elasticity/elastic.py @@ -13,24 +13,22 @@ import numpy as np import sympy as sp -from scipy.integrate import quad -from scipy.optimize import root -from scipy.special import factorial - from pymatgen.analysis.elasticity.strain import Strain from pymatgen.analysis.elasticity.stress import Stress from pymatgen.core.tensors import DEFAULT_QUAD, SquareTensor, Tensor, TensorCollection, get_uvec from pymatgen.core.units import Unit from pymatgen.util.due import Doi, due +from scipy.integrate import quad +from scipy.optimize import root +from scipy.special import factorial if TYPE_CHECKING: from collections.abc import Sequence from typing import Literal from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.core import Structure + from typing_extensions import Self __author__ = "Joseph Montoya" @@ -484,7 +482,7 @@ def from_pseudoinverse(cls, strains, stresses) -> Self: @classmethod def from_independent_strains(cls, strains, stresses, eq_stress=None, vasp=False, tol: float = 1e-10) -> Self: """ - Constructs the elastic tensor least-squares fit of independent strains + Constructs the elastic tensor least-squares fit of independent strains. Args: strains (list of Strains): list of strain objects to fit @@ -874,15 +872,15 @@ def diff_fit(strains, stresses, eq_stress=None, order=2, tol: float = 1e-10): dei_dsi = np.zeros((order - 1, 6, len(strain_state_dict))) for idx, (strain_state, data) in enumerate(strain_state_dict.items()): hvec = data["strains"][:, strain_state.index(1)] - for ord in range(1, order): - coef = get_diff_coeff(hvec, ord) - dei_dsi[ord - 1, :, idx] = np.dot(coef, data["stresses"]) + for _ord in range(1, order): + coef = get_diff_coeff(hvec, _ord) + dei_dsi[_ord - 1, :, idx] = np.dot(coef, data["stresses"]) m, _absent = generate_pseudo(list(strain_state_dict), order) - for ord in range(1, order): - cvec, carr = get_symbol_list(ord + 1) - svec = np.ravel(dei_dsi[ord - 1].T) - cmap = dict(zip(cvec, np.dot(m[ord - 1], svec))) + for _ord in range(1, order): + cvec, carr = get_symbol_list(_ord + 1) + svec = np.ravel(dei_dsi[_ord - 1].T) + cmap = dict(zip(cvec, np.dot(m[_ord - 1], svec))) c_list.append(v_subs(carr, cmap)) return [Tensor.from_voigt(c) for c in c_list] diff --git a/pymatgen/analysis/elasticity/strain.py b/src/pymatgen/analysis/elasticity/strain.py similarity index 99% rename from pymatgen/analysis/elasticity/strain.py rename to src/pymatgen/analysis/elasticity/strain.py index 99fe716a249..13092b5daf2 100644 --- a/pymatgen/analysis/elasticity/strain.py +++ b/src/pymatgen/analysis/elasticity/strain.py @@ -12,7 +12,6 @@ import numpy as np import scipy - from pymatgen.core.lattice import Lattice from pymatgen.core.tensors import SquareTensor, symmetry_reduce @@ -21,9 +20,8 @@ from typing import Literal from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.core.structure import Structure + from typing_extensions import Self __author__ = "Joseph Montoya" __copyright__ = "Copyright 2012, The Materials Project" diff --git a/pymatgen/analysis/elasticity/stress.py b/src/pymatgen/analysis/elasticity/stress.py similarity index 99% rename from pymatgen/analysis/elasticity/stress.py rename to src/pymatgen/analysis/elasticity/stress.py index 3e5765130ca..720eb00dc4f 100644 --- a/pymatgen/analysis/elasticity/stress.py +++ b/src/pymatgen/analysis/elasticity/stress.py @@ -9,7 +9,6 @@ from typing import TYPE_CHECKING import numpy as np - from pymatgen.core.tensors import SquareTensor if TYPE_CHECKING: diff --git a/pymatgen/analysis/energy_models.py b/src/pymatgen/analysis/energy_models.py similarity index 95% rename from pymatgen/analysis/energy_models.py rename to src/pymatgen/analysis/energy_models.py index 03a32cabe17..501287f7f01 100644 --- a/pymatgen/analysis/energy_models.py +++ b/src/pymatgen/analysis/energy_models.py @@ -10,14 +10,12 @@ from typing import TYPE_CHECKING from monty.json import MSONable - from pymatgen.analysis.ewald import EwaldSummation from pymatgen.symmetry.analyzer import SpacegroupAnalyzer if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.core import Structure + from typing_extensions import Self __version__ = "0.1" @@ -29,7 +27,7 @@ class EnergyModel(MSONable, abc.ABC): def get_energy(self, structure) -> float: """ Args: - structure: Structure + structure: Structure. Returns: Energy value @@ -76,7 +74,7 @@ def __init__(self, real_space_cut=None, recip_space_cut=None, eta=None, acc_fact def get_energy(self, structure: Structure): """ Args: - structure: Structure + structure: Structure. Returns: Energy value @@ -91,7 +89,7 @@ def get_energy(self, structure: Structure): return e.total_energy def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "version": __version__, "@module": type(self).__module__, @@ -125,7 +123,7 @@ def __init__(self, symprec: float = 0.1, angle_tolerance=5): def get_energy(self, structure: Structure): """ Args: - structure: Structure + structure: Structure. Returns: Energy value @@ -134,7 +132,7 @@ def get_energy(self, structure: Structure): return -spg_analyzer.get_space_group_number() def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "version": __version__, "@module": type(self).__module__, @@ -161,7 +159,7 @@ def __init__(self, j, max_radius): def get_energy(self, structure: Structure): """ Args: - structure: Structure + structure: Structure. Returns: Energy value @@ -175,7 +173,7 @@ def get_energy(self, structure: Structure): return energy def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "version": __version__, "@module": type(self).__module__, @@ -194,7 +192,7 @@ class NsitesModel(EnergyModel): def get_energy(self, structure: Structure): """ Args: - structure: Structure + structure: Structure. Returns: Energy value @@ -202,7 +200,7 @@ def get_energy(self, structure: Structure): return len(structure) def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "version": __version__, "@module": type(self).__module__, diff --git a/pymatgen/analysis/eos.py b/src/pymatgen/analysis/eos.py similarity index 98% rename from pymatgen/analysis/eos.py rename to src/pymatgen/analysis/eos.py index 01e10854289..fc526884537 100644 --- a/pymatgen/analysis/eos.py +++ b/src/pymatgen/analysis/eos.py @@ -13,10 +13,9 @@ from typing import TYPE_CHECKING import numpy as np -from scipy.optimize import leastsq, minimize - from pymatgen.core.units import FloatWithUnit from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig, pretty_plot +from scipy.optimize import leastsq, minimize if TYPE_CHECKING: from typing import ClassVar @@ -118,7 +117,7 @@ def func(self, volume): def __call__(self, volume: float) -> float: """ Args: - volume (float | list[float]): volume(s) in Ang^3 + volume (float | list[float]): volume(s) in Ang^3. Returns: Compute EOS with this volume. @@ -534,15 +533,15 @@ class EOS: eos_fit.plot() """ - MODELS: ClassVar = dict( - murnaghan=Murnaghan, - birch=Birch, - birch_murnaghan=BirchMurnaghan, - pourier_tarantola=PourierTarantola, - vinet=Vinet, - deltafactor=DeltaFactor, - numerical_eos=NumericalEOS, - ) + MODELS: ClassVar = { + "murnaghan": Murnaghan, + "birch": Birch, + "birch_murnaghan": BirchMurnaghan, + "pourier_tarantola": PourierTarantola, + "vinet": Vinet, + "deltafactor": DeltaFactor, + "numerical_eos": NumericalEOS, + } def __init__(self, eos_name="murnaghan"): """ diff --git a/pymatgen/analysis/ewald.py b/src/pymatgen/analysis/ewald.py similarity index 99% rename from pymatgen/analysis/ewald.py rename to src/pymatgen/analysis/ewald.py index 651389b0f12..46fb6c523ee 100644 --- a/pymatgen/analysis/ewald.py +++ b/src/pymatgen/analysis/ewald.py @@ -11,11 +11,10 @@ import numpy as np from monty.json import MSONable -from scipy import constants -from scipy.special import comb, erfc - from pymatgen.core.structure import Structure from pymatgen.util.due import Doi, due +from scipy import constants +from scipy.special import comb, erfc if TYPE_CHECKING: from typing import Any @@ -622,7 +621,6 @@ def get_next_index(cls, matrix, manipulation, indices_left): """Get an index that should have the most negative effect on the matrix sum. """ - f = manipulation[0] indices = list(indices_left.intersection(manipulation[2])) sums = np.sum(matrix[indices], axis=1) diff --git a/pymatgen/analysis/excitation.py b/src/pymatgen/analysis/excitation.py similarity index 100% rename from pymatgen/analysis/excitation.py rename to src/pymatgen/analysis/excitation.py diff --git a/pymatgen/analysis/ferroelectricity/__init__.py b/src/pymatgen/analysis/ferroelectricity/__init__.py similarity index 100% rename from pymatgen/analysis/ferroelectricity/__init__.py rename to src/pymatgen/analysis/ferroelectricity/__init__.py diff --git a/pymatgen/analysis/ferroelectricity/polarization.py b/src/pymatgen/analysis/ferroelectricity/polarization.py similarity index 99% rename from pymatgen/analysis/ferroelectricity/polarization.py rename to src/pymatgen/analysis/ferroelectricity/polarization.py index 398fee58930..2e0175fdf3b 100644 --- a/pymatgen/analysis/ferroelectricity/polarization.py +++ b/src/pymatgen/analysis/ferroelectricity/polarization.py @@ -48,17 +48,15 @@ from typing import TYPE_CHECKING import numpy as np -from scipy.interpolate import UnivariateSpline - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure +from scipy.interpolate import UnivariateSpline if TYPE_CHECKING: from collections.abc import Sequence - from typing_extensions import Self - from pymatgen.core.sites import PeriodicSite + from typing_extensions import Self __author__ = "Tess Smidt" @@ -422,7 +420,7 @@ class EnergyTrend: def __init__(self, energies): """ Args: - energies: Energies + energies: Energies. """ self.energies = energies diff --git a/pymatgen/analysis/fragmenter.py b/src/pymatgen/analysis/fragmenter.py similarity index 99% rename from pymatgen/analysis/fragmenter.py rename to src/pymatgen/analysis/fragmenter.py index 7458a46dfeb..98ad92a2b24 100644 --- a/pymatgen/analysis/fragmenter.py +++ b/src/pymatgen/analysis/fragmenter.py @@ -7,7 +7,6 @@ from typing import TYPE_CHECKING from monty.json import MSONable - from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender from pymatgen.io.babel import BabelMolAdaptor diff --git a/pymatgen/analysis/functional_groups.py b/src/pymatgen/analysis/functional_groups.py similarity index 99% rename from pymatgen/analysis/functional_groups.py rename to src/pymatgen/analysis/functional_groups.py index f21f3ea894b..94f4cce6f17 100644 --- a/pymatgen/analysis/functional_groups.py +++ b/src/pymatgen/analysis/functional_groups.py @@ -83,7 +83,7 @@ def __init__(self, molecule, optimize=False): self.molgraph = molecule else: - raise ValueError("Input to FunctionalGroupExtractor must be str, Molecule, or MoleculeGraph.") + raise TypeError("Input to FunctionalGroupExtractor must be str, Molecule, or MoleculeGraph.") if self.molgraph is None: self.molgraph = MoleculeGraph.from_local_env_strategy(self.molecule, OpenBabelNN()) diff --git a/pymatgen/analysis/gb/__init__.py b/src/pymatgen/analysis/gb/__init__.py similarity index 100% rename from pymatgen/analysis/gb/__init__.py rename to src/pymatgen/analysis/gb/__init__.py diff --git a/pymatgen/analysis/gb/grain.py b/src/pymatgen/analysis/gb/grain.py similarity index 100% rename from pymatgen/analysis/gb/grain.py rename to src/pymatgen/analysis/gb/grain.py diff --git a/pymatgen/analysis/graphs.py b/src/pymatgen/analysis/graphs.py similarity index 99% rename from pymatgen/analysis/graphs.py rename to src/pymatgen/analysis/graphs.py index 1722aea1720..998db8a72bf 100644 --- a/pymatgen/analysis/graphs.py +++ b/src/pymatgen/analysis/graphs.py @@ -20,13 +20,12 @@ from monty.json import MSONable from networkx.drawing.nx_agraph import write_dot from networkx.readwrite import json_graph -from scipy.spatial import KDTree -from scipy.stats import describe - from pymatgen.core import Lattice, Molecule, PeriodicSite, Structure from pymatgen.core.structure import FunctionalGroups from pymatgen.util.coord import lattice_points_in_supercell from pymatgen.vis.structure_vtk import EL_COLORS +from scipy.spatial import KDTree +from scipy.stats import describe try: import igraph @@ -39,11 +38,10 @@ from igraph import Graph from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.analysis.local_env import NearNeighbors from pymatgen.core import Species from pymatgen.util.typing import Tuple3Ints + from typing_extensions import Self logger = logging.getLogger(__name__) @@ -313,17 +311,17 @@ def with_local_env_strategy(cls, *args, **kwargs): @property def name(self) -> str: - """Name of graph""" + """Name of graph.""" return self.graph.graph["name"] @property def edge_weight_name(self) -> str: - """Name of the edge weight property of graph""" + """Name of the edge weight property of graph.""" return self.graph.graph["edge_weight_name"] @property def edge_weight_unit(self): - """Units of the edge weight property of graph""" + """Units of the edge weight property of graph.""" return self.graph.graph["edge_weight_units"] def add_edge( @@ -769,10 +767,10 @@ def get_connected_sites(self, n: int, jimage: Tuple3Ints = (0, 0, 0)) -> list[Co out_edges = [(u, v, d, "out") for u, v, d in self.graph.out_edges(n, data=True)] in_edges = [(u, v, d, "in") for u, v, d in self.graph.in_edges(n, data=True)] - for u, v, data, dir in out_edges + in_edges: + for u, v, data, dirc in out_edges + in_edges: to_jimage = data["to_jimage"] - if dir == "in": + if dirc == "in": u, v = v, u to_jimage = np.multiply(-1, to_jimage) @@ -1331,7 +1329,7 @@ def __repr__(self): return out def __len__(self): - """length of Structure / number of nodes in graph""" + """Length of Structure / number of nodes in graph.""" return len(self.structure) def sort(self, key=None, reverse: bool = False) -> None: @@ -1768,17 +1766,17 @@ def with_local_env_strategy(cls, *args, **kwargs): @property def name(self): - """Name of graph""" + """Name of graph.""" return self.graph.graph["name"] @property def edge_weight_name(self): - """Name of the edge weight property of graph""" + """Name of the edge weight property of graph.""" return self.graph.graph["edge_weight_name"] @property def edge_weight_unit(self): - """Units of the edge weight property of graph""" + """Units of the edge weight property of graph.""" return self.graph.graph["edge_weight_units"] def add_edge( @@ -2421,8 +2419,8 @@ def find_rings(self, including=None) -> list[list[tuple[int, int]]]: for cycle in cycles_nodes: edges = [] - for idx, itm in enumerate(cycle, start=-1): - edges.append((cycle[idx], itm)) + for idx, itm in enumerate(cycle): + edges.append((cycle[idx - 1], itm)) cycles_edges.append(edges) return cycles_edges @@ -2433,9 +2431,10 @@ def get_connected_sites(self, n): Index is the index of the corresponding site in the original structure, weight can be None if not defined. + Args: n: index of Site in Molecule - jimage: lattice vector of site + jimage: lattice vector of site. Returns: list of ConnectedSite tuples, @@ -2717,7 +2716,7 @@ def __repr__(self) -> str: return out def __len__(self) -> int: - """length of Molecule / number of nodes in graph""" + """Length of Molecule / number of nodes in graph.""" return len(self.molecule) def sort(self, key: Callable[[Molecule], float] | None = None, reverse: bool = False) -> None: diff --git a/pymatgen/analysis/hhi.py b/src/pymatgen/analysis/hhi.py similarity index 99% rename from pymatgen/analysis/hhi.py rename to src/pymatgen/analysis/hhi.py index 85708e78366..b893fe3a131 100644 --- a/pymatgen/analysis/hhi.py +++ b/src/pymatgen/analysis/hhi.py @@ -14,7 +14,6 @@ import os from monty.design_patterns import singleton - from pymatgen.core import Composition, Element __author__ = "Anubhav Jain" diff --git a/pymatgen/analysis/hhi_data.csv b/src/pymatgen/analysis/hhi_data.csv similarity index 100% rename from pymatgen/analysis/hhi_data.csv rename to src/pymatgen/analysis/hhi_data.csv diff --git a/pymatgen/analysis/icsd_bv.yaml b/src/pymatgen/analysis/icsd_bv.yaml similarity index 100% rename from pymatgen/analysis/icsd_bv.yaml rename to src/pymatgen/analysis/icsd_bv.yaml diff --git a/pymatgen/analysis/interface_reactions.py b/src/pymatgen/analysis/interface_reactions.py similarity index 98% rename from pymatgen/analysis/interface_reactions.py rename to src/pymatgen/analysis/interface_reactions.py index ffdf0a06c8b..908cd538ff0 100644 --- a/pymatgen/analysis/interface_reactions.py +++ b/src/pymatgen/analysis/interface_reactions.py @@ -15,7 +15,6 @@ from monty.json import MSONable from pandas import DataFrame from plotly.graph_objects import Figure, Scatter - from pymatgen.analysis.phase_diagram import GrandPotentialPhaseDiagram, PhaseDiagram from pymatgen.analysis.reaction_calculator import Reaction from pymatgen.core.composition import Composition @@ -92,7 +91,7 @@ def __init__( bypass_grand_warning = kwargs.get("bypass_grand_warning", False) if isinstance(pd, GrandPotentialPhaseDiagram) and not bypass_grand_warning: - raise ValueError( + raise TypeError( "Please use the GrandPotentialInterfacialReactivity " "class for interfacial reactions with open elements!" ) @@ -338,17 +337,16 @@ def _get_plotly_figure(self) -> Figure: hoverinfo="none", ) - annotations = self._get_plotly_annotations(x, energy, reactions) # type: ignore + annotations = self._get_plotly_annotations(x, energy, reactions) - min_idx = energy.index(min(energy)) # type: ignore + min_idx = energy.index(min(energy)) x_min = x.pop(min_idx) e_min = energy.pop(min_idx) rxn_min = reactions.pop(min_idx) labels = [ - f"{htmlify(str(r))}
                                                                                        \u0394Erxn = {round(e, 3)} eV/atom" # type: ignore - for r, e in zip(reactions, energy) + f"{htmlify(str(r))}
                                                                                        \u0394Erxn = {round(e, 3)} eV/atom" for r, e in zip(reactions, energy) ] markers = Scatter( @@ -367,7 +365,7 @@ def _get_plotly_figure(self) -> Figure: hoverlabel={"bgcolor": "navy"}, ) - min_label = f"{htmlify(str(rxn_min))}
                                                                                        \u0394Erxn = {round(e_min, 3)} eV/atom" # type: ignore + min_label = f"{htmlify(str(rxn_min))}
                                                                                        \u0394Erxn = {round(e_min, 3)} eV/atom" minimum = Scatter( x=[x_min], @@ -572,7 +570,8 @@ def labels(self): @property def minimum(self): """The minimum reaction energy E_min and corresponding mixing ratio x_min - as tuple[float, float]: (x_min, E_min).""" + as tuple[float, float]: (x_min, E_min). + """ return min(((x, energy) for _, x, energy, _, _ in self.get_kinks()), key=lambda tup: tup[1]) @property @@ -625,9 +624,9 @@ def __init__( warning message. """ if not isinstance(grand_pd, GrandPotentialPhaseDiagram): - raise ValueError("Please use the InterfacialReactivity class if using a regular phase diagram!") + raise TypeError("Please use the InterfacialReactivity class if using a regular phase diagram!") if not isinstance(pd_non_grand, PhaseDiagram): - raise ValueError("Please provide non-grand phase diagram to compute no_mixing_energy!") + raise TypeError("Please provide non-grand phase diagram to compute no_mixing_energy!") super().__init__( c1=c1, c2=c2, pd=grand_pd, norm=norm, use_hull_energy=use_hull_energy, bypass_grand_warning=True diff --git a/pymatgen/analysis/interfaces/__init__.py b/src/pymatgen/analysis/interfaces/__init__.py similarity index 100% rename from pymatgen/analysis/interfaces/__init__.py rename to src/pymatgen/analysis/interfaces/__init__.py diff --git a/pymatgen/analysis/interfaces/coherent_interfaces.py b/src/pymatgen/analysis/interfaces/coherent_interfaces.py similarity index 99% rename from pymatgen/analysis/interfaces/coherent_interfaces.py rename to src/pymatgen/analysis/interfaces/coherent_interfaces.py index 3e145fc5618..e52dab38e04 100644 --- a/pymatgen/analysis/interfaces/coherent_interfaces.py +++ b/src/pymatgen/analysis/interfaces/coherent_interfaces.py @@ -7,12 +7,11 @@ import numpy as np from numpy.testing import assert_allclose -from scipy.linalg import polar - from pymatgen.analysis.elasticity.strain import Deformation from pymatgen.analysis.interfaces.zsl import ZSLGenerator, fast_norm from pymatgen.core.interface import Interface, label_termination from pymatgen.core.surface import SlabGenerator +from scipy.linalg import polar if TYPE_CHECKING: from collections.abc import Iterator, Sequence diff --git a/pymatgen/analysis/interfaces/substrate_analyzer.py b/src/pymatgen/analysis/interfaces/substrate_analyzer.py similarity index 99% rename from pymatgen/analysis/interfaces/substrate_analyzer.py rename to src/pymatgen/analysis/interfaces/substrate_analyzer.py index 4d6f3ecf431..62b2a4a5152 100644 --- a/pymatgen/analysis/interfaces/substrate_analyzer.py +++ b/src/pymatgen/analysis/interfaces/substrate_analyzer.py @@ -11,10 +11,9 @@ if TYPE_CHECKING: from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.core import Structure from pymatgen.util.typing import Tuple3Ints + from typing_extensions import Self @dataclass @@ -95,7 +94,7 @@ class SubstrateAnalyzer(ZSLGenerator): """ def __init__(self, film_max_miller=1, substrate_max_miller=1, **kwargs): - """Initialize the substrate analyzer + """Initialize the substrate analyzer. Args: zslgen (ZSLGenerator): Defaults to a ZSLGenerator with standard diff --git a/pymatgen/analysis/interfaces/zsl.py b/src/pymatgen/analysis/interfaces/zsl.py similarity index 98% rename from pymatgen/analysis/interfaces/zsl.py rename to src/pymatgen/analysis/interfaces/zsl.py index 65cebe57058..fdd17dbcdb0 100644 --- a/pymatgen/analysis/interfaces/zsl.py +++ b/src/pymatgen/analysis/interfaces/zsl.py @@ -8,7 +8,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.util.due import Doi, due from pymatgen.util.numba import njit @@ -91,7 +90,7 @@ def __init__( ): """ Initialize a Zur Super Lattice Generator for a specific film and - substrate + substrate. Args: max_area_ratio_tol(float): Max tolerance on ratio of @@ -112,7 +111,7 @@ def generate_sl_transformation_sets(self, film_area, substrate_area): """Generate transformation sets for film/substrate pair given the area of the unit cell area for the film and substrate. The transformation sets map the film and substrate unit cells to super - lattices with a maximum area + lattices with a maximum area. Args: film_area (int): the unit cell area for the film @@ -183,9 +182,7 @@ def get_equiv_transformations(self, transformation_sets, film_vectors, substrate yield [f, s, f_trans, s_trans] def __call__(self, film_vectors, substrate_vectors, lowest=False) -> Iterator[ZSLMatch]: - """ - Runs the ZSL algorithm to generate all possible matching - """ + """Runs the ZSL algorithm to generate all possible matching.""" film_area = vec_area(*film_vectors) substrate_area = vec_area(*substrate_vectors) diff --git a/pymatgen/analysis/ionic_radii.json b/src/pymatgen/analysis/ionic_radii.json similarity index 100% rename from pymatgen/analysis/ionic_radii.json rename to src/pymatgen/analysis/ionic_radii.json diff --git a/pymatgen/analysis/local_env.py b/src/pymatgen/analysis/local_env.py similarity index 99% rename from pymatgen/analysis/local_env.py rename to src/pymatgen/analysis/local_env.py index cad13415668..d4acd5a7d2f 100644 --- a/pymatgen/analysis/local_env.py +++ b/src/pymatgen/analysis/local_env.py @@ -19,13 +19,12 @@ import numpy as np from monty.dev import deprecated, requires from monty.serialization import loadfn -from ruamel.yaml import YAML -from scipy.spatial import Voronoi - from pymatgen.analysis.bond_valence import BV_PARAMS, BVAnalyzer from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph from pymatgen.analysis.molecule_structure_comparator import CovalentRadius from pymatgen.core import Element, IStructure, PeriodicNeighbor, PeriodicSite, Site, Species, Structure +from ruamel.yaml import YAML +from scipy.spatial import Voronoi try: from openbabel import openbabel @@ -35,10 +34,9 @@ if TYPE_CHECKING: from typing import Any - from typing_extensions import Self - from pymatgen.core.composition import SpeciesLike from pymatgen.util.typing import Tuple3Ints + from typing_extensions import Self __author__ = "Shyue Ping Ong, Geoffroy Hautier, Sai Jayaraman, " @@ -220,7 +218,7 @@ def _handle_disorder(structure: Structure, on_disorder: on_disorder_options): # As a workaround, we create a new structure with majority species on each site. structure = structure.copy() # make a copy so we don't mutate the original structure for idx, site in enumerate(structure): - max_specie = max(site.species, key=site.species.get) # type: ignore + max_specie = max(site.species, key=site.species.get) max_val = site.species[max_specie] if max_val <= 0.5: if on_disorder == "take_majority_strict": @@ -590,6 +588,10 @@ def get_bonded_structure( """ Obtain a StructureGraph object using this NearNeighbor class. Requires pip install networkx. + NOTE: The StructureGraph will not contain sites or bonds that are equivalent under lattice + vector translations. For more details please see the following discussion: + https://github.com/materialsproject/pymatgen/issues/3888 + Args: structure: Structure object. decorate (bool): whether to annotate site properties with order parameters using neighbors @@ -621,7 +623,7 @@ def get_bonded_structure( structure, self, weights=weights, edge_properties=edge_properties ) - # sets the attributes + # Set the attributes struct_graph.set_node_attributes() return struct_graph @@ -655,7 +657,7 @@ def get_local_order_parameters(self, structure: Structure, n: int): params.append(tmp) lsops = LocalStructOrderParams(types, parameters=params) sites = [structure[n], *self.get_nn(structure, n)] - lostop_vals = lsops.get_order_parameters(sites, 0, indices_neighs=list(range(1, cn + 1))) # type: ignore + lostop_vals = lsops.get_order_parameters(sites, 0, indices_neighs=list(range(1, cn + 1))) # type: ignore[call-overload, arg-type] dct = {} for idx, lsop in enumerate(lostop_vals): dct[names[idx]] = lsop @@ -769,7 +771,7 @@ def get_voronoi_polyhedra(self, structure: Structure, n: int): if self.cutoff >= max_cutoff: if exc.args and "vertex" in exc.args[0]: # pass through the error raised by _extract_cell_info - raise exc + raise raise RuntimeError("Error in Voronoi neighbor finding; max cutoff exceeded") self.cutoff = min(self.cutoff * 2, max_cutoff + 0.001) return cell_info @@ -817,14 +819,14 @@ def get_all_voronoi_polyhedra(self, structure: Structure): indices.extend([(x[2],) + x[3] for x in neighs]) # Get the non-duplicates (using the site indices for numerical stability) - indices = np.array(indices, dtype=int) # type: ignore + indices = np.array(indices, dtype=int) indices, uniq_inds = np.unique(indices, return_index=True, axis=0) # type: ignore[assignment] sites = [sites[idx] for idx in uniq_inds] # Sort array such that atoms in the root image are first # Exploit the fact that the array is sorted by the unique operation such that # the images associated with atom 0 are first, followed by atom 1, etc. - (root_images,) = np.nonzero(np.abs(indices[:, 1:]).max(axis=1) == 0) # type: ignore + (root_images,) = np.nonzero(np.abs(indices[:, 1:]).max(axis=1) == 0) # type: ignore[call-overload] del indices # Save memory (tessellations can be costly) @@ -1243,7 +1245,7 @@ def extend_structure_molecules(self) -> bool: def get_max_bond_distance(self, el1_sym, el2_sym): """ - Use Jmol algorithm to determine bond length from atomic parameters + Use Jmol algorithm to determine bond length from atomic parameters. Args: el1_sym (str): symbol of atom 1 @@ -1486,7 +1488,7 @@ def get_nn_info(self, structure: Structure, n: int): return siw - def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> StructureGraph: # type: ignore + def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> StructureGraph: # type: ignore[override] """ Obtain a MoleculeGraph object using this NearNeighbor class. Requires the optional dependency networkx @@ -1633,7 +1635,7 @@ def get_nn_info(self, structure: Structure, n: int): return siw - def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> MoleculeGraph: # type: ignore + def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> MoleculeGraph: # type: ignore[override] """ Obtain a MoleculeGraph object using this NearNeighbor class. @@ -2874,7 +2876,7 @@ def get_order_parameters( for j, neigh in enumerate(neighsites): rij.append(neigh.coords - centvec) dist.append(float(np.linalg.norm(rij[j]))) - rij_norm.append(rij[j] / dist[j]) # type: ignore + rij_norm.append(rij[j] / dist[j]) if self._computerjks: for j, neigh in enumerate(neighsites): rjk.append([]) @@ -2890,7 +2892,7 @@ def get_order_parameters( rjknorm[j].append(rjk[j][kk] / distjk[j][kk]) kk += 1 # Initialize OP list and, then, calculate OPs. - ops = [0.0 for t in self._types] + ops: list[float | None] = [0.0 for t in self._types] # norms = [[[] for j in range(nneigh)] for t in self._types] # First, coordination number and distance-based OPs. @@ -2947,8 +2949,8 @@ def get_order_parameters( # Zimmermann et al., J. Am. Chem. Soc., under revision, 2015). if self._geomops: gaussthetak: list[float] = [0 for _t in self._types] # not used by all OPs - qsp_theta = [[[] for _j in range(n_neighbors)] for _t in self._types] # type: ignore - norms = [[[] for _j in range(n_neighbors)] for _t in self._types] # type: ignore + qsp_theta: list[list[list]] = [[[] for _j in range(n_neighbors)] for _t in self._types] + norms: list[list[list]] = [[[] for _j in range(n_neighbors)] for _t in self._types] ipi = 1 / math.pi piover2 = math.pi / 2.0 onethird = 1 / 3 @@ -3254,7 +3256,8 @@ def get_order_parameters( for j in range(n_neighbors): ops[idx] += sum(qsp_theta[idx][j]) tmp_norm += float(sum(norms[idx][j])) - ops[idx] = ops[idx] / tmp_norm if tmp_norm > 1.0e-12 else None # type: ignore + ops[idx] = ops[idx] / tmp_norm if tmp_norm > 1.0e-12 else None # type: ignore[operator] + elif typ in { "T", "tri_pyr", @@ -3283,16 +3286,18 @@ def get_order_parameters( qsp_theta[idx][j][k] / norms[idx][j][k] if norms[idx][j][k] > 1.0e-12 else 0.0 ) ops[idx] = max(qsp_theta[idx][j]) if j == 0 else max(ops[idx], *qsp_theta[idx][j]) + elif typ == "bcc": ops[idx] = 0.0 for j in range(n_neighbors): ops[idx] += sum(qsp_theta[idx][j]) if n_neighbors > 3: - ops[idx] = ops[idx] / float( + ops[idx] = ops[idx] / float( # type: ignore[operator] 0.5 * float(n_neighbors * (6 + (n_neighbors - 2) * (n_neighbors - 3))) ) else: ops[idx] = None # type: ignore[call-overload] + elif typ == "sq_pyr_legacy": if n_neighbors > 1: dmean = np.mean(dist) @@ -3302,7 +3307,7 @@ def get_order_parameters( acc = acc + math.exp(-0.5 * tmp * tmp) for j in range(n_neighbors): ops[idx] = max(qsp_theta[idx][j]) if j == 0 else max(ops[idx], *qsp_theta[idx][j]) - ops[idx] = acc * ops[idx] / float(n_neighbors) + ops[idx] = acc * ops[idx] / float(n_neighbors) # type: ignore[operator] # nneigh * (nneigh - 1)) else: ops[idx] = None # type: ignore[call-overload] @@ -3334,15 +3339,15 @@ def get_order_parameters( else: ops[idx] = 1.0 if typ == "reg_tri": - a = 2 * math.asin(b / (2 * math.sqrt(h * h + (b / (2 * math.cos(3 * math.pi / 18))) ** 2))) # type: ignore + a = 2 * math.asin(b / (2 * math.sqrt(h * h + (b / (2 * math.cos(3 * math.pi / 18))) ** 2))) nmax = 3 else: - a = 2 * math.asin(b / (2 * math.sqrt(h * h + dhalf * dhalf))) # type: ignore + a = 2 * math.asin(b / (2 * math.sqrt(h * h + dhalf * dhalf))) nmax = 4 for j in range(min([n_neighbors, nmax])): - ops[idx] = ops[idx] * math.exp(-0.5 * ((aijs[j] - a) * self._params[idx][0]) ** 2) + ops[idx] = ops[idx] * math.exp(-0.5 * ((aijs[j] - a) * self._params[idx][0]) ** 2) # type: ignore[operator] return ops @@ -3759,7 +3764,7 @@ class CrystalNN(NearNeighbors): Please note that the default weights have been benchmarked for inorganic crystal structures. For MOFs or molecular crystals, weights and cutoffs likely will need to be adapted. A starting point could be: - CrystalNN(x_diff_weight = 1.5, search_cutoff = 4.5) + CrystalNN(x_diff_weight = 1.5, search_cutoff = 4.5). """ class NNData(NamedTuple): @@ -3995,7 +4000,7 @@ def get_nn_data(self, structure: Structure, n: int, length=None): return self.transform_to_length(self.NNData(nn, cn_weights, cn_nninfo), length) - def get_cn(self, structure: Structure, n: int, **kwargs) -> float: # type: ignore + def get_cn(self, structure: Structure, n: int, **kwargs) -> float: # type: ignore[override] """Get coordination number, CN, of site with index n in structure. Args: @@ -4073,7 +4078,7 @@ def _semicircle_integral(dist_bins, idx): @staticmethod def transform_to_length(nn_data, length): """ - Given NNData, transforms data to the specified fingerprint length + Given NNData, transforms data to the specified fingerprint length. Args: nn_data: (NNData) @@ -4301,7 +4306,7 @@ def extend_structure_molecules(self) -> bool: """ return True - def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> StructureGraph: # type: ignore + def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> StructureGraph: # type: ignore[override] """ Args: structure (Structure): Input structure diff --git a/pymatgen/analysis/magnetism/__init__.py b/src/pymatgen/analysis/magnetism/__init__.py similarity index 100% rename from pymatgen/analysis/magnetism/__init__.py rename to src/pymatgen/analysis/magnetism/__init__.py diff --git a/pymatgen/analysis/magnetism/analyzer.py b/src/pymatgen/analysis/magnetism/analyzer.py similarity index 99% rename from pymatgen/analysis/magnetism/analyzer.py rename to src/pymatgen/analysis/magnetism/analyzer.py index a983da40ca0..59359e773fd 100644 --- a/pymatgen/analysis/magnetism/analyzer.py +++ b/src/pymatgen/analysis/magnetism/analyzer.py @@ -13,10 +13,6 @@ import numpy as np from monty.serialization import loadfn -from ruamel.yaml.error import MarkedYAMLError -from scipy.signal import argrelextrema -from scipy.stats import gaussian_kde - from pymatgen.core.structure import DummySpecies, Element, Species, Structure from pymatgen.electronic_structure.core import Magmom from pymatgen.symmetry.analyzer import SpacegroupAnalyzer @@ -24,6 +20,9 @@ from pymatgen.transformations.advanced_transformations import MagOrderingTransformation, MagOrderParameterConstraint from pymatgen.transformations.standard_transformations import AutoOxiStateDecorationTransformation from pymatgen.util.due import Doi, due +from ruamel.yaml.error import MarkedYAMLError +from scipy.signal import argrelextrema +from scipy.stats import gaussian_kde if TYPE_CHECKING: from typing import Any @@ -266,8 +265,8 @@ def __init__( elif overwrite_magmom_mode == OverwriteMagmomMode.normalize.value and magmoms[idx] != 0: magmoms[idx] = int(magmoms[idx] / abs(magmoms[idx])) - # round magmoms, used to smooth out computational data - magmoms = self._round_magmoms(magmoms, round_magmoms) if round_magmoms else magmoms # type: ignore + # Round magmoms, used to smooth out computational data + magmoms = self._round_magmoms(magmoms, round_magmoms) if round_magmoms else magmoms if set_net_positive: sign = np.sum(magmoms) diff --git a/pymatgen/analysis/magnetism/default_magmoms.yaml b/src/pymatgen/analysis/magnetism/default_magmoms.yaml similarity index 100% rename from pymatgen/analysis/magnetism/default_magmoms.yaml rename to src/pymatgen/analysis/magnetism/default_magmoms.yaml diff --git a/pymatgen/analysis/magnetism/heisenberg.py b/src/pymatgen/analysis/magnetism/heisenberg.py similarity index 99% rename from pymatgen/analysis/magnetism/heisenberg.py rename to src/pymatgen/analysis/magnetism/heisenberg.py index 35f4c12f116..ac627f903b1 100644 --- a/pymatgen/analysis/magnetism/heisenberg.py +++ b/src/pymatgen/analysis/magnetism/heisenberg.py @@ -15,7 +15,6 @@ import pandas as pd from monty.json import MSONable, jsanitize from monty.serialization import dumpfn - from pymatgen.analysis.graphs import StructureGraph from pymatgen.analysis.local_env import MinimumDistanceNN from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer, Ordering diff --git a/pymatgen/analysis/magnetism/jahnteller.py b/src/pymatgen/analysis/magnetism/jahnteller.py similarity index 99% rename from pymatgen/analysis/magnetism/jahnteller.py rename to src/pymatgen/analysis/magnetism/jahnteller.py index b102c3c352f..90727f19e15 100644 --- a/pymatgen/analysis/magnetism/jahnteller.py +++ b/src/pymatgen/analysis/magnetism/jahnteller.py @@ -7,7 +7,6 @@ from typing import TYPE_CHECKING, Literal, cast import numpy as np - from pymatgen.analysis.bond_valence import BVAnalyzer from pymatgen.analysis.local_env import LocalStructOrderParams, get_neighbors_of_site_with_index from pymatgen.core import Species, get_el_sp @@ -348,7 +347,7 @@ def _get_number_of_d_electrons(species: Species) -> float: elec = species.element.full_electronic_structure if len(elec) < 4 or elec[-1][1] != "s" or elec[-2][1] != "d": raise AttributeError(f"Invalid element {species.symbol} for crystal field calculation.") - n_electrons = int(elec[-1][2] + elec[-2][2] - species.oxi_state) # type: ignore + n_electrons = int(elec[-1][2] + elec[-2][2] - species.oxi_state) # type: ignore[operator] if n_electrons < 0 or n_electrons > 10: raise AttributeError(f"Invalid oxidation state {species.oxi_state} for element {species.symbol}") diff --git a/pymatgen/analysis/molecule_matcher.py b/src/pymatgen/analysis/molecule_matcher.py similarity index 99% rename from pymatgen/analysis/molecule_matcher.py rename to src/pymatgen/analysis/molecule_matcher.py index a8da516d5a5..1b779e6898c 100644 --- a/pymatgen/analysis/molecule_matcher.py +++ b/src/pymatgen/analysis/molecule_matcher.py @@ -22,14 +22,12 @@ import numpy as np from monty.dev import requires from monty.json import MSONable +from pymatgen.core.structure import Molecule from scipy.optimize import linear_sum_assignment from scipy.spatial.distance import cdist -from pymatgen.core.structure import Molecule - try: from openbabel import openbabel - from pymatgen.io.babel import BabelMolAdaptor except ImportError: openbabel = BabelMolAdaptor = None # type: ignore[misc] diff --git a/pymatgen/analysis/molecule_structure_comparator.py b/src/pymatgen/analysis/molecule_structure_comparator.py similarity index 77% rename from pymatgen/analysis/molecule_structure_comparator.py rename to src/pymatgen/analysis/molecule_structure_comparator.py index a3907fd08d7..28400b65a34 100644 --- a/pymatgen/analysis/molecule_structure_comparator.py +++ b/src/pymatgen/analysis/molecule_structure_comparator.py @@ -14,7 +14,6 @@ from typing import TYPE_CHECKING from monty.json import MSONable - from pymatgen.util.due import Doi, due if TYPE_CHECKING: @@ -39,104 +38,104 @@ class CovalentRadius: Beatriz C. et al. Dalton Trans. 2008, 2832-2838. https://doi.org/10.1039/b801115j """ - radius: ClassVar = dict( - H=0.31, - He=0.28, - Li=1.28, - Be=0.96, - B=0.84, - C=0.73, - N=0.71, - O=0.66, - F=0.57, - Ne=0.58, - Na=1.66, - Mg=1.41, - Al=1.21, - Si=1.11, - P=1.07, - S=1.05, - Cl=1.02, - Ar=1.06, - K=2.03, - Ca=1.76, - Sc=1.70, - Ti=1.60, - V=1.53, - Cr=1.39, - Mn=1.50, - Fe=1.42, - Co=1.38, - Ni=1.24, - Cu=1.32, - Zn=1.22, - Ga=1.22, - Ge=1.20, - As=1.19, - Se=1.20, - Br=1.20, - Kr=1.16, - Rb=2.20, - Sr=1.95, - Y=1.90, - Zr=1.75, - Nb=1.64, - Mo=1.54, - Tc=1.47, - Ru=1.46, - Rh=1.42, - Pd=1.39, - Ag=1.45, - Cd=1.44, - In=1.42, - Sn=1.39, - Sb=1.39, - Te=1.38, - I=1.39, - Xe=1.40, - Cs=2.44, - Ba=2.15, - La=2.07, - Ce=2.04, - Pr=2.03, - Nd=2.01, - Pm=1.99, - Sm=1.98, - Eu=1.98, - Gd=1.96, - Tb=1.94, - Dy=1.92, - Ho=1.92, - Er=1.89, - Tm=1.90, - Yb=1.87, - Lu=1.87, - Hf=1.75, - Ta=1.70, - W=1.62, - Re=1.51, - Os=1.44, - Ir=1.41, - Pt=1.36, - Au=1.36, - Hg=1.32, - Tl=1.45, - Pb=1.46, - Bi=1.48, - Po=1.40, - At=1.50, - Rn=1.50, - Fr=2.60, - Ra=2.21, - Ac=2.15, - Th=2.06, - Pa=2, - U=1.96, - Np=1.90, - Pu=1.87, - Am=1.80, - Cm=1.69, - ) + radius: ClassVar = { + "H": 0.31, + "He": 0.28, + "Li": 1.28, + "Be": 0.96, + "B": 0.84, + "C": 0.73, + "N": 0.71, + "O": 0.66, + "F": 0.57, + "Ne": 0.58, + "Na": 1.66, + "Mg": 1.41, + "Al": 1.21, + "Si": 1.11, + "P": 1.07, + "S": 1.05, + "Cl": 1.02, + "Ar": 1.06, + "K": 2.03, + "Ca": 1.76, + "Sc": 1.70, + "Ti": 1.60, + "V": 1.53, + "Cr": 1.39, + "Mn": 1.50, + "Fe": 1.42, + "Co": 1.38, + "Ni": 1.24, + "Cu": 1.32, + "Zn": 1.22, + "Ga": 1.22, + "Ge": 1.20, + "As": 1.19, + "Se": 1.20, + "Br": 1.20, + "Kr": 1.16, + "Rb": 2.20, + "Sr": 1.95, + "Y": 1.90, + "Zr": 1.75, + "Nb": 1.64, + "Mo": 1.54, + "Tc": 1.47, + "Ru": 1.46, + "Rh": 1.42, + "Pd": 1.39, + "Ag": 1.45, + "Cd": 1.44, + "In": 1.42, + "Sn": 1.39, + "Sb": 1.39, + "Te": 1.38, + "I": 1.39, + "Xe": 1.40, + "Cs": 2.44, + "Ba": 2.15, + "La": 2.07, + "Ce": 2.04, + "Pr": 2.03, + "Nd": 2.01, + "Pm": 1.99, + "Sm": 1.98, + "Eu": 1.98, + "Gd": 1.96, + "Tb": 1.94, + "Dy": 1.92, + "Ho": 1.92, + "Er": 1.89, + "Tm": 1.90, + "Yb": 1.87, + "Lu": 1.87, + "Hf": 1.75, + "Ta": 1.70, + "W": 1.62, + "Re": 1.51, + "Os": 1.44, + "Ir": 1.41, + "Pt": 1.36, + "Au": 1.36, + "Hg": 1.32, + "Tl": 1.45, + "Pb": 1.46, + "Bi": 1.48, + "Po": 1.40, + "At": 1.50, + "Rn": 1.50, + "Fr": 2.60, + "Ra": 2.21, + "Ac": 2.15, + "Th": 2.06, + "Pa": 2, + "U": 1.96, + "Np": 1.90, + "Pu": 1.87, + "Am": 1.80, + "Cm": 1.69, + } class MoleculeStructureComparator(MSONable): diff --git a/pymatgen/analysis/nmr.py b/src/pymatgen/analysis/nmr.py similarity index 98% rename from pymatgen/analysis/nmr.py rename to src/pymatgen/analysis/nmr.py index de10dd6370a..91a7ccd21d4 100644 --- a/pymatgen/analysis/nmr.py +++ b/src/pymatgen/analysis/nmr.py @@ -5,7 +5,6 @@ from typing import TYPE_CHECKING, NamedTuple import numpy as np - from pymatgen.core import Site, Species from pymatgen.core.tensors import SquareTensor from pymatgen.core.units import FloatWithUnit @@ -238,6 +237,6 @@ def coupling_constant(self, specie): elif isinstance(specie, Species): quad_pol_mom = specie.get_nmr_quadrupole_moment() else: - raise ValueError("Invalid species provided for quadrupolar coupling constant calculations") + raise TypeError("Invalid species provided for quadrupolar coupling constant calculations") return (e * quad_pol_mom * Vzz / planks_constant).to("MHz") diff --git a/pymatgen/analysis/op_params.yaml b/src/pymatgen/analysis/op_params.yaml similarity index 100% rename from pymatgen/analysis/op_params.yaml rename to src/pymatgen/analysis/op_params.yaml diff --git a/pymatgen/analysis/phase_diagram.py b/src/pymatgen/analysis/phase_diagram.py similarity index 98% rename from pymatgen/analysis/phase_diagram.py rename to src/pymatgen/analysis/phase_diagram.py index 5557b85d6c5..6369e2369a0 100644 --- a/pymatgen/analysis/phase_diagram.py +++ b/src/pymatgen/analysis/phase_diagram.py @@ -21,11 +21,6 @@ from matplotlib.colors import LinearSegmentedColormap, Normalize from matplotlib.font_manager import FontProperties from monty.json import MontyDecoder, MSONable -from scipy import interpolate -from scipy.optimize import minimize -from scipy.spatial import ConvexHull -from tqdm import tqdm - from pymatgen.analysis.reaction_calculator import Reaction, ReactionError from pymatgen.core import DummySpecies, Element, get_el_sp from pymatgen.core.composition import Composition @@ -34,6 +29,10 @@ from pymatgen.util.due import Doi, due from pymatgen.util.plotting import pretty_plot from pymatgen.util.string import htmlify, latexify +from scipy import interpolate +from scipy.optimize import minimize +from scipy.spatial import ConvexHull +from tqdm import tqdm if TYPE_CHECKING: from collections.abc import Collection, Iterator, Sequence @@ -904,7 +903,6 @@ def get_decomp_and_phase_separation_energy( } # NOTE calling PhaseDiagram is only reasonable if the composition has fewer than 5 elements - # TODO can we call PatchedPhaseDiagram here? inner_hull = PhaseDiagram(reduced_space) competing_entries = inner_hull.stable_entries | {*self._get_stable_entries_in_space(entry_elems)} @@ -1037,8 +1035,6 @@ def get_critical_compositions(self, comp1, comp2): if np.all(c1 == c2): return [comp1.copy(), comp2.copy()] - # NOTE made into method to facilitate inheritance of this method - # in PatchedPhaseDiagram if approximate solution can be found. intersections = self._get_simplex_intersections(c1, c2) # find position along line @@ -1620,29 +1616,21 @@ def __init__( # Add the elemental references inds.extend([min_entries.index(el) for el in el_refs.values()]) - self.qhull_entries = tuple(min_entries[idx] for idx in inds) + qhull_entries = tuple(min_entries[idx] for idx in inds) # make qhull spaces frozensets since they become keys to self.pds dict and frozensets are hashable # prevent repeating elements in chemical space and avoid the ordering problem (i.e. Fe-O == O-Fe automatically) - self._qhull_spaces = tuple(frozenset(entry.elements) for entry in self.qhull_entries) + qhull_spaces = tuple(frozenset(entry.elements) for entry in qhull_entries) # Get all unique chemical spaces - spaces = {s for s in self._qhull_spaces if len(s) > 1} + spaces = {s for s in qhull_spaces if len(s) > 1} # Remove redundant chemical spaces - if not keep_all_spaces and len(spaces) > 1: - max_size = max(len(s) for s in spaces) - - systems = set() - # NOTE reduce the number of comparisons by only comparing to larger sets - for idx in range(2, max_size + 1): - test = (s for s in spaces if len(s) == idx) - refer = (s for s in spaces if len(s) > idx) - systems |= {t for t in test if not any(t.issubset(r) for r in refer)} - - spaces = systems + spaces = self.remove_redundant_spaces(spaces, keep_all_spaces) # TODO comprhys: refactor to have self._compute method to allow serialization - self.spaces = sorted(spaces, key=len, reverse=False) # Calculate pds for smaller dimension spaces first + self.spaces = sorted(spaces, key=len, reverse=True) # Calculate pds for smaller dimension spaces last + self.qhull_entries = qhull_entries + self._qhull_spaces = qhull_spaces self.pds = dict(self._get_pd_patch_for_space(s) for s in tqdm(self.spaces, disable=not verbose)) self.all_entries = all_entries self.el_refs = el_refs @@ -1676,7 +1664,19 @@ def __contains__(self, item: frozenset[Element]) -> bool: return item in self.pds def as_dict(self) -> dict[str, Any]: - """ + """Write the entries and elements used to construct the PatchedPhaseDiagram + to a dictionary. + + NOTE unlike PhaseDiagram the computation involved in constructing the + PatchedPhaseDiagram is not saved on serialisation. This is done because + hierarchically calling the `PhaseDiagram.as_dict()` method would break the + link in memory between entries in overlapping patches leading to a + ballooning of the amount of memory used. + + NOTE For memory efficiency the best way to store patched phase diagrams is + via pickling. As this allows all the entries in overlapping patches to share + the same id in memory when unpickling. + Returns: dict[str, Any]: MSONable dictionary representation of PatchedPhaseDiagram. """ @@ -1689,7 +1689,18 @@ def as_dict(self) -> dict[str, Any]: @classmethod def from_dict(cls, dct: dict) -> Self: - """ + """Reconstruct PatchedPhaseDiagram from dictionary serialisation. + + NOTE unlike PhaseDiagram the computation involved in constructing the + PatchedPhaseDiagram is not saved on serialisation. This is done because + hierarchically calling the `PhaseDiagram.as_dict()` method would break the + link in memory between entries in overlapping patches leading to a + ballooning of the amount of memory used. + + NOTE For memory efficiency the best way to store patched phase diagrams is + via pickling. As this allows all the entries in overlapping patches to share + the same id in memory when unpickling. + Args: dct (dict): dictionary representation of PatchedPhaseDiagram. @@ -1700,9 +1711,23 @@ def from_dict(cls, dct: dict) -> Self: elements = [Element.from_dict(elem) for elem in dct["elements"]] return cls(entries, elements) + @staticmethod + def remove_redundant_spaces(spaces, keep_all_spaces=False): + if keep_all_spaces or len(spaces) <= 1: + return spaces + + # Sort spaces by size in descending order and pre-compute lengths + sorted_spaces = sorted(spaces, key=len, reverse=True) + + result = [] + for i, space_i in enumerate(sorted_spaces): + if not any(space_i.issubset(larger_space) for larger_space in sorted_spaces[:i]): + result.append(space_i) + + return result + # NOTE following methods are inherited unchanged from PhaseDiagram: # __repr__, - # as_dict, # all_entries_hulldata, # unstable_entries, # stable_entries, @@ -1772,8 +1797,6 @@ def get_equilibrium_reaction_energy(self, entry: Entry) -> float: """ return self.get_phase_separation_energy(entry, stable_only=True) - # NOTE the following functions are not implemented for PatchedPhaseDiagram - def get_decomp_and_e_above_hull( self, entry: PDEntry, @@ -1788,6 +1811,20 @@ def get_decomp_and_e_above_hull( entry=entry, allow_negative=allow_negative, check_stable=check_stable, on_error=on_error ) + def _get_pd_patch_for_space(self, space: frozenset[Element]) -> tuple[frozenset[Element], PhaseDiagram]: + """ + Args: + space (frozenset[Element]): chemical space of the form A-B-X. + + Returns: + space, PhaseDiagram for the given chemical space + """ + space_entries = [e for e, s in zip(self.qhull_entries, self._qhull_spaces) if space.issuperset(s)] + + return space, PhaseDiagram(space_entries) + + # NOTE the following functions are not implemented for PatchedPhaseDiagram + def _get_facet_and_simplex(self): """Not Implemented - See PhaseDiagram.""" raise NotImplementedError("_get_facet_and_simplex() not implemented for PatchedPhaseDiagram") @@ -1836,18 +1873,6 @@ def get_chempot_range_stability_phase(self): """Not Implemented - See PhaseDiagram.""" raise NotImplementedError("get_chempot_range_stability_phase() not implemented for PatchedPhaseDiagram") - def _get_pd_patch_for_space(self, space: frozenset[Element]) -> tuple[frozenset[Element], PhaseDiagram]: - """ - Args: - space (frozenset[Element]): chemical space of the form A-B-X. - - Returns: - space, PhaseDiagram for the given chemical space - """ - space_entries = [e for e, s in zip(self.qhull_entries, self._qhull_spaces) if space.issuperset(s)] - - return space, PhaseDiagram(space_entries) - class ReactionDiagram: """ @@ -2492,7 +2517,7 @@ def get_contour_pd_plot(self): return ax - @property # type: ignore + @property @lru_cache(1) # noqa: B019 def pd_plot_data(self): """ diff --git a/pymatgen/analysis/piezo.py b/src/pymatgen/analysis/piezo.py similarity index 99% rename from pymatgen/analysis/piezo.py rename to src/pymatgen/analysis/piezo.py index 2f168e1eef4..7a5b32ac8d0 100644 --- a/pymatgen/analysis/piezo.py +++ b/src/pymatgen/analysis/piezo.py @@ -6,7 +6,6 @@ from typing import TYPE_CHECKING import numpy as np - from pymatgen.core.tensors import Tensor if TYPE_CHECKING: diff --git a/pymatgen/analysis/piezo_sensitivity.py b/src/pymatgen/analysis/piezo_sensitivity.py similarity index 99% rename from pymatgen/analysis/piezo_sensitivity.py rename to src/pymatgen/analysis/piezo_sensitivity.py index 64e2c01bc7c..d5b4f232199 100644 --- a/pymatgen/analysis/piezo_sensitivity.py +++ b/src/pymatgen/analysis/piezo_sensitivity.py @@ -7,7 +7,6 @@ import numpy as np from monty.dev import requires - from pymatgen.core.tensors import Tensor from pymatgen.symmetry.analyzer import SpacegroupAnalyzer @@ -534,7 +533,7 @@ def get_asum_FCM(self, fcm: np.ndarray, numiter: int = 15): pastrow = 0 total = np.zeros([3, 3]) for col in range(n_sites): - total = total + X[0:3, col * 3 : col * 3 + 3] + total = total + X[:3, col * 3 : col * 3 + 3] total = total / (n_sites) for op in operations: diff --git a/pymatgen/analysis/pourbaix_diagram.py b/src/pymatgen/analysis/pourbaix_diagram.py similarity index 99% rename from pymatgen/analysis/pourbaix_diagram.py rename to src/pymatgen/analysis/pourbaix_diagram.py index 55203146f63..dad540db5fb 100644 --- a/pymatgen/analysis/pourbaix_diagram.py +++ b/src/pymatgen/analysis/pourbaix_diagram.py @@ -16,9 +16,6 @@ import numpy as np from monty.json import MontyDecoder, MSONable -from scipy.spatial import ConvexHull, HalfspaceIntersection -from scipy.special import comb - from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram from pymatgen.analysis.reaction_calculator import Reaction, ReactionError from pymatgen.core import Composition, Element @@ -29,6 +26,8 @@ from pymatgen.util.due import Doi, due from pymatgen.util.plotting import pretty_plot from pymatgen.util.string import Stringify +from scipy.spatial import ConvexHull, HalfspaceIntersection +from scipy.special import comb if TYPE_CHECKING: from typing import Any @@ -255,9 +254,7 @@ def __repr__(self): class MultiEntry(PourbaixEntry): - """ - PourbaixEntry-like object for constructing multi-elemental Pourbaix diagrams. - """ + """PourbaixEntry-like object for constructing multi-elemental Pourbaix diagrams.""" def __init__(self, entry_list, weights=None): """Initialize a MultiEntry. @@ -778,7 +775,7 @@ def get_pourbaix_domains(pourbaix_entries, limits=None): return pourbaix_domains, pourbaix_domain_vertices def find_stable_entry(self, pH, V): - """Find stable entry at a pH,V condition + """Find stable entry at a pH,V condition. Args: pH (float): pH to find stable entry diff --git a/pymatgen/analysis/prototypes.py b/src/pymatgen/analysis/prototypes.py similarity index 99% rename from pymatgen/analysis/prototypes.py rename to src/pymatgen/analysis/prototypes.py index a9cdf29c70c..6423e53170c 100644 --- a/pymatgen/analysis/prototypes.py +++ b/src/pymatgen/analysis/prototypes.py @@ -17,7 +17,6 @@ from typing import TYPE_CHECKING from monty.serialization import loadfn - from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.util.due import Doi, due diff --git a/pymatgen/analysis/quasiharmonic.py b/src/pymatgen/analysis/quasiharmonic.py similarity index 99% rename from pymatgen/analysis/quasiharmonic.py rename to src/pymatgen/analysis/quasiharmonic.py index d1c7612fecf..f7b8aa08a05 100644 --- a/pymatgen/analysis/quasiharmonic.py +++ b/src/pymatgen/analysis/quasiharmonic.py @@ -15,15 +15,14 @@ import numpy as np from monty.dev import deprecated +from pymatgen.analysis.eos import EOS, PolynomialEOS +from pymatgen.core.units import FloatWithUnit +from pymatgen.util.due import Doi, due from scipy.constants import physical_constants from scipy.integrate import quadrature from scipy.misc import derivative from scipy.optimize import minimize -from pymatgen.analysis.eos import EOS, PolynomialEOS -from pymatgen.core.units import FloatWithUnit -from pymatgen.util.due import Doi, due - __author__ = "Kiran Mathew, Brandon Bocklund" __credits__ = "Cormac Toher" diff --git a/pymatgen/analysis/quasirrho.py b/src/pymatgen/analysis/quasirrho.py similarity index 97% rename from pymatgen/analysis/quasirrho.py rename to src/pymatgen/analysis/quasirrho.py index b7be8bb64c1..5846f19339b 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/src/pymatgen/analysis/quasirrho.py @@ -5,7 +5,7 @@ """ A module to calculate free energies using the Quasi-Rigid Rotor Harmonic Oscillator approximation. Modified from a script by Steven Wheeler. -See: Grimme, S. Chem. Eur. J. 2012, 18, 9955 +See: Grimme, S. Chem. Eur. J. 2012, 18, 9955. """ from __future__ import annotations @@ -15,16 +15,14 @@ import numpy as np import scipy.constants as const - from pymatgen.core.units import kb as kb_ev from pymatgen.util.due import Doi, due if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.core import Molecule from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.qchem.outputs import QCOutput + from typing_extensions import Self __author__ = "Alex Epstein" __copyright__ = "Copyright 2020, The Materials Project" @@ -49,7 +47,7 @@ def get_avg_mom_inertia(mol): """ - Calculate the average moment of inertia of a molecule + Calculate the average moment of inertia of a molecule. Args: mol (Molecule): Pymatgen Molecule @@ -137,7 +135,7 @@ def __init__( def from_gaussian_output(cls, output: GaussianOutput, **kwargs) -> Self: """ Args: - output (GaussianOutput): Pymatgen GaussianOutput object + output (GaussianOutput): Pymatgen GaussianOutput object. Returns: QuasiRRHO: QuasiRRHO class instantiated from a Gaussian Output @@ -152,7 +150,7 @@ def from_gaussian_output(cls, output: GaussianOutput, **kwargs) -> Self: def from_qc_output(cls, output: QCOutput, **kwargs) -> Self: """ Args: - output (QCOutput): Pymatgen QCOutput object + output (QCOutput): Pymatgen QCOutput object. Returns: QuasiRRHO: QuasiRRHO class instantiated from a QChem Output @@ -175,7 +173,7 @@ def _get_quasirrho_thermo( self, mol: Molecule, mult: int, sigma_r: int, frequencies: list[float], elec_energy: float ) -> None: """ - Calculate Quasi-RRHO thermochemistry + Calculate Quasi-RRHO thermochemistry. Args: mol (Molecule): Pymatgen molecule diff --git a/pymatgen/analysis/reaction_calculator.py b/src/pymatgen/analysis/reaction_calculator.py similarity index 99% rename from pymatgen/analysis/reaction_calculator.py rename to src/pymatgen/analysis/reaction_calculator.py index a98876d6615..638e9189318 100644 --- a/pymatgen/analysis/reaction_calculator.py +++ b/src/pymatgen/analysis/reaction_calculator.py @@ -10,18 +10,16 @@ import numpy as np from monty.fractions import gcd_float from monty.json import MontyDecoder, MSONable -from uncertainties import ufloat - from pymatgen.core.composition import Composition from pymatgen.entries.computed_entries import ComputedEntry +from uncertainties import ufloat if TYPE_CHECKING: from collections.abc import Mapping - from typing_extensions import Self - from pymatgen.core import Element, Species from pymatgen.util.typing import CompositionLike + from typing_extensions import Self __author__ = "Shyue Ping Ong, Anubhav Jain" __copyright__ = "Copyright 2011, The Materials Project" @@ -283,8 +281,8 @@ def from_str(cls, rxn_str: str) -> Self: def get_comp_amt(comp_str): return { - Composition(m.group(2)): float(m.group(1) or 1) - for m in re.finditer(r"([\d\.]*(?:[eE]-?[\d\.]+)?)\s*([A-Z][\w\.\(\)]*)", comp_str) + Composition(match[2]): float(match[1] or 1) + for match in re.finditer(r"([\d\.]*(?:[eE]-?[\d\.]+)?)\s*([A-Z][\w\.\(\)]*)", comp_str) } return BalancedReaction(get_comp_amt(rct_str), get_comp_amt(prod_str)) diff --git a/pymatgen/analysis/solar/__init__.py b/src/pymatgen/analysis/solar/__init__.py similarity index 100% rename from pymatgen/analysis/solar/__init__.py rename to src/pymatgen/analysis/solar/__init__.py diff --git a/pymatgen/analysis/solar/am1.5G.dat b/src/pymatgen/analysis/solar/am1.5G.dat similarity index 100% rename from pymatgen/analysis/solar/am1.5G.dat rename to src/pymatgen/analysis/solar/am1.5G.dat diff --git a/pymatgen/analysis/solar/slme.py b/src/pymatgen/analysis/solar/slme.py similarity index 96% rename from pymatgen/analysis/solar/slme.py rename to src/pymatgen/analysis/solar/slme.py index dcc7065c421..976ef49b701 100644 --- a/pymatgen/analysis/solar/slme.py +++ b/src/pymatgen/analysis/solar/slme.py @@ -17,11 +17,14 @@ import numpy as np from scipy import constants from scipy.constants import physical_constants, speed_of_light -from scipy.integrate import simps -from scipy.interpolate import interp1d +try: + from scipy.integrate import simpson +except ImportError: + from scipy.integrate import simps as simpson from pymatgen.io.vasp.outputs import Vasprun from pymatgen.util.due import Doi, due +from scipy.interpolate import interp1d due.cite( Doi("10.1021/acs.chemmater.9b02166"), @@ -187,7 +190,7 @@ def slme( solar_spectra_photon_flux = solar_spectra_irradiance * (solar_spectra_wavelength_meters / (h * c)) # Calculation of total solar power incoming - power_in = simps(solar_spectra_irradiance, solar_spectra_wavelength) + power_in = simpson(solar_spectra_irradiance, x=solar_spectra_wavelength) # calculation of blackbody irradiance spectra # units of W/(m**3), different than solar_spectra_irradiance!!! (This @@ -232,15 +235,15 @@ def slme( J_0_r = ( e * np.pi - * simps( + * simpson( blackbody_photon_flux * absorbed_by_wavelength, - solar_spectra_wavelength_meters, + x=solar_spectra_wavelength_meters, ) ) J_0 = J_0_r / fr - J_sc = e * simps(solar_spectra_photon_flux * absorbed_by_wavelength, solar_spectra_wavelength) + J_sc = e * simpson(solar_spectra_photon_flux * absorbed_by_wavelength, x=solar_spectra_wavelength) def J(V): return J_sc - J_0 * (np.exp(e * V / (k * temperature)) - 1.0) diff --git a/pymatgen/analysis/structure_analyzer.py b/src/pymatgen/analysis/structure_analyzer.py similarity index 99% rename from pymatgen/analysis/structure_analyzer.py rename to src/pymatgen/analysis/structure_analyzer.py index 45bc60da98d..a044216444a 100644 --- a/pymatgen/analysis/structure_analyzer.py +++ b/src/pymatgen/analysis/structure_analyzer.py @@ -10,11 +10,10 @@ import matplotlib.pyplot as plt import numpy as np -from scipy.spatial import Voronoi - from pymatgen.analysis.local_env import JmolNN, VoronoiNN from pymatgen.core import Composition, Element, PeriodicSite, Species from pymatgen.symmetry.analyzer import SpacegroupAnalyzer +from scipy.spatial import Voronoi if TYPE_CHECKING: from pymatgen.core import Structure diff --git a/pymatgen/analysis/structure_matcher.py b/src/pymatgen/analysis/structure_matcher.py similarity index 99% rename from pymatgen/analysis/structure_matcher.py rename to src/pymatgen/analysis/structure_matcher.py index a2640c127ee..7a2650bef71 100644 --- a/pymatgen/analysis/structure_matcher.py +++ b/src/pymatgen/analysis/structure_matcher.py @@ -8,7 +8,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.core import Composition, Lattice, Structure, get_el_sp from pymatgen.optimization.linear_assignment import LinearAssignment from pymatgen.util.coord import lattice_points_in_supercell @@ -18,9 +17,8 @@ from collections.abc import Mapping, Sequence from typing import Literal - from typing_extensions import Self - from pymatgen.util.typing import SpeciesLike + from typing_extensions import Self __author__ = "William Davidson Richards, Stephen Dacek, Shyue Ping Ong" __copyright__ = "Copyright 2011, The Materials Project" @@ -81,7 +79,7 @@ def get_hash(self, composition): def from_dict(cls, dct: dict) -> Self: """ Args: - dct (dict): Dict representation + dct (dict): Dict representation. Returns: Comparator. @@ -100,7 +98,7 @@ def from_dict(cls, dct: dict) -> Self: raise ValueError("Invalid Comparator dict") def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "version": __version__, "@module": type(self).__module__, @@ -834,7 +832,7 @@ def s_hash(s): return all_groups def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "version": __version__, "@module": type(self).__module__, @@ -855,7 +853,7 @@ def as_dict(self): def from_dict(cls, dct: dict) -> Self: """ Args: - dct (dict): Dict representation + dct (dict): Dict representation. Returns: StructureMatcher @@ -899,7 +897,7 @@ def _anonymous_match( List of (mapping, match) """ if not isinstance(self._comparator, SpeciesComparator): - raise ValueError("Anonymous fitting currently requires SpeciesComparator") + raise TypeError("Anonymous fitting currently requires SpeciesComparator") # check that species lists are comparable sp1 = struct1.elements diff --git a/pymatgen/analysis/structure_prediction/DLS_bond_params.yaml b/src/pymatgen/analysis/structure_prediction/DLS_bond_params.yaml similarity index 100% rename from pymatgen/analysis/structure_prediction/DLS_bond_params.yaml rename to src/pymatgen/analysis/structure_prediction/DLS_bond_params.yaml diff --git a/pymatgen/analysis/structure_prediction/__init__.py b/src/pymatgen/analysis/structure_prediction/__init__.py similarity index 100% rename from pymatgen/analysis/structure_prediction/__init__.py rename to src/pymatgen/analysis/structure_prediction/__init__.py diff --git a/pymatgen/analysis/structure_prediction/data/lambda.json b/src/pymatgen/analysis/structure_prediction/data/lambda.json similarity index 100% rename from pymatgen/analysis/structure_prediction/data/lambda.json rename to src/pymatgen/analysis/structure_prediction/data/lambda.json diff --git a/pymatgen/analysis/structure_prediction/data/pair_correlation.json b/src/pymatgen/analysis/structure_prediction/data/pair_correlation.json similarity index 100% rename from pymatgen/analysis/structure_prediction/data/pair_correlation.json rename to src/pymatgen/analysis/structure_prediction/data/pair_correlation.json diff --git a/pymatgen/analysis/structure_prediction/dopant_predictor.py b/src/pymatgen/analysis/structure_prediction/dopant_predictor.py similarity index 99% rename from pymatgen/analysis/structure_prediction/dopant_predictor.py rename to src/pymatgen/analysis/structure_prediction/dopant_predictor.py index e21603e13ee..dcc750ec9f3 100644 --- a/pymatgen/analysis/structure_prediction/dopant_predictor.py +++ b/src/pymatgen/analysis/structure_prediction/dopant_predictor.py @@ -5,7 +5,6 @@ import warnings import numpy as np - from pymatgen.analysis.structure_prediction.substitution_probability import SubstitutionPredictor from pymatgen.core import Element, Species diff --git a/pymatgen/analysis/structure_prediction/substitution_probability.py b/src/pymatgen/analysis/structure_prediction/substitution_probability.py similarity index 99% rename from pymatgen/analysis/structure_prediction/substitution_probability.py rename to src/pymatgen/analysis/structure_prediction/substitution_probability.py index bcdcd8598e5..75720ce9419 100644 --- a/pymatgen/analysis/structure_prediction/substitution_probability.py +++ b/src/pymatgen/analysis/structure_prediction/substitution_probability.py @@ -1,6 +1,4 @@ -""" -This module provides classes for representing species substitution probabilities. -""" +"""This module provides classes for representing species substitution probabilities.""" from __future__ import annotations @@ -15,7 +13,6 @@ from typing import TYPE_CHECKING from monty.design_patterns import cached_class - from pymatgen.core import Species, get_el_sp from pymatgen.util.due import Doi, due diff --git a/pymatgen/analysis/structure_prediction/substitutor.py b/src/pymatgen/analysis/structure_prediction/substitutor.py similarity index 99% rename from pymatgen/analysis/structure_prediction/substitutor.py rename to src/pymatgen/analysis/structure_prediction/substitutor.py index 2921355d637..c36df98f030 100644 --- a/pymatgen/analysis/structure_prediction/substitutor.py +++ b/src/pymatgen/analysis/structure_prediction/substitutor.py @@ -9,7 +9,6 @@ from typing import TYPE_CHECKING from monty.json import MSONable - from pymatgen.alchemy.filters import RemoveDuplicatesFilter, RemoveExistingFilter from pymatgen.alchemy.materials import TransformedStructure from pymatgen.alchemy.transmuters import StandardTransmuter diff --git a/pymatgen/analysis/structure_prediction/volume_predictor.py b/src/pymatgen/analysis/structure_prediction/volume_predictor.py similarity index 99% rename from pymatgen/analysis/structure_prediction/volume_predictor.py rename to src/pymatgen/analysis/structure_prediction/volume_predictor.py index dd749e8416a..5ce74b652f4 100644 --- a/pymatgen/analysis/structure_prediction/volume_predictor.py +++ b/src/pymatgen/analysis/structure_prediction/volume_predictor.py @@ -7,7 +7,6 @@ import numpy as np from monty.serialization import loadfn - from pymatgen.analysis.bond_valence import BVAnalyzer from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core import Structure diff --git a/pymatgen/analysis/surface_analysis.py b/src/pymatgen/analysis/surface_analysis.py similarity index 99% rename from pymatgen/analysis/surface_analysis.py rename to src/pymatgen/analysis/surface_analysis.py index c251e44c479..f395f90afd0 100644 --- a/pymatgen/analysis/surface_analysis.py +++ b/src/pymatgen/analysis/surface_analysis.py @@ -20,7 +20,7 @@ Computational Materials, 3(1), 14. https://doi.org/10.1038/s41524-017-0017-z -TODO: +Todo: - Still assumes individual elements have their own chempots in a molecular adsorbate instead of considering a single chempot for a single molecular adsorbate. E.g. for an OH @@ -42,9 +42,6 @@ import matplotlib.pyplot as plt import numpy as np -from sympy import Symbol -from sympy.solvers import linsolve, solve - from pymatgen.analysis.wulff import WulffShape from pymatgen.core import Structure from pymatgen.core.composition import Composition @@ -54,11 +51,12 @@ from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.due import Doi, due from pymatgen.util.plotting import pretty_plot +from sympy import Symbol +from sympy.solvers import linsolve, solve if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.util.typing import Tuple3Ints + from typing_extensions import Self EV_PER_ANG2_TO_JOULES_PER_M2 = 16.0217656 @@ -872,10 +870,10 @@ def chempot_vs_gamma_plot_one( mark = "--" if ucell_comp != clean_comp else "-" delu_dict = self.set_all_variables(delu_dict, delu_default) - delu_dict[ref_delu] = chempot_range[0] # type: ignore + delu_dict[ref_delu] = chempot_range[0] # type: ignore[index] gamma_min = self.as_coeffs_dict[entry] gamma_min = gamma_min if type(gamma_min).__name__ == "float" else sub_chempots(gamma_min, delu_dict) - delu_dict[ref_delu] = chempot_range[1] # type: ignore + delu_dict[ref_delu] = chempot_range[1] # type: ignore[index] gamma_max = self.as_coeffs_dict[entry] gamma_max = gamma_max if type(gamma_max).__name__ == "float" else sub_chempots(gamma_max, delu_dict) gamma_range = [gamma_min, gamma_max] @@ -1465,7 +1463,7 @@ def get_locpot_along_slab_plot(self, label_energies=True, plt=None, label_fontsi def get_labels(self, plt, label_fontsize=10): """ - Handles the optional labelling of the plot with relevant quantities + Handles the optional labelling of the plot with relevant quantities. Args: plt (plt): Plot of the locpot vs c axis diff --git a/pymatgen/analysis/thermochemistry.py b/src/pymatgen/analysis/thermochemistry.py similarity index 100% rename from pymatgen/analysis/thermochemistry.py rename to src/pymatgen/analysis/thermochemistry.py diff --git a/pymatgen/analysis/topological/__init__.py b/src/pymatgen/analysis/topological/__init__.py similarity index 100% rename from pymatgen/analysis/topological/__init__.py rename to src/pymatgen/analysis/topological/__init__.py diff --git a/pymatgen/analysis/topological/spillage.py b/src/pymatgen/analysis/topological/spillage.py similarity index 99% rename from pymatgen/analysis/topological/spillage.py rename to src/pymatgen/analysis/topological/spillage.py index d0da47ccfe1..e088b98553b 100644 --- a/pymatgen/analysis/topological/spillage.py +++ b/src/pymatgen/analysis/topological/spillage.py @@ -8,7 +8,6 @@ from __future__ import annotations import numpy as np - from pymatgen.io.vasp.outputs import Wavecar diff --git a/pymatgen/analysis/transition_state.py b/src/pymatgen/analysis/transition_state.py similarity index 99% rename from pymatgen/analysis/transition_state.py rename to src/pymatgen/analysis/transition_state.py index 5dbbe1fbb54..e7c6d9b2924 100644 --- a/pymatgen/analysis/transition_state.py +++ b/src/pymatgen/analysis/transition_state.py @@ -15,12 +15,11 @@ import matplotlib.pyplot as plt import numpy as np from monty.json import MSONable, jsanitize -from scipy.interpolate import CubicSpline - from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core import Structure from pymatgen.io.vasp import Outcar from pymatgen.util.plotting import pretty_plot +from scipy.interpolate import CubicSpline if TYPE_CHECKING: from typing_extensions import Self diff --git a/pymatgen/analysis/vesta_cutoffs.yaml b/src/pymatgen/analysis/vesta_cutoffs.yaml similarity index 100% rename from pymatgen/analysis/vesta_cutoffs.yaml rename to src/pymatgen/analysis/vesta_cutoffs.yaml diff --git a/pymatgen/analysis/wulff.py b/src/pymatgen/analysis/wulff.py similarity index 99% rename from pymatgen/analysis/wulff.py rename to src/pymatgen/analysis/wulff.py index d5365068fe8..23a6986d87f 100644 --- a/pymatgen/analysis/wulff.py +++ b/src/pymatgen/analysis/wulff.py @@ -25,11 +25,10 @@ import matplotlib.pyplot as plt import numpy as np import plotly.graph_objects as go -from scipy.spatial import ConvexHull - from pymatgen.core.structure import Structure from pymatgen.util.coord import get_angle from pymatgen.util.string import unicodeify_spacegroup +from scipy.spatial import ConvexHull if TYPE_CHECKING: from pymatgen.core.lattice import Lattice @@ -46,7 +45,7 @@ def hkl_tuple_to_str(hkl): """ - Prepare for display on plots "(hkl)" for surfaces + Prepare for display on plots "(hkl)" for surfaces. Args: hkl: in the form of [h, k, l] or (h, k, l). @@ -268,7 +267,6 @@ def _get_colors(self, color_set, alpha, off_color, custom_colors=None): Returns: tuple: color_list, color_proxy, color_proxy_on_wulff, miller_on_wulff, e_surf_on_wulff_list """ - color_list = [off_color] * len(self.hkl_list) color_proxy_on_wulff = [] miller_on_wulff = [] @@ -311,7 +309,7 @@ def show(self, *args, **kwargs): *args: Passed to get_plot. **kwargs: Passed to get_plot. """ - self.get_plot(*args, **kwargs).show() + self.get_plot(*args, **kwargs).get_figure().show() def get_line_in_facet(self, facet): """Get the sorted pts in a facet used to draw a line.""" diff --git a/pymatgen/analysis/xas/__init__.py b/src/pymatgen/analysis/xas/__init__.py similarity index 100% rename from pymatgen/analysis/xas/__init__.py rename to src/pymatgen/analysis/xas/__init__.py diff --git a/pymatgen/analysis/xas/spectrum.py b/src/pymatgen/analysis/xas/spectrum.py similarity index 99% rename from pymatgen/analysis/xas/spectrum.py rename to src/pymatgen/analysis/xas/spectrum.py index 007c4596642..97af8b85282 100644 --- a/pymatgen/analysis/xas/spectrum.py +++ b/src/pymatgen/analysis/xas/spectrum.py @@ -7,11 +7,10 @@ from typing import TYPE_CHECKING import numpy as np -from scipy.interpolate import interp1d - from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core.spectrum import Spectrum from pymatgen.symmetry.analyzer import SpacegroupAnalyzer +from scipy.interpolate import interp1d if TYPE_CHECKING: from typing import Literal diff --git a/pymatgen/analysis/xps.py b/src/pymatgen/analysis/xps.py similarity index 99% rename from pymatgen/analysis/xps.py rename to src/pymatgen/analysis/xps.py index 1aca37a1eee..4e9acff9540 100644 --- a/pymatgen/analysis/xps.py +++ b/src/pymatgen/analysis/xps.py @@ -25,15 +25,13 @@ import numpy as np import pandas as pd - from pymatgen.core import Element from pymatgen.core.spectrum import Spectrum from pymatgen.util.due import Doi, due if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.electronic_structure.dos import CompleteDos + from typing_extensions import Self due.cite( diff --git a/pymatgen/apps/__init__.py b/src/pymatgen/apps/__init__.py similarity index 100% rename from pymatgen/apps/__init__.py rename to src/pymatgen/apps/__init__.py diff --git a/pymatgen/apps/battery/__init__.py b/src/pymatgen/apps/battery/__init__.py similarity index 100% rename from pymatgen/apps/battery/__init__.py rename to src/pymatgen/apps/battery/__init__.py diff --git a/pymatgen/apps/battery/analyzer.py b/src/pymatgen/apps/battery/analyzer.py similarity index 99% rename from pymatgen/apps/battery/analyzer.py rename to src/pymatgen/apps/battery/analyzer.py index 2543b44da92..3d08e147c35 100644 --- a/pymatgen/apps/battery/analyzer.py +++ b/src/pymatgen/apps/battery/analyzer.py @@ -6,7 +6,6 @@ from collections import defaultdict import scipy.constants as const - from pymatgen.core import Composition, Element, Species __author__ = "Anubhav Jain" diff --git a/pymatgen/apps/battery/battery_abc.py b/src/pymatgen/apps/battery/battery_abc.py similarity index 99% rename from pymatgen/apps/battery/battery_abc.py rename to src/pymatgen/apps/battery/battery_abc.py index 78f4d984498..8465f85445f 100644 --- a/pymatgen/apps/battery/battery_abc.py +++ b/src/pymatgen/apps/battery/battery_abc.py @@ -12,9 +12,8 @@ from typing import TYPE_CHECKING from monty.json import MSONable -from scipy.constants import N_A - from pymatgen.core import Composition, Element +from scipy.constants import N_A if TYPE_CHECKING: from pymatgen.entries.computed_entries import ComputedEntry diff --git a/pymatgen/apps/battery/conversion_battery.py b/src/pymatgen/apps/battery/conversion_battery.py similarity index 99% rename from pymatgen/apps/battery/conversion_battery.py rename to src/pymatgen/apps/battery/conversion_battery.py index b84da63efd6..ee274bcd40d 100644 --- a/pymatgen/apps/battery/conversion_battery.py +++ b/src/pymatgen/apps/battery/conversion_battery.py @@ -5,20 +5,18 @@ from dataclasses import dataclass from typing import TYPE_CHECKING -from scipy.constants import N_A - from pymatgen.analysis.phase_diagram import PhaseDiagram from pymatgen.analysis.reaction_calculator import BalancedReaction from pymatgen.apps.battery.battery_abc import AbstractElectrode, AbstractVoltagePair from pymatgen.core import Composition, Element from pymatgen.core.units import Charge, Time +from scipy.constants import N_A if TYPE_CHECKING: from collections.abc import Iterable - from typing_extensions import Self - from pymatgen.entries.computed_entries import ComputedEntry + from typing_extensions import Self @dataclass diff --git a/pymatgen/apps/battery/insertion_battery.py b/src/pymatgen/apps/battery/insertion_battery.py similarity index 99% rename from pymatgen/apps/battery/insertion_battery.py rename to src/pymatgen/apps/battery/insertion_battery.py index 76631f53368..5f073fbc916 100644 --- a/pymatgen/apps/battery/insertion_battery.py +++ b/src/pymatgen/apps/battery/insertion_battery.py @@ -9,13 +9,12 @@ from typing import TYPE_CHECKING from monty.json import MontyDecoder -from scipy.constants import N_A - from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram from pymatgen.apps.battery.battery_abc import AbstractElectrode, AbstractVoltagePair from pymatgen.core import Composition, Element from pymatgen.core.units import Charge, Time from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry +from scipy.constants import N_A if TYPE_CHECKING: from collections.abc import Iterable diff --git a/pymatgen/apps/battery/plotter.py b/src/pymatgen/apps/battery/plotter.py similarity index 99% rename from pymatgen/apps/battery/plotter.py rename to src/pymatgen/apps/battery/plotter.py index f8725ef25e6..150f413784b 100644 --- a/pymatgen/apps/battery/plotter.py +++ b/src/pymatgen/apps/battery/plotter.py @@ -6,7 +6,6 @@ import matplotlib.pyplot as plt import plotly.graph_objects as go - from pymatgen.util.plotting import pretty_plot if TYPE_CHECKING: diff --git a/pymatgen/apps/borg/__init__.py b/src/pymatgen/apps/borg/__init__.py similarity index 100% rename from pymatgen/apps/borg/__init__.py rename to src/pymatgen/apps/borg/__init__.py diff --git a/pymatgen/apps/borg/hive.py b/src/pymatgen/apps/borg/hive.py similarity index 99% rename from pymatgen/apps/borg/hive.py rename to src/pymatgen/apps/borg/hive.py index a90380d0dee..87aaeeb2500 100644 --- a/pymatgen/apps/borg/hive.py +++ b/src/pymatgen/apps/borg/hive.py @@ -12,7 +12,6 @@ from monty.io import zopen from monty.json import MSONable - from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.vasp.inputs import Incar, Poscar, Potcar diff --git a/pymatgen/apps/borg/queen.py b/src/pymatgen/apps/borg/queen.py similarity index 100% rename from pymatgen/apps/borg/queen.py rename to src/pymatgen/apps/borg/queen.py diff --git a/pymatgen/cli/__init__.py b/src/pymatgen/cli/__init__.py similarity index 100% rename from pymatgen/cli/__init__.py rename to src/pymatgen/cli/__init__.py diff --git a/pymatgen/cli/feff_plot_cross_section.py b/src/pymatgen/cli/feff_plot_cross_section.py similarity index 99% rename from pymatgen/cli/feff_plot_cross_section.py rename to src/pymatgen/cli/feff_plot_cross_section.py index a9a59f3a650..2bf9d89fe23 100755 --- a/pymatgen/cli/feff_plot_cross_section.py +++ b/src/pymatgen/cli/feff_plot_cross_section.py @@ -7,7 +7,6 @@ import argparse import matplotlib.pyplot as plt - from pymatgen.io.feff.outputs import Xmu from pymatgen.util.plotting import pretty_plot diff --git a/pymatgen/cli/feff_plot_dos.py b/src/pymatgen/cli/feff_plot_dos.py similarity index 100% rename from pymatgen/cli/feff_plot_dos.py rename to src/pymatgen/cli/feff_plot_dos.py diff --git a/pymatgen/cli/get_environment.py b/src/pymatgen/cli/get_environment.py similarity index 100% rename from pymatgen/cli/get_environment.py rename to src/pymatgen/cli/get_environment.py diff --git a/pymatgen/cli/pmg.py b/src/pymatgen/cli/pmg.py similarity index 99% rename from pymatgen/cli/pmg.py rename to src/pymatgen/cli/pmg.py index 491d4ab2c11..1ee6a93ed7e 100755 --- a/pymatgen/cli/pmg.py +++ b/src/pymatgen/cli/pmg.py @@ -7,8 +7,6 @@ import argparse import itertools -from tabulate import tabulate, tabulate_formats - from pymatgen.cli.pmg_analyze import analyze from pymatgen.cli.pmg_config import configure_pmg from pymatgen.cli.pmg_plot import plot @@ -17,6 +15,7 @@ from pymatgen.core import SETTINGS from pymatgen.core.structure import Structure from pymatgen.io.vasp import Incar, Potcar +from tabulate import tabulate, tabulate_formats def parse_view(args): diff --git a/pymatgen/cli/pmg_analyze.py b/src/pymatgen/cli/pmg_analyze.py similarity index 97% rename from pymatgen/cli/pmg_analyze.py rename to src/pymatgen/cli/pmg_analyze.py index 132e447b8c3..4db3fbcb2f6 100644 --- a/pymatgen/cli/pmg_analyze.py +++ b/src/pymatgen/cli/pmg_analyze.py @@ -7,11 +7,10 @@ import os import re -from tabulate import tabulate - from pymatgen.apps.borg.hive import SimpleVaspToComputedEntryDrone, VaspToComputedEntryDrone from pymatgen.apps.borg.queen import BorgQueen from pymatgen.io.vasp import Outcar +from tabulate import tabulate __author__ = "Shyue Ping Ong" __copyright__ = "Copyright 2012, The Materials Project" @@ -91,11 +90,11 @@ def get_energies(rootdir, reanalyze, verbose, quick, sort, fmt): return 0 -def get_magnetizations(dir: str, ion_list: list[int]): +def get_magnetizations(dirc: str, ion_list: list[int]): """Get magnetization info from OUTCARs. Args: - dir (str): Directory name + dirc (str): Directory name ion_list (list[int]): List of ions to obtain magnetization information for. Returns: @@ -103,7 +102,7 @@ def get_magnetizations(dir: str, ion_list: list[int]): """ data = [] max_row = 0 - for parent, _subdirs, files in os.walk(dir): + for parent, _subdirs, files in os.walk(dirc): for file in files: if re.match(r"OUTCAR*", file): try: diff --git a/pymatgen/cli/pmg_config.py b/src/pymatgen/cli/pmg_config.py similarity index 96% rename from pymatgen/cli/pmg_config.py rename to src/pymatgen/cli/pmg_config.py index d3c135b7c71..8a0f4a04317 100755 --- a/pymatgen/cli/pmg_config.py +++ b/src/pymatgen/cli/pmg_config.py @@ -13,11 +13,10 @@ from monty.json import jsanitize from monty.serialization import dumpfn, loadfn -from ruamel import yaml - from pymatgen.core import OLD_SETTINGS_FILE, SETTINGS_FILE, Element from pymatgen.io.cp2k.inputs import GaussianTypeOrbitalBasisSet, GthPotential from pymatgen.io.cp2k.utils import chunk +from ruamel import yaml if TYPE_CHECKING: from argparse import Namespace @@ -26,7 +25,7 @@ def setup_cp2k_data(cp2k_data_dirs: list[str]) -> None: """Setup CP2K basis and potential data directory.""" - data_dir, target_dir = (os.path.abspath(dir) for dir in cp2k_data_dirs) + data_dir, target_dir = (os.path.abspath(dirc) for dirc in cp2k_data_dirs) try: os.mkdir(target_dir) except OSError: @@ -74,9 +73,7 @@ def setup_cp2k_data(cp2k_data_dirs: list[str]) -> None: try: basis = GaussianTypeOrbitalBasisSet.from_str(chk) basis.filename = os.path.basename(basis_file) - settings[basis.element.symbol]["basis_sets"][basis.get_hash()] = jsanitize( # type: ignore - basis, strict=True - ) + settings[basis.element.symbol]["basis_sets"][basis.get_hash()] = jsanitize(basis, strict=True) # type: ignore[union-attr] except ValueError: # Chunk was readable, but the element is not pmg recognized continue @@ -146,17 +143,17 @@ def setup_potcars(potcar_dirs: list[str]): shutil.copy(fname, dest) ext = fname.split(".")[-1] if ext.upper() in ["Z", "GZ"]: - with subprocess.Popen(["gunzip", dest]) as p: - p.communicate() + with subprocess.Popen(["gunzip", dest]) as process: + process.communicate() elif ext.upper() == "BZ2": - with subprocess.Popen(["bunzip2", dest]) as p: - p.communicate() + with subprocess.Popen(["bunzip2", dest]) as process: + process.communicate() if subdir == "Osmium": subdir = "Os" dest = os.path.join(base_dir, f"POTCAR.{subdir}") shutil.move(f"{base_dir}/POTCAR", dest) - with subprocess.Popen(["gzip", "-f", dest]) as p: - p.communicate() + with subprocess.Popen(["gzip", "-f", dest]) as process: + process.communicate() except Exception as exc: print(f"An error has occurred. Message is {exc}. Trying to continue... ") @@ -273,7 +270,7 @@ def add_config_var(tokens: list[str], backup_suffix: str) -> None: print(f"Existing {rc_path} backed up to {rc_path}{backup_suffix}") dct = loadfn(rc_path) special_vals = {"true": True, "false": False, "none": None, "null": None} - for key, val in zip(tokens[0::2], tokens[1::2]): + for key, val in zip(tokens[::2], tokens[1::2]): dct[key] = special_vals.get(val.lower(), val) dumpfn(dct, rc_path) print(f"New {rc_path} written!") diff --git a/pymatgen/cli/pmg_plot.py b/src/pymatgen/cli/pmg_plot.py similarity index 99% rename from pymatgen/cli/pmg_plot.py rename to src/pymatgen/cli/pmg_plot.py index 89d0fa269ae..56e7d629660 100755 --- a/pymatgen/cli/pmg_plot.py +++ b/src/pymatgen/cli/pmg_plot.py @@ -5,7 +5,6 @@ from __future__ import annotations import matplotlib.pyplot as plt - from pymatgen.analysis.diffraction.xrd import XRDCalculator from pymatgen.core.structure import Structure from pymatgen.electronic_structure.plotter import DosPlotter diff --git a/pymatgen/cli/pmg_potcar.py b/src/pymatgen/cli/pmg_potcar.py similarity index 100% rename from pymatgen/cli/pmg_potcar.py rename to src/pymatgen/cli/pmg_potcar.py diff --git a/pymatgen/cli/pmg_structure.py b/src/pymatgen/cli/pmg_structure.py similarity index 99% rename from pymatgen/cli/pmg_structure.py rename to src/pymatgen/cli/pmg_structure.py index 3f85040fede..b8046b699ce 100755 --- a/pymatgen/cli/pmg_structure.py +++ b/src/pymatgen/cli/pmg_structure.py @@ -4,11 +4,10 @@ from __future__ import annotations -from tabulate import tabulate - from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher from pymatgen.core.structure import Structure from pymatgen.symmetry.analyzer import SpacegroupAnalyzer +from tabulate import tabulate __author__ = "Shyue Ping Ong" __copyright__ = "Copyright 2012, The Materials Project" diff --git a/pymatgen/command_line/OxideTersoffPotentials b/src/pymatgen/command_line/OxideTersoffPotentials similarity index 100% rename from pymatgen/command_line/OxideTersoffPotentials rename to src/pymatgen/command_line/OxideTersoffPotentials diff --git a/pymatgen/command_line/__init__.py b/src/pymatgen/command_line/__init__.py similarity index 100% rename from pymatgen/command_line/__init__.py rename to src/pymatgen/command_line/__init__.py diff --git a/pymatgen/command_line/bader_caller.py b/src/pymatgen/command_line/bader_caller.py similarity index 98% rename from pymatgen/command_line/bader_caller.py rename to src/pymatgen/command_line/bader_caller.py index 27bca78353b..c85baf861ed 100644 --- a/pymatgen/command_line/bader_caller.py +++ b/src/pymatgen/command_line/bader_caller.py @@ -17,7 +17,6 @@ import shutil import subprocess import warnings -from datetime import datetime from glob import glob from pathlib import Path from shutil import which @@ -28,7 +27,6 @@ from monty.dev import deprecated from monty.shutil import decompress_file from monty.tempfile import ScratchDir - from pymatgen.io.common import VolumetricData from pymatgen.io.vasp.inputs import Potcar from pymatgen.io.vasp.outputs import Chgcar @@ -36,9 +34,8 @@ if TYPE_CHECKING: from typing import Any - from typing_extensions import Self - from pymatgen.core import Structure + from typing_extensions import Self __author__ = "shyuepingong" __version__ = "0.1" @@ -244,13 +241,6 @@ def _parse_atomic_densities(self) -> list[dict]: "shift" is the shift used to center the atomic charge density, and "dim" is the dimension of the original charge density. """ - # Deprecation tracker - if ( - datetime(2025, 2, 26) < datetime.now() - and os.getenv("CI") - and os.getenv("GITHUB_REPOSITORY") == "materialsproject/pymatgen" - ): - raise RuntimeError("This method should have been removed, see #3656.") def slice_from_center(data: np.ndarray, x_width: int, y_width: int, z_width: int) -> np.ndarray: """Slices a central window from the data array.""" diff --git a/pymatgen/command_line/bush.lib b/src/pymatgen/command_line/bush.lib similarity index 100% rename from pymatgen/command_line/bush.lib rename to src/pymatgen/command_line/bush.lib diff --git a/pymatgen/command_line/chargemol_caller.py b/src/pymatgen/command_line/chargemol_caller.py similarity index 99% rename from pymatgen/command_line/chargemol_caller.py rename to src/pymatgen/command_line/chargemol_caller.py index d9b17a27404..a22e4b345a0 100644 --- a/pymatgen/command_line/chargemol_caller.py +++ b/src/pymatgen/command_line/chargemol_caller.py @@ -51,7 +51,6 @@ import numpy as np from monty.tempfile import ScratchDir - from pymatgen.core import Element from pymatgen.io.vasp.inputs import Potcar from pymatgen.io.vasp.outputs import Chgcar diff --git a/pymatgen/command_line/critic2_caller.py b/src/pymatgen/command_line/critic2_caller.py similarity index 99% rename from pymatgen/command_line/critic2_caller.py rename to src/pymatgen/command_line/critic2_caller.py index 6d43959576d..9855345d7ff 100644 --- a/pymatgen/command_line/critic2_caller.py +++ b/src/pymatgen/command_line/critic2_caller.py @@ -52,18 +52,16 @@ from monty.json import MSONable from monty.serialization import loadfn from monty.tempfile import ScratchDir -from scipy.spatial import KDTree - from pymatgen.analysis.graphs import StructureGraph from pymatgen.core import DummySpecies from pymatgen.io.vasp.inputs import Potcar from pymatgen.io.vasp.outputs import Chgcar, VolumetricData from pymatgen.util.due import Doi, due +from scipy.spatial import KDTree if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.core import Structure + from typing_extensions import Self logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__) @@ -351,7 +349,7 @@ class CriticalPoint(MSONable): def __init__( self, index, - type, + type, # noqa: A002 frac_coords, point_group, multiplicity, diff --git a/pymatgen/command_line/enumlib_caller.py b/src/pymatgen/command_line/enumlib_caller.py similarity index 98% rename from pymatgen/command_line/enumlib_caller.py rename to src/pymatgen/command_line/enumlib_caller.py index e8db875440d..619060b8386 100644 --- a/pymatgen/command_line/enumlib_caller.py +++ b/src/pymatgen/command_line/enumlib_caller.py @@ -39,7 +39,6 @@ from monty.dev import requires from monty.fractions import lcm from monty.tempfile import ScratchDir - from pymatgen.core import DummySpecies, PeriodicSite, Structure from pymatgen.io.vasp.inputs import Poscar from pymatgen.symmetry.analyzer import SpacegroupAnalyzer @@ -273,14 +272,14 @@ def get_sg_info(ss): file.write("\n".join(output)) def _run_multienum(self): - with subprocess.Popen([enum_cmd], stdout=subprocess.PIPE, stdin=subprocess.PIPE, close_fds=True) as p: + with subprocess.Popen([enum_cmd], stdout=subprocess.PIPE, stdin=subprocess.PIPE, close_fds=True) as process: if self.timeout: timed_out = False - timer = Timer(self.timeout * 60, lambda p: p.kill(), [p]) + timer = Timer(self.timeout * 60, lambda p: p.kill(), [process]) try: timer.start() - output = p.communicate()[0].decode("utf-8") + output = process.communicate()[0].decode("utf-8") finally: if not timer.is_alive(): timed_out = True @@ -290,7 +289,7 @@ def _run_multienum(self): raise TimeoutError("Enumeration took too long") else: - output = p.communicate()[0].decode("utf-8") + output = process.communicate()[0].decode("utf-8") count = 0 start_count = False diff --git a/pymatgen/command_line/gulp_caller.py b/src/pymatgen/command_line/gulp_caller.py similarity index 99% rename from pymatgen/command_line/gulp_caller.py rename to src/pymatgen/command_line/gulp_caller.py index b13912f2433..fa3e250b99a 100644 --- a/pymatgen/command_line/gulp_caller.py +++ b/src/pymatgen/command_line/gulp_caller.py @@ -10,7 +10,6 @@ import subprocess from monty.tempfile import ScratchDir - from pymatgen.analysis.bond_valence import BVAnalyzer from pymatgen.core import Element, Lattice, Structure from pymatgen.symmetry.analyzer import SpacegroupAnalyzer diff --git a/pymatgen/command_line/lewis.lib b/src/pymatgen/command_line/lewis.lib similarity index 100% rename from pymatgen/command_line/lewis.lib rename to src/pymatgen/command_line/lewis.lib diff --git a/pymatgen/command_line/mcsqs_caller.py b/src/pymatgen/command_line/mcsqs_caller.py similarity index 98% rename from pymatgen/command_line/mcsqs_caller.py rename to src/pymatgen/command_line/mcsqs_caller.py index 657060d6dec..980f04e2f13 100644 --- a/pymatgen/command_line/mcsqs_caller.py +++ b/src/pymatgen/command_line/mcsqs_caller.py @@ -13,7 +13,6 @@ from typing import TYPE_CHECKING, NamedTuple from monty.dev import requires - from pymatgen.core.structure import Structure if TYPE_CHECKING: @@ -178,8 +177,8 @@ def _parse_sqs_path(path) -> Sqs: detected_instances = len(list(path.glob("bestsqs*[0-9]*.out"))) # Convert best SQS structure to CIF file and pymatgen Structure - with Popen("str2cif < bestsqs.out > bestsqs.cif", shell=True, cwd=path) as p: - p.communicate() + with Popen("str2cif < bestsqs.out > bestsqs.cif", shell=True, cwd=path) as process: + process.communicate() with warnings.catch_warnings(): warnings.simplefilter("ignore") @@ -200,8 +199,8 @@ def _parse_sqs_path(path) -> Sqs: sqs_out = f"bestsqs{idx + 1}.out" sqs_cif = f"bestsqs{idx + 1}.cif" corr_out = f"bestcorr{idx + 1}.out" - with Popen(f"str2cif < {sqs_out} > {sqs_cif}", shell=True, cwd=path) as p: - p.communicate() + with Popen(f"str2cif < {sqs_out} > {sqs_cif}", shell=True, cwd=path) as process: + process.communicate() sqs = Structure.from_file(path / sqs_out) with open(path / corr_out) as file: lines = file.readlines() diff --git a/pymatgen/command_line/vampire_caller.py b/src/pymatgen/command_line/vampire_caller.py similarity index 99% rename from pymatgen/command_line/vampire_caller.py rename to src/pymatgen/command_line/vampire_caller.py index 8709088514d..44aa50c3895 100644 --- a/pymatgen/command_line/vampire_caller.py +++ b/src/pymatgen/command_line/vampire_caller.py @@ -21,7 +21,6 @@ import pandas as pd from monty.dev import requires from monty.json import MSONable - from pymatgen.analysis.magnetism.heisenberg import HeisenbergMapper __author__ = "ncfrey" diff --git a/pymatgen/core/__init__.py b/src/pymatgen/core/__init__.py similarity index 90% rename from pymatgen/core/__init__.py rename to src/pymatgen/core/__init__.py index 2459aa7e534..c1f047de11c 100644 --- a/pymatgen/core/__init__.py +++ b/src/pymatgen/core/__init__.py @@ -7,8 +7,6 @@ from importlib.metadata import PackageNotFoundError, version from typing import Any -from ruamel.yaml import YAML - from pymatgen.core.composition import Composition from pymatgen.core.lattice import Lattice from pymatgen.core.operations import SymmOp @@ -16,6 +14,7 @@ from pymatgen.core.sites import PeriodicSite, Site from pymatgen.core.structure import IMolecule, IStructure, Molecule, PeriodicNeighbor, SiteCollection, Structure from pymatgen.core.units import ArrayWithUnit, FloatWithUnit, Unit +from ruamel.yaml import YAML __author__ = "Pymatgen Development Team" __email__ = "pymatgen@googlegroups.com" @@ -59,6 +58,13 @@ def _load_pmg_settings() -> dict[str, Any]: elif key in ("VASP_PSP_DIR", "MAPI_KEY", "DEFAULT_FUNCTIONAL"): settings[f"PMG_{key}"] = val + for key, val in settings.items(): + if key.endswith("_DIR"): + # Enables the use of $HOME and ~ in paths. + val = os.path.expanduser(val) + val = os.path.expandvars(val) + settings[key] = val + return settings diff --git a/pymatgen/core/bond_lengths.json b/src/pymatgen/core/bond_lengths.json similarity index 100% rename from pymatgen/core/bond_lengths.json rename to src/pymatgen/core/bond_lengths.json diff --git a/pymatgen/core/bonds.py b/src/pymatgen/core/bonds.py similarity index 99% rename from pymatgen/core/bonds.py rename to src/pymatgen/core/bonds.py index ac3c4b7bbf6..7faed475c54 100644 --- a/pymatgen/core/bonds.py +++ b/src/pymatgen/core/bonds.py @@ -228,4 +228,4 @@ def get_bond_length( f"No order {bond_order} bond lengths between {sp1} and {sp2} found in " "database. Returning sum of atomic radius." ) - return sp1.atomic_radius + sp2.atomic_radius # type: ignore + return sp1.atomic_radius + sp2.atomic_radius # type: ignore[operator] diff --git a/pymatgen/core/composition.py b/src/pymatgen/core/composition.py similarity index 95% rename from pymatgen/core/composition.py rename to src/pymatgen/core/composition.py index aefdb5045d7..8eaa6a5400d 100644 --- a/pymatgen/core/composition.py +++ b/src/pymatgen/core/composition.py @@ -18,7 +18,6 @@ from monty.fractions import gcd, gcd_float from monty.json import MSONable from monty.serialization import loadfn - from pymatgen.core.periodic_table import DummySpecies, Element, ElementType, Species, get_el_sp from pymatgen.core.units import Mass from pymatgen.util.string import Stringify, formula_double_format @@ -27,9 +26,8 @@ from collections.abc import Generator, Iterator from typing import Any, ClassVar - from typing_extensions import Self - from pymatgen.util.typing import SpeciesLike + from typing_extensions import Self module_dir = os.path.dirname(os.path.abspath(__file__)) @@ -81,19 +79,19 @@ class Composition(collections.abc.Hashable, collections.abc.Mapping, MSONable, S # Special formula handling for peroxides and certain elements. This is so # that formula output does not write LiO instead of Li2O2 for example. - special_formulas: ClassVar[dict[str, str]] = dict( - LiO="Li2O2", - NaO="Na2O2", - KO="K2O2", - HO="H2O2", - CsO="Cs2O2", - RbO="Rb2O2", - O="O2", - N="N2", - F="F2", - Cl="Cl2", - H="H2", - ) + special_formulas: ClassVar[dict[str, str]] = { + "LiO": "Li2O2", + "NaO": "Na2O2", + "KO": "K2O2", + "HO": "H2O2", + "CsO": "Cs2O2", + "RbO": "Rb2O2", + "O": "O2", + "N": "N2", + "F": "F2", + "Cl": "Cl2", + "H": "H2", + } oxi_prob = None # prior probability of oxidation used by oxi_state_guesses @@ -193,10 +191,10 @@ def __eq__(self, other: object) -> bool: return all(abs(amt - other[el]) <= type(self).amount_tolerance for el, amt in self.items()) def __ge__(self, other: object) -> bool: - """Composition greater than or equal to. We consider compositions A >= B - if all elements in B are in A and the amount of each element in A is - greater than or equal to the amount of the element in B within - Composition.amount_tolerance. + """Composition greater than or equal to. We sort the elements in the compositions in order of + electronegativity. The amount of the most electropositive element that is not equal within a certain + tolerance factor is used to make a comparison. Note that an element not present in a Composition has an implied + amount of 0. Should ONLY be used for defining a sort order (the behavior is probably not what you'd expect). """ @@ -767,11 +765,12 @@ def oxi_state_guesses( element's common oxidation states, e.g. {"V": [2,3,4,5]} target_charge (int): the desired total charge on the structure. Default is 0 signifying charge balance. - all_oxi_states (bool): if True, an element defaults to - all oxidation states in pymatgen Element.icsd_oxidation_states. - Otherwise, default is Element.common_oxidation_states. Note - that the full oxidation state list is *very* inclusive and - can produce nonsensical results. + all_oxi_states (bool): if True, all oxidation states of an element, even rare ones, are used in the search + for guesses. However, the full oxidation state list is *very* inclusive and can produce nonsensical + results. If False, the icsd_oxidation_states list is used when present, or the common_oxidation_states + is used when icsd_oxidation_states is not present. These oxidation states lists comprise more + commonly occurring oxidation states and results in more reliable guesses, albeit at the cost of + missing some uncommon situations. The default is False. max_sites (int): if possible, will reduce Compositions to at most this many sites to speed up oxidation state guesses. If the composition cannot be reduced to this many sites a ValueError @@ -859,11 +858,12 @@ def add_charges_from_oxi_state_guesses( element's common oxidation states, e.g. {"V": [2, 3, 4, 5]} target_charge (float): the desired total charge on the structure. Default is 0 signifying charge balance. - all_oxi_states (bool): If True, an element defaults to - all oxidation states in pymatgen Element.icsd_oxidation_states. - Otherwise, default is Element.common_oxidation_states. Note - that the full oxidation state list is *very* inclusive and - can produce nonsensical results. + all_oxi_states (bool): if True, all oxidation states of an element, even rare ones, are used in the search + for guesses. However, the full oxidation state list is *very* inclusive and can produce nonsensical + results. If False, the icsd_oxidation_states list is used when present, or the common_oxidation_states + is used when icsd_oxidation_states is not present. These oxidation states lists comprise more + commonly occurring oxidation states and results in more reliable guesses, albeit at the cost of + missing some uncommon situations. The default is False. max_sites (int): If possible, will reduce Compositions to at most this many sites to speed up oxidation state guesses. If the composition cannot be reduced to this many sites a ValueError @@ -916,15 +916,15 @@ def _get_oxi_state_guesses( calculation of the most likely oxidation states Args: - oxi_states_override (dict): dict of str->list to override an - element's common oxidation states, e.g. {"V": [2,3,4,5]} - target_charge (float): the desired total charge on the structure. - Default is 0 signifying charge balance. - all_oxi_states (bool): if True, an element defaults to - all oxidation states in pymatgen Element.icsd_oxidation_states. - Otherwise, default is Element.common_oxidation_states. Note - that the full oxidation state list is *very* inclusive and - can produce nonsensical results. + oxi_states_override (dict): dict of str->list to override an element's common oxidation states, e.g. + {"V": [2,3,4,5]}. + target_charge (float): the desired total charge on the structure. Default is 0 signifying charge balance. + all_oxi_states (bool): if True, all oxidation states of an element, even rare ones, are used in the search + for guesses. However, the full oxidation state list is *very* inclusive and can produce nonsensical + results. If False, the icsd_oxidation_states list is used when present, or the common_oxidation_states + is used when icsd_oxidation_states is not present. These oxidation states lists comprise more + commonly occurring oxidation states and results in more reliable guesses, albeit at the cost of + missing some uncommon situations. The default is False. max_sites (int): if possible, will reduce Compositions to at most this many sites to speed up oxidation state guesses. If the composition cannot be reduced to this many sites a ValueError @@ -980,7 +980,7 @@ def _get_oxi_state_guesses( elif all_oxi_states: oxids = Element(el).oxidation_states else: - oxids = Element(el).icsd_oxidation_states or Element(el).oxidation_states + oxids = Element(el).icsd_oxidation_states or Element(el).common_oxidation_states # Get all possible combinations of oxidation states # and sum each combination @@ -1135,7 +1135,7 @@ def _parse_chomp_and_rank(match, formula: str, m_dict: dict[str, float], m_point el = match[1] if len(el) > 2 or len(el) < 1: raise ValueError("Invalid element symbol entered!") - amt = float(match.group(2)) if match.group(2).strip() != "" else 1 + amt = float(match[2]) if match[2].strip() != "" else 1 # convert the element string to proper [uppercase,lowercase] format # and award points if it is already in that format diff --git a/pymatgen/core/func_groups.json b/src/pymatgen/core/func_groups.json similarity index 100% rename from pymatgen/core/func_groups.json rename to src/pymatgen/core/func_groups.json diff --git a/pymatgen/core/interface.py b/src/pymatgen/core/interface.py similarity index 99% rename from pymatgen/core/interface.py rename to src/pymatgen/core/interface.py index d7d5c8eccf3..2856130e014 100644 --- a/pymatgen/core/interface.py +++ b/src/pymatgen/core/interface.py @@ -15,9 +15,6 @@ import numpy as np from monty.fractions import lcm from numpy.testing import assert_allclose -from scipy.cluster.hierarchy import fcluster, linkage -from scipy.spatial.distance import squareform - from pymatgen.analysis.adsorption import AdsorbateSiteFinder from pymatgen.core.lattice import Lattice from pymatgen.core.sites import PeriodicSite, Site @@ -25,16 +22,17 @@ from pymatgen.core.surface import Slab from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.typing import Tuple3Ints +from scipy.cluster.hierarchy import fcluster, linkage +from scipy.spatial.distance import squareform if TYPE_CHECKING: from collections.abc import Sequence from typing import Any, Callable from numpy.typing import ArrayLike, NDArray - from typing_extensions import Self - from pymatgen.core import Element from pymatgen.util.typing import CompositionLike, Matrix3D, MillerIndex, Tuple3Floats, Vector3D + from typing_extensions import Self Tuple4Ints = tuple[int, int, int, int] logger = logging.getLogger(__name__) @@ -698,7 +696,7 @@ def gb_from_parameters( list(top_grain.frac_coords) + list(bottom_grain.frac_coords), ) t_and_b_dis = t_and_b.lattice.get_all_distances( - t_and_b.frac_coords[0:n_sites], t_and_b.frac_coords[n_sites : n_sites * 2] + t_and_b.frac_coords[:n_sites], t_and_b.frac_coords[n_sites : n_sites * 2] ) index_incident = np.nonzero(t_and_b_dis < np.min(t_and_b_dis) + tol_coi) @@ -1444,7 +1442,7 @@ def enum_sigma_hex( v = 2 * v1 + u1 w = w1 else: - u, v, w = r_axis + u, v, w = r_axis # type: ignore[misc] # Make sure mu, mv are coprime integers if c2_a2_ratio is None: @@ -1557,7 +1555,7 @@ def enum_sigma_rho( # Make sure math.(r_axis) == 1 if reduce(math.gcd, r_axis) != 1: r_axis = cast(Tuple3Ints, tuple([round(x / reduce(math.gcd, r_axis)) for x in r_axis])) - u, v, w = r_axis + u, v, w = r_axis # type: ignore[misc] # Make sure mu, mv are coprime integers if ratio_alpha is None: diff --git a/pymatgen/core/ion.py b/src/pymatgen/core/ion.py similarity index 99% rename from pymatgen/core/ion.py rename to src/pymatgen/core/ion.py index ec246d1ca34..c3d7cf3271c 100644 --- a/pymatgen/core/ion.py +++ b/src/pymatgen/core/ion.py @@ -7,7 +7,6 @@ from typing import TYPE_CHECKING from monty.json import MSONable - from pymatgen.core.composition import Composition, reduce_formula from pymatgen.util.string import Stringify, charge_string, formula_double_format diff --git a/pymatgen/core/lattice.py b/src/pymatgen/core/lattice.py similarity index 99% rename from pymatgen/core/lattice.py rename to src/pymatgen/core/lattice.py index 50fcb50b22c..89f28628e6d 100644 --- a/pymatgen/core/lattice.py +++ b/src/pymatgen/core/lattice.py @@ -16,19 +16,17 @@ import numpy as np from monty.dev import deprecated from monty.json import MSONable -from scipy.spatial import Voronoi - from pymatgen.util.coord import pbc_shortest_vectors from pymatgen.util.due import Doi, due +from scipy.spatial import Voronoi if TYPE_CHECKING: from collections.abc import Iterator from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.core.operations import SymmOp from pymatgen.util.typing import MillerIndex, PbcLike, Vector3D + from typing_extensions import Self __author__ = "Shyue Ping Ong, Michael Kocher" __copyright__ = "Copyright 2011, The Materials Project" @@ -1504,7 +1502,7 @@ def get_points_in_sphere_old( center = np.array(center) # Prepare the list of output atoms - n = len(frac_points) # type: ignore + n = len(frac_points) frac_coords = np.array(frac_points) % 1 indices = np.arange(n) @@ -1623,13 +1621,13 @@ def get_distance_and_image( """ if jimage is None: v, d2 = pbc_shortest_vectors(self, frac_coords1, frac_coords2, return_d2=True) - fc = self.get_fractional_coords(v[0][0]) + frac_coords1 - frac_coords2 # type: ignore + fc = self.get_fractional_coords(v[0][0]) + frac_coords1 - frac_coords2 fc = np.array(np.round(fc), dtype=int) return np.sqrt(d2[0, 0]), fc jimage = np.array(jimage) - mapped_vec = self.get_cartesian_coords(jimage + frac_coords2 - frac_coords1) # type: ignore - return np.linalg.norm(mapped_vec), jimage # type: ignore + mapped_vec = self.get_cartesian_coords(jimage + frac_coords2 - frac_coords1) + return np.linalg.norm(mapped_vec), jimage def get_miller_index_from_coords( self, @@ -1660,7 +1658,7 @@ def get_miller_index_from_coords( tuple: The Miller index. """ if coords_are_cartesian: - coords = [self.get_fractional_coords(c) for c in coords] # type: ignore + coords = [self.get_fractional_coords(c) for c in coords] coords = np.asarray(coords) g = coords.sum(axis=0) / coords.shape[0] @@ -1837,12 +1835,12 @@ def get_points_in_spheres( valid_images = np.concatenate(valid_images, axis=0) else: - valid_coords = all_coords # type: ignore + valid_coords = all_coords valid_images = [[0, 0, 0]] * len(valid_coords) - valid_indices = np.arange(len(valid_coords)) # type: ignore + valid_indices = np.arange(len(valid_coords)) # Divide the valid 3D space into cubes and compute the cube ids - all_cube_index = _compute_cube_index(valid_coords, global_min, r) # type: ignore + all_cube_index = _compute_cube_index(valid_coords, global_min, r) nx, ny, nz = _compute_cube_index(global_max, global_min, r) + 1 all_cube_index = _three_to_one(all_cube_index, ny, nz) site_cube_index = _three_to_one(_compute_cube_index(center_coords, global_min, r), ny, nz) diff --git a/pymatgen/core/libxc_docs.json b/src/pymatgen/core/libxc_docs.json similarity index 100% rename from pymatgen/core/libxc_docs.json rename to src/pymatgen/core/libxc_docs.json diff --git a/pymatgen/core/libxcfunc.py b/src/pymatgen/core/libxcfunc.py similarity index 100% rename from pymatgen/core/libxcfunc.py rename to src/pymatgen/core/libxcfunc.py diff --git a/pymatgen/core/molecular_orbitals.py b/src/pymatgen/core/molecular_orbitals.py similarity index 100% rename from pymatgen/core/molecular_orbitals.py rename to src/pymatgen/core/molecular_orbitals.py diff --git a/pymatgen/core/operations.py b/src/pymatgen/core/operations.py similarity index 99% rename from pymatgen/core/operations.py rename to src/pymatgen/core/operations.py index a96be8d2c09..c67603c288f 100644 --- a/pymatgen/core/operations.py +++ b/src/pymatgen/core/operations.py @@ -10,7 +10,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.electronic_structure.core import Magmom from pymatgen.util.due import Doi, due from pymatgen.util.string import transformation_to_string @@ -367,7 +366,7 @@ def reflection(normal: ArrayLike, origin: ArrayLike = (0, 0, 0)) -> SymmOp: u, v, w = normal translation = np.eye(4) - translation[0:3, 3] = -np.array(origin) + translation[:3, 3] = -np.array(origin) xx = 1 - 2 * u**2 yy = 1 - 2 * v**2 @@ -394,7 +393,7 @@ def inversion(origin: ArrayLike = (0, 0, 0)) -> SymmOp: """ mat = -np.eye(4) mat[3, 3] = 1 - mat[0:3, 3] = 2 * np.array(origin) + mat[:3, 3] = 2 * np.array(origin) return SymmOp(mat) @staticmethod diff --git a/src/pymatgen/core/periodic_table.json b/src/pymatgen/core/periodic_table.json new file mode 100644 index 00000000000..e0b56082370 --- /dev/null +++ b/src/pymatgen/core/periodic_table.json @@ -0,0 +1,16930 @@ +{ + "Ac": { + "Atomic mass": 227, + "Atomic no": 89, + "Atomic orbitals": { + "1s": -3443.110367, + "2p": -572.7627, + "2s": -592.622878, + "3d": -119.541743, + "3p": -137.654394, + "3s": -147.320716, + "4d": -23.57061, + "4f": -12.278225, + "4p": -31.761846, + "4s": -36.15826, + "5d": -3.222752, + "5p": -6.06511, + "5s": -7.713078, + "6d": -0.137786, + "6p": -0.744524, + "6s": -1.19698, + "7s": -0.126551 + }, + "Atomic radius": 1.95, + "Atomic radius calculated": "no data", + "Boiling point": "3573 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "10070 kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].6d1.7s2", + "3": "[Xe].4f14.5d10.6s2.6p6" + }, + "Ionic radii": { + "3": 1.26 + }, + "Liquid range": "2250 K", + "Melting point": "1323 K", + "Mendeleev no": 48, + "Mineral hardness": "no data", + "Molar volume": "22.55 cm3", + "Name": "Actinium", + "Oxidation states": [ + 3 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.26, + "ionic_radius": 1.12 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "12 W m-1 K-1", + "Van der waals radius": 2.47, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.1, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.878, + "iupac_ordering": 32, + "IUPAC ordering": 32, + "Ground level": "2D3/2", + "Ionization energies": [ + 5.380226, + 11.75, + 17.431, + 44.8, + 55, + 67, + 79, + 98.9, + 113.9, + 143.9, + 161.1, + 233, + 255, + 279, + 305, + 330, + 355, + 390, + 416, + 444, + 470, + 610, + 640, + 670, + 710, + 780, + 820, + 920, + 950, + 1030, + 1100, + 1170, + 1240, + 1310, + 1380, + 1460, + 1530, + 1610, + 1680, + 1750, + 1820, + 1900, + 1970, + 2298, + 2362, + 2430, + 2503, + 2572, + 2639, + 2762, + 2833, + 2908, + 2980, + 3264, + 3334, + 3409, + 3479, + 3811, + 3893, + 4093, + 4175, + 6767, + 6923, + 7088, + 7265, + 7430, + 7600, + 7950, + 8120, + 8310, + 8480, + 8970, + 9120, + 9290, + 9440, + 10480, + 10660, + 11030, + 11200, + 23480, + 23890, + 24340, + 24760, + 28610, + 29160, + 29850, + 30293.1, + 119938.6, + 122062.9 + ], + "Electron affinity": 0.35 + }, + "Ag": { + "Atomic mass": 107.8682, + "Atomic no": 47, + "Atomic orbitals": { + "1s": -900.324578, + "2p": -120.913351, + "2s": -129.859807, + "3d": -13.367803, + "3p": -20.06763, + "3s": -23.678437, + "4d": -0.298706, + "4p": -2.086602, + "4s": -3.22309, + "5s": -0.157407 + }, + "Atomic radius": 1.6, + "Atomic radius calculated": 1.65, + "Boiling point": "2435 K", + "Brinell hardness": "24.5 MN m-2", + "Bulk modulus": "100 GPa", + "Coefficient of linear thermal expansion": "18.9 x10-6K-1", + "Common oxidation states": [ + 1 + ], + "Critical temperature": "no data K", + "Density of solid": "10490 kg m-3", + "Electrical resistivity": "1.63 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d10.5s1", + "1": "[Kr].4d10" + }, + "ICSD oxidation states": [ + 1, + 2, + 3 + ], + "Ionic radii": { + "1": 1.29, + "2": 1.08, + "3": 0.89 + }, + "Liquid range": "1200.07 K", + "Melting point": "1234.93 K", + "Mendeleev no": 71, + "Mineral hardness": "2.5", + "Molar volume": "10.27 cm3", + "Name": "Silver", + "Oxidation states": [ + 1, + 2, + 3 + ], + "Poissons ratio": "0.37", + "Reflectivity": "97 %", + "Refractive index": "no data", + "Rigidity modulus": "30 GPa", + "Shannon radii": { + "1": { + "II": { + "": { + "crystal_radius": 0.81, + "ionic_radius": 0.67 + } + }, + "IV": { + "": { + "crystal_radius": 1.14, + "ionic_radius": 1 + } + }, + "IVSQ": { + "": { + "crystal_radius": 1.16, + "ionic_radius": 1.02 + } + }, + "V": { + "": { + "crystal_radius": 1.23, + "ionic_radius": 1.09 + } + }, + "VI": { + "": { + "crystal_radius": 1.29, + "ionic_radius": 1.15 + } + }, + "VII": { + "": { + "crystal_radius": 1.36, + "ionic_radius": 1.22 + } + }, + "VIII": { + "": { + "crystal_radius": 1.42, + "ionic_radius": 1.28 + } + } + }, + "2": { + "IVSQ": { + "": { + "crystal_radius": 0.93, + "ionic_radius": 0.79 + } + }, + "VI": { + "": { + "crystal_radius": 1.08, + "ionic_radius": 0.94 + } + } + }, + "3": { + "IVSQ": { + "": { + "crystal_radius": 0.81, + "ionic_radius": 0.67 + } + }, + "VI": { + "": { + "crystal_radius": 0.89, + "ionic_radius": 0.75 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "430 W m-1 K-1", + "Van der waals radius": 2.11, + "Velocity of sound": "2600 m s-1", + "Vickers hardness": "251 MN m-2", + "X": 1.93, + "Youngs modulus": "83 GPa", + "Metallic radius": 1.445, + "iupac_ordering": 72, + "IUPAC ordering": 72, + "Ground level": "2S1/2", + "Ionization energies": [ + 7.576234, + 21.4844, + 34.8, + 49, + 65, + 82, + 106, + 125, + 145.1, + 167, + 188, + 271.46, + 294, + 321, + 347, + 381, + 408.43, + 469, + 500.87, + 885, + 946, + 1013, + 1082, + 1149, + 1231, + 1308, + 1382, + 1460, + 1535, + 1747, + 1810.5, + 1888, + 1979, + 2077, + 2131, + 2302, + 2371.99, + 5558, + 5753, + 5966, + 6170, + 6551, + 6785, + 7082, + 7271.298, + 30097.318, + 30965.698 + ], + "Electron affinity": 1.304473 + }, + "Al": { + "Atomic mass": 26.9815386, + "Atomic no": 13, + "Atomic orbitals": { + "1s": -55.156044, + "2p": -2.564018, + "2s": -3.934827, + "3p": -0.102545, + "3s": -0.286883 + }, + "Atomic radius": 1.25, + "Atomic radius calculated": 1.18, + "Boiling point": "2792 K", + "Brinell hardness": "245 MN m-2", + "Bulk modulus": "76 GPa", + "Coefficient of linear thermal expansion": "23.1 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "2700 kg m-3", + "Electrical resistivity": "2.7 10-8 Ω m", + "Electronic structure": { + "0": "[Ne].3s2.3p1", + "3": "1s2.2s2.2p6" + }, + "ICSD oxidation states": [ + 3 + ], + "Ionic radii": { + "3": 0.675 + }, + "Liquid range": "1858.53 K", + "Melting point": "933.47 K", + "Mendeleev no": 80, + "Mineral hardness": "2.75", + "Molar volume": "10.00 cm3", + "Name": "Aluminum", + "Oxidation states": [ + 1, + 3 + ], + "Poissons ratio": "0.35", + "Reflectivity": "71 %", + "Refractive index": "no data", + "Rigidity modulus": "26 GPa", + "Shannon radii": { + "3": { + "IV": { + "": { + "crystal_radius": 0.53, + "ionic_radius": 0.39 + } + }, + "V": { + "": { + "crystal_radius": 0.62, + "ionic_radius": 0.48 + } + }, + "VI": { + "": { + "crystal_radius": 0.675, + "ionic_radius": 0.535 + } + } + } + }, + "Superconduction temperature": "1.175 K", + "Thermal conductivity": "235 W m-1 K-1", + "Van der waals radius": 1.84, + "Velocity of sound": "5100 m s-1", + "Vickers hardness": "167 MN m-2", + "X": 1.61, + "Youngs modulus": "70 GPa", + "NMR Quadrupole Moment": { + "Al-27": 146.6 + }, + "Metallic radius": 1.43, + "iupac_ordering": 80, + "IUPAC ordering": 80, + "Ground level": "2P°1/2", + "Ionization energies": [ + 5.985769, + 18.82855, + 28.447642, + 119.9924, + 153.8252, + 190.49, + 241.76, + 284.64, + 330.21, + 398.65, + 442.005, + 2085.97702, + 2304.14007 + ], + "Electron affinity": 0.432835 + }, + "Am": { + "Atomic mass": 243, + "Atomic no": 95, + "Atomic orbitals": "no data", + "Atomic radius": 1.75, + "Atomic radius calculated": "no data", + "Boiling point": "2880 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f7.7s2", + "3": "[Rn].5f6" + }, + "Ionic radii": { + "2": 1.4, + "3": 1.115, + "4": 0.99 + }, + "Liquid range": "1431 K", + "Melting point": "1449 K", + "Mendeleev no": 42, + "Mineral hardness": "no data", + "Molar volume": "17.63 cm3", + "Name": "Americium", + "Oxidation states": [ + 2, + 3, + 4, + 5, + 6 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "2": { + "VII": { + "": { + "crystal_radius": 1.35, + "ionic_radius": 1.21 + } + }, + "VIII": { + "": { + "crystal_radius": 1.4, + "ionic_radius": 1.26 + } + }, + "IX": { + "": { + "crystal_radius": 1.45, + "ionic_radius": 1.31 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 1.115, + "ionic_radius": 0.975 + } + }, + "VIII": { + "": { + "crystal_radius": 1.23, + "ionic_radius": 1.09 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.99, + "ionic_radius": 0.85 + } + }, + "VIII": { + "": { + "crystal_radius": 1.09, + "ionic_radius": 0.95 + } + } + } + }, + "Superconduction temperature": "0.6 K", + "Thermal conductivity": "10 W m-1 K-1", + "Van der waals radius": 2.44, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.3, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.73, + "iupac_ordering": 26, + "IUPAC ordering": 26, + "Ground level": "8S°7/2", + "Ionization energies": [ + 5.97381, + 11.7, + 21.7, + 36.8, + 50, + 67.9, + 95, + 110, + 125, + 141, + 163, + 184, + 206, + 225, + 242, + 284, + 305, + 424, + 451, + 481, + 511, + 541, + 571, + 616, + 646, + 680, + 711, + 870, + 900, + 940, + 980, + 1090, + 1130, + 1240, + 1280, + 1410, + 1490, + 1570, + 1650, + 1730, + 1820, + 1900, + 1980, + 2070, + 2160, + 2240, + 2320, + 2410, + 2480, + 2874, + 2946, + 3021, + 3101, + 3178, + 3251, + 3402, + 3479, + 3563, + 3641, + 3956, + 4033, + 4115, + 4191, + 4642, + 4733, + 4960, + 5050, + 8040, + 8210, + 8390, + 8590, + 8770, + 8950, + 9380, + 9560, + 9770, + 9960, + 10490, + 10650, + 10830, + 11000, + 12400, + 12600, + 13000, + 13190, + 27110, + 27550, + 28040, + 28500, + 33700, + 34300, + 35100, + 35549.4, + 139769.5, + 142161 + ], + "Electron affinity": 0.1 + }, + "Ar": { + "Atomic mass": 39.948, + "Atomic no": 18, + "Atomic orbitals": { + "1s": -113.800134, + "2p": -8.443439, + "2s": -10.794172, + "3p": -0.38233, + "3s": -0.883384 + }, + "Atomic radius": 0.71, + "Atomic radius calculated": 0.71, + "Boiling point": "87.3 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Critical temperature": "150.8 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Ne].3s2.3p6" + }, + "Liquid range": "3.5 K", + "Max oxidation state": 0, + "Melting point": "83.8 K", + "Mendeleev no": 3, + "Min oxidation state": 0, + "Mineral hardness": "no data", + "Molar volume": "22.56 cm3", + "Name": "Argon", + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000281", + "Rigidity modulus": "no data GPa", + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.01772 W m-1 K-1", + "Van der waals radius": 1.88, + "Velocity of sound": "319 m s-1", + "Vickers hardness": "no data MN m-2", + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 3, + "IUPAC ordering": 3, + "Ground level": "1S0", + "Ionization energies": [ + 15.7596119, + 27.62967, + 40.735, + 59.58, + 74.84, + 91.29, + 124.41, + 143.4567, + 422.6, + 479.76, + 540.4, + 619, + 685.5, + 755.13, + 855.5, + 918.375, + 4120.6657, + 4426.2229 + ], + "Electron affinity": -1.02 + }, + "As": { + "Atomic mass": 74.9216, + "Atomic no": 33, + "Atomic orbitals": { + "1s": -423.336658, + "2p": -47.527869, + "2s": -53.093086, + "3d": -1.542767, + "3p": -4.851725, + "3s": -6.730755, + "4p": -0.197497, + "4s": -0.52367 + }, + "Atomic radius": 1.15, + "Atomic radius calculated": 1.14, + "Boiling point": "887 K", + "Brinell hardness": "1440 MN m-2", + "Bulk modulus": "22 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -3, + 3, + 5 + ], + "Critical temperature": "1700 K", + "Density of solid": "5727 kg m-3", + "Electrical resistivity": "33 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d10.4s2.4p3", + "3": "[Ar].3d10.4s2", + "5": "[Ar].3d10", + "-3": "[Ar].3d10.4s2.4p6" + }, + "ICSD oxidation states": [ + 2, + 3, + 5, + -2, + -3, + -1 + ], + "Ionic radii": { + "3": 0.72, + "5": 0.6 + }, + "Liquid range": "203 K", + "Melting point": "1090 K", + "Mendeleev no": 89, + "Mineral hardness": "3.5", + "Molar volume": "12.95 cm3", + "Name": "Arsenic", + "Oxidation states": [ + -3, + 2, + 3, + 5 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.001552", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.72, + "ionic_radius": 0.58 + } + } + }, + "5": { + "IV": { + "": { + "crystal_radius": 0.475, + "ionic_radius": 0.335 + } + }, + "VI": { + "": { + "crystal_radius": 0.6, + "ionic_radius": 0.46 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "50 W m-1 K-1", + "Van der waals radius": 1.85, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.18, + "Youngs modulus": "8 GPa", + "Metallic radius": "no data", + "iupac_ordering": 89, + "IUPAC ordering": 89, + "Ground level": "4S°3/2", + "Ionization energies": [ + 9.78855, + 18.5892, + 28.349, + 50.15, + 62.77, + 121.19, + 147, + 180, + 213, + 247, + 296, + 333, + 375, + 418, + 460, + 587.6, + 628.8, + 672.9, + 728.9, + 774, + 814, + 911.7, + 956.79, + 2356.9, + 2486, + 2626, + 2766, + 2938, + 3088.1, + 3287, + 3411.643, + 14447.678, + 15028.907 + ], + "Electron affinity": 0.80482 + }, + "At": { + "Atomic mass": 210, + "Atomic no": 85, + "Atomic orbitals": { + "1s": -3127.390276, + "2p": -513.044243, + "2s": -531.81835, + "3d": -103.060375, + "3p": -119.995013, + "3s": -129.035542, + "4d": -18.295162, + "4f": -8.063483, + "4p": -25.778264, + "4s": -29.809515, + "5d": -1.643758, + "5p": -4.027061, + "5s": -5.453383, + "6p": -0.255453, + "6s": -0.560189 + }, + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -1, + 1 + ], + "Critical temperature": "no data K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d10.6s2.6p5", + "1": "[Xe].4f14.5d10.6s2.6p4", + "-1": "[Xe].4f14.5d10.6s2.6p6" + }, + "Ionic radii": { + "7": 0.76 + }, + "Liquid range": "no data K", + "Melting point": "575 K", + "Mendeleev no": 96, + "Mineral hardness": "no data", + "Molar volume": "no data cm3", + "Name": "Astatine", + "Oxidation states": [ + -1, + 1, + 3, + 5 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "7": { + "VI": { + "": { + "crystal_radius": 0.76, + "ionic_radius": 0.62 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "2 (estimate)W m-1 K-1", + "Van der waals radius": 2.02, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.2, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 98, + "IUPAC ordering": 98, + "Ground level": "2P°3/2", + "Ionization energies": [ + 9.31751, + 17.88, + 26.58, + 39.65, + 50.39, + 72, + 85.1, + 130.1, + 149, + 169, + 192.1, + 212, + 236, + 263, + 287, + 311, + 335, + 452, + 481, + 510, + 540, + 600, + 630, + 720, + 750, + 790, + 860, + 920, + 990, + 1050, + 1120, + 1180, + 1250, + 1320, + 1380, + 1450, + 1510, + 1590, + 1650, + 1948, + 2007, + 2071, + 2139, + 2203, + 2266, + 2373, + 2439, + 2510, + 2576, + 2841, + 2905, + 2977, + 3042, + 3312, + 3388, + 3573, + 3649, + 5976, + 6122, + 6279, + 6445, + 6604, + 6759, + 7068, + 7230, + 7410, + 7570, + 8030, + 8180, + 8330, + 8480, + 9330, + 9500, + 9830, + 9990, + 21210, + 21600, + 22030, + 22420, + 25580, + 26090, + 26730, + 27139, + 107923.4, + 109886 + ], + "Electron affinity": 2.415787 + }, + "Au": { + "Atomic mass": 196.966569, + "Atomic no": 79, + "Atomic orbitals": { + "1s": -2683.508245, + "2p": -430.725701, + "2s": -447.888973, + "3d": -81.511751, + "3p": -96.707, + "3s": -104.824516, + "4d": -12.131815, + "4f": -3.486824, + "4p": -18.578652, + "4s": -22.078357, + "5d": -0.304738, + "5p": -2.002495, + "5s": -3.113936, + "6s": -0.162334 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.74, + "Boiling point": "3129 K", + "Brinell hardness": "2450 MN m-2", + "Bulk modulus": "220 GPa", + "Coefficient of linear thermal expansion": "14.2 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "19300 kg m-3", + "Electrical resistivity": "2.2 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d10.6s1", + "3": "[Xe].4f14.5d8" + }, + "Ionic radii": { + "1": 1.51, + "3": 0.99, + "5": 0.71 + }, + "Liquid range": "1791.67 K", + "Melting point": "1337.33 K", + "Mendeleev no": 70, + "Mineral hardness": "2.5", + "Molar volume": "10.21 cm3", + "Name": "Gold", + "Oxidation states": [ + -1, + 1, + 2, + 3, + 5 + ], + "Poissons ratio": "0.44", + "Reflectivity": "95 %", + "Refractive index": "no data", + "Rigidity modulus": "27 GPa", + "Shannon radii": { + "1": { + "VI": { + "": { + "crystal_radius": 1.51, + "ionic_radius": 1.37 + } + } + }, + "3": { + "IVSQ": { + "": { + "crystal_radius": 0.82, + "ionic_radius": 0.68 + } + }, + "VI": { + "": { + "crystal_radius": 0.99, + "ionic_radius": 0.85 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.71, + "ionic_radius": 0.57 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "320 W m-1 K-1", + "Van der waals radius": 2.14, + "Velocity of sound": "1740 m s-1", + "Vickers hardness": "216 MN m-2", + "X": 2.54, + "Youngs modulus": "78 GPa", + "Metallic radius": 1.442, + "iupac_ordering": 71, + "IUPAC ordering": 71, + "Ground level": "2S1/2", + "Ionization energies": [ + 9.225554, + 20.203, + 30, + 45, + 60, + 74, + 94, + 112, + 130.1, + 149, + 168.2, + 248, + 275, + 299, + 324, + 365, + 392, + 433, + 487, + 520, + 550, + 600, + 650, + 710, + 760, + 820, + 870, + 930, + 990, + 1040, + 1100, + 1150, + 1210, + 1475, + 1527, + 1584, + 1644, + 1702, + 1758, + 1845, + 1904, + 1967, + 2026, + 2261, + 2320, + 2383, + 2443, + 2640, + 2708, + 2870, + 2941, + 4888, + 5013, + 5156, + 5307, + 5452, + 5594, + 5846, + 5994, + 6156, + 6305, + 6724, + 6854, + 6997, + 7130, + 7760, + 7910, + 8210, + 8360, + 18040, + 18400, + 18790, + 19150, + 21470, + 21920, + 22500, + 22868.1, + 91515.82, + 93254.3 + ], + "Electron affinity": 2.30861025 + }, + "B": { + "Atomic mass": 10.811, + "Atomic no": 5, + "Atomic orbitals": { + "1s": -6.564347, + "2p": -0.136603, + "2s": -0.344701 + }, + "Atomic radius": 0.85, + "Atomic radius calculated": 0.87, + "Boiling point": "4200 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "320 GPa", + "Coefficient of linear thermal expansion": "6 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "2460 kg m-3", + "Electrical resistivity": "> 101210-8 Ω m", + "Electronic structure": { + "0": "[He].2s2.2p1", + "3": "1s2" + }, + "ICSD oxidation states": [ + 3, + -3 + ], + "Ionic radii": { + "3": 0.41 + }, + "Liquid range": "1851 K", + "Melting point": "2349 K", + "Mendeleev no": 86, + "Mineral hardness": "9.3", + "Molar volume": "4.39 cm3", + "Name": "Boron", + "Oxidation states": [ + 1, + 2, + 3 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "III": { + "": { + "crystal_radius": 0.15, + "ionic_radius": 0.01 + } + }, + "IV": { + "": { + "crystal_radius": 0.25, + "ionic_radius": 0.11 + } + }, + "VI": { + "": { + "crystal_radius": 0.41, + "ionic_radius": 0.27 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "27 W m-1 K-1", + "Van der waals radius": 1.92, + "Velocity of sound": "16200 m s-1", + "Vickers hardness": "49000 MN m-2", + "X": 2.04, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "B-10": 84.59, + "B-11": 40.59 + }, + "Metallic radius": "no data", + "iupac_ordering": 81, + "IUPAC ordering": 81, + "Ground level": "2P°1/2", + "Ionization energies": [ + 8.298019, + 25.15483, + 37.93059, + 259.3715, + 340.2260229 + ], + "Electron affinity": 0.27972325 + }, + "Ba": { + "Atomic mass": 137.327, + "Atomic no": 56, + "Atomic orbitals": { + "1s": -1305.743258, + "2p": -189.598483, + "2s": -200.844444, + "3d": -28.528933, + "3p": -37.536931, + "3s": -42.359434, + "4d": -3.432441, + "4p": -6.497622, + "4s": -8.257061, + "5p": -0.698605, + "5s": -1.157159, + "6s": -0.118967 + }, + "Atomic radius": 2.15, + "Atomic radius calculated": 2.53, + "Boiling point": "2143 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "9.6 GPa", + "Coefficient of linear thermal expansion": "20.6 x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "3510 kg m-3", + "Electrical resistivity": "34 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].6s2", + "2": "[Kr].4d10.5s2.5p6" + }, + "ICSD oxidation states": [ + 2 + ], + "Ionic radii": { + "2": 1.49 + }, + "Liquid range": "1143 K", + "Melting point": "1000 K", + "Mendeleev no": 14, + "Mineral hardness": "1.25", + "Molar volume": "38.16 cm3", + "Name": "Barium", + "Oxidation states": [ + 2 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "4.9 GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1.49, + "ionic_radius": 1.35 + } + }, + "VII": { + "": { + "crystal_radius": 1.52, + "ionic_radius": 1.38 + } + }, + "VIII": { + "": { + "crystal_radius": 1.56, + "ionic_radius": 1.42 + } + }, + "IX": { + "": { + "crystal_radius": 1.61, + "ionic_radius": 1.47 + } + }, + "X": { + "": { + "crystal_radius": 1.66, + "ionic_radius": 1.52 + } + }, + "XI": { + "": { + "crystal_radius": 1.71, + "ionic_radius": 1.57 + } + }, + "XII": { + "": { + "crystal_radius": 1.75, + "ionic_radius": 1.61 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "18 W m-1 K-1", + "Van der waals radius": 2.68, + "Velocity of sound": "1620 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 0.89, + "Youngs modulus": "13 GPa", + "Metallic radius": 2.236, + "iupac_ordering": 13, + "IUPAC ordering": 13, + "Ground level": "1S0", + "Ionization energies": [ + 5.2116646, + 10.003826, + 35.8438, + 47, + 58, + 71, + 86, + 101, + 130.5, + 146.52, + 241, + 267.1, + 296, + 325, + 354, + 390, + 422, + 455, + 488, + 520, + 646, + 679, + 717, + 752, + 809, + 846, + 935, + 976.62, + 1695, + 1776, + 1864, + 1958, + 2047, + 2142, + 2256, + 2349, + 2452, + 2547, + 2814, + 2901, + 2994, + 3081, + 3266, + 3363, + 3546, + 3640, + 8326, + 8565, + 8831, + 9077, + 9739, + 10023, + 10376, + 10616.42, + 43485.366, + 44561.47 + ], + "Electron affinity": 0.144626 + }, + "Be": { + "Atomic mass": 9.012182, + "Atomic no": 4, + "Atomic orbitals": { + "1s": -3.856411, + "2s": -0.205744 + }, + "Atomic radius": 1.05, + "Atomic radius calculated": 1.12, + "Boiling point": "2742 K", + "Brinell hardness": "600 MN m-2", + "Bulk modulus": "130 GPa", + "Coefficient of linear thermal expansion": "11.3 x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "1848 kg m-3", + "Electrical resistivity": "3.8 10-8 Ω m", + "Electronic structure": { + "0": "[He].2s2", + "2": "1s2" + }, + "ICSD oxidation states": [ + 2 + ], + "Ionic radii": { + "2": 0.59 + }, + "Liquid range": "1182 K", + "Melting point": "1560 K", + "Mendeleev no": 77, + "Mineral hardness": "5.5", + "Molar volume": "4.85 cm3", + "Name": "Beryllium", + "Oxidation states": [ + 2 + ], + "Poissons ratio": "0.032", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "132 GPa", + "Shannon radii": { + "2": { + "III": { + "": { + "crystal_radius": 0.3, + "ionic_radius": 0.16 + } + }, + "IV": { + "": { + "crystal_radius": 0.41, + "ionic_radius": 0.27 + } + }, + "VI": { + "": { + "crystal_radius": 0.59, + "ionic_radius": 0.45 + } + } + } + }, + "Superconduction temperature": "0.026 K", + "Thermal conductivity": "190 W m-1 K-1", + "Van der waals radius": 1.53, + "Velocity of sound": "13000 m s-1", + "Vickers hardness": "1670 MN m-2", + "X": 1.57, + "Youngs modulus": "287 GPa", + "NMR Quadrupole Moment": { + "Be-9": 52.88 + }, + "Metallic radius": 1.12, + "iupac_ordering": 17, + "IUPAC ordering": 17, + "Ground level": "1S0", + "Ionization energies": [ + 9.322699, + 18.21115, + 153.896205, + 217.7185861 + ], + "Electron affinity": -0.52 + }, + "Bi": { + "Atomic mass": 208.9804, + "Atomic no": 83, + "Atomic orbitals": { + "1s": -2975.550959, + "2p": -484.716359, + "2s": -502.950758, + "3d": -95.532476, + "3p": -111.883393, + "3s": -120.613998, + "4d": -16.084817, + "4f": -6.382744, + "4p": -23.218641, + "4s": -27.07034, + "5d": -1.139408, + "5p": -3.293637, + "5s": -4.611934, + "6p": -0.180198, + "6s": -0.426129 + }, + "Atomic radius": 1.6, + "Atomic radius calculated": 1.43, + "Boiling point": "1837 K", + "Brinell hardness": "94.2 MN m-2", + "Bulk modulus": "31 GPa", + "Coefficient of linear thermal expansion": "13.4 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "9780 kg m-3", + "Electrical resistivity": "130 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d10.6s2.6p3", + "3": "[Xe].4f14.5d10.6s2" + }, + "ICSD oxidation states": [ + 1, + 2, + 3, + 5 + ], + "Ionic radii": { + "3": 1.17, + "5": 0.9 + }, + "Liquid range": "1292.6 K", + "Melting point": "544.4 K", + "Mendeleev no": 87, + "Mineral hardness": "2.25", + "Molar volume": "21.31 cm3", + "Name": "Bismuth", + "Oxidation states": [ + -3, + 3, + 5 + ], + "Poissons ratio": "0.33", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "12 GPa", + "Shannon radii": { + "3": { + "V": { + "": { + "crystal_radius": 1.1, + "ionic_radius": 0.96 + } + }, + "VI": { + "": { + "crystal_radius": 1.17, + "ionic_radius": 1.03 + } + }, + "VIII": { + "": { + "crystal_radius": 1.31, + "ionic_radius": 1.17 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.9, + "ionic_radius": 0.76 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "8 W m-1 K-1", + "Van der waals radius": 2.07, + "Velocity of sound": "1790 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.02, + "Youngs modulus": "32 GPa", + "Metallic radius": 1.82, + "iupac_ordering": 87, + "IUPAC ordering": 87, + "Ground level": "4S°3/2", + "Ionization energies": [ + 7.285516, + 16.703, + 25.57075, + 45.37, + 54.856, + 88.4, + 103, + 122, + 143, + 161.1, + 183, + 208, + 229, + 252, + 272.6, + 370.2, + 409, + 436, + 464, + 520, + 550, + 620, + 660, + 690, + 750, + 810, + 870, + 930, + 990, + 1060, + 1120, + 1180, + 1250, + 1310, + 1380, + 1440, + 1500, + 1784, + 1840, + 1902, + 1967, + 2029, + 2090, + 2190, + 2253, + 2321, + 2385, + 2641, + 2703, + 2771, + 2835, + 3078, + 3151, + 3329, + 3401.8, + 5599, + 5740, + 5892, + 6054, + 6208, + 6358, + 6648, + 6804, + 6977, + 7137, + 7580, + 7720, + 7870, + 8010, + 8780, + 8950, + 9270, + 9430, + 20130, + 20500, + 20920, + 21300, + 24150, + 24640, + 25260, + 25656.9, + 102251.76, + 104132.8 + ], + "Electron affinity": 0.94236213 + }, + "Bk": { + "Atomic mass": 247, + "Atomic no": 97, + "Atomic orbitals": "no data", + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "14780 kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f9.7s2", + "3": "[Rn].5f8" + }, + "Ionic radii": { + "3": 1.1, + "4": 0.97 + }, + "Liquid range": "no data K", + "Melting point": "1259 K", + "Mendeleev no": 40, + "Mineral hardness": "no data", + "Molar volume": "16.84 cm3", + "Name": "Berkelium", + "Oxidation states": [ + 3, + 4 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.1, + "ionic_radius": 0.96 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.97, + "ionic_radius": 0.83 + } + }, + "VIII": { + "": { + "crystal_radius": 1.07, + "ionic_radius": 0.93 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "10 W m-1 K-1", + "Van der waals radius": 2.44, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.3, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.703, + "iupac_ordering": 24, + "IUPAC ordering": 24, + "Ground level": "6H°15/2", + "Ionization energies": [ + 6.19785, + 11.9, + 21.6, + 36, + 56, + 70.1, + 90, + 114, + 130, + 147, + 171, + 195, + 218, + 240, + 259, + 279, + 303, + 339, + 361, + 497, + 526, + 557, + 590, + 621, + 652, + 700, + 733, + 768, + 800, + 960, + 1000, + 1040, + 1080, + 1200, + 1240, + 1360, + 1410, + 1550, + 1630, + 1720, + 1800, + 1890, + 1970, + 2050, + 2140, + 2240, + 2320, + 2410, + 2490, + 2580, + 2670, + 3080, + 3154, + 3232, + 3315, + 3393, + 3469, + 3630, + 3709, + 3797, + 3877, + 4202, + 4281, + 4365, + 4445, + 4940, + 5040, + 5270, + 5360, + 8500, + 8670, + 8850, + 9050, + 9240, + 9420, + 9880, + 10070, + 10280, + 10480, + 11020, + 11190, + 11380, + 11550, + 13090, + 13300, + 13720, + 13910, + 28380, + 28800, + 29300, + 29800, + 35500, + 36200, + 37000, + 37457.6, + 146904.7, + 149398 + ], + "Electron affinity": -1.72 + }, + "Br": { + "Atomic mass": 79.904, + "Atomic no": 35, + "Atomic orbitals": { + "1s": -480.182643, + "2p": -55.67796, + "2s": -61.710022, + "3d": -2.52211, + "3p": -6.298805, + "3s": -8.409057, + "4p": -0.295334, + "4s": -0.720066 + }, + "Atomic radius": 1.15, + "Atomic radius calculated": 0.94, + "Boiling point": "332 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "1.9 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -1, + 1, + 3, + 5, + 7 + ], + "Critical temperature": "586 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "> 101810-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d10.4s2.4p5", + "-1": "[Ar].3d10.4s2.4p6", + "1": "[Ar].3d10.4s2.4p4", + "3": "[Ar].3d10.4s2.4p2", + "5": "[Ar].3d10.4s2", + "7": "[Ar].3d10" + }, + "ICSD oxidation states": [ + 5, + -1 + ], + "Ionic radii": { + "3": 0.73, + "5": 0.45, + "7": 0.53, + "-1": 1.82 + }, + "Liquid range": "66.2 K", + "Melting point": "265.8 K", + "Mendeleev no": 98, + "Mineral hardness": "no data", + "Molar volume": "19.78 cm3", + "Name": "Bromine", + "Oxidation states": [ + -1, + 1, + 3, + 4, + 5, + 7 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.001132", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "IVSQ": { + "": { + "crystal_radius": 0.73, + "ionic_radius": 0.59 + } + } + }, + "5": { + "IIIPY": { + "": { + "crystal_radius": 0.45, + "ionic_radius": 0.31 + } + } + }, + "7": { + "IV": { + "": { + "crystal_radius": 0.39, + "ionic_radius": 0.25 + } + }, + "VI": { + "": { + "crystal_radius": 0.53, + "ionic_radius": 0.39 + } + } + }, + "-1": { + "VI": { + "": { + "crystal_radius": 1.82, + "ionic_radius": 1.96 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.12 W m-1 K-1", + "Van der waals radius": 1.85, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.96, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.14, + "iupac_ordering": 100, + "IUPAC ordering": 100, + "Ground level": "2P°3/2", + "Ionization energies": [ + 11.81381, + 21.591, + 34.871, + 47.782, + 59.595, + 87.39, + 103.03, + 192.61, + 224, + 261, + 301, + 338, + 393, + 436, + 481, + 530, + 577, + 716.3, + 761, + 809.8, + 870, + 920.8, + 963, + 1070.6, + 1119.17, + 2731.4, + 2869, + 3021, + 3169, + 3361, + 3523.1, + 3735, + 3868.986, + 16317.011, + 16937.127 + ], + "Electron affinity": 3.3635883 + }, + "C": { + "Atomic mass": 12.0107, + "Atomic no": 6, + "Atomic orbitals": { + "1s": -9.947718, + "2p": -0.199186, + "2s": -0.500866 + }, + "Atomic radius": 0.7, + "Atomic radius calculated": 0.67, + "Boiling point": "4300 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "33 GPa", + "Coefficient of linear thermal expansion": "7.1 x10-6K-1", + "Common oxidation states": [ + -4, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "2267 kg m-3", + "Electrical resistivity": "about 1000 - direction dependent10-8 Ω m", + "Electronic structure": { + "0": "[He].2s2.2p2", + "-4": "[He].2s2.2p6", + "4": "1s2" + }, + "ICSD oxidation states": [ + 2, + 3, + 4, + -4, + -3, + -2 + ], + "Ionic radii": { + "4": 0.3 + }, + "Liquid range": "500 K", + "Melting point": "3800 K", + "Mendeleev no": 95, + "Mineral hardness": "0.5 (graphite; diamond is 10.0)(no units)", + "Molar volume": "5.29 cm3", + "Name": "Carbon", + "Oxidation states": [ + -4, + -3, + -2, + -1, + 1, + 2, + 3, + 4 + ], + "Poissons ratio": "no data", + "Reflectivity": "27 %", + "Refractive index": "2.417 (diamond)(no units)", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "4": { + "III": { + "": { + "crystal_radius": 0.06, + "ionic_radius": -0.08 + } + }, + "IV": { + "": { + "crystal_radius": 0.29, + "ionic_radius": 0.15 + } + }, + "VI": { + "": { + "crystal_radius": 0.3, + "ionic_radius": 0.16 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "140 W m-1 K-1", + "Van der waals radius": 1.7, + "Velocity of sound": "18350 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.55, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "C-11": 33.27 + }, + "Metallic radius": "no data", + "iupac_ordering": 86, + "IUPAC ordering": 86, + "Ground level": "3P0", + "Ionization energies": [ + 11.260288, + 24.383154, + 47.88778, + 64.49352, + 392.090518, + 489.993198 + ], + "Electron affinity": 1.262113612 + }, + "Ca": { + "Atomic mass": 40.078, + "Atomic no": 20, + "Atomic orbitals": { + "1s": -143.935181, + "2p": -12.285376, + "2s": -15.046905, + "3p": -1.030572, + "3s": -1.706331, + "4s": -0.141411 + }, + "Atomic radius": 1.8, + "Atomic radius calculated": 1.94, + "Boiling point": "1757 K", + "Brinell hardness": "167 MN m-2", + "Bulk modulus": "17 GPa", + "Coefficient of linear thermal expansion": "22.3 x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "1550 kg m-3", + "Electrical resistivity": "3.4 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].4s2", + "2": "[Ne].3s2.3p6" + }, + "ICSD oxidation states": [ + 2 + ], + "Ionic radii": { + "2": 1.14 + }, + "Liquid range": "642 K", + "Melting point": "1115 K", + "Mendeleev no": 16, + "Mineral hardness": "1.75", + "Molar volume": "26.20 cm3", + "Name": "Calcium", + "Oxidation states": [ + 2 + ], + "Poissons ratio": "0.31", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "7.4 GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1.14, + "ionic_radius": 1 + } + }, + "VII": { + "": { + "crystal_radius": 1.2, + "ionic_radius": 1.06 + } + }, + "VIII": { + "": { + "crystal_radius": 1.26, + "ionic_radius": 1.12 + } + }, + "IX": { + "": { + "crystal_radius": 1.32, + "ionic_radius": 1.18 + } + }, + "X": { + "": { + "crystal_radius": 1.37, + "ionic_radius": 1.23 + } + }, + "XII": { + "": { + "crystal_radius": 1.48, + "ionic_radius": 1.34 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "200 W m-1 K-1", + "Van der waals radius": 2.31, + "Velocity of sound": "3810 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1, + "Youngs modulus": "20 GPa", + "NMR Quadrupole Moment": { + "Ca-41": -66.5, + "Ca-43": -40.8 + }, + "Metallic radius": 1.976, + "iupac_ordering": 15, + "IUPAC ordering": 15, + "Ground level": "1S0", + "Ionization energies": [ + 6.11315547, + 11.871719, + 50.91316, + 67.2732, + 84.34, + 108.78, + 127.21, + 147.24, + 188.54, + 211.275, + 591.6, + 658.2, + 728.6, + 817.2, + 894, + 973.7, + 1086.8, + 1157.726, + 5128.8578, + 5469.8616 + ], + "Electron affinity": 0.024551 + }, + "Cd": { + "Atomic mass": 112.411, + "Atomic no": 48, + "Atomic orbitals": { + "1s": -941.476646, + "2p": -127.63512, + "2s": -136.83249, + "3d": -14.685252, + "3p": -21.637522, + "3s": -25.379908, + "4d": -0.47053, + "4p": -2.39526, + "4s": -3.596069, + "5s": -0.204228 + }, + "Atomic radius": 1.55, + "Atomic radius calculated": 1.61, + "Boiling point": "1040 K", + "Brinell hardness": "203 MN m-2", + "Bulk modulus": "42 GPa", + "Coefficient of linear thermal expansion": "30.8 x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "8650 kg m-3", + "Electrical resistivity": "7 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d10.5s2", + "2": "[Kr].4d10" + }, + "ICSD oxidation states": [ + 2 + ], + "Ionic radii": { + "2": 1.09 + }, + "Liquid range": "445.78 K", + "Melting point": "594.22 K", + "Mendeleev no": 75, + "Mineral hardness": "2.0", + "Molar volume": "13.00 cm3", + "Name": "Cadmium", + "Oxidation states": [ + 1, + 2 + ], + "Poissons ratio": "0.30", + "Reflectivity": "67 %", + "Refractive index": "no data", + "Rigidity modulus": "19 GPa", + "Shannon radii": { + "2": { + "IV": { + "": { + "crystal_radius": 0.92, + "ionic_radius": 0.78 + } + }, + "V": { + "": { + "crystal_radius": 1.01, + "ionic_radius": 0.87 + } + }, + "VI": { + "": { + "crystal_radius": 1.09, + "ionic_radius": 0.95 + } + }, + "VII": { + "": { + "crystal_radius": 1.17, + "ionic_radius": 1.03 + } + }, + "VIII": { + "": { + "crystal_radius": 1.24, + "ionic_radius": 1.1 + } + }, + "XII": { + "": { + "crystal_radius": 1.45, + "ionic_radius": 1.31 + } + } + } + }, + "Superconduction temperature": "0.517 K", + "Thermal conductivity": "97 W m-1 K-1", + "Van der waals radius": 2.18, + "Velocity of sound": "2310 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.69, + "Youngs modulus": "50 GPa", + "Metallic radius": 1.51, + "iupac_ordering": 75, + "IUPAC ordering": 75, + "Ground level": "1S0", + "Ionization energies": [ + 8.99382, + 16.908313, + 37.468, + 51, + 67.9, + 87, + 105, + 130.1, + 150, + 173, + 195, + 218, + 305, + 329, + 358, + 385, + 421, + 452.6, + 513, + 546.19, + 963, + 1026, + 1095, + 1167, + 1237, + 1320, + 1401, + 1477, + 1558, + 1635, + 1852, + 1917.9, + 1998, + 2091, + 2195, + 2250, + 2427, + 2498.62, + 5839, + 6039, + 6257, + 6460, + 6869, + 7109, + 7414, + 7607.95, + 31451.062, + 32341.49 + ], + "Electron affinity": -0.72 + }, + "Ce": { + "Atomic mass": 140.116, + "Atomic no": 58, + "Atomic orbitals": { + "1s": -1406.148284, + "2p": -206.925148, + "2s": -218.684842, + "3d": -32.412569, + "3p": -41.938282, + "3s": -47.035283, + "4d": -4.192548, + "4f": -0.337442, + "4p": -7.532106, + "4s": -9.432744, + "5d": -0.14055, + "5p": -0.85011, + "5s": -1.369728, + "6s": -0.133974 + }, + "Atomic radius": 1.85, + "Atomic radius calculated": "no data", + "Boiling point": "3633 K", + "Brinell hardness": "412 MN m-2", + "Bulk modulus": "22 GPa", + "Coefficient of linear thermal expansion": "6.3 x10-6K-1", + "Common oxidation states": [ + 3, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "6689 kg m-3", + "Electrical resistivity": "74 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f1.5d1.6s2", + "3": "[Xe].4f1", + "4": "[Cd].5p6" + }, + "ICSD oxidation states": [ + 3, + 4 + ], + "Ionic radii": { + "3": 1.15, + "4": 1.01 + }, + "Liquid range": "2565 K", + "Melting point": "1068 K", + "Mendeleev no": 32, + "Mineral hardness": "2.5", + "Molar volume": "20.69 cm3", + "Name": "Cerium", + "Oxidation states": [ + 2, + 3, + 4 + ], + "Poissons ratio": "0.24", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "14 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.15, + "ionic_radius": 1.01 + } + }, + "VII": { + "": { + "crystal_radius": 1.21, + "ionic_radius": 1.07 + } + }, + "VIII": { + "": { + "crystal_radius": 1.283, + "ionic_radius": 1.143 + } + }, + "IX": { + "": { + "crystal_radius": 1.336, + "ionic_radius": 1.196 + } + }, + "X": { + "": { + "crystal_radius": 1.39, + "ionic_radius": 1.25 + } + }, + "XII": { + "": { + "crystal_radius": 1.48, + "ionic_radius": 1.34 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 1.01, + "ionic_radius": 0.87 + } + }, + "VIII": { + "": { + "crystal_radius": 1.11, + "ionic_radius": 0.97 + } + }, + "X": { + "": { + "crystal_radius": 1.21, + "ionic_radius": 1.07 + } + }, + "XII": { + "": { + "crystal_radius": 1.28, + "ionic_radius": 1.14 + } + } + } + }, + "Superconduction temperature": "0.022 (under pressure)K", + "Thermal conductivity": "11 W m-1 K-1", + "Van der waals radius": 2.42, + "Velocity of sound": "2100 m s-1", + "Vickers hardness": "270 MN m-2", + "X": 1.12, + "Youngs modulus": "34 GPa", + "Metallic radius": 1.707, + "iupac_ordering": 46, + "IUPAC ordering": 46, + "Ground level": "1G°4", + "Ionization energies": [ + 5.5386, + 10.956, + 20.1974, + 36.906, + 65.55, + 77.6, + 91, + 106, + 125, + 140, + 172, + 192.24, + 312, + 340, + 371, + 403, + 435, + 472, + 509, + 543, + 579, + 613, + 749, + 785, + 824, + 862, + 924, + 965, + 1060, + 1103.5, + 1908, + 1994, + 2087, + 2185, + 2280, + 2378, + 2500, + 2600, + 2706, + 2806, + 3087, + 3176, + 3274, + 3366, + 3570, + 3672, + 3865, + 3963, + 9020, + 9269, + 9545, + 9803, + 10542, + 10840, + 11210, + 11459.85, + 46840.306, + 47965.72 + ], + "Electron affinity": 0.572 + }, + "Cf": { + "Atomic mass": 251, + "Atomic no": 98, + "Atomic orbitals": "no data", + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "15100 kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f10.7s2", + "3": "[Rn].5f9" + }, + "Ionic radii": { + "3": 1.09, + "4": 0.961 + }, + "Liquid range": "no data K", + "Melting point": "1173 K", + "Mendeleev no": 39, + "Mineral hardness": "no data", + "Molar volume": "16.50 cm3", + "Name": "Californium", + "Oxidation states": [ + 2, + 3, + 4 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.09, + "ionic_radius": 0.95 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.961, + "ionic_radius": 0.821 + } + }, + "VIII": { + "": { + "crystal_radius": 1.06, + "ionic_radius": 0.92 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "no data W m-1 K-1", + "Van der waals radius": 2.45, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.3, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.86, + "iupac_ordering": 23, + "IUPAC ordering": 23, + "Ground level": "5I8", + "Ionization energies": [ + 6.28166, + 12, + 22.4, + 37.7, + 51.9, + 75, + 91, + 112.9, + 133, + 152, + 178, + 201, + 225, + 247, + 265, + 286, + 310, + 334, + 368, + 390, + 536, + 566, + 597, + 630, + 662, + 695, + 744, + 778, + 814, + 847, + 1010, + 1050, + 1090, + 1120, + 1250, + 1300, + 1420, + 1470, + 1620, + 1700, + 1790, + 1880, + 1960, + 2050, + 2130, + 2220, + 2320, + 2410, + 2490, + 2580, + 2670, + 2750, + 3186, + 3261, + 3340, + 3424, + 3503, + 3581, + 3747, + 3828, + 3915, + 3998, + 4329, + 4407, + 4494, + 4570, + 5100, + 5190, + 5430, + 5520, + 8730, + 8900, + 9090, + 9290, + 9480, + 9660, + 10140, + 10330, + 10550, + 10740, + 11300, + 11470, + 11650, + 11820, + 13450, + 13660, + 14080, + 14280, + 29000, + 29500, + 30000, + 30500, + 36500, + 37100, + 37900, + 38443.5, + 150579.3, + 153124 + ], + "Electron affinity": -1.01 + }, + "Cl": { + "Atomic mass": 35.453, + "Atomic no": 17, + "Atomic orbitals": { + "1s": -100.369229, + "2p": -7.039982, + "2s": -9.187993, + "3p": -0.32038, + "3s": -0.754458 + }, + "Atomic radius": 1, + "Atomic radius calculated": 0.79, + "Boiling point": "239.11 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "1.1 (liquid)GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -1, + 1, + 3, + 5, + 7 + ], + "Critical temperature": "417 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "> 101010-8 Ω m", + "Electronic structure": { + "0": "[Ne].3s2.3p5", + "-1": "[Ne].3s2.3p6", + "1": "[Ne].3s2.3p4", + "3": "[Ne].3s2.3p2", + "5": "[Ne].3s2", + "7": "1s2.2s2.2p6" + }, + "ICSD oxidation states": [ + -1 + ], + "Ionic radii": { + "5": 0.26, + "7": 0.41, + "-1": 1.67 + }, + "Liquid range": "67.51 K", + "Melting point": "171.6 K", + "Mendeleev no": 99, + "Mineral hardness": "no data", + "Molar volume": "17.39 cm3", + "Name": "Chlorine", + "Oxidation states": [ + -1, + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000773", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "5": { + "IIIPY": { + "": { + "crystal_radius": 0.26, + "ionic_radius": 0.12 + } + } + }, + "7": { + "IV": { + "": { + "crystal_radius": 0.22, + "ionic_radius": 0.08 + } + }, + "VI": { + "": { + "crystal_radius": 0.41, + "ionic_radius": 0.27 + } + } + }, + "-1": { + "VI": { + "": { + "crystal_radius": 1.67, + "ionic_radius": 1.81 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.0089 W m-1 K-1", + "Van der waals radius": 1.75, + "Velocity of sound": "206 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 3.16, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "Cl-35": -81.65, + "Cl-37": -64.35 + }, + "Metallic radius": "no data", + "iupac_ordering": 101, + "IUPAC ordering": 101, + "Ground level": "2P°3/2", + "Ionization energies": [ + 12.967633, + 23.81364, + 39.8, + 53.24, + 67.68, + 96.94, + 114.2013, + 348.306, + 400.851, + 456.7, + 530, + 591.58, + 656.3, + 750.23, + 809.198, + 3658.3438, + 3946.2909 + ], + "Electron affinity": 3.61272528 + }, + "Cm": { + "Atomic mass": 247, + "Atomic no": 96, + "Atomic orbitals": "no data", + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "3383 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "13510 kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f7.6d1.7s2", + "3": "[Rn].5f7" + }, + "Ionic radii": { + "3": 1.11, + "4": 0.99 + }, + "Liquid range": "1770 K", + "Melting point": "1613 K", + "Mendeleev no": 41, + "Mineral hardness": "no data", + "Molar volume": "18.05 cm3", + "Name": "Curium", + "Oxidation states": [ + 3, + 4 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.11, + "ionic_radius": 0.97 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.99, + "ionic_radius": 0.85 + } + }, + "VIII": { + "": { + "crystal_radius": 1.09, + "ionic_radius": 0.95 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "8.8 W m-1 K-1", + "Van der waals radius": 2.45, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.3, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.743, + "iupac_ordering": 25, + "IUPAC ordering": 25, + "Ground level": "9D°2", + "Ionization energies": [ + 5.99141, + 12.4, + 20.1, + 37.7, + 51, + 69.1, + 97, + 112, + 128, + 144, + 167, + 190, + 213, + 235, + 253, + 272, + 311, + 332, + 460, + 489, + 518, + 550, + 580, + 611, + 657, + 689, + 723, + 755, + 910, + 950, + 990, + 1030, + 1140, + 1180, + 1300, + 1340, + 1480, + 1560, + 1650, + 1730, + 1810, + 1890, + 1980, + 2060, + 2160, + 2240, + 2320, + 2410, + 2490, + 2580, + 2976, + 3050, + 3125, + 3207, + 3284, + 3360, + 3515, + 3593, + 3679, + 3758, + 4078, + 4156, + 4239, + 4317, + 4791, + 4880, + 5110, + 5200, + 8270, + 8440, + 8620, + 8820, + 9000, + 9180, + 9630, + 9820, + 10020, + 10220, + 10760, + 10920, + 11100, + 11270, + 12740, + 12950, + 13350, + 13550, + 27740, + 28180, + 28700, + 29100, + 34600, + 35200, + 36000, + 36493, + 143299.6, + 145743 + ], + "Electron affinity": 0.28 + }, + "Co": { + "Atomic mass": 58.933195, + "Atomic no": 27, + "Atomic orbitals": { + "1s": -275.616639, + "2p": -28.152095, + "2s": -32.379758, + "3d": -0.322368, + "3p": -2.388285, + "3s": -3.651812, + "4s": -0.204497 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.52, + "Boiling point": "3200 K", + "Brinell hardness": "700 MN m-2", + "Bulk modulus": "180 GPa", + "Coefficient of linear thermal expansion": "13.0 x10-6K-1", + "Common oxidation states": [ + 2, + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "8900 kg m-3", + "Electrical resistivity": "6 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d7.4s2", + "2": "[Ar].3d7", + "3": "[Ar].3d6" + }, + "ICSD oxidation states": [ + 1, + 2, + 3, + 4 + ], + "Ionic radii": { + "2": 0.885, + "3": 0.75, + "4": 0.67 + }, + "Ionic radii hs": { + "2": 0.885, + "3": 0.75, + "4": 0.67 + }, + "Ionic radii ls": { + "2": 0.79, + "3": 0.685 + }, + "Liquid range": "1432 K", + "Melting point": "1768 K", + "Mendeleev no": 64, + "Mineral hardness": "5.0", + "Molar volume": "6.67 cm3", + "Name": "Cobalt", + "Oxidation states": [ + -1, + 1, + 2, + 3, + 4, + 5 + ], + "Poissons ratio": "0.31", + "Reflectivity": "67 %", + "Refractive index": "no data", + "Rigidity modulus": "75 GPa", + "Shannon radii": { + "2": { + "IV": { + "High Spin": { + "crystal_radius": 0.72, + "ionic_radius": 0.58 + } + }, + "V": { + "": { + "crystal_radius": 0.81, + "ionic_radius": 0.67 + } + }, + "VI": { + "Low Spin": { + "crystal_radius": 0.79, + "ionic_radius": 0.65 + }, + "High Spin": { + "crystal_radius": 0.885, + "ionic_radius": 0.745 + } + }, + "VIII": { + "": { + "crystal_radius": 1.04, + "ionic_radius": 0.9 + } + } + }, + "3": { + "VI": { + "High Spin": { + "crystal_radius": 0.75, + "ionic_radius": 0.61 + }, + "Low Spin": { + "crystal_radius": 0.685, + "ionic_radius": 0.545 + } + } + }, + "4": { + "IV": { + "": { + "crystal_radius": 0.54, + "ionic_radius": 0.4 + } + }, + "VI": { + "High Spin": { + "crystal_radius": 0.67, + "ionic_radius": 0.53 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "100 W m-1 K-1", + "Van der waals radius": 2, + "Velocity of sound": "4720 m s-1", + "Vickers hardness": "1043 MN m-2", + "X": 1.88, + "Youngs modulus": "209 GPa", + "NMR Quadrupole Moment": { + "Co-59": 420.3 + }, + "Metallic radius": 1.25, + "iupac_ordering": 67, + "IUPAC ordering": 67, + "Ground level": "4F9/2", + "Ionization energies": [ + 7.88101, + 17.0844, + 33.5, + 51.27, + 79.5, + 102, + 128.9, + 157.8, + 186.14, + 275.4, + 305.32, + 336.1, + 378.5, + 410, + 441.1, + 511.96, + 546.588, + 1397.2, + 1504.5, + 1606, + 1724, + 1844, + 1960.8, + 2119.4, + 2218.876, + 9544.1833, + 10012.122 + ], + "Electron affinity": 0.662265 + }, + "Cr": { + "Atomic mass": 51.9961, + "Atomic no": 24, + "Atomic orbitals": { + "1s": -213.881191, + "2p": -20.526273, + "2s": -24.113457, + "3d": -0.118123, + "3p": -1.65423, + "3s": -2.649085, + "4s": -0.150445 + }, + "Atomic radius": 1.4, + "Atomic radius calculated": 1.66, + "Boiling point": "2944 K", + "Brinell hardness": "1120 MN m-2", + "Bulk modulus": "160 GPa", + "Coefficient of linear thermal expansion": "4.9 x10-6K-1", + "Common oxidation states": [ + 3, + 6 + ], + "Critical temperature": "no data K", + "Density of solid": "7140 kg m-3", + "Electrical resistivity": "12.7 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d5.4s1", + "2": "[Ar].3d4", + "3": "[Ar].3d3", + "6": "[Ne].3s2.3p6" + }, + "ICSD oxidation states": [ + 2, + 3, + 4, + 5, + 6 + ], + "Ionic radii": { + "2": 0.94 + }, + "Ionic radii hs": { + "2": 0.94 + }, + "Ionic radii ls": { + "2": 0.87, + "3": 0.755, + "4": 0.69, + "5": 0.63, + "6": 0.58 + }, + "Liquid range": "764 K", + "Melting point": "2180 K", + "Mendeleev no": 57, + "Mineral hardness": "8.5", + "Molar volume": "7.23 cm3", + "Name": "Chromium", + "Oxidation states": [ + -2, + -1, + 1, + 2, + 3, + 4, + 5, + 6 + ], + "Poissons ratio": "0.21", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "115 GPa", + "Shannon radii": { + "2": { + "VI": { + "Low Spin": { + "crystal_radius": 0.87, + "ionic_radius": 0.73 + }, + "High Spin": { + "crystal_radius": 0.94, + "ionic_radius": 0.8 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 0.755, + "ionic_radius": 0.615 + } + } + }, + "4": { + "IV": { + "": { + "crystal_radius": 0.55, + "ionic_radius": 0.41 + } + }, + "VI": { + "": { + "crystal_radius": 0.69, + "ionic_radius": 0.55 + } + } + }, + "5": { + "IV": { + "": { + "crystal_radius": 0.485, + "ionic_radius": 0.345 + } + }, + "VI": { + "": { + "crystal_radius": 0.63, + "ionic_radius": 0.49 + } + }, + "VIII": { + "": { + "crystal_radius": 0.71, + "ionic_radius": 0.57 + } + } + }, + "6": { + "IV": { + "": { + "crystal_radius": 0.4, + "ionic_radius": 0.26 + } + }, + "VI": { + "": { + "crystal_radius": 0.58, + "ionic_radius": 0.44 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "94 W m-1 K-1", + "Van der waals radius": 2.06, + "Velocity of sound": "5940 m s-1", + "Vickers hardness": "1060 MN m-2", + "X": 1.66, + "Youngs modulus": "279 GPa", + "NMR Quadrupole Moment": { + "Cr-53": -150.5 + }, + "Metallic radius": 1.285, + "iupac_ordering": 58, + "IUPAC ordering": 58, + "Ground level": "7S3", + "Ionization energies": [ + 6.76651, + 16.486305, + 30.959, + 49.16, + 69.46, + 90.6349, + 160.29, + 184.76, + 209.5, + 244.5, + 270.8, + 296.7, + 354.7, + 384.163, + 1011.6, + 1097.2, + 1188, + 1294.8, + 1394.5, + 1495.1, + 1634.1, + 1721.183, + 7481.8628, + 7894.7992 + ], + "Electron affinity": 0.6758412 + }, + "Cs": { + "Atomic mass": 132.9054519, + "Atomic no": 55, + "Atomic orbitals": { + "1s": -1256.738791, + "2p": -180.995344, + "2s": -191.981873, + "3d": -26.418398, + "3p": -35.166423, + "3s": -39.851584, + "4d": -2.848386, + "4p": -5.769326, + "4s": -7.455966, + "5p": -0.504903, + "5s": -0.915819, + "6s": -0.078699 + }, + "Atomic radius": 2.6, + "Atomic radius calculated": 2.98, + "Boiling point": "944 K", + "Brinell hardness": "0.14 MN m-2", + "Bulk modulus": "1.6 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 1 + ], + "Critical temperature": "1938 K", + "Density of solid": "1879 kg m-3", + "Electrical resistivity": "21 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].6s1", + "1": "[Kr].4d10.5s2.5p6" + }, + "ICSD oxidation states": [ + 1 + ], + "Ionic radii": { + "1": 1.81 + }, + "Liquid range": "642.41 K", + "Melting point": "301.59 K", + "Mendeleev no": 8, + "Mineral hardness": "0.2", + "Molar volume": "70.94 cm3", + "Name": "Cesium", + "Oxidation states": [ + 1 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "1": { + "VI": { + "": { + "crystal_radius": 1.81, + "ionic_radius": 1.67 + } + }, + "VIII": { + "": { + "crystal_radius": 1.88, + "ionic_radius": 1.74 + } + }, + "IX": { + "": { + "crystal_radius": 1.92, + "ionic_radius": 1.78 + } + }, + "X": { + "": { + "crystal_radius": 1.95, + "ionic_radius": 1.81 + } + }, + "XI": { + "": { + "crystal_radius": 1.99, + "ionic_radius": 1.85 + } + }, + "XII": { + "": { + "crystal_radius": 2.02, + "ionic_radius": 1.88 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "36 W m-1 K-1", + "Van der waals radius": 3.43, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 0.79, + "Youngs modulus": "1.7 GPa", + "Metallic radius": 2.719, + "iupac_ordering": 7, + "IUPAC ordering": 7, + "Ground level": "2S1/2", + "Ionization energies": [ + 3.89390572743, + 23.15745, + 33.195, + 43, + 56, + 69.1, + 82.9, + 110.1, + 125.61, + 213.3, + 233, + 261, + 289, + 316, + 352, + 382, + 413, + 445, + 476, + 597, + 629, + 666, + 700, + 753, + 791, + 875, + 916.1, + 1592, + 1672, + 1757, + 1848, + 1936, + 2029, + 2137, + 2230, + 2329, + 2422, + 2683, + 2767, + 2859, + 2945, + 3118, + 3214, + 3392, + 3485, + 7989, + 8224, + 8484, + 8726, + 9350, + 9629, + 9974, + 10208.78, + 41861.075, + 42912.99 + ], + "Electron affinity": 0.47163025 + }, + "Cu": { + "Atomic mass": 63.546, + "Atomic no": 29, + "Atomic orbitals": { + "1s": -320.78852, + "2p": -33.481247, + "2s": -38.14131, + "3d": -0.202272, + "3p": -2.609244, + "3s": -4.057453, + "4s": -0.172056 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.45, + "Boiling point": "3200 K", + "Brinell hardness": "874 MN m-2", + "Bulk modulus": "140 GPa", + "Coefficient of linear thermal expansion": "16.5 x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "8920 kg m-3", + "Electrical resistivity": "1.72 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d10.4s1", + "1": "[Ar].3d10", + "2": "[Ar].3d9", + "3": "[Ar].3d8" + }, + "ICSD oxidation states": [ + 1, + 2, + 3 + ], + "Ionic radii": { + "1": 0.91, + "2": 0.87, + "3": 0.68 + }, + "Liquid range": "1842.23 K", + "Melting point": "1357.77 K", + "Mendeleev no": 72, + "Mineral hardness": "3.0", + "Molar volume": "7.11 cm3", + "Name": "Copper", + "Oxidation states": [ + 1, + 2, + 3, + 4 + ], + "Poissons ratio": "0.34", + "Reflectivity": "90 %", + "Refractive index": "no data", + "Rigidity modulus": "48 GPa", + "Shannon radii": { + "1": { + "II": { + "": { + "crystal_radius": 0.6, + "ionic_radius": 0.46 + } + }, + "IV": { + "": { + "crystal_radius": 0.74, + "ionic_radius": 0.6 + } + }, + "VI": { + "": { + "crystal_radius": 0.91, + "ionic_radius": 0.77 + } + } + }, + "2": { + "IV": { + "": { + "crystal_radius": 0.71, + "ionic_radius": 0.57 + } + }, + "IVSQ": { + "": { + "crystal_radius": 0.71, + "ionic_radius": 0.57 + } + }, + "V": { + "": { + "crystal_radius": 0.79, + "ionic_radius": 0.65 + } + }, + "VI": { + "": { + "crystal_radius": 0.87, + "ionic_radius": 0.73 + } + } + }, + "3": { + "VI": { + "Low Spin": { + "crystal_radius": 0.68, + "ionic_radius": 0.54 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "400 W m-1 K-1", + "Van der waals radius": 1.96, + "Velocity of sound": "3570 m s-1", + "Vickers hardness": "369 MN m-2", + "X": 1.9, + "Youngs modulus": "130 GPa", + "NMR Quadrupole Moment": { + "Cu-63": -220.15, + "Cu-65": -204.14 + }, + "Metallic radius": 1.278, + "iupac_ordering": 73, + "IUPAC ordering": 73, + "Ground level": "2S1/2", + "Ionization energies": [ + 7.72638, + 20.29239, + 36.841, + 57.38, + 79.8, + 103, + 139, + 166, + 198, + 232.2, + 265.33, + 367, + 401, + 436, + 483.1, + 518.7, + 552.8, + 632.5, + 670.608, + 1690.5, + 1800, + 1918, + 2044, + 2179.4, + 2307.3, + 2479.1, + 2586.954, + 11062.4313, + 11567.613 + ], + "Electron affinity": 1.235784 + }, + "Dy": { + "Atomic mass": 162.5, + "Atomic no": 66, + "Atomic orbitals": { + "1s": -1843.229585, + "2p": -281.558531, + "2s": -295.342856, + "3d": -47.4867, + "3p": -59.091931, + "3s": -65.299442, + "4d": -5.686352, + "4f": -0.265302, + "4p": -10.094091, + "4s": -12.551251, + "5p": -0.90349, + "5s": -1.547977, + "6s": -0.132769 + }, + "Atomic radius": 1.75, + "Atomic radius calculated": 2.28, + "Boiling point": "2840 K", + "Brinell hardness": "500 MN m-2", + "Bulk modulus": "41 GPa", + "Coefficient of linear thermal expansion": "9.9 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "8551 kg m-3", + "Electrical resistivity": "92.6 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f10.6s2", + "3": "[Xe].4f9" + }, + "ICSD oxidation states": [ + 3 + ], + "Ionic radii": { + "2": 1.21, + "3": 1.052 + }, + "Liquid range": "1160 K", + "Melting point": "1680 K", + "Mendeleev no": 24, + "Mineral hardness": "no data", + "Molar volume": "19.01 cm3", + "Name": "Dysprosium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "0.25", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "25 GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1.21, + "ionic_radius": 1.07 + } + }, + "VII": { + "": { + "crystal_radius": 1.27, + "ionic_radius": 1.13 + } + }, + "VIII": { + "": { + "crystal_radius": 1.33, + "ionic_radius": 1.19 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 1.052, + "ionic_radius": 0.912 + } + }, + "VII": { + "": { + "crystal_radius": 1.11, + "ionic_radius": 0.97 + } + }, + "VIII": { + "": { + "crystal_radius": 1.167, + "ionic_radius": 1.027 + } + }, + "IX": { + "": { + "crystal_radius": 1.223, + "ionic_radius": 1.083 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "11 W m-1 K-1", + "Van der waals radius": 2.31, + "Velocity of sound": "2710 m s-1", + "Vickers hardness": "540 MN m-2", + "X": 1.22, + "Youngs modulus": "61 GPa", + "Metallic radius": 1.773, + "iupac_ordering": 38, + "IUPAC ordering": 38, + "Ground level": "5I8", + "Ionization energies": [ + 5.93905, + 11.647, + 22.89, + 41.23, + 62.1, + 93, + 110, + 127, + 152, + 170, + 192, + 224, + 259, + 279, + 300, + 332, + 366, + 399, + 431, + 464.9, + 664, + 702, + 743, + 786, + 827, + 872, + 924, + 969, + 1014, + 1059, + 1232, + 1275, + 1325, + 1371, + 1468, + 1520, + 1638, + 1691.7, + 2882, + 2987, + 3098, + 3217, + 3331, + 3445, + 3607, + 3725, + 3852, + 3970, + 4303, + 4407, + 4523, + 4629, + 4945, + 5066, + 5296, + 5412, + 12081, + 12370, + 12690, + 12986, + 14144, + 14495, + 14936, + 15228.06, + 61736.56, + 63073.5 + ], + "Electron affinity": 0.352 + }, + "Er": { + "Atomic mass": 167.259, + "Atomic no": 68, + "Atomic orbitals": { + "1s": -1961.799176, + "2p": -302.01827, + "2s": -316.310631, + "3d": -51.682149, + "3p": -63.818655, + "3s": -70.310142, + "4d": -6.127443, + "4f": -0.278577, + "4p": -10.819574, + "4s": -13.423547, + "5p": -0.935202, + "5s": -1.616073, + "6s": -0.134905 + }, + "Atomic radius": 1.75, + "Atomic radius calculated": 2.26, + "Boiling point": "3141 K", + "Brinell hardness": "814 MN m-2", + "Bulk modulus": "44 GPa", + "Coefficient of linear thermal expansion": "12.2 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "9066 kg m-3", + "Electrical resistivity": "86.0 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f12.6s2", + "3": "[Xe].4f11" + }, + "ICSD oxidation states": [ + 3 + ], + "Ionic radii": { + "3": 1.03 + }, + "Liquid range": "1371 K", + "Melting point": "1802 K", + "Mendeleev no": 22, + "Mineral hardness": "no data", + "Molar volume": "18.46 cm3", + "Name": "Erbium", + "Oxidation states": [ + 3 + ], + "Poissons ratio": "0.24", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "28 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.03, + "ionic_radius": 0.89 + } + }, + "VII": { + "": { + "crystal_radius": 1.085, + "ionic_radius": 0.945 + } + }, + "VIII": { + "": { + "crystal_radius": 1.144, + "ionic_radius": 1.004 + } + }, + "IX": { + "": { + "crystal_radius": 1.202, + "ionic_radius": 1.062 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "15 W m-1 K-1", + "Van der waals radius": 2.29, + "Velocity of sound": "2830 m s-1", + "Vickers hardness": "589 MN m-2", + "X": 1.24, + "Youngs modulus": "70 GPa", + "Metallic radius": 1.756, + "iupac_ordering": 36, + "IUPAC ordering": 36, + "Ground level": "3H6", + "Ionization energies": [ + 6.1077, + 11.916, + 22.7, + 42.42, + 65.1, + 96, + 114, + 131, + 158, + 177, + 201, + 235, + 268, + 290, + 311, + 345, + 381, + 415, + 450, + 486, + 520, + 555, + 770, + 810, + 853, + 899, + 943, + 989, + 1046, + 1092, + 1142, + 1188, + 1370, + 1416, + 1468, + 1516, + 1625, + 1678, + 1803, + 1858.5, + 3157, + 3265, + 3381, + 3505, + 3624, + 3742, + 3916, + 4038, + 4170, + 4294, + 4639, + 4748, + 4866, + 4978, + 5329, + 5455, + 5695, + 5815, + 12918, + 13217, + 13548, + 13855, + 15146, + 15511, + 15971, + 16274.56, + 65848.24, + 67241.9 + ], + "Electron affinity": 0.312 + }, + "Es": { + "Atomic mass": 252, + "Atomic no": 99, + "Atomic orbitals": "no data", + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f11.7s2", + "3": "[Rn].5f10" + }, + "Liquid range": "no data K", + "Melting point": "1133 K", + "Mendeleev no": 38, + "Mineral hardness": "no data", + "Molar volume": "28.52 cm3", + "Name": "Einsteinium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Superconduction temperature": "no data K", + "Thermal conductivity": "no data W m-1 K-1", + "Van der waals radius": 2.45, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.3, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.86, + "iupac_ordering": 22, + "IUPAC ordering": 22, + "Ground level": "4I°15/2", + "Ionization energies": [ + 6.36758, + 12.2, + 22.7, + 38.8, + 54.1, + 71, + 97, + 112.9, + 137, + 157, + 180, + 206, + 231, + 252, + 270, + 294, + 317, + 342, + 367, + 398, + 421, + 576, + 606, + 638, + 672, + 705, + 738, + 790, + 824, + 861, + 895, + 1060, + 1100, + 1140, + 1180, + 1310, + 1360, + 1480, + 1530, + 1690, + 1780, + 1870, + 1950, + 2040, + 2130, + 2220, + 2300, + 2410, + 2490, + 2580, + 2680, + 2760, + 2850, + 3294, + 3370, + 3449, + 3535, + 3616, + 3694, + 3866, + 3947, + 4038, + 4120, + 4456, + 4537, + 4620, + 4700, + 5260, + 5350, + 5600, + 5690, + 8960, + 9140, + 9330, + 9530, + 9720, + 9910, + 10400, + 10590, + 10810, + 11010, + 11570, + 11740, + 11930, + 12110, + 13810, + 14030, + 14460, + 14700, + 29700, + 30100, + 30700, + 31100, + 37400, + 38100, + 38900, + 39451.4, + 154328.1, + 156926 + ], + "Electron affinity": -0.3 + }, + "Eu": { + "Atomic mass": 151.964, + "Atomic no": 63, + "Atomic orbitals": { + "1s": -1672.309322, + "2p": -252.176697, + "2s": -265.199534, + "3d": -41.465518, + "3p": -52.281987, + "3s": -58.068128, + "4d": -5.03242, + "4f": -0.232773, + "4p": -9.025455, + "4s": -11.267747, + "5p": -0.853575, + "5s": -1.444087, + "6s": -0.129426 + }, + "Atomic radius": 1.85, + "Atomic radius calculated": 2.31, + "Boiling point": "1800 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "8.3 GPa", + "Coefficient of linear thermal expansion": "35 x10-6K-1", + "Common oxidation states": [ + 2, + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "5244 kg m-3", + "Electrical resistivity": "90 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f7.6s2", + "2": "[Xe].4f7", + "3": "[Xe].4f6" + }, + "ICSD oxidation states": [ + 2, + 3 + ], + "Ionic radii": { + "2": 1.31, + "3": 1.087 + }, + "Liquid range": "701 K", + "Melting point": "1099 K", + "Mendeleev no": 18, + "Mineral hardness": "no data", + "Molar volume": "28.97 cm3", + "Name": "Europium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "0.15", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "7.9 GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1.31, + "ionic_radius": 1.17 + } + }, + "VII": { + "": { + "crystal_radius": 1.34, + "ionic_radius": 1.2 + } + }, + "VIII": { + "": { + "crystal_radius": 1.39, + "ionic_radius": 1.25 + } + }, + "IX": { + "": { + "crystal_radius": 1.44, + "ionic_radius": 1.3 + } + }, + "X": { + "": { + "crystal_radius": 1.49, + "ionic_radius": 1.35 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 1.087, + "ionic_radius": 0.947 + } + }, + "VII": { + "": { + "crystal_radius": 1.15, + "ionic_radius": 1.01 + } + }, + "VIII": { + "": { + "crystal_radius": 1.206, + "ionic_radius": 1.066 + } + }, + "IX": { + "": { + "crystal_radius": 1.26, + "ionic_radius": 1.12 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "14 W m-1 K-1", + "Van der waals radius": 2.35, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "167 MN m-2", + "X": 1.2, + "Youngs modulus": "18 GPa", + "Metallic radius": 2.041, + "iupac_ordering": 41, + "IUPAC ordering": 41, + "Ground level": "8S°7/2", + "Ionization energies": [ + 5.670385, + 11.24, + 24.84, + 42.94, + 63.2, + 89, + 105, + 120, + 144, + 161, + 183, + 213, + 243, + 263, + 281, + 311, + 344.4, + 518, + 553, + 590, + 630, + 667, + 709, + 755, + 795, + 838, + 879, + 1037, + 1078, + 1124, + 1167, + 1249, + 1296, + 1406, + 1456.06, + 2495, + 2591, + 2697, + 2807, + 2914, + 3022, + 3168, + 3279, + 3398, + 3510, + 3823, + 3921, + 4031, + 4131, + 4400, + 4513, + 4729, + 4838, + 10880, + 11153, + 11457, + 11739, + 12718, + 13050, + 13462, + 13738.58, + 55865.92, + 57120.64 + ], + "Electron affinity": 0.11613 + }, + "F": { + "Atomic mass": 18.9984032, + "Atomic no": 9, + "Atomic orbitals": { + "1s": -24.189391, + "2p": -0.415606, + "2s": -1.086859 + }, + "Atomic radius": 0.5, + "Atomic radius calculated": 0.42, + "Boiling point": "85.03 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -1 + ], + "Critical temperature": "144 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[He].2s2.2p5", + "-1": "[He].2s2.2p6" + }, + "ICSD oxidation states": [ + -1 + ], + "Ionic radii": { + "7": 0.22, + "-1": 1.19 + }, + "Liquid range": "31.5 K", + "Melting point": "53.53 K", + "Mendeleev no": 102, + "Mineral hardness": "no data", + "Molar volume": "11.20 cm3", + "Name": "Fluorine", + "Oxidation states": [ + -1 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000195", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "7": { + "VI": { + "": { + "crystal_radius": 0.22, + "ionic_radius": 0.08 + } + } + }, + "-1": { + "II": { + "": { + "crystal_radius": 1.145, + "ionic_radius": 1.285 + } + }, + "III": { + "": { + "crystal_radius": 1.16, + "ionic_radius": 1.3 + } + }, + "IV": { + "": { + "crystal_radius": 1.17, + "ionic_radius": 1.31 + } + }, + "VI": { + "": { + "crystal_radius": 1.19, + "ionic_radius": 1.33 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.0277 W m-1 K-1", + "Van der waals radius": 1.47, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 3.98, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "F-19": -94.2 + }, + "Metallic radius": "no data", + "iupac_ordering": 102, + "IUPAC ordering": 102, + "Ground level": "2P°3/2", + "Ionization energies": [ + 17.42282, + 34.97081, + 62.70798, + 87.175, + 114.249, + 157.16311, + 185.1868, + 953.89805, + 1103.11748 + ], + "Electron affinity": 3.401189824 + }, + "Fe": { + "Atomic mass": 55.845, + "Atomic no": 26, + "Atomic orbitals": { + "1s": -254.225505, + "2p": -25.551766, + "2s": -29.56486, + "3d": -0.295049, + "3p": -2.187523, + "3s": -3.360621, + "4s": -0.197978 + }, + "Atomic radius": 1.4, + "Atomic radius calculated": 1.56, + "Boiling point": "3134 K", + "Brinell hardness": "490 MN m-2", + "Bulk modulus": "170 GPa", + "Coefficient of linear thermal expansion": "11.8 x10-6K-1", + "Common oxidation states": [ + 2, + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "7874 kg m-3", + "Electrical resistivity": "10 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d6.4s2", + "2": "[Ar].3d6", + "3": "[Ar].3d5" + }, + "ICSD oxidation states": [ + 2, + 3 + ], + "Ionic radii": { + "2": 0.92, + "3": 0.785 + }, + "Ionic radii hs": { + "2": 0.92, + "3": 0.785 + }, + "Ionic radii ls": { + "2": 0.75, + "3": 0.69, + "4": 0.725, + "6": 0.39 + }, + "Liquid range": "1323 K", + "Melting point": "1811 K", + "Mendeleev no": 61, + "Mineral hardness": "4.0", + "Molar volume": "7.09 cm3", + "Name": "Iron", + "Oxidation states": [ + -2, + -1, + 1, + 2, + 3, + 4, + 5, + 6 + ], + "Poissons ratio": "0.29", + "Reflectivity": "65 %", + "Refractive index": "no data", + "Rigidity modulus": "82 GPa", + "Shannon radii": { + "2": { + "IV": { + "High Spin": { + "crystal_radius": 0.77, + "ionic_radius": 0.63 + } + }, + "IVSQ": { + "High Spin": { + "crystal_radius": 0.78, + "ionic_radius": 0.64 + } + }, + "VI": { + "Low Spin": { + "crystal_radius": 0.75, + "ionic_radius": 0.61 + }, + "High Spin": { + "crystal_radius": 0.92, + "ionic_radius": 0.78 + } + }, + "VIII": { + "High Spin": { + "crystal_radius": 1.06, + "ionic_radius": 0.92 + } + } + }, + "3": { + "IV": { + "High Spin": { + "crystal_radius": 0.63, + "ionic_radius": 0.49 + } + }, + "V": { + "": { + "crystal_radius": 0.72, + "ionic_radius": 0.58 + } + }, + "VI": { + "Low Spin": { + "crystal_radius": 0.69, + "ionic_radius": 0.55 + }, + "High Spin": { + "crystal_radius": 0.785, + "ionic_radius": 0.645 + } + }, + "VIII": { + "High Spin": { + "crystal_radius": 0.92, + "ionic_radius": 0.78 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.725, + "ionic_radius": 0.585 + } + } + }, + "6": { + "IV": { + "": { + "crystal_radius": 0.39, + "ionic_radius": 0.25 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "80 W m-1 K-1", + "Van der waals radius": 2.04, + "Velocity of sound": "4910 m s-1", + "Vickers hardness": "608 MN m-2", + "X": 1.83, + "Youngs modulus": "211 GPa", + "NMR Quadrupole Moment": { + "Fe-57": 160 + }, + "Metallic radius": 1.277, + "iupac_ordering": 64, + "IUPAC ordering": 64, + "Ground level": "5D4", + "Ionization energies": [ + 7.9024681, + 16.19921, + 30.651, + 54.91, + 75, + 98.985, + 124.976, + 151.06, + 233.6, + 262.1, + 290.9, + 330.8, + 361, + 392.2, + 456.2, + 489.312, + 1262.7, + 1357.8, + 1460, + 1575.6, + 1687, + 1798.4, + 1950.4, + 2045.759, + 8828.1879, + 9277.6818 + ], + "Electron affinity": 0.15323634 + }, + "Fm": { + "Atomic mass": 257, + "Atomic no": 100, + "Atomic orbitals": "no data", + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f12.7s2", + "3": "[Rn].5f11" + }, + "Liquid range": "no data K", + "Melting point": "about 1800 K", + "Mendeleev no": 37, + "Mineral hardness": "no data", + "Molar volume": "no data cm3", + "Name": "Fermium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Superconduction temperature": "no data K", + "Thermal conductivity": "no data W m-1 K-1", + "Van der waals radius": 2.45, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.3, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 21, + "IUPAC ordering": 21, + "Ground level": "3H6", + "Ionization energies": [ + 6.5, + 12.4, + 23.2, + 39.3, + 55, + 74, + 93, + 120, + 136, + 162, + 185, + 209, + 237, + 257, + 276, + 300, + 326, + 351, + 377, + 402, + 430, + 453, + 616, + 647, + 680, + 716, + 749, + 782, + 837, + 871, + 909, + 944, + 1110, + 1150, + 1190, + 1230, + 1370, + 1420, + 1550, + 1600, + 1770, + 1850, + 1940, + 2030, + 2120, + 2210, + 2300, + 2390, + 2490, + 2590, + 2680, + 2760, + 2850, + 2950, + 3403, + 3480, + 3561, + 3647, + 3730, + 3810, + 3986, + 4070, + 4160, + 4245, + 4586, + 4670, + 4760, + 4840, + 5420, + 5510, + 5760, + 5860, + 9200, + 9370, + 9570, + 9770, + 9970, + 10160, + 10660, + 10860, + 11080, + 11280, + 11850, + 12020, + 12220, + 12390, + 14180, + 14400, + 14800, + 15000, + 30300, + 30800, + 31300, + 31800, + 38400, + 39100, + 40000, + 40482.2, + 158152.5, + 160804 + ], + "Electron affinity": 0.35 + }, + "Fr": { + "Atomic mass": 223, + "Atomic no": 87, + "Atomic orbitals": { + "1s": -3283.263399, + "2p": -542.41424, + "2s": -561.73045, + "3d": -111.085223, + "3p": -128.607136, + "3s": -137.959632, + "4d": -20.812462, + "4f": -10.050648, + "4p": -28.648131, + "4s": -32.861013, + "5d": -2.360991, + "5p": -4.97328, + "5s": -6.509516, + "6p": -0.466197, + "6s": -0.841848, + "7s": -0.076176 + }, + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 1 + ], + "Critical temperature": "no data K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].7s1", + "1": "[Hg].6p6" + }, + "Ionic radii": { + "1": 1.94 + }, + "Liquid range": "no data K", + "Melting point": "maybe about 300 K", + "Mendeleev no": 7, + "Mineral hardness": "no data", + "Molar volume": "no data cm3", + "Name": "Francium", + "Oxidation states": [ + 1 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "1": { + "VI": { + "": { + "crystal_radius": 1.94, + "ionic_radius": 1.8 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "no data W m-1 K-1", + "Van der waals radius": 3.48, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 0.7, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 6, + "IUPAC ordering": 6, + "Ground level": "2S1/2", + "Ionization energies": [ + 4.0727411, + 22.4, + 33.5, + 39.1, + 50, + 67, + 80, + 106, + 120, + 179, + 200, + 222.1, + 245, + 269, + 293, + 324, + 349, + 375, + 400, + 530, + 560, + 590, + 620, + 690, + 720, + 810, + 850, + 910, + 980, + 1040, + 1110, + 1180, + 1250, + 1320, + 1380, + 1460, + 1530, + 1600, + 1670, + 1740, + 1810, + 2119, + 2182, + 2247, + 2317, + 2384, + 2450, + 2564, + 2631, + 2706, + 2774, + 3049, + 3115, + 3190, + 3257, + 3556, + 3635, + 3828, + 3907, + 6365, + 6516, + 6678, + 6849, + 7013, + 7172, + 7500, + 7670, + 7850, + 8020, + 8500, + 8640, + 8800, + 8950, + 9890, + 10070, + 10420, + 10590, + 22330, + 22730, + 23170, + 23570, + 27060, + 27590, + 28260, + 28683.4, + 113817.2, + 115859 + ], + "Electron affinity": 0.486 + }, + "Ga": { + "Atomic mass": 69.723, + "Atomic no": 31, + "Atomic orbitals": { + "1s": -370.170639, + "2p": -40.093339, + "2s": -45.200869, + "3d": -0.736204, + "3p": -3.584666, + "3s": -5.241645, + "4p": -0.101634, + "4s": -0.328019 + }, + "Atomic radius": 1.3, + "Atomic radius calculated": 1.36, + "Boiling point": "2477 K", + "Brinell hardness": "60 MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "120 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "5904 kg m-3", + "Electrical resistivity": "about 14 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d10.4s2.4p1", + "3": "[Ar].3d10" + }, + "ICSD oxidation states": [ + 2, + 3 + ], + "Ionic radii": { + "3": 0.76 + }, + "Liquid range": "2174.09 K", + "Melting point": "302.91 K", + "Mendeleev no": 81, + "Mineral hardness": "1.5", + "Molar volume": "11.80 cm3", + "Name": "Gallium", + "Oxidation states": [ + 1, + 2, + 3 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "IV": { + "": { + "crystal_radius": 0.61, + "ionic_radius": 0.47 + } + }, + "V": { + "": { + "crystal_radius": 0.69, + "ionic_radius": 0.55 + } + }, + "VI": { + "": { + "crystal_radius": 0.76, + "ionic_radius": 0.62 + } + } + } + }, + "Superconduction temperature": "1.083 K", + "Thermal conductivity": "29 W m-1 K-1", + "Van der waals radius": 1.87, + "Velocity of sound": "2740 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.81, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.35, + "iupac_ordering": 79, + "IUPAC ordering": 79, + "Ground level": "2P°1/2", + "Ionization energies": [ + 5.999302, + 20.51514, + 30.72576, + 63.241, + 86.01, + 112.7, + 140.8, + 169.9, + 211, + 244, + 280, + 319, + 356, + 471.2, + 508.8, + 548.3, + 599.8, + 640, + 677, + 765.7, + 807.308, + 2010, + 2129, + 2258, + 2391, + 2543.9, + 2683, + 2868, + 2984.426, + 12696.5575, + 13239.489 + ], + "Electron affinity": 0.3012011 + }, + "Gd": { + "Atomic mass": 157.25, + "Atomic no": 64, + "Atomic orbitals": { + "1s": -1728.625195, + "2p": -262.081616, + "2s": -275.36313, + "3d": -43.754556, + "3p": -54.836922, + "3s": -60.764408, + "4d": -5.531835, + "4f": -0.489012, + "4p": -9.669866, + "4s": -11.986486, + "5d": -0.12722, + "5p": -0.978749, + "5s": -1.608477, + "6s": -0.143627 + }, + "Atomic radius": 1.8, + "Atomic radius calculated": 2.33, + "Boiling point": "3523 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "38 GPa", + "Coefficient of linear thermal expansion": "9.4 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "7901 kg m-3", + "Electrical resistivity": "131 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f7.5d1.6s2", + "3": "[Xe].4f7" + }, + "ICSD oxidation states": [ + 3 + ], + "Ionic radii": { + "3": 1.075 + }, + "Liquid range": "1938 K", + "Melting point": "1585 K", + "Mendeleev no": 27, + "Mineral hardness": "no data", + "Molar volume": "19.90 cm3", + "Name": "Gadolinium", + "Oxidation states": [ + 1, + 2, + 3 + ], + "Poissons ratio": "0.26", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "22 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.078, + "ionic_radius": 0.938 + } + }, + "VII": { + "": { + "crystal_radius": 1.14, + "ionic_radius": 1 + } + }, + "VIII": { + "": { + "crystal_radius": 1.193, + "ionic_radius": 1.053 + } + }, + "IX": { + "": { + "crystal_radius": 1.247, + "ionic_radius": 1.107 + } + } + } + }, + "Superconduction temperature": "1.083 K", + "Thermal conductivity": "11 W m-1 K-1", + "Van der waals radius": 2.34, + "Velocity of sound": "2680 m s-1", + "Vickers hardness": "570 MN m-2", + "X": 1.2, + "Youngs modulus": "55 GPa", + "Metallic radius": 1.802, + "iupac_ordering": 40, + "IUPAC ordering": 40, + "Ground level": "9D°2", + "Ionization energies": [ + 6.1498, + 12.076, + 20.54, + 44.44, + 64.8, + 89, + 106, + 123, + 144, + 165, + 183, + 213, + 246, + 268, + 288, + 319, + 352, + 384.4, + 565, + 601, + 639, + 680, + 719, + 761, + 810, + 851, + 895, + 937, + 1100, + 1142, + 1189, + 1233, + 1321, + 1368, + 1481, + 1532.3, + 2621, + 2720, + 2827, + 2941, + 3050, + 3160, + 3312, + 3424, + 3546, + 3660, + 3980, + 4080, + 4191, + 4294, + 4578, + 4693, + 4914, + 5025, + 11273, + 11552, + 11861, + 12147, + 13183, + 13521, + 13943, + 14224.57, + 57783.9, + 59065.53 + ], + "Electron affinity": 0.137 + }, + "Ge": { + "Atomic mass": 72.64, + "Atomic no": 32, + "Atomic orbitals": { + "1s": -396.292991, + "2p": -43.720129, + "2s": -49.055282, + "3d": -1.117316, + "3p": -4.194822, + "3s": -5.961472, + "4p": -0.149882, + "4s": -0.426523 + }, + "Atomic radius": 1.25, + "Atomic radius calculated": 1.25, + "Boiling point": "3093 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "6 x10-6K-1", + "Common oxidation states": [ + -4, + 2, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "5323 kg m-3", + "Electrical resistivity": "about 50000 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d10.4s2.4p2", + "-4": "[Ar].3d10.4s2.4p6", + "2": "[Ar].3d10.4s2", + "4": "[Ar].3d10" + }, + "ICSD oxidation states": [ + 2, + 3, + 4 + ], + "Ionic radii": { + "2": 0.87, + "4": 0.67 + }, + "Liquid range": "1881.6 K", + "Melting point": "1211.4 K", + "Mendeleev no": 84, + "Mineral hardness": "6.0", + "Molar volume": "13.63 cm3", + "Name": "Germanium", + "Oxidation states": [ + -4, + 1, + 2, + 3, + 4 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 0.87, + "ionic_radius": 0.73 + } + } + }, + "4": { + "IV": { + "": { + "crystal_radius": 0.53, + "ionic_radius": 0.39 + } + }, + "VI": { + "": { + "crystal_radius": 0.67, + "ionic_radius": 0.53 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "60 W m-1 K-1", + "Van der waals radius": 2.11, + "Velocity of sound": "5400 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.01, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.39, + "iupac_ordering": 84, + "IUPAC ordering": 84, + "Ground level": "3P0", + "Ionization energies": [ + 7.899435, + 15.93461, + 34.0576, + 45.7155, + 90.5, + 115.9, + 144.9, + 176.4, + 212.5, + 252.1, + 286, + 326, + 367, + 407, + 527.9, + 567.3, + 609.1, + 662.8, + 706.7, + 744, + 837.1, + 880.44, + 2180.1, + 2304, + 2439, + 2575, + 2737.1, + 2881.9, + 3074, + 3194.293, + 13557.4208, + 14119.43 + ], + "Electron affinity": 1.232676413 + }, + "H": { + "Atomic mass": 1.00794, + "Atomic mass no": 1, + "Atomic no": 1, + "Atomic orbitals": { + "1s": -0.233471 + }, + "Atomic radius": 0.25, + "Atomic radius calculated": 0.53, + "Boiling point": "20.28 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -1, + 1 + ], + "Critical temperature": "33 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "1s1", + "-1": "1s2", + "1": null + }, + "ICSD oxidation states": [ + 1, + -1 + ], + "Is named isotope": false, + "Liquid range": "6.27 K", + "Melting point": "14.01 K", + "Mendeleev no": 103, + "Mineral hardness": "no data", + "Molar volume": "11.42 cm3", + "Name": "Hydrogen", + "Oxidation states": [ + -1, + 1 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000132 (gas; liquid 1.12)(no units)", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "1": { + "I": { + "": { + "crystal_radius": -0.24, + "ionic_radius": -0.38 + } + }, + "II": { + "": { + "crystal_radius": -0.04, + "ionic_radius": -0.18 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.1805 W m-1 K-1", + "Van der waals radius": 1.1, + "Velocity of sound": "1270 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.2, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "H-2": 2.86 + }, + "Metallic radius": "no data", + "iupac_ordering": 92, + "IUPAC ordering": 92, + "Ground level": "2S1/2", + "Ionization energies": [ + 13.598434599702 + ], + "Electron affinity": 0.754598 + }, + "He": { + "Atomic mass": 4.002602, + "Atomic no": 2, + "Atomic orbitals": { + "1s": -0.570425 + }, + "Atomic radius": "no data", + "Atomic radius calculated": 0.31, + "Boiling point": "4.22 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Critical temperature": "5.19 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "1s2" + }, + "Liquid range": "3.27 K", + "Max oxidation state": 0, + "Melting point": "0.95 K", + "Mendeleev no": 1, + "Min oxidation state": 0, + "Mineral hardness": "no data", + "Molar volume": "21.0 cm3", + "Name": "Helium", + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000035 (gas; liquid 1.028)(no units)", + "Rigidity modulus": "no data GPa", + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.1513 W m-1 K-1", + "Van der waals radius": 1.4, + "Velocity of sound": "970 m s-1", + "Vickers hardness": "no data MN m-2", + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 5, + "IUPAC ordering": 5, + "Ground level": "1S0", + "Ionization energies": [ + 24.587389011, + 54.417765486 + ], + "Electron affinity": -0.52 + }, + "Hf": { + "Atomic mass": 178.49, + "Atomic no": 72, + "Atomic orbitals": { + "1s": -2210.65199, + "2p": -345.687023, + "2s": -361.006527, + "3d": -61.231443, + "3p": -74.452656, + "3s": -81.522812, + "4d": -7.676638, + "4f": -0.871574, + "4p": -12.971211, + "4s": -15.883625, + "5d": -0.143805, + "5p": -1.246441, + "5s": -2.049828, + "6s": -0.166465 + }, + "Atomic radius": 1.55, + "Atomic radius calculated": 2.08, + "Boiling point": "4876 K", + "Brinell hardness": "1700 MN m-2", + "Bulk modulus": "110 GPa", + "Coefficient of linear thermal expansion": "5.9 x10-6K-1", + "Common oxidation states": [ + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "13310 kg m-3", + "Electrical resistivity": "34 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d2.6s2", + "4": "[Xe].4f14" + }, + "ICSD oxidation states": [ + 4 + ], + "Ionic radii": { + "4": 0.85 + }, + "Liquid range": "2370 K", + "Melting point": "2506 K", + "Mendeleev no": 50, + "Mineral hardness": "5.5", + "Molar volume": "13.44 cm3", + "Name": "Hafnium", + "Oxidation states": [ + 2, + 3, + 4 + ], + "Poissons ratio": "0.37", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "30 GPa", + "Shannon radii": { + "4": { + "IV": { + "": { + "crystal_radius": 0.72, + "ionic_radius": 0.58 + } + }, + "VI": { + "": { + "crystal_radius": 0.85, + "ionic_radius": 0.71 + } + }, + "VII": { + "": { + "crystal_radius": 0.9, + "ionic_radius": 0.76 + } + }, + "VIII": { + "": { + "crystal_radius": 0.97, + "ionic_radius": 0.83 + } + } + } + }, + "Superconduction temperature": "0.128 K", + "Thermal conductivity": "23 W m-1 K-1", + "Van der waals radius": 2.23, + "Velocity of sound": "3010 m s-1", + "Vickers hardness": "1760 MN m-2", + "X": 1.3, + "Youngs modulus": "78 GPa", + "Metallic radius": 1.58, + "iupac_ordering": 50, + "IUPAC ordering": 50, + "Ground level": "3F2", + "Ionization energies": [ + 6.82507, + 14.61, + 22.55, + 33.37, + 68.37, + 98, + 118, + 137, + 157, + 187, + 209, + 230, + 270, + 310, + 334, + 359, + 399, + 440, + 481, + 520, + 570, + 610, + 650, + 690, + 730, + 772, + 1002, + 1047, + 1094, + 1146, + 1195, + 1245, + 1311, + 1362, + 1417, + 1467, + 1669, + 1719, + 1776, + 1827, + 1963, + 2022, + 2159, + 2218.9, + 3741, + 3858, + 3984, + 4118, + 4246, + 4372, + 4573, + 4703, + 4846, + 4980, + 5350, + 5468, + 5595, + 5713, + 6149, + 6284, + 6545, + 6674, + 14678, + 14999, + 15351, + 15680, + 17280, + 17680, + 18180, + 18502.32, + 74565.93, + 76077.8 + ], + "Electron affinity": 0.17807 + }, + "Hg": { + "Atomic mass": 200.59, + "Atomic no": 80, + "Atomic orbitals": { + "1s": -2755.022637, + "2p": -443.848676, + "2s": -461.27864, + "3d": -84.845492, + "3p": -100.328031, + "3s": -108.597921, + "4d": -13.019221, + "4f": -4.110291, + "4p": -19.636187, + "4s": -23.222921, + "5d": -0.452552, + "5p": -2.261975, + "5s": -3.423486, + "6s": -0.205137 + }, + "Atomic radius": 1.5, + "Atomic radius calculated": 1.71, + "Boiling point": "629.88 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "25 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 1, + 2 + ], + "Critical temperature": "1750 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "96 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d10.6s2", + "1": "[Xe].4f14.5d10.6s1", + "2": "[Xe].4f14.5d10" + }, + "ICSD oxidation states": [ + 1, + 2 + ], + "Ionic radii": { + "1": 1.33, + "2": 1.16 + }, + "Liquid range": "395.56 K", + "Melting point": "234.32 K", + "Mendeleev no": 74, + "Mineral hardness": "1.5", + "Molar volume": "14.09 cm3", + "Name": "Mercury", + "Oxidation states": [ + 1, + 2, + 4 + ], + "Poissons ratio": "no data", + "Reflectivity": "73 %", + "Refractive index": "1.000933", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "1": { + "III": { + "": { + "crystal_radius": 1.11, + "ionic_radius": 0.97 + } + }, + "VI": { + "": { + "crystal_radius": 1.33, + "ionic_radius": 1.19 + } + } + }, + "2": { + "II": { + "": { + "crystal_radius": 0.83, + "ionic_radius": 0.69 + } + }, + "IV": { + "": { + "crystal_radius": 1.1, + "ionic_radius": 0.96 + } + }, + "VI": { + "": { + "crystal_radius": 1.16, + "ionic_radius": 1.02 + } + }, + "VIII": { + "": { + "crystal_radius": 1.28, + "ionic_radius": 1.14 + } + } + } + }, + "Superconduction temperature": "3.95 K", + "Thermal conductivity": "8.3 W m-1 K-1", + "Van der waals radius": 2.23, + "Velocity of sound": "1407 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "Hg-201": 387.6 + }, + "Metallic radius": 1.51, + "iupac_ordering": 74, + "IUPAC ordering": 74, + "Ground level": "1S0", + "Ionization energies": [ + 10.437504, + 18.75688, + 34.49, + 48.55, + 61.2, + 76.6, + 93, + 113.9, + 134, + 153, + 173, + 192.7, + 276.9, + 307, + 332, + 357, + 402, + 429, + 477, + 530, + 560, + 590, + 650, + 710, + 760, + 820, + 880, + 930, + 990, + 1050, + 1110, + 1160, + 1220, + 1280, + 1549, + 1603, + 1661, + 1723, + 1780, + 1839, + 1928, + 1989, + 2052, + 2113, + 2354, + 2412, + 2478, + 2539, + 2745, + 2815, + 2981, + 3049.9, + 5055, + 5191, + 5335, + 5490, + 5636, + 5780, + 6041, + 6192, + 6356, + 6508, + 6933, + 7066, + 7211, + 7350, + 8010, + 8160, + 8470, + 8620, + 18550, + 18910, + 19310, + 19680, + 22120, + 22580, + 23170, + 23544.1, + 94124.7, + 95897.7 + ], + "Electron affinity": -0.52 + }, + "Ho": { + "Atomic mass": 164.93032, + "Atomic no": 67, + "Atomic orbitals": { + "1s": -1902.051908, + "2p": -291.700994, + "2s": -305.739294, + "3d": -49.565996, + "3p": -61.436304, + "3s": -67.785492, + "4d": -5.906195, + "4f": -0.272677, + "4p": -10.455303, + "4s": -12.985498, + "5p": -0.919463, + "5s": -1.582088, + "6s": -0.133845 + }, + "Atomic radius": 1.75, + "Atomic radius calculated": "no data", + "Boiling point": "2993 K", + "Brinell hardness": "746 MN m-2", + "Bulk modulus": "40 GPa", + "Coefficient of linear thermal expansion": "11.2 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "8795 kg m-3", + "Electrical resistivity": "81.4 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f11.6s2", + "3": "[Xe].4f10" + }, + "ICSD oxidation states": [ + 3 + ], + "Ionic radii": { + "3": 1.041 + }, + "Liquid range": "1259 K", + "Melting point": "1734 K", + "Mendeleev no": 23, + "Mineral hardness": "no data", + "Molar volume": "18.74 cm3", + "Name": "Holmium", + "Oxidation states": [ + 3 + ], + "Poissons ratio": "0.23", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "26 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.041, + "ionic_radius": 0.901 + } + }, + "VIII": { + "": { + "crystal_radius": 1.155, + "ionic_radius": 1.015 + } + }, + "IX": { + "": { + "crystal_radius": 1.212, + "ionic_radius": 1.072 + } + }, + "X": { + "": { + "crystal_radius": 1.26, + "ionic_radius": 1.12 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "16 W m-1 K-1", + "Van der waals radius": 2.3, + "Velocity of sound": "2760 m s-1", + "Vickers hardness": "481 MN m-2", + "X": 1.23, + "Youngs modulus": "65 GPa", + "Metallic radius": 1.765, + "iupac_ordering": 37, + "IUPAC ordering": 37, + "Ground level": "4I°15/2", + "Ionization energies": [ + 6.0215, + 11.781, + 22.79, + 42.52, + 63.9, + 95, + 112, + 129, + 155, + 173, + 197, + 229, + 263, + 284, + 305, + 340, + 373, + 408, + 441, + 475, + 510, + 715, + 755, + 797, + 842, + 885, + 929, + 985, + 1029, + 1077, + 1122, + 1300, + 1346, + 1395, + 1443, + 1545, + 1598, + 1719, + 1773.6, + 3018, + 3125, + 3238, + 3359, + 3476, + 3592, + 3760, + 3880, + 4009, + 4131, + 4469, + 4576, + 4693, + 4802, + 5135, + 5258, + 5494, + 5611, + 12495, + 12790, + 13116, + 13417, + 14639, + 14998, + 15448, + 15745.77, + 63772.43, + 65136.8 + ], + "Electron affinity": 0.338 + }, + "I": { + "Atomic mass": 126.90447, + "Atomic no": 53, + "Atomic orbitals": { + "1s": -1161.787047, + "2p": -164.603788, + "2s": -175.073804, + "3d": -22.600693, + "3p": -30.831092, + "3s": -35.243351, + "4d": -1.938179, + "4p": -4.572522, + "4s": -6.115811, + "5p": -0.267904, + "5s": -0.596339 + }, + "Atomic radius": 1.4, + "Atomic radius calculated": 1.15, + "Boiling point": "457.4 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "7.7 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -1, + 1, + 3, + 5, + 7 + ], + "Critical temperature": "819 K", + "Density of solid": "4940 kg m-3", + "Electrical resistivity": "> 101510-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d10.5s2.5p5", + "-1": "[Kr].4d10.5s2.5p6", + "1": "[Kr].4d10.5s2.5p4", + "3": "[Kr].4d10.5s2.5p2", + "5": "[Kr].4d10.5s2", + "7": "[Kr].4d10" + }, + "ICSD oxidation states": [ + 5, + -1 + ], + "Ionic radii": { + "5": 1.09, + "7": 0.67, + "-1": 2.06 + }, + "Liquid range": "70.55 K", + "Melting point": "386.85 K", + "Mendeleev no": 97, + "Mineral hardness": "no data", + "Molar volume": "25.72 cm3", + "Name": "Iodine", + "Oxidation states": [ + -1, + 1, + 3, + 5, + 7 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "5": { + "IIIPY": { + "": { + "crystal_radius": 0.58, + "ionic_radius": 0.44 + } + }, + "VI": { + "": { + "crystal_radius": 1.09, + "ionic_radius": 0.95 + } + } + }, + "7": { + "IV": { + "": { + "crystal_radius": 0.56, + "ionic_radius": 0.42 + } + }, + "VI": { + "": { + "crystal_radius": 0.67, + "ionic_radius": 0.53 + } + } + }, + "-1": { + "VI": { + "": { + "crystal_radius": 2.06, + "ionic_radius": 2.2 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.449 W m-1 K-1", + "Van der waals radius": 1.98, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.66, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "I-127": -696.12, + "I-129": -604.1 + }, + "Metallic radius": "no data", + "iupac_ordering": 99, + "IUPAC ordering": 99, + "Ground level": "2P°3/2", + "Ionization energies": [ + 10.45126, + 19.13126, + 29.57, + 40.357, + 51.52, + 74.4, + 87.61, + 150.81, + 171, + 197, + 220.9, + 247, + 279, + 307, + 335, + 365, + 393, + 505, + 535, + 569, + 601, + 649, + 683, + 762, + 800.8, + 1397, + 1472, + 1553, + 1639, + 1720, + 1812, + 1911, + 1999, + 2093, + 2181, + 2431, + 2510, + 2598, + 2680, + 2836, + 2926, + 3096, + 3185.5, + 7337, + 7563, + 7811, + 8044, + 8601, + 8867, + 9196, + 9421.1, + 38716.996, + 39721.41 + ], + "Electron affinity": 3.05905238 + }, + "In": { + "Atomic mass": 114.818, + "Atomic no": 49, + "Atomic orbitals": { + "1s": -983.647445, + "2p": -134.628845, + "2s": -144.078357, + "3d": -16.139823, + "3p": -23.345778, + "3s": -27.2206, + "4d": -0.730481, + "4p": -2.795832, + "4s": -4.062639, + "5p": -0.101782, + "5s": -0.290497 + }, + "Atomic radius": 1.55, + "Atomic radius calculated": 1.56, + "Boiling point": "2345 K", + "Brinell hardness": "8.83 MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "32.1 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "7310 kg m-3", + "Electrical resistivity": "8 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d10.5s2.5p1", + "3": "[Kr].4d10" + }, + "ICSD oxidation states": [ + 1, + 2, + 3 + ], + "Ionic radii": { + "3": 0.94 + }, + "Liquid range": "1915.25 K", + "Melting point": "429.75 K", + "Mendeleev no": 79, + "Mineral hardness": "1.2", + "Molar volume": "15.76 cm3", + "Name": "Indium", + "Oxidation states": [ + 1, + 2, + 3 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "IV": { + "": { + "crystal_radius": 0.76, + "ionic_radius": 0.62 + } + }, + "VI": { + "": { + "crystal_radius": 0.94, + "ionic_radius": 0.8 + } + }, + "VIII": { + "": { + "crystal_radius": 1.06, + "ionic_radius": 0.92 + } + } + } + }, + "Superconduction temperature": "3.41 K", + "Thermal conductivity": "82 W m-1 K-1", + "Van der waals radius": 1.93, + "Velocity of sound": "1215 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.78, + "Youngs modulus": "11 GPa", + "NMR Quadrupole Moment": { + "In-113": 759.8, + "In-115": 770.8 + }, + "Metallic radius": 1.67, + "iupac_ordering": 78, + "IUPAC ordering": 78, + "Ground level": "2P°1/2", + "Ionization energies": [ + 5.7863557, + 18.87041, + 28.04415, + 55.45, + 69.3, + 90, + 109, + 130.1, + 156, + 178, + 201, + 226, + 249, + 341, + 368, + 396, + 425, + 462, + 497.1, + 560, + 593.38, + 1043, + 1109, + 1181, + 1255, + 1328, + 1413, + 1496, + 1575, + 1659, + 1738, + 1961, + 2028.5, + 2111, + 2207, + 2317, + 2373, + 2555, + 2628.77, + 6126, + 6331, + 6554, + 6770, + 7196, + 7442, + 7754, + 7953.14, + 32837.592, + 33750.31 + ], + "Electron affinity": 0.383926 + }, + "Ir": { + "Atomic mass": 192.217, + "Atomic no": 77, + "Atomic orbitals": { + "1s": -2543.761342, + "2p": -405.526834, + "2s": -422.159424, + "3d": -75.485027, + "3p": -90.108427, + "3s": -97.923081, + "4d": -10.856593, + "4f": -2.738339, + "4p": -16.966578, + "4s": -20.29429, + "5d": -0.335189, + "5p": -1.883349, + "5s": -2.909174, + "6s": -0.195511 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.8, + "Boiling point": "4701 K", + "Brinell hardness": "1670 MN m-2", + "Bulk modulus": "320 GPa", + "Coefficient of linear thermal expansion": "6.4 x10-6K-1", + "Common oxidation states": [ + 3, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "22650 kg m-3", + "Electrical resistivity": "4.7 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d7.6s2", + "3": "[Xe].4f14.5d6", + "4": "[Xe].4f14.5d5" + }, + "ICSD oxidation states": [ + 3, + 4, + 5 + ], + "Ionic radii": { + "3": 0.82, + "4": 0.765, + "5": 0.71 + }, + "Liquid range": "1962 K", + "Melting point": "2739 K", + "Mendeleev no": 66, + "Mineral hardness": "6.5", + "Molar volume": "8.52 cm3", + "Name": "Iridium", + "Oxidation states": [ + -3, + -1, + 1, + 2, + 3, + 4, + 5, + 6 + ], + "Poissons ratio": "0.26", + "Reflectivity": "78 %", + "Refractive index": "no data", + "Rigidity modulus": "210 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.82, + "ionic_radius": 0.68 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.765, + "ionic_radius": 0.625 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.71, + "ionic_radius": 0.57 + } + } + } + }, + "Superconduction temperature": "0.11 K", + "Thermal conductivity": "150 W m-1 K-1", + "Van der waals radius": 2.13, + "Velocity of sound": "4825 m s-1", + "Vickers hardness": "1760 MN m-2", + "X": 2.2, + "Youngs modulus": "528 GPa", + "Metallic radius": 1.357, + "iupac_ordering": 65, + "IUPAC ordering": 65, + "Ground level": "4F9/2", + "Ionization energies": [ + 8.96702, + 17, + 28, + 40, + 57, + 72, + 89, + 105, + 122.7, + 194.8, + 217, + 240, + 264, + 303, + 329, + 356, + 407, + 445, + 472, + 510, + 560, + 610, + 670, + 720, + 770, + 820, + 870, + 920, + 980, + 1030, + 1080, + 1331, + 1381, + 1436, + 1493, + 1548, + 1603, + 1684, + 1739, + 1801, + 1857, + 2083, + 2139, + 2201, + 2258, + 2435, + 2500, + 2656, + 2720.4, + 4540, + 4668, + 4806, + 4952, + 5092, + 5229, + 5466, + 5609, + 5765, + 5910, + 6315, + 6441, + 6580, + 6708, + 7274, + 7421, + 7710, + 7850, + 17040, + 17390, + 17770, + 18120, + 20210, + 20650, + 21200, + 21556.6, + 86438.9, + 88113.3 + ], + "Electron affinity": 1.5643615 + }, + "K": { + "Atomic mass": 39.0983, + "Atomic no": 19, + "Atomic orbitals": { + "1s": -128.414957, + "2p": -10.283851, + "2s": -12.839001, + "3p": -0.693776, + "3s": -1.281897, + "4s": -0.088815 + }, + "Atomic radius": 2.2, + "Atomic radius calculated": 2.43, + "Boiling point": "1032 K", + "Brinell hardness": "0.363 MN m-2", + "Bulk modulus": "3.1 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 1 + ], + "Critical temperature": "2223 K", + "Density of solid": "856 kg m-3", + "Electrical resistivity": "7.5 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].4s1", + "1": "[Ne].3s2.3p6" + }, + "ICSD oxidation states": [ + 1 + ], + "Ionic radii": { + "1": 1.52 + }, + "Liquid range": "695.47 K", + "Melting point": "336.53 K", + "Mendeleev no": 10, + "Mineral hardness": "0.4", + "Molar volume": "45.94 cm3", + "Name": "Potassium", + "Oxidation states": [ + -1, + 1 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "1.3 GPa", + "Shannon radii": { + "1": { + "IV": { + "": { + "crystal_radius": 1.51, + "ionic_radius": 1.37 + } + }, + "VI": { + "": { + "crystal_radius": 1.52, + "ionic_radius": 1.38 + } + }, + "VII": { + "": { + "crystal_radius": 1.6, + "ionic_radius": 1.46 + } + }, + "VIII": { + "": { + "crystal_radius": 1.65, + "ionic_radius": 1.51 + } + }, + "IX": { + "": { + "crystal_radius": 1.69, + "ionic_radius": 1.55 + } + }, + "X": { + "": { + "crystal_radius": 1.73, + "ionic_radius": 1.59 + } + }, + "XII": { + "": { + "crystal_radius": 1.78, + "ionic_radius": 1.64 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "100 W m-1 K-1", + "Van der waals radius": 2.75, + "Velocity of sound": "2000 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 0.82, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "K-39": 58.5, + "K-40": -73, + "K-41": 71.1 + }, + "Metallic radius": 2.381, + "iupac_ordering": 9, + "IUPAC ordering": 9, + "Ground level": "2S1/2", + "Ionization energies": [ + 4.34066373, + 31.625, + 45.8031, + 60.917, + 82.66, + 99.44, + 117.56, + 154.87, + 175.8174, + 503.67, + 565.6, + 631.1, + 714.7, + 786.3, + 860.92, + 967.7, + 1034.542, + 4610.87018, + 4934.0484 + ], + "Electron affinity": 0.50145913 + }, + "Kr": { + "Atomic mass": 83.798, + "Atomic no": 36, + "Atomic orbitals": { + "1s": -509.982989, + "2p": -60.017328, + "2s": -66.285953, + "3d": -3.074109, + "3p": -7.086634, + "3s": -9.315192, + "4p": -0.34634, + "4s": -0.820574 + }, + "Atomic radius": "no data", + "Atomic radius calculated": 0.88, + "Boiling point": "119.93 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Critical temperature": "209.4 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d10.4s2.4p6" + }, + "Liquid range": "4.14 K", + "Max oxidation state": 0, + "Melting point": "115.79 K", + "Mendeleev no": 4, + "Min oxidation state": 0, + "Mineral hardness": "no data", + "Molar volume": "27.99 cm3", + "Name": "Krypton", + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000427", + "Rigidity modulus": "no data GPa", + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.00943 W m-1 K-1", + "Van der waals radius": 2.02, + "Velocity of sound": "1120 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 3, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 2, + "IUPAC ordering": 2, + "Ground level": "1S0", + "Ionization energies": [ + 13.9996055, + 24.35984, + 35.838, + 50.85, + 64.69, + 78.49, + 109.13, + 125.802, + 233, + 268, + 308, + 350, + 391, + 446, + 492, + 540, + 591, + 640, + 785, + 831.6, + 882.8, + 945, + 999, + 1042, + 1155, + 1205.23, + 2928.9, + 3072, + 3228, + 3380, + 3584, + 3752, + 3971, + 4109.083, + 17296.421, + 17936.209 + ], + "Electron affinity": -1.02 + }, + "La": { + "Atomic mass": 138.90547, + "Atomic no": 57, + "Atomic orbitals": { + "1s": -1355.622446, + "2p": -198.325243, + "2s": -209.831151, + "3d": -30.626696, + "3p": -39.895838, + "3s": -44.856283, + "4d": -3.95801, + "4p": -7.167724, + "4s": -9.000543, + "5d": -0.141085, + "5p": -0.824498, + "5s": -1.324936, + "6s": -0.132233 + }, + "Atomic radius": 1.95, + "Atomic radius calculated": "no data", + "Boiling point": "3743 K", + "Brinell hardness": "363 MN m-2", + "Bulk modulus": "28 GPa", + "Coefficient of linear thermal expansion": "12.1 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "6146 kg m-3", + "Electrical resistivity": "61.5 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].5d1.6s2", + "3": "[Cd].5p6" + }, + "ICSD oxidation states": [ + 2, + 3 + ], + "Ionic radii": { + "3": 1.172 + }, + "Liquid range": "2550 K", + "Melting point": "1193 K", + "Mendeleev no": 33, + "Mineral hardness": "2.5", + "Molar volume": "22.39 cm3", + "Name": "Lanthanum", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "0.28", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "14 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.172, + "ionic_radius": 1.032 + } + }, + "VII": { + "": { + "crystal_radius": 1.24, + "ionic_radius": 1.1 + } + }, + "VIII": { + "": { + "crystal_radius": 1.3, + "ionic_radius": 1.16 + } + }, + "IX": { + "": { + "crystal_radius": 1.356, + "ionic_radius": 1.216 + } + }, + "X": { + "": { + "crystal_radius": 1.41, + "ionic_radius": 1.27 + } + }, + "XII": { + "": { + "crystal_radius": 1.5, + "ionic_radius": 1.36 + } + } + } + }, + "Superconduction temperature": "6.00 K", + "Thermal conductivity": "13 W m-1 K-1", + "Van der waals radius": 2.43, + "Velocity of sound": "2475 m s-1", + "Vickers hardness": "491 MN m-2", + "X": 1.1, + "Youngs modulus": "37 GPa", + "NMR Quadrupole Moment": { + "La-139": 200.6 + }, + "Metallic radius": 1.877, + "iupac_ordering": 47, + "IUPAC ordering": 47, + "Ground level": "2D3/2", + "Ionization energies": [ + 5.5769, + 11.18496, + 19.1773, + 49.95, + 61.6, + 74, + 88, + 105, + 119, + 151.4, + 168.77, + 275, + 303, + 332, + 364, + 393, + 431, + 464, + 498, + 533, + 566, + 696, + 731, + 770, + 806, + 865, + 906, + 995, + 1039.09, + 1800, + 1884, + 1974, + 2069, + 2162, + 2259, + 2377, + 2473, + 2577, + 2674, + 2950, + 3036, + 3133, + 3222, + 3416, + 3515, + 3704, + 3800, + 8669, + 8914, + 9184, + 9437, + 10136, + 10426, + 10789, + 11033.4, + 45144.996, + 46245.6 + ], + "Electron affinity": 0.5575462 + }, + "Li": { + "Atomic mass": 6.941, + "Atomic no": 3, + "Atomic orbitals": { + "1s": -1.878564, + "2s": -0.10554 + }, + "Atomic radius": 1.45, + "Atomic radius calculated": 1.67, + "Boiling point": "1615 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "11 GPa", + "Coefficient of linear thermal expansion": "46 x10-6K-1", + "Common oxidation states": [ + 1 + ], + "Critical temperature": "3223 K", + "Density of solid": "535 kg m-3", + "Electrical resistivity": "9.5 10-8 Ω m", + "Electronic structure": { + "0": "[He].2s1", + "1": "1s2" + }, + "ICSD oxidation states": [ + 1 + ], + "Ionic radii": { + "1": 0.9 + }, + "Liquid range": "1161.31 K", + "Melting point": "453.69 K", + "Mendeleev no": 12, + "Mineral hardness": "0.6", + "Molar volume": "13.02 cm3", + "Name": "Lithium", + "Oxidation states": [ + 1 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "4.2 GPa", + "Shannon radii": { + "1": { + "IV": { + "": { + "crystal_radius": 0.73, + "ionic_radius": 0.59 + } + }, + "VI": { + "": { + "crystal_radius": 0.9, + "ionic_radius": 0.76 + } + }, + "VIII": { + "": { + "crystal_radius": 1.06, + "ionic_radius": 0.92 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "85 W m-1 K-1", + "Van der waals radius": 1.82, + "Velocity of sound": "6000 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 0.98, + "Youngs modulus": "4.9 GPa", + "NMR Quadrupole Moment": { + "Li-6": -0.808, + "Li-7": -40.1 + }, + "Metallic radius": 1.52, + "iupac_ordering": 11, + "IUPAC ordering": 11, + "Ground level": "2S1/2", + "Ionization energies": [ + 5.391714996, + 75.640097, + 122.45435914 + ], + "Electron affinity": 0.61804922 + }, + "Lr": { + "Atomic mass": 262, + "Atomic no": 103, + "Atomic orbitals": "no data", + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f14.7s2.7p1", + "3": "[Rn].5f14" + }, + "Liquid range": "no data K", + "Melting point": "about 1900 K", + "Mendeleev no": 34, + "Mineral hardness": "no data", + "Molar volume": "no data cm3", + "Name": "Lawrencium", + "Oxidation states": [ + 3 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Superconduction temperature": "no data K", + "Thermal conductivity": "no data W m-1 K-1", + "Van der waals radius": "no data", + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.3, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 18, + "IUPAC ordering": 18, + "Ground level": "2P°1/2", + "Ionization energies": [ + 4.96, + 14.54, + 21.8, + 43.6, + 56, + 80, + 96, + 121, + 143, + 165, + 197, + 216, + 244, + 269, + 290, + 322, + 344, + 374, + 403, + 431, + 459, + 487, + 510, + 540, + 560, + 745, + 779, + 814, + 852, + 888, + 922, + 985, + 1020, + 1061, + 1098, + 1280, + 1320, + 1360, + 1410, + 1570, + 1620, + 1760, + 1810, + 2010, + 2100, + 2190, + 2290, + 2380, + 2470, + 2570, + 2670, + 2780, + 2860, + 2960, + 3060, + 3150, + 3250, + 3741, + 3821, + 3906, + 3996, + 4082, + 4165, + 4360, + 4448, + 4540, + 4630, + 4990, + 5070, + 5160, + 5250, + 5920, + 6030, + 6290, + 6390, + 9920, + 10110, + 10310, + 10520, + 10720, + 10920, + 11470, + 11680, + 11910, + 12120, + 12710, + 12890, + 13090, + 13300, + 15300, + 15600, + 16000, + 16200, + 32400, + 32900, + 33400, + 33900, + 41600, + 42300, + 43200, + 43759, + null, + 172930 + ], + "Electron affinity": -0.31 + }, + "Lu": { + "Atomic mass": 174.967, + "Atomic no": 71, + "Atomic orbitals": { + "1s": -2146.885351, + "2p": -334.330902, + "2s": -349.390492, + "3d": -58.592982, + "3p": -71.538779, + "3s": -78.462398, + "4d": -7.113364, + "4f": -0.568096, + "4p": -12.250904, + "4s": -15.08337, + "5d": -0.103686, + "5p": -1.111991, + "5s": -1.872086, + "6s": -0.155112 + }, + "Atomic radius": 1.75, + "Atomic radius calculated": 2.17, + "Boiling point": "3675 K", + "Brinell hardness": "893 MN m-2", + "Bulk modulus": "48 GPa", + "Coefficient of linear thermal expansion": "9.9 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "9841 kg m-3", + "Electrical resistivity": "58 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d1.6s2", + "3": "[Xe].4f14" + }, + "ICSD oxidation states": [ + 3 + ], + "Ionic radii": { + "3": 1.001 + }, + "Liquid range": "1750 K", + "Melting point": "1925 K", + "Mendeleev no": 20, + "Mineral hardness": "no data", + "Molar volume": "17.78 cm3", + "Name": "Lutetium", + "Oxidation states": [ + 3 + ], + "Poissons ratio": "0.26", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "27 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.001, + "ionic_radius": 0.861 + } + }, + "VIII": { + "": { + "crystal_radius": 1.117, + "ionic_radius": 0.977 + } + }, + "IX": { + "": { + "crystal_radius": 1.172, + "ionic_radius": 1.032 + } + } + } + }, + "Superconduction temperature": "0.022 K", + "Thermal conductivity": "16 W m-1 K-1", + "Van der waals radius": 2.24, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "1160 MN m-2", + "X": 1.27, + "Youngs modulus": "69 GPa", + "Metallic radius": 1.735, + "iupac_ordering": 33, + "IUPAC ordering": 33, + "Ground level": "2D3/2", + "Ionization energies": [ + 5.425871, + 14.13, + 20.9594, + 45.249, + 66.8, + 98, + 117, + 136, + 159, + 185, + 205, + 238, + 276, + 305, + 328, + 361, + 399, + 438, + 476, + 520, + 560, + 600, + 630, + 670, + 713, + 941, + 985, + 1032, + 1081, + 1130, + 1178, + 1242, + 1292, + 1345, + 1395, + 1591, + 1641, + 1696, + 1747, + 1875, + 1933, + 2067, + 2125.5, + 3590, + 3706, + 3828, + 3960, + 4086, + 4211, + 4403, + 4532, + 4673, + 4803, + 5168, + 5282, + 5408, + 5525, + 5937, + 6070, + 6326, + 6452, + 14228, + 14542, + 14890, + 15211, + 16730, + 17120, + 17610, + 17928.05, + 72322.91, + 73804.8 + ], + "Electron affinity": 0.23887 + }, + "Md": { + "Atomic mass": 258, + "Atomic no": 101, + "Atomic orbitals": "no data", + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f13.7s2", + "3": "[Rn].5f12" + }, + "Liquid range": "no data K", + "Melting point": "about 1100 K", + "Mendeleev no": 36, + "Mineral hardness": "no data", + "Molar volume": "no data cm3", + "Name": "Mendelevium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Superconduction temperature": "no data K", + "Thermal conductivity": "no data W m-1 K-1", + "Van der waals radius": 2.46, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.3, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 20, + "IUPAC ordering": 20, + "Ground level": "2F°7/2", + "Ionization energies": [ + 6.58, + 12.4, + 24.3, + 40, + 54.1, + 76, + 96, + 115.1, + 143.9, + 162, + 187, + 215, + 240, + 260, + 282, + 307, + 334, + 360, + 386, + 412, + 438, + 462, + 486, + 659, + 690, + 723, + 760, + 794, + 828, + 885, + 920, + 958, + 994, + 1160, + 1210, + 1250, + 1290, + 1430, + 1480, + 1620, + 1660, + 1840, + 1930, + 2020, + 2110, + 2200, + 2290, + 2390, + 2480, + 2580, + 2680, + 2760, + 2860, + 2950, + 3050, + 3513, + 3592, + 3675, + 3762, + 3845, + 3926, + 4109, + 4194, + 4286, + 4371, + 4720, + 4800, + 4890, + 4970, + 5580, + 5680, + 5930, + 6030, + 9430, + 9620, + 9810, + 10020, + 10220, + 10410, + 10930, + 11130, + 11350, + 11560, + 12130, + 12310, + 12500, + 12680, + 14560, + 14800, + 15200, + 15400, + 31000, + 31500, + 32000, + 32500, + 39500, + 40100, + 41000, + 41548, + null, + 164764 + ], + "Electron affinity": 0.98 + }, + "Mg": { + "Atomic mass": 24.305, + "Atomic no": 12, + "Atomic orbitals": { + "1s": -45.973167, + "2p": -1.71897, + "2s": -2.903746, + "3s": -0.175427 + }, + "Atomic radius": 1.5, + "Atomic radius calculated": 1.45, + "Boiling point": "1363 K", + "Brinell hardness": "260 MN m-2", + "Bulk modulus": "45 GPa", + "Coefficient of linear thermal expansion": "8.2 x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "1738 kg m-3", + "Electrical resistivity": "4.4 10-8 Ω m", + "Electronic structure": { + "0": "[Ne].3s2", + "2": "[He].2s2.2p6" + }, + "ICSD oxidation states": [ + 2 + ], + "Ionic radii": { + "2": 0.86 + }, + "Liquid range": "440 K", + "Melting point": "923 K", + "Mendeleev no": 73, + "Mineral hardness": "2.5", + "Molar volume": "14.00 cm3", + "Name": "Magnesium", + "Oxidation states": [ + 1, + 2 + ], + "Poissons ratio": "0.29", + "Reflectivity": "74 %", + "Refractive index": "no data", + "Rigidity modulus": "17 GPa", + "Shannon radii": { + "2": { + "IV": { + "": { + "crystal_radius": 0.71, + "ionic_radius": 0.57 + } + }, + "V": { + "": { + "crystal_radius": 0.8, + "ionic_radius": 0.66 + } + }, + "VI": { + "": { + "crystal_radius": 0.86, + "ionic_radius": 0.72 + } + }, + "VIII": { + "": { + "crystal_radius": 1.03, + "ionic_radius": 0.89 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "160 W m-1 K-1", + "Van der waals radius": 1.73, + "Velocity of sound": "4602 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.31, + "Youngs modulus": "45 GPa", + "NMR Quadrupole Moment": { + "Mg-25": 199.4 + }, + "Metallic radius": 1.6, + "iupac_ordering": 16, + "IUPAC ordering": 16, + "Ground level": "1S0", + "Ionization energies": [ + 7.646236, + 15.035271, + 80.1436, + 109.2654, + 141.33, + 186.76, + 225.02, + 265.924, + 327.99, + 367.489, + 1761.80488, + 1962.66366 + ], + "Electron affinity": -0.42 + }, + "Mn": { + "Atomic mass": 54.938045, + "Atomic no": 25, + "Atomic orbitals": { + "1s": -233.696912, + "2p": -23.066297, + "2s": -26.866646, + "3d": -0.26654, + "3p": -1.99145, + "3s": -3.076637, + "4s": -0.191136 + }, + "Atomic radius": 1.4, + "Atomic radius calculated": 1.61, + "Boiling point": "2334 K", + "Brinell hardness": "196 MN m-2", + "Bulk modulus": "120 GPa", + "Coefficient of linear thermal expansion": "21.7 x10-6K-1", + "Common oxidation states": [ + 2, + 4, + 7 + ], + "Critical temperature": "no data K", + "Density of solid": "7470 kg m-3", + "Electrical resistivity": "144 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d5.4s2", + "2": "[Ar].3d5", + "3": "[Ar].3d4", + "4": "[Ar].3d3", + "7": "[Ne].3s2.3p6" + }, + "ICSD oxidation states": [ + 2, + 3, + 4, + 7 + ], + "Ionic radii": { + "2": 0.97, + "3": 0.785, + "4": 0.67, + "5": 0.47, + "6": 0.395, + "7": 0.6 + }, + "Ionic radii hs": { + "2": 0.97, + "3": 0.785 + }, + "Ionic radii ls": { + "2": 0.81, + "3": 0.72, + "4": 0.67, + "5": 0.47, + "6": 0.395, + "7": 0.6 + }, + "Liquid range": "815 K", + "Melting point": "1519 K", + "Mendeleev no": 60, + "Mineral hardness": "6.0", + "Molar volume": "7.35 cm3", + "Name": "Manganese", + "Oxidation states": [ + -3, + -2, + -1, + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "2": { + "IV": { + "High Spin": { + "crystal_radius": 0.8, + "ionic_radius": 0.66 + } + }, + "V": { + "High Spin": { + "crystal_radius": 0.89, + "ionic_radius": 0.75 + } + }, + "VI": { + "Low Spin": { + "crystal_radius": 0.81, + "ionic_radius": 0.67 + }, + "High Spin": { + "crystal_radius": 0.97, + "ionic_radius": 0.83 + } + }, + "VII": { + "High Spin": { + "crystal_radius": 1.04, + "ionic_radius": 0.9 + } + }, + "VIII": { + "": { + "crystal_radius": 1.1, + "ionic_radius": 0.96 + } + } + }, + "3": { + "V": { + "": { + "crystal_radius": 0.72, + "ionic_radius": 0.58 + } + }, + "VI": { + "Low Spin": { + "crystal_radius": 0.72, + "ionic_radius": 0.58 + }, + "High Spin": { + "crystal_radius": 0.785, + "ionic_radius": 0.645 + } + } + }, + "4": { + "IV": { + "": { + "crystal_radius": 0.53, + "ionic_radius": 0.39 + } + }, + "VI": { + "": { + "crystal_radius": 0.67, + "ionic_radius": 0.53 + } + } + }, + "5": { + "IV": { + "": { + "crystal_radius": 0.47, + "ionic_radius": 0.33 + } + } + }, + "6": { + "IV": { + "": { + "crystal_radius": 0.395, + "ionic_radius": 0.255 + } + } + }, + "7": { + "IV": { + "": { + "crystal_radius": 0.39, + "ionic_radius": 0.25 + } + }, + "VI": { + "": { + "crystal_radius": 0.6, + "ionic_radius": 0.46 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "7.8 W m-1 K-1", + "Van der waals radius": 2.05, + "Velocity of sound": "5150 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.55, + "Youngs modulus": "198 GPa", + "NMR Quadrupole Moment": { + "Mn-55": 330.1 + }, + "Metallic radius": 1.292, + "iupac_ordering": 61, + "IUPAC ordering": 61, + "Ground level": "6S5/2", + "Ionization energies": [ + 7.434038, + 15.63999, + 33.668, + 51.21, + 72.41, + 95.604, + 119.203, + 195.5, + 221.89, + 248.6, + 286.1, + 314.4, + 343.6, + 402.95, + 435.172, + 1133.7, + 1224.1, + 1320.3, + 1430.9, + 1537.2, + 1643.2, + 1788.7, + 1879.873, + 8140.7872, + 8571.9488 + ], + "Electron affinity": -0.52 + }, + "Mo": { + "Atomic mass": 95.94, + "Atomic no": 42, + "Atomic orbitals": { + "1s": -709.232119, + "2p": -90.791541, + "2s": -98.503638, + "3d": -8.257721, + "3p": -13.71481, + "3s": -16.681545, + "4d": -0.153347, + "4p": -1.39005, + "4s": -2.234824, + "5s": -0.14788 + }, + "Atomic radius": 1.45, + "Atomic radius calculated": 1.9, + "Boiling point": "4912 K", + "Brinell hardness": "1500 MN m-2", + "Bulk modulus": "230 GPa", + "Coefficient of linear thermal expansion": "4.8 x10-6K-1", + "Common oxidation states": [ + 4, + 6 + ], + "Critical temperature": "no data K", + "Density of solid": "10280 kg m-3", + "Electrical resistivity": "5.5 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d5.5s1", + "3": "[Kr].4d3", + "4": "[Kr].4d2", + "6": "[Ar].3d10.4s2.4p6" + }, + "ICSD oxidation states": [ + 2, + 3, + 4, + 5, + 6 + ], + "Ionic radii": { + "3": 0.83, + "4": 0.79, + "5": 0.75, + "6": 0.73 + }, + "Liquid range": "2016 K", + "Melting point": "2896 K", + "Mendeleev no": 56, + "Mineral hardness": "5.5", + "Molar volume": "9.38 cm3", + "Name": "Molybdenum", + "Oxidation states": [ + -2, + -1, + 1, + 2, + 3, + 4, + 5, + 6 + ], + "Poissons ratio": "0.31", + "Reflectivity": "58 %", + "Refractive index": "no data", + "Rigidity modulus": "20 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.83, + "ionic_radius": 0.69 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.79, + "ionic_radius": 0.65 + } + } + }, + "5": { + "IV": { + "": { + "crystal_radius": 0.6, + "ionic_radius": 0.46 + } + }, + "VI": { + "": { + "crystal_radius": 0.75, + "ionic_radius": 0.61 + } + } + }, + "6": { + "IV": { + "": { + "crystal_radius": 0.55, + "ionic_radius": 0.41 + } + }, + "V": { + "": { + "crystal_radius": 0.64, + "ionic_radius": 0.5 + } + }, + "VI": { + "": { + "crystal_radius": 0.73, + "ionic_radius": 0.59 + } + }, + "VII": { + "": { + "crystal_radius": 0.87, + "ionic_radius": 0.73 + } + } + } + }, + "Superconduction temperature": "0.915 K", + "Thermal conductivity": "139 W m-1 K-1", + "Van der waals radius": 2.17, + "Velocity of sound": "6190 m s-1", + "Vickers hardness": "1530 MN m-2", + "X": 2.16, + "Youngs modulus": "329 GPa", + "Metallic radius": 1.402, + "iupac_ordering": 57, + "IUPAC ordering": 57, + "Ground level": "7S3", + "Ionization energies": [ + 7.09243, + 16.16, + 27.13, + 40.33, + 54.417, + 68.82704, + 125.638, + 143.6, + 164.12, + 186.3, + 209.3, + 230.28, + 279.1, + 302.6, + 544, + 591, + 646, + 702, + 758, + 829, + 890, + 953, + 1019, + 1082, + 1263, + 1319.6, + 1385.1, + 1462, + 1537, + 1587, + 1730.1, + 1790.93, + 4259, + 4430, + 4618, + 4800, + 5084, + 5287, + 5548, + 5713.194, + 23810.654, + 24572.156 + ], + "Electron affinity": 0.74733 + }, + "N": { + "Atomic mass": 14.0067, + "Atomic no": 7, + "Atomic orbitals": { + "1s": -14.011501, + "2p": -0.266297, + "2s": -0.676151 + }, + "Atomic radius": 0.65, + "Atomic radius calculated": 0.56, + "Boiling point": "77.36 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -3, + 3, + 5 + ], + "Critical temperature": "126.2 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[He].2s2.2p3", + "-3": "[He].2s2.2p6", + "3": "1s2.2s2", + "5": "1s2" + }, + "ICSD oxidation states": [ + 1, + 3, + 5, + -1, + -3, + -2 + ], + "Ionic radii": { + "3": 0.3, + "5": 0.27, + "-3": 1.32 + }, + "Liquid range": "14.31 K", + "Melting point": "63.05 K", + "Mendeleev no": 100, + "Mineral hardness": "no data", + "Molar volume": "13.54 cm3", + "Name": "Nitrogen", + "Oxidation states": [ + -3, + -2, + -1, + 1, + 2, + 3, + 4, + 5 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000298 (gas; liquid 1.197)(no units)", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.3, + "ionic_radius": 0.16 + } + } + }, + "5": { + "III": { + "": { + "crystal_radius": 0.044, + "ionic_radius": -0.104 + } + }, + "VI": { + "": { + "crystal_radius": 0.27, + "ionic_radius": 0.13 + } + } + }, + "-3": { + "IV": { + "": { + "crystal_radius": 1.32, + "ionic_radius": 1.46 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.02583 W m-1 K-1", + "Van der waals radius": 1.55, + "Velocity of sound": "333.6 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 3.04, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "N-14": 20.44 + }, + "Metallic radius": "no data", + "iupac_ordering": 91, + "IUPAC ordering": 91, + "Ground level": "4S°3/2", + "Ionization energies": [ + 14.53413, + 29.60125, + 47.4453, + 77.4735, + 97.8901, + 552.06733, + 667.046121 + ], + "Electron affinity": -0.07 + }, + "Na": { + "Atomic mass": 22.98976928, + "Atomic no": 11, + "Atomic orbitals": { + "1s": -37.719975, + "2p": -1.060636, + "2s": -2.063401, + "3s": -0.103415 + }, + "Atomic radius": 1.8, + "Atomic radius calculated": 1.9, + "Boiling point": "1156 K", + "Brinell hardness": "0.69 MN m-2", + "Bulk modulus": "6.3 GPa", + "Coefficient of linear thermal expansion": "71 x10-6K-1", + "Common oxidation states": [ + 1 + ], + "Critical temperature": "2573 K", + "Density of solid": "968 kg m-3", + "Electrical resistivity": "4.9 10-8 Ω m", + "Electronic structure": { + "0": "[Ne].3s1", + "1": "[He].2s2.2p6" + }, + "ICSD oxidation states": [ + 1 + ], + "Ionic radii": { + "1": 1.16 + }, + "Liquid range": "785.13 K", + "Melting point": "370.87 K", + "Mendeleev no": 11, + "Mineral hardness": "0.5", + "Molar volume": "23.78 cm3", + "Name": "Sodium", + "Oxidation states": [ + -1, + 1 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "3.3 GPa", + "Shannon radii": { + "1": { + "IV": { + "": { + "crystal_radius": 1.13, + "ionic_radius": 0.99 + } + }, + "V": { + "": { + "crystal_radius": 1.14, + "ionic_radius": 1 + } + }, + "VI": { + "": { + "crystal_radius": 1.16, + "ionic_radius": 1.02 + } + }, + "VII": { + "": { + "crystal_radius": 1.26, + "ionic_radius": 1.12 + } + }, + "VIII": { + "": { + "crystal_radius": 1.32, + "ionic_radius": 1.18 + } + }, + "IX": { + "": { + "crystal_radius": 1.38, + "ionic_radius": 1.24 + } + }, + "XII": { + "": { + "crystal_radius": 1.53, + "ionic_radius": 1.39 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "140 W m-1 K-1", + "Van der waals radius": 2.27, + "Velocity of sound": "3200 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 0.93, + "Youngs modulus": "10 GPa", + "NMR Quadrupole Moment": { + "Na-23": 104.1 + }, + "Metallic radius": 1.86, + "iupac_ordering": 10, + "IUPAC ordering": 10, + "Ground level": "2S1/2", + "Ionization energies": [ + 5.13907696, + 47.28636, + 71.62, + 98.936, + 138.404, + 172.23, + 208.504, + 264.192, + 299.856, + 1465.134502, + 1648.7022 + ], + "Electron affinity": 0.54792625 + }, + "Nb": { + "Atomic mass": 92.90638, + "Atomic no": 41, + "Atomic orbitals": { + "1s": -673.76253, + "2p": -85.272175, + "2s": -92.74086, + "3d": -7.339839, + "3p": -12.552855, + "3s": -15.393727, + "4d": -0.125252, + "4p": -1.250049, + "4s": -2.036693, + "5s": -0.144272 + }, + "Atomic radius": 1.45, + "Atomic radius calculated": 1.98, + "Boiling point": "5017 K", + "Brinell hardness": "736 MN m-2", + "Bulk modulus": "170 GPa", + "Coefficient of linear thermal expansion": "7.3 x10-6K-1", + "Common oxidation states": [ + 5 + ], + "Critical temperature": "no data K", + "Density of solid": "8570 kg m-3", + "Electrical resistivity": "15.2 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d4.5s1", + "5": "[Ar].3d10.4s2.4p6" + }, + "ICSD oxidation states": [ + 2, + 3, + 4, + 5 + ], + "Ionic radii": { + "3": 0.86, + "4": 0.82, + "5": 0.78 + }, + "Liquid range": "2267 K", + "Melting point": "2750 K", + "Mendeleev no": 53, + "Mineral hardness": "6.0", + "Molar volume": "10.83 cm3", + "Name": "Niobium", + "Oxidation states": [ + -1, + 2, + 3, + 4, + 5 + ], + "Poissons ratio": "0.40", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "38 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.86, + "ionic_radius": 0.72 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.82, + "ionic_radius": 0.68 + } + }, + "VIII": { + "": { + "crystal_radius": 0.93, + "ionic_radius": 0.79 + } + } + }, + "5": { + "IV": { + "": { + "crystal_radius": 0.62, + "ionic_radius": 0.48 + } + }, + "VI": { + "": { + "crystal_radius": 0.78, + "ionic_radius": 0.64 + } + }, + "VII": { + "": { + "crystal_radius": 0.83, + "ionic_radius": 0.69 + } + }, + "VIII": { + "": { + "crystal_radius": 0.88, + "ionic_radius": 0.74 + } + } + } + }, + "Superconduction temperature": "9.25 K", + "Thermal conductivity": "54 W m-1 K-1", + "Van der waals radius": 2.18, + "Velocity of sound": "3480 m s-1", + "Vickers hardness": "1320 MN m-2", + "X": 1.6, + "Youngs modulus": "105 GPa", + "Metallic radius": 1.473, + "iupac_ordering": 54, + "IUPAC ordering": 54, + "Ground level": "6D1/2", + "Ionization energies": [ + 6.75885, + 14.32, + 25.04, + 37.611, + 50.5728, + 102.069, + 119.1, + 136, + 159.2, + 180, + 200.28, + 246.1, + 268.59, + 482.5, + 530, + 581, + 636, + 688, + 758, + 816, + 877, + 940, + 1000, + 1176, + 1230.6, + 1293.7, + 1368, + 1439, + 1488, + 1625.9, + 1684.97, + 4020.1, + 4187, + 4369, + 4540, + 4815, + 5011, + 5265, + 5426.066, + 22648.046, + 23388.801 + ], + "Electron affinity": 0.917407 + }, + "Nd": { + "Atomic mass": 144.242, + "Atomic no": 60, + "Atomic orbitals": { + "1s": -1509.698955, + "2p": -224.351816, + "2s": -236.613572, + "3d": -35.754515, + "3p": -45.791219, + "3s": -51.161263, + "4d": -4.377027, + "4f": -0.179508, + "4p": -7.96782, + "4s": -10.000891, + "5p": -0.798503, + "5s": -1.334934, + "6s": -0.125796 + }, + "Atomic radius": 1.85, + "Atomic radius calculated": 2.06, + "Boiling point": "3373 K", + "Brinell hardness": "265 MN m-2", + "Bulk modulus": "32 GPa", + "Coefficient of linear thermal expansion": "9.6 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "6800 kg m-3", + "Electrical resistivity": "64.3 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f4.6s2", + "3": "[Xe].4f3" + }, + "ICSD oxidation states": [ + 2, + 3 + ], + "Ionic radii": { + "2": 1.43, + "3": 1.123 + }, + "Liquid range": "2076 K", + "Melting point": "1297 K", + "Mendeleev no": 30, + "Mineral hardness": "no data", + "Molar volume": "20.59 cm3", + "Name": "Neodymium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "0.28", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "16 GPa", + "Shannon radii": { + "2": { + "VIII": { + "": { + "crystal_radius": 1.43, + "ionic_radius": 1.29 + } + }, + "IX": { + "": { + "crystal_radius": 1.49, + "ionic_radius": 1.35 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 1.123, + "ionic_radius": 0.983 + } + }, + "VIII": { + "": { + "crystal_radius": 1.249, + "ionic_radius": 1.109 + } + }, + "IX": { + "": { + "crystal_radius": 1.303, + "ionic_radius": 1.163 + } + }, + "XII": { + "": { + "crystal_radius": 1.41, + "ionic_radius": 1.27 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "17 W m-1 K-1", + "Van der waals radius": 2.39, + "Velocity of sound": "2330 m s-1", + "Vickers hardness": "343 MN m-2", + "X": 1.14, + "Youngs modulus": "41 GPa", + "Metallic radius": 1.821, + "iupac_ordering": 44, + "IUPAC ordering": 44, + "Ground level": "5I4", + "Ionization energies": [ + 5.525, + 10.783, + 22.09, + 40.6, + 60, + 84, + 99, + 114, + 136, + 152, + 168, + 195, + 221, + 243, + 389, + 420, + 453, + 489, + 522, + 562, + 602, + 638, + 678, + 714, + 859, + 896, + 939, + 978, + 1049, + 1092, + 1191, + 1238.42, + 2134, + 2224, + 2321, + 2425, + 2525, + 2627, + 2758, + 2861, + 2974, + 3078, + 3371, + 3465, + 3567, + 3662, + 3891, + 3997, + 4198, + 4302, + 9742, + 10002, + 10288, + 10555, + 11384, + 11694, + 12082, + 12341.66, + 50339.59, + 51515.58 + ], + "Electron affinity": 0.0974933 + }, + "Ne": { + "Atomic mass": 20.1797, + "Atomic no": 10, + "Atomic orbitals": { + "1s": -30.305855, + "2p": -0.498034, + "2s": -1.322809 + }, + "Atomic radius": "no data", + "Atomic radius calculated": 0.38, + "Boiling point": "27.07 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Critical temperature": "44.4 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[He].2s2.2p6" + }, + "Liquid range": "2.51 K", + "Max oxidation state": 0, + "Melting point": "24.56 K", + "Mendeleev no": 2, + "Min oxidation state": 0, + "Mineral hardness": "no data", + "Molar volume": "13.23 cm3", + "Name": "Neon", + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000067", + "Rigidity modulus": "no data GPa", + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.0491 W m-1 K-1", + "Van der waals radius": 1.54, + "Velocity of sound": "936 m s-1", + "Vickers hardness": "no data MN m-2", + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "Ne-21": 101.55 + }, + "Metallic radius": "no data", + "iupac_ordering": 4, + "IUPAC ordering": 4, + "Ground level": "1S0", + "Ionization energies": [ + 21.564541, + 40.96297, + 63.4233, + 97.19, + 126.247, + 157.934, + 207.271, + 239.097, + 1195.80784, + 1362.19916 + ], + "Electron affinity": -1.22 + }, + "Ni": { + "Atomic mass": 58.6934, + "Atomic no": 28, + "Atomic orbitals": { + "1s": -297.870824, + "2p": -30.868027, + "2s": -35.312112, + "3d": -0.348699, + "3p": -2.594158, + "3s": -3.950717, + "4s": -0.210764 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.49, + "Boiling point": "3186 K", + "Brinell hardness": "700 MN m-2", + "Bulk modulus": "180 GPa", + "Coefficient of linear thermal expansion": "13.4 x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "8908 kg m-3", + "Electrical resistivity": "7.2 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d8.4s2", + "2": "[Ar].3d8", + "3": "[Ar].3d7" + }, + "ICSD oxidation states": [ + 1, + 2, + 3, + 4 + ], + "Ionic radii": { + "3": 0.74 + }, + "Ionic radii hs": { + "3": 0.74 + }, + "Ionic radii ls": { + "2": 0.83, + "3": 0.7, + "4": 0.62 + }, + "Liquid range": "1458 K", + "Melting point": "1728 K", + "Mendeleev no": 67, + "Mineral hardness": "4.0", + "Molar volume": "6.59 cm3", + "Name": "Nickel", + "Oxidation states": [ + -1, + 1, + 2, + 3, + 4 + ], + "Poissons ratio": "0.31", + "Reflectivity": "72 %", + "Refractive index": "no data", + "Rigidity modulus": "76 GPa", + "Shannon radii": { + "2": { + "IV": { + "": { + "crystal_radius": 0.69, + "ionic_radius": 0.55 + } + }, + "IVSQ": { + "": { + "crystal_radius": 0.63, + "ionic_radius": 0.49 + } + }, + "V": { + "": { + "crystal_radius": 0.77, + "ionic_radius": 0.63 + } + }, + "VI": { + "": { + "crystal_radius": 0.83, + "ionic_radius": 0.69 + } + } + }, + "3": { + "VI": { + "Low Spin": { + "crystal_radius": 0.7, + "ionic_radius": 0.56 + }, + "High Spin": { + "crystal_radius": 0.74, + "ionic_radius": 0.6 + } + } + }, + "4": { + "VI": { + "Low Spin": { + "crystal_radius": 0.62, + "ionic_radius": 0.48 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "91 W m-1 K-1", + "Van der waals radius": 1.97, + "Velocity of sound": "4970 m s-1", + "Vickers hardness": "638 MN m-2", + "X": 1.91, + "Youngs modulus": "200 GPa", + "NMR Quadrupole Moment": { + "Ni-61": 162.15 + }, + "Metallic radius": 1.246, + "iupac_ordering": 70, + "IUPAC ordering": 70, + "Ground level": "3F4", + "Ionization energies": [ + 7.639878, + 18.168838, + 35.187, + 54.92, + 76.06, + 108, + 132, + 162, + 193.2, + 224.7, + 319.5, + 351.6, + 384.5, + 429.3, + 462.8, + 495.4, + 571.07, + 607.02, + 1541, + 1646, + 1758, + 1880, + 2008.1, + 2130.5, + 2295.6, + 2399.259, + 10288.8862, + 10775.386 + ], + "Electron affinity": 1.1571612 + }, + "No": { + "Atomic mass": 259, + "Atomic no": 102, + "Atomic orbitals": "no data", + "Atomic radius": "no data", + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f14.7s2", + "3": "[Rn].5f13" + }, + "Liquid range": "no data K", + "Melting point": "about 1100 K", + "Mendeleev no": 35, + "Mineral hardness": "no data", + "Molar volume": "no data cm3", + "Name": "Nobelium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1.24, + "ionic_radius": 1.1 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "no data W m-1 K-1", + "Van der waals radius": 2.46, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.3, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 19, + "IUPAC ordering": 19, + "Ground level": "1S0", + "Ionization energies": [ + 6.62621, + 12.93, + 25.8, + 41.5, + 60, + 74, + 97, + 119, + 140, + 170, + 187, + 216, + 246, + 267, + 285, + 312, + 341, + 367, + 394, + 422, + 448, + 475, + 496, + 520, + 701, + 734, + 768, + 805, + 840, + 875, + 934, + 969, + 1010, + 1045, + 1220, + 1260, + 1300, + 1350, + 1500, + 1550, + 1680, + 1730, + 1920, + 2010, + 2110, + 2200, + 2290, + 2380, + 2470, + 2570, + 2680, + 2760, + 2860, + 2950, + 3050, + 3140, + 3627, + 3705, + 3790, + 3878, + 3962, + 4045, + 4234, + 4320, + 4413, + 4500, + 4850, + 4930, + 5030, + 5110, + 5750, + 5850, + 6110, + 6210, + 9680, + 9860, + 10060, + 10270, + 10470, + 10660, + 11200, + 11410, + 11630, + 11840, + 12420, + 12600, + 12800, + 12980, + 15000, + 15200, + 15600, + 15800, + 31700, + 32200, + 32700, + 33200, + 40500, + 41200, + 42100, + 42632, + null, + 168806 + ], + "Electron affinity": -2.33 + }, + "Np": { + "Atomic mass": 237, + "Atomic no": 93, + "Atomic orbitals": "no data", + "Atomic radius": 1.75, + "Atomic radius calculated": "no data", + "Boiling point": "4273 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 5 + ], + "Critical temperature": "no data K", + "Density of solid": "20450 kg m-3", + "Electrical resistivity": "120 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f4.6d1.7s2", + "5": "[Rn].5f2" + }, + "Ionic radii": { + "2": 1.24, + "3": 1.15, + "4": 1.01, + "5": 0.89, + "6": 0.86, + "7": 0.85 + }, + "Liquid range": "3363 K", + "Melting point": "910 K", + "Mendeleev no": 44, + "Mineral hardness": "no data", + "Molar volume": "11.59 cm3", + "Name": "Neptunium", + "Oxidation states": [ + 3, + 4, + 5, + 6, + 7 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1.24, + "ionic_radius": 1.1 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 1.15, + "ionic_radius": 1.01 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 1.01, + "ionic_radius": 0.87 + } + }, + "VIII": { + "": { + "crystal_radius": 1.12, + "ionic_radius": 0.98 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.89, + "ionic_radius": 0.75 + } + } + }, + "6": { + "VI": { + "": { + "crystal_radius": 0.86, + "ionic_radius": 0.72 + } + } + }, + "7": { + "VI": { + "": { + "crystal_radius": 0.85, + "ionic_radius": 0.71 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "6 W m-1 K-1", + "Van der waals radius": 2.39, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.36, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.503, + "iupac_ordering": 28, + "IUPAC ordering": 28, + "Ground level": "6L11/2", + "Ionization energies": [ + 6.26554, + 11.5, + 19.7, + 33.8, + 48, + 65, + 92, + 107, + 121, + 136, + 151, + 179, + 196, + 233, + 252, + 355, + 382, + 408, + 438, + 466, + 495, + 535, + 565, + 596, + 626, + 770, + 810, + 850, + 880, + 980, + 1020, + 1130, + 1170, + 1280, + 1360, + 1430, + 1510, + 1590, + 1670, + 1740, + 1820, + 1910, + 1990, + 2070, + 2140, + 2230, + 2310, + 2675, + 2745, + 2817, + 2894, + 2969, + 3041, + 3181, + 3255, + 3338, + 3413, + 3718, + 3792, + 3872, + 3947, + 4353, + 4441, + 4658, + 4744, + 7610, + 7770, + 7950, + 8130, + 8310, + 8480, + 8890, + 9070, + 9270, + 9450, + 9970, + 10130, + 10300, + 10470, + 11730, + 11930, + 12320, + 12500, + 25870, + 26300, + 26770, + 27210, + 31910, + 32500, + 33300, + 33722.2, + 132901.8, + 135202 + ], + "Electron affinity": 0.48 + }, + "O": { + "Atomic mass": 15.9994, + "Atomic no": 8, + "Atomic orbitals": { + "1s": -18.758245, + "2p": -0.338381, + "2s": -0.871362 + }, + "Atomic radius": 0.6, + "Atomic radius calculated": 0.48, + "Boiling point": "90.2 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -2 + ], + "Critical temperature": "154.6 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[He].2s2.2p4", + "-2": "[He].2s2.2p6" + }, + "ICSD oxidation states": [ + -2 + ], + "Ionic radii": { + "-2": 1.26 + }, + "Liquid range": "35.4 K", + "Melting point": "54.8 K", + "Mendeleev no": 101, + "Mineral hardness": "no data", + "Molar volume": "17.36 cm3", + "Name": "Oxygen", + "Oxidation states": [ + -2, + -1, + 1, + 2 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000271 (gas; liquid 1.221)(no units)", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "-2": { + "II": { + "": { + "crystal_radius": 1.21, + "ionic_radius": 1.35 + } + }, + "III": { + "": { + "crystal_radius": 1.22, + "ionic_radius": 1.36 + } + }, + "IV": { + "": { + "crystal_radius": 1.24, + "ionic_radius": 1.38 + } + }, + "VI": { + "": { + "crystal_radius": 1.26, + "ionic_radius": 1.4 + } + }, + "VIII": { + "": { + "crystal_radius": 1.28, + "ionic_radius": 1.42 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.02658 W m-1 K-1", + "Van der waals radius": 1.52, + "Velocity of sound": "317.5 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 3.44, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "O-17": -25.58 + }, + "Metallic radius": "no data", + "iupac_ordering": 97, + "IUPAC ordering": 97, + "Ground level": "3P2", + "Ionization energies": [ + 13.618055, + 35.12112, + 54.93554, + 77.4135, + 113.899, + 138.1189, + 739.32683, + 871.409883 + ], + "Electron affinity": 1.4611053 + }, + "Os": { + "Atomic mass": 190.23, + "Atomic no": 76, + "Atomic orbitals": { + "1s": -2475.238617, + "2p": -393.15408, + "2s": -409.522396, + "3d": -72.497183, + "3p": -86.837047, + "3s": -94.501324, + "4d": -10.176082, + "4f": -2.321175, + "4p": -16.119671, + "4s": -19.362527, + "5d": -0.296791, + "5p": -1.757404, + "5s": -2.738293, + "6s": -0.191489 + }, + "Atomic radius": 1.3, + "Atomic radius calculated": 1.85, + "Boiling point": "5285 K", + "Brinell hardness": "3920 MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "5.1 x10-6K-1", + "Common oxidation states": [ + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "22610 kg m-3", + "Electrical resistivity": "8.1 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d6.6s2", + "4": "[Xe].4f14.5d4" + }, + "Ionic radii": { + "4": 0.77, + "5": 0.715, + "6": 0.685, + "7": 0.665, + "8": 0.53 + }, + "Liquid range": "1979 K", + "Melting point": "3306 K", + "Mendeleev no": 63, + "Mineral hardness": "7.0", + "Molar volume": "8.42 cm3", + "Name": "Osmium", + "Oxidation states": [ + -2, + -1, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8 + ], + "Poissons ratio": "0.25", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "222 GPa", + "Shannon radii": { + "4": { + "VI": { + "": { + "crystal_radius": 0.77, + "ionic_radius": 0.63 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.715, + "ionic_radius": 0.575 + } + } + }, + "6": { + "V": { + "": { + "crystal_radius": 0.63, + "ionic_radius": 0.49 + } + }, + "VI": { + "": { + "crystal_radius": 0.685, + "ionic_radius": 0.545 + } + } + }, + "7": { + "VI": { + "": { + "crystal_radius": 0.665, + "ionic_radius": 0.525 + } + } + }, + "8": { + "IV": { + "": { + "crystal_radius": 0.53, + "ionic_radius": 0.39 + } + } + } + }, + "Superconduction temperature": "0.66 K", + "Thermal conductivity": "88 W m-1 K-1", + "Van der waals radius": 2.16, + "Velocity of sound": "4940 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.2, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.352, + "iupac_ordering": 62, + "IUPAC ordering": 62, + "Ground level": "5D4", + "Ionization energies": [ + 8.43823, + 17, + 25, + 41, + 55, + 70.1, + 85.1, + 102.02, + 168.7, + 190, + 213, + 235, + 269, + 298, + 322, + 367, + 410, + 436, + 470, + 520, + 570, + 620, + 670, + 720, + 770, + 820, + 870, + 920, + 970, + 1015, + 1262, + 1311, + 1364, + 1420, + 1474, + 1528, + 1606, + 1660, + 1720, + 1776, + 1996, + 2052, + 2112, + 2168, + 2336, + 2400, + 2552, + 2615.5, + 4374, + 4501, + 4635, + 4779, + 4917, + 5052, + 5280, + 5421, + 5575, + 5717, + 6115, + 6240, + 6376, + 6503, + 7039, + 7185, + 7468, + 7610, + 16560, + 16900, + 17270, + 17620, + 19600, + 20030, + 20570, + 20920.6, + 83976.21, + 85614.4 + ], + "Electron affinity": 1.0778013 + }, + "P": { + "Atomic mass": 30.973762, + "Atomic no": 15, + "Atomic orbitals": { + "1s": -76.061897, + "2p": -4.576617, + "2s": -6.329346, + "3p": -0.20608, + "3s": -0.512364 + }, + "Atomic radius": 1, + "Atomic radius calculated": 0.98, + "Boiling point": "550 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "11 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -3, + 3, + 5 + ], + "Critical temperature": "994 K", + "Density of solid": "1823 kg m-3", + "Electrical resistivity": "about 10 10-8 Ω m", + "Electronic structure": { + "0": "[Ne].3s2.3p3", + "-3": "[Ne].3s2.3p6", + "3": "[Ne].3s2", + "5": "1s2.2s2.2p6" + }, + "ICSD oxidation states": [ + 3, + 4, + 5, + -2, + -3, + -1 + ], + "Ionic radii": { + "3": 0.58, + "5": 0.52 + }, + "Liquid range": "232.7 K", + "Melting point": "(white P) 317.3 K", + "Mendeleev no": 90, + "Mineral hardness": "no data", + "Molar volume": "17.02 cm3", + "Name": "Phosphorus", + "Oxidation states": [ + -3, + -2, + -1, + 1, + 2, + 3, + 4, + 5 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.001212", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.58, + "ionic_radius": 0.44 + } + } + }, + "5": { + "IV": { + "": { + "crystal_radius": 0.31, + "ionic_radius": 0.17 + } + }, + "V": { + "": { + "crystal_radius": 0.43, + "ionic_radius": 0.29 + } + }, + "VI": { + "": { + "crystal_radius": 0.52, + "ionic_radius": 0.38 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.236 W m-1 K-1", + "Van der waals radius": 1.8, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.19, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 90, + "IUPAC ordering": 90, + "Ground level": "4S°3/2", + "Ionization energies": [ + 10.486686, + 19.76949, + 30.20264, + 51.44387, + 65.02511, + 220.43, + 263.57, + 309.6, + 372.31, + 424.4, + 479.44, + 560.62, + 611.741, + 2816.90879, + 3069.8416 + ], + "Electron affinity": 0.7466071 + }, + "Pa": { + "Atomic mass": 231.03588, + "Atomic no": 91, + "Atomic orbitals": { + "1s": -3606.333629, + "2p": -603.470278, + "2s": -623.870431, + "3d": -127.781168, + "3p": -146.485678, + "3s": -156.466742, + "4d": -25.933121, + "4f": -14.105747, + "4p": -34.48293, + "4s": -39.064507, + "5d": -3.659928, + "5f": -0.316813, + "5p": -6.709821, + "5s": -8.463463, + "6d": -0.142481, + "6p": -0.799756, + "6s": -1.287232, + "7s": -0.129653 + }, + "Atomic radius": 1.8, + "Atomic radius calculated": "no data", + "Boiling point": "no data K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 5 + ], + "Critical temperature": "no data K", + "Density of solid": "15370 kg m-3", + "Electrical resistivity": "18 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f2.6d1.7s2", + "5": "[Hg].6p6" + }, + "Ionic radii": { + "3": 1.16, + "4": 1.04, + "5": 0.92 + }, + "Liquid range": "no data K", + "Melting point": "1841 K", + "Mendeleev no": 46, + "Mineral hardness": "no data", + "Molar volume": "15.18 cm3", + "Name": "Protactinium", + "Oxidation states": [ + 3, + 4, + 5 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.18, + "ionic_radius": 1.04 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 1.04, + "ionic_radius": 0.9 + } + }, + "VIII": { + "": { + "crystal_radius": 1.15, + "ionic_radius": 1.01 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.92, + "ionic_radius": 0.78 + } + }, + "VIII": { + "": { + "crystal_radius": 1.05, + "ionic_radius": 0.91 + } + }, + "IX": { + "": { + "crystal_radius": 1.09, + "ionic_radius": 0.95 + } + } + } + }, + "Superconduction temperature": "1.4 K", + "Thermal conductivity": "47 W m-1 K-1", + "Van der waals radius": 2.1, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.5, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.642, + "iupac_ordering": 30, + "IUPAC ordering": 30, + "Ground level": "4K11/2", + "Ionization energies": [ + 5.89, + 11.9, + 18.6, + 30.9, + 44.3, + 72, + 85.1, + 98.9, + 111, + 137, + 153, + 187, + 203, + 292, + 316, + 342, + 369, + 395, + 423, + 460, + 488, + 518, + 546, + 690, + 720, + 760, + 790, + 880, + 920, + 1020, + 1060, + 1150, + 1220, + 1300, + 1370, + 1450, + 1520, + 1600, + 1670, + 1760, + 1830, + 1910, + 1980, + 2060, + 2130, + 2483, + 2550, + 2620, + 2696, + 2766, + 2837, + 2968, + 3040, + 3119, + 3193, + 3488, + 3558, + 3637, + 3709, + 4077, + 4161, + 4370, + 4454, + 7181, + 7341, + 7510, + 7690, + 7870, + 8040, + 8410, + 8590, + 8780, + 8960, + 9460, + 9620, + 9790, + 9950, + 11100, + 11290, + 11660, + 11840, + 24660, + 25080, + 25540, + 25970, + 30230, + 30800, + 31520, + 31971.6, + 126296.6, + 128507.1 + ], + "Electron affinity": 0.55 + }, + "Pb": { + "Atomic mass": 207.2, + "Atomic no": 82, + "Atomic orbitals": { + "1s": -2901.078061, + "2p": -470.877785, + "2s": -488.843335, + "3d": -91.889924, + "3p": -107.950391, + "3s": -116.526852, + "4d": -15.030026, + "4f": -5.592532, + "4p": -21.990564, + "4s": -25.75333, + "5d": -0.902393, + "5p": -2.941657, + "5s": -4.206797, + "6p": -0.141831, + "6s": -0.357187 + }, + "Atomic radius": 1.8, + "Atomic radius calculated": 1.54, + "Boiling point": "2022 K", + "Brinell hardness": "38.3 MN m-2", + "Bulk modulus": "46 GPa", + "Coefficient of linear thermal expansion": "28.9 x10-6K-1", + "Common oxidation states": [ + 2, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "11340 kg m-3", + "Electrical resistivity": "21 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d10.6s2.6p2", + "2": "[Xe].4f14.5d10.6s2", + "4": "[Xe].4f14.5d10" + }, + "ICSD oxidation states": [ + 2, + 4 + ], + "Ionic radii": { + "2": 1.33, + "4": 0.915 + }, + "Liquid range": "1421.39 K", + "Melting point": "600.61 K", + "Mendeleev no": 82, + "Mineral hardness": "1.5", + "Molar volume": "18.26 cm3", + "Name": "Lead", + "Oxidation states": [ + -4, + 2, + 4 + ], + "Poissons ratio": "0.44", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "5.6 GPa", + "Shannon radii": { + "2": { + "IVPY": { + "": { + "crystal_radius": 1.12, + "ionic_radius": 0.98 + } + }, + "VI": { + "": { + "crystal_radius": 1.33, + "ionic_radius": 1.19 + } + }, + "VII": { + "": { + "crystal_radius": 1.37, + "ionic_radius": 1.23 + } + }, + "VIII": { + "": { + "crystal_radius": 1.43, + "ionic_radius": 1.29 + } + }, + "IX": { + "": { + "crystal_radius": 1.49, + "ionic_radius": 1.35 + } + }, + "X": { + "": { + "crystal_radius": 1.54, + "ionic_radius": 1.4 + } + }, + "XI": { + "": { + "crystal_radius": 1.59, + "ionic_radius": 1.45 + } + }, + "XII": { + "": { + "crystal_radius": 1.63, + "ionic_radius": 1.49 + } + } + }, + "4": { + "IV": { + "": { + "crystal_radius": 0.79, + "ionic_radius": 0.65 + } + }, + "V": { + "": { + "crystal_radius": 0.87, + "ionic_radius": 0.73 + } + }, + "VI": { + "": { + "crystal_radius": 0.915, + "ionic_radius": 0.775 + } + }, + "VIII": { + "": { + "crystal_radius": 1.08, + "ionic_radius": 0.94 + } + } + } + }, + "Superconduction temperature": "7.2 K", + "Thermal conductivity": "35 W m-1 K-1", + "Van der waals radius": 2.02, + "Velocity of sound": "1260 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.33, + "Youngs modulus": "16 GPa", + "Metallic radius": 1.75, + "iupac_ordering": 82, + "IUPAC ordering": 82, + "Ground level": "1/2,1/2)0", + "Ionization energies": [ + 7.4166799, + 15.032499, + 31.9373, + 42.33256, + 68.8, + 82.9, + 100.1, + 120, + 138, + 158, + 182, + 203, + 224, + 245.1, + 338.1, + 374, + 401, + 427, + 478, + 507, + 570, + 610, + 650, + 690, + 750, + 810, + 870, + 930, + 990, + 1050, + 1120, + 1180, + 1240, + 1300, + 1360, + 1430, + 1704, + 1760, + 1819, + 1884, + 1945, + 2004, + 2101, + 2163, + 2230, + 2292, + 2543, + 2605, + 2671, + 2735, + 2965, + 3036, + 3211, + 3282.1, + 5414, + 5555, + 5703, + 5862, + 6015, + 6162, + 6442, + 6597, + 6767, + 6924, + 7362, + 7500, + 7650, + 7790, + 8520, + 8680, + 9000, + 9150, + 19590, + 19970, + 20380, + 20750, + 23460, + 23940, + 24550, + 24938.2, + 99491.85, + 101336.4 + ], + "Electron affinity": 0.3567212 + }, + "Pd": { + "Atomic mass": 106.42, + "Atomic no": 46, + "Atomic orbitals": { + "1s": -860.134909, + "2p": -114.408286, + "2s": -123.105078, + "3d": -12.132197, + "3p": -18.580798, + "3s": -22.060898, + "4d": -0.160771, + "4p": -1.815215, + "4s": -2.889173 + }, + "Atomic radius": 1.4, + "Atomic radius calculated": 1.69, + "Boiling point": "3236 K", + "Brinell hardness": "37.3 MN m-2", + "Bulk modulus": "180 GPa", + "Coefficient of linear thermal expansion": "11.8 x10-6K-1", + "Common oxidation states": [ + 2, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "12023 kg m-3", + "Electrical resistivity": "10.8 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d10", + "2": "[Kr].4d8", + "4": "[Kr].4d6" + }, + "ICSD oxidation states": [ + 2, + 4 + ], + "Ionic radii": { + "1": 0.73, + "2": 1, + "3": 0.9, + "4": 0.755 + }, + "Liquid range": "1407.95 K", + "Melting point": "1828.05 K", + "Mendeleev no": 69, + "Mineral hardness": "4.75", + "Molar volume": "8.56 cm3", + "Name": "Palladium", + "Oxidation states": [ + 2, + 4 + ], + "Poissons ratio": "0.39", + "Reflectivity": "72 %", + "Refractive index": "no data", + "Rigidity modulus": "44 GPa", + "Shannon radii": { + "1": { + "II": { + "": { + "crystal_radius": 0.73, + "ionic_radius": 0.59 + } + } + }, + "2": { + "IVSQ": { + "": { + "crystal_radius": 0.78, + "ionic_radius": 0.64 + } + }, + "VI": { + "": { + "crystal_radius": 1, + "ionic_radius": 0.86 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 0.9, + "ionic_radius": 0.76 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.755, + "ionic_radius": 0.615 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "72 W m-1 K-1", + "Van der waals radius": 2.1, + "Velocity of sound": "3070 m s-1", + "Vickers hardness": "461 MN m-2", + "X": 2.2, + "Youngs modulus": "121 GPa", + "Metallic radius": 1.376, + "iupac_ordering": 69, + "IUPAC ordering": 69, + "Ground level": "1S0", + "Ionization energies": [ + 8.336839, + 19.43, + 32.93, + 46, + 61, + 84.1, + 101, + 120, + 141, + 159.9, + 238.57, + 260, + 286, + 311, + 342, + 369.1, + 427, + 457.5, + 810, + 869, + 933, + 1000, + 1065, + 1145, + 1218, + 1290, + 1366, + 1438, + 1644, + 1706.2, + 1781.3, + 1869, + 1962, + 2016, + 2181, + 2248.87, + 5284, + 5475, + 5683, + 5880, + 6242, + 6469, + 6759, + 6943.097, + 28776.034, + 29622.6 + ], + "Electron affinity": 0.5621412 + }, + "Pm": { + "Atomic mass": 145, + "Atomic no": 61, + "Atomic orbitals": { + "1s": -1562.980284, + "2p": -233.455114, + "2s": -245.970548, + "3d": -37.625433, + "3p": -47.921132, + "3s": -53.429311, + "4d": -4.596822, + "4f": -0.200159, + "4p": -8.320495, + "4s": -10.422756, + "5p": -0.817702, + "5s": -1.372265, + "6s": -0.127053 + }, + "Atomic radius": 1.85, + "Atomic radius calculated": 2.05, + "Boiling point": "3273 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "33 GPa", + "Coefficient of linear thermal expansion": "11 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "7264 kg m-3", + "Electrical resistivity": "about 75 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f5.6s2", + "3": "[Xe].4f4" + }, + "Ionic radii": { + "3": 1.11 + }, + "Liquid range": "1900 K", + "Melting point": "1373 K", + "Mendeleev no": 29, + "Mineral hardness": "no data", + "Molar volume": "20.23 cm3", + "Name": "Promethium", + "Oxidation states": [ + 3 + ], + "Poissons ratio": "0.28", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "18 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.11, + "ionic_radius": 0.97 + } + }, + "VIII": { + "": { + "crystal_radius": 1.233, + "ionic_radius": 1.093 + } + }, + "IX": { + "": { + "crystal_radius": 1.284, + "ionic_radius": 1.144 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "15 W m-1 K-1", + "Van der waals radius": 2.38, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.13, + "Youngs modulus": "46 GPa", + "Metallic radius": 1.811, + "iupac_ordering": 43, + "IUPAC ordering": 43, + "Ground level": "6H°5/2", + "Ionization energies": [ + 5.58187, + 10.938, + 22.44, + 41.17, + 61.7, + 85, + 101, + 116, + 138, + 155, + 174, + 202, + 229, + 248, + 269, + 430, + 462, + 497, + 534, + 569, + 609, + 651, + 689, + 730, + 767, + 916, + 956, + 998, + 1040, + 1113, + 1158, + 1261, + 1308.7, + 2251, + 2344, + 2443, + 2549, + 2652, + 2755, + 2892, + 2997, + 3112, + 3219, + 3519, + 3613, + 3718, + 3816, + 4056, + 4166, + 4371, + 4476, + 10115, + 10378, + 10671, + 10942, + 11819, + 12136, + 12532, + 12797.26, + 52144.29, + 53346.1 + ], + "Electron affinity": 0.129 + }, + "Po": { + "Atomic mass": 210, + "Atomic no": 84, + "Atomic orbitals": { + "1s": -3050.988417, + "2p": -498.77192, + "2s": -517.275843, + "3d": -99.256068, + "3p": -115.898384, + "3s": -124.783683, + "4d": -17.173307, + "4f": -7.206499, + "4p": -24.481337, + "4s": -28.42254, + "5d": -1.386458, + "5p": -3.655382, + "5s": -5.027447, + "6p": -0.217889, + "6s": -0.493528 + }, + "Atomic radius": 1.9, + "Atomic radius calculated": 1.35, + "Boiling point": "1235 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -2, + 2, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "9196 kg m-3", + "Electrical resistivity": "40 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d10.6s2.6p4", + "-2": "[Xe].4f14.5d10.6s2.6p6", + "2": "[Xe].4f14.5d10.6s2.6p2", + "4": "[Xe].4f14.5d10.6s2" + }, + "Ionic radii": { + "4": 1.08, + "6": 0.81 + }, + "Liquid range": "708 K", + "Melting point": "527 K", + "Mendeleev no": 91, + "Mineral hardness": "no data", + "Molar volume": "22.97 cm3", + "Name": "Polonium", + "Oxidation states": [ + -2, + 2, + 4, + 6 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "4": { + "VI": { + "": { + "crystal_radius": 1.08, + "ionic_radius": 0.94 + } + }, + "VIII": { + "": { + "crystal_radius": 1.22, + "ionic_radius": 1.08 + } + } + }, + "6": { + "VI": { + "": { + "crystal_radius": 0.81, + "ionic_radius": 0.67 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "20 W m-1 K-1", + "Van der waals radius": 1.97, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.53, + "iupac_ordering": 93, + "IUPAC ordering": 93, + "Ground level": "3P2", + "Ionization energies": [ + 8.41807, + 19.3, + 27.3, + 36, + 57, + 69.1, + 108, + 125, + 146.1, + 166, + 186, + 209, + 235, + 257, + 281, + 304, + 416, + 444, + 473, + 502, + 560, + 590, + 670, + 700, + 740, + 800, + 870, + 930, + 990, + 1060, + 1120, + 1180, + 1250, + 1320, + 1380, + 1440, + 1510, + 1570, + 1865, + 1923, + 1986, + 2052, + 2115, + 2177, + 2281, + 2345, + 2414, + 2480, + 2740, + 2803, + 2873, + 2938, + 3194, + 3268, + 3450, + 3524.2, + 5785, + 5930, + 6084, + 6248, + 6405, + 6557, + 6856, + 7015, + 7191, + 7350, + 7810, + 7950, + 8100, + 8240, + 9050, + 9220, + 9550, + 9710, + 20670, + 21050, + 21470, + 21860, + 24860, + 25360, + 25990, + 26390.4, + 105064.3, + 106982.7 + ], + "Electron affinity": 1.407 + }, + "Pr": { + "Atomic mass": 140.90765, + "Atomic no": 59, + "Atomic orbitals": { + "1s": -1457.338067, + "2p": -215.418313, + "2s": -227.426363, + "3d": -33.913996, + "3p": -43.692548, + "3s": -48.924994, + "4d": -4.154228, + "4f": -0.155138, + "4p": -7.613108, + "4s": -9.577447, + "5p": -0.778046, + "5s": -1.296106, + "6s": -0.124465 + }, + "Atomic radius": 1.85, + "Atomic radius calculated": 2.47, + "Boiling point": "3563 K", + "Brinell hardness": "481 MN m-2", + "Bulk modulus": "29 GPa", + "Coefficient of linear thermal expansion": "6.7 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "6640 kg m-3", + "Electrical resistivity": "70 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f3.6s2", + "3": "[Xe].4f2" + }, + "ICSD oxidation states": [ + 3, + 4 + ], + "Ionic radii": { + "3": 1.13, + "4": 0.99 + }, + "Liquid range": "2355 K", + "Melting point": "1208 K", + "Mendeleev no": 31, + "Mineral hardness": "no data", + "Molar volume": "20.80 cm3", + "Name": "Praseodymium", + "Oxidation states": [ + 2, + 3, + 4 + ], + "Poissons ratio": "0.28", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "15 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.13, + "ionic_radius": 0.99 + } + }, + "VIII": { + "": { + "crystal_radius": 1.266, + "ionic_radius": 1.126 + } + }, + "IX": { + "": { + "crystal_radius": 1.319, + "ionic_radius": 1.179 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.99, + "ionic_radius": 0.85 + } + }, + "VIII": { + "": { + "crystal_radius": 1.1, + "ionic_radius": 0.96 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "13 W m-1 K-1", + "Van der waals radius": 2.4, + "Velocity of sound": "2280 m s-1", + "Vickers hardness": "400 MN m-2", + "X": 1.13, + "Youngs modulus": "37 GPa", + "Metallic radius": 1.828, + "iupac_ordering": 45, + "IUPAC ordering": 45, + "Ground level": "4I°9/2", + "Ionization energies": [ + 5.4702, + 10.631, + 21.6237, + 38.981, + 57.53, + 82, + 97, + 112, + 131, + 148, + 162, + 196, + 217.02, + 350, + 378, + 412, + 445, + 478, + 516, + 554, + 590, + 627, + 663, + 803, + 840, + 880, + 920, + 985, + 1028, + 1124, + 1169.9, + 2019, + 2108, + 2202, + 2304, + 2400, + 2501, + 2628, + 2729, + 2838, + 2941, + 3227, + 3319, + 3419, + 3512, + 3729, + 3832, + 4030, + 4130, + 9378, + 9632, + 9913, + 10175, + 10959, + 11262, + 11641, + 11895.89, + 48571.71, + 49722.25 + ], + "Electron affinity": 0.1092346 + }, + "Pt": { + "Atomic mass": 195.084, + "Atomic no": 78, + "Atomic orbitals": { + "1s": -2613.096532, + "2p": -417.96053, + "2s": -434.858003, + "3d": -78.400271, + "3p": -93.309108, + "3s": -101.274869, + "4d": -11.419476, + "4f": -3.038049, + "4p": -17.697297, + "4s": -21.110651, + "5d": -0.273634, + "5p": -1.884256, + "5s": -2.950526, + "6s": -0.161308 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.77, + "Boiling point": "4098 K", + "Brinell hardness": "392 MN m-2", + "Bulk modulus": "230 GPa", + "Coefficient of linear thermal expansion": "8.8 x10-6K-1", + "Common oxidation states": [ + 2, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "21090 kg m-3", + "Electrical resistivity": "10.6 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d9.6s1", + "2": "[Xe].4f14.5d8", + "4": "[Xe].4f14.5d6" + }, + "Ionic radii": { + "2": 0.94, + "4": 0.765, + "5": 0.71 + }, + "Liquid range": "2056.6 K", + "Melting point": "2041.4 K", + "Mendeleev no": 68, + "Mineral hardness": "3.5", + "Molar volume": "9.09 cm3", + "Name": "Platinum", + "Oxidation states": [ + -2, + 2, + 4, + 5, + 6 + ], + "Poissons ratio": "0.38", + "Reflectivity": "73 %", + "Refractive index": "no data", + "Rigidity modulus": "61 GPa", + "Shannon radii": { + "2": { + "IVSQ": { + "": { + "crystal_radius": 0.74, + "ionic_radius": 0.6 + } + }, + "VI": { + "": { + "crystal_radius": 0.94, + "ionic_radius": 0.8 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.765, + "ionic_radius": 0.625 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.71, + "ionic_radius": 0.57 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "72 W m-1 K-1", + "Van der waals radius": 2.13, + "Velocity of sound": "2680 m s-1", + "Vickers hardness": "549 MN m-2", + "X": 2.28, + "Youngs modulus": "168 GPa", + "Metallic radius": 1.387, + "iupac_ordering": 68, + "IUPAC ordering": 68, + "Ground level": "3D3", + "Ionization energies": [ + 8.95883, + 18.56, + 29, + 43, + 56, + 75, + 91, + 109, + 126, + 144.9, + 220.4, + 245, + 269, + 293, + 332, + 358, + 392, + 445, + 479, + 507, + 550, + 610, + 660, + 710, + 760, + 820, + 870, + 930, + 980, + 1040, + 1090, + 1140, + 1402, + 1454, + 1509, + 1567, + 1624, + 1680, + 1763, + 1821, + 1883, + 1941, + 2171, + 2228, + 2291, + 2350, + 2536, + 2603, + 2762, + 2827.8, + 4715, + 4839, + 4980, + 5128, + 5270, + 5410, + 5654, + 5800, + 5959, + 6106, + 6517, + 6646, + 6787, + 6918, + 7512, + 7660, + 7960, + 8100, + 17540, + 17890, + 18280, + 18630, + 20840, + 21280, + 21840, + 22205.7, + 88955.18, + 90659.7 + ], + "Electron affinity": 2.125105 + }, + "Pu": { + "Atomic mass": 244, + "Atomic no": 94, + "Atomic orbitals": "no data", + "Atomic radius": 1.75, + "Atomic radius calculated": "no data", + "Boiling point": "3503 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "19816 kg m-3", + "Electrical resistivity": "150 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f6.7s2", + "4": "[Rn].5f4" + }, + "Ionic radii": { + "3": 1.14, + "4": 1, + "5": 0.88, + "6": 0.85 + }, + "Liquid range": "2590.5 K", + "Melting point": "912.5 K", + "Mendeleev no": 43, + "Mineral hardness": "no data", + "Molar volume": "12.29 cm3", + "Name": "Plutonium", + "Oxidation states": [ + 3, + 4, + 5, + 6, + 7 + ], + "Poissons ratio": "0.21", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "43 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.14, + "ionic_radius": 1 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 1, + "ionic_radius": 0.86 + } + }, + "VIII": { + "": { + "crystal_radius": 1.1, + "ionic_radius": 0.96 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.88, + "ionic_radius": 0.74 + } + } + }, + "6": { + "VI": { + "": { + "crystal_radius": 0.85, + "ionic_radius": 0.71 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "6 W m-1 K-1", + "Van der waals radius": 2.43, + "Velocity of sound": "2260 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.28, + "Youngs modulus": "96 GPa", + "Metallic radius": 1.523, + "iupac_ordering": 27, + "IUPAC ordering": 27, + "Ground level": "7F0", + "Ionization energies": [ + 6.02576, + 11.5, + 21.1, + 35, + 49, + 80, + 95, + 109, + 124, + 139, + 159, + 179, + 200, + 219, + 258, + 278, + 389, + 416, + 444, + 474, + 503, + 532, + 575, + 605, + 637, + 668, + 820, + 850, + 890, + 930, + 1030, + 1070, + 1180, + 1220, + 1340, + 1420, + 1500, + 1580, + 1660, + 1740, + 1820, + 1890, + 1990, + 2070, + 2150, + 2230, + 2310, + 2390, + 2774, + 2844, + 2918, + 2997, + 3072, + 3146, + 3290, + 3366, + 3449, + 3527, + 3836, + 3911, + 3993, + 4068, + 4496, + 4585, + 4807, + 4890, + 7830, + 7990, + 8170, + 8360, + 8540, + 8710, + 9130, + 9310, + 9520, + 9700, + 10230, + 10390, + 10570, + 10730, + 12060, + 12260, + 12660, + 12840, + 26480, + 26920, + 27400, + 27840, + 32800, + 33400, + 34100, + 34625.8, + 136299.2, + 138646 + ], + "Electron affinity": -0.5 + }, + "Ra": { + "Atomic mass": 226, + "Atomic no": 88, + "Atomic orbitals": { + "1s": -3362.736563, + "2p": -557.513214, + "2s": -577.101208, + "3d": -115.306476, + "3p": -133.12325, + "3s": -142.632426, + "4d": -22.208125, + "4f": -11.181066, + "4p": -30.221208, + "4s": -34.525628, + "5d": -2.819853, + "5p": -5.547203, + "5s": -7.139137, + "6p": -0.634674, + "6s": -1.05135, + "7s": -0.113732 + }, + "Atomic radius": 2.15, + "Atomic radius calculated": "no data", + "Boiling point": "2010 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "5000 kg m-3", + "Electrical resistivity": "100 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].7s2", + "2": "[Hg].6p6" + }, + "Ionic radii": { + "2": 1.62 + }, + "Liquid range": "1037 K", + "Melting point": "973 K", + "Mendeleev no": 13, + "Mineral hardness": "no data", + "Molar volume": "41.09 cm3", + "Name": "Radium", + "Oxidation states": [ + 2 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "2": { + "VIII": { + "": { + "crystal_radius": 1.62, + "ionic_radius": 1.48 + } + }, + "XII": { + "": { + "crystal_radius": 1.84, + "ionic_radius": 1.7 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "19 W m-1 K-1", + "Van der waals radius": 2.83, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 0.9, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "Ra-223": 1210.3 + }, + "Metallic radius": 2.293, + "iupac_ordering": 12, + "IUPAC ordering": 12, + "Ground level": "1S0", + "Ionization energies": [ + 5.2784239, + 10.14718, + 31, + 41, + 52.9, + 64, + 82, + 97, + 124, + 140, + 204.9, + 227, + 250, + 274, + 299, + 324, + 356, + 382, + 409, + 435, + 570, + 600, + 630, + 660, + 740, + 770, + 860, + 900, + 970, + 1040, + 1110, + 1180, + 1250, + 1320, + 1390, + 1460, + 1530, + 1610, + 1680, + 1750, + 1820, + 1880, + 2208, + 2271, + 2338, + 2409, + 2477, + 2544, + 2662, + 2731, + 2806, + 2876, + 3155, + 3224, + 3298, + 3368, + 3682, + 3762, + 3959, + 4040, + 6565, + 6718, + 6881, + 7056, + 7222, + 7380, + 7720, + 7890, + 8080, + 8250, + 8730, + 8880, + 9040, + 9200, + 10190, + 10360, + 10720, + 10890, + 22900, + 23300, + 23750, + 24160, + 27830, + 28370, + 29050, + 29479.8, + 116848.7, + 118931.3 + ], + "Electron affinity": 0.1 + }, + "Rb": { + "Atomic mass": 85.4678, + "Atomic no": 37, + "Atomic orbitals": { + "1s": -540.957115, + "2p": -64.784678, + "2s": -71.291202, + "3d": -3.915508, + "3p": -8.165416, + "3s": -10.513861, + "4p": -0.59217, + "4s": -1.135051, + "5s": -0.085375 + }, + "Atomic radius": 2.35, + "Atomic radius calculated": 2.65, + "Boiling point": "961 K", + "Brinell hardness": "0.216 MN m-2", + "Bulk modulus": "2.5 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 1 + ], + "Critical temperature": "2093 K", + "Density of solid": "1532 kg m-3", + "Electrical resistivity": "13.3 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].5s1", + "1": "[Ar].3d10.4s2.4p6" + }, + "ICSD oxidation states": [ + 1 + ], + "Ionic radii": { + "1": 1.66 + }, + "Liquid range": "648.54 K", + "Melting point": "312.46 K", + "Mendeleev no": 9, + "Mineral hardness": "0.3", + "Molar volume": "55.76 cm3", + "Name": "Rubidium", + "Oxidation states": [ + 1 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "1": { + "VI": { + "": { + "crystal_radius": 1.66, + "ionic_radius": 1.52 + } + }, + "VII": { + "": { + "crystal_radius": 1.7, + "ionic_radius": 1.56 + } + }, + "VIII": { + "": { + "crystal_radius": 1.75, + "ionic_radius": 1.61 + } + }, + "IX": { + "": { + "crystal_radius": 1.77, + "ionic_radius": 1.63 + } + }, + "X": { + "": { + "crystal_radius": 1.8, + "ionic_radius": 1.66 + } + }, + "XI": { + "": { + "crystal_radius": 1.83, + "ionic_radius": 1.69 + } + }, + "XII": { + "": { + "crystal_radius": 1.86, + "ionic_radius": 1.72 + } + }, + "XIV": { + "": { + "crystal_radius": 1.97, + "ionic_radius": 1.83 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "58 W m-1 K-1", + "Van der waals radius": 3.03, + "Velocity of sound": "1300 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 0.82, + "Youngs modulus": "2.4 GPa", + "Metallic radius": 2.537, + "iupac_ordering": 8, + "IUPAC ordering": 8, + "Ground level": "2S1/2", + "Ionization energies": [ + 4.1771281, + 27.28954, + 39.247, + 52.2, + 68.44, + 82.9, + 98.67, + 132.79, + 150.628, + 277.12, + 313.1, + 356, + 400, + 443, + 502, + 550, + 601, + 654, + 706, + 857, + 905.3, + 958.9, + 1024, + 1080, + 1125, + 1242.5, + 1294.57, + 3133.3, + 3281, + 3443, + 3600, + 3815, + 3988, + 4214, + 4356.865, + 18305.884, + 18965.516 + ], + "Electron affinity": 0.48591621 + }, + "Re": { + "Atomic mass": 186.207, + "Atomic no": 75, + "Atomic orbitals": { + "1s": -2407.665572, + "2p": -380.982869, + "2s": -397.087707, + "3d": -69.57676, + "3p": -83.634578, + "3s": -91.149193, + "4d": -9.516816, + "4f": -1.92508, + "4p": -15.295495, + "4s": -18.454325, + "5d": -0.258639, + "5p": -1.631227, + "5s": -2.567348, + "6s": -0.186859 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.88, + "Boiling point": "5869 K", + "Brinell hardness": "1320 MN m-2", + "Bulk modulus": "370 GPa", + "Coefficient of linear thermal expansion": "6.2 x10-6K-1", + "Common oxidation states": [ + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "21020 kg m-3", + "Electrical resistivity": "18 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d5.6s2", + "4": "[Xe].4f14.5d3" + }, + "ICSD oxidation states": [ + 3, + 4, + 5, + 6, + 7 + ], + "Ionic radii": { + "4": 0.77, + "5": 0.72, + "6": 0.69, + "7": 0.67 + }, + "Liquid range": "2410 K", + "Melting point": "3459 K", + "Mendeleev no": 58, + "Mineral hardness": "7.0", + "Molar volume": "8.86 cm3", + "Name": "Rhenium", + "Oxidation states": [ + -3, + -1, + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "Poissons ratio": "0.30", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "178 GPa", + "Shannon radii": { + "4": { + "VI": { + "": { + "crystal_radius": 0.77, + "ionic_radius": 0.63 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.72, + "ionic_radius": 0.58 + } + } + }, + "6": { + "VI": { + "": { + "crystal_radius": 0.69, + "ionic_radius": 0.55 + } + } + }, + "7": { + "IV": { + "": { + "crystal_radius": 0.52, + "ionic_radius": 0.38 + } + }, + "VI": { + "": { + "crystal_radius": 0.67, + "ionic_radius": 0.53 + } + } + } + }, + "Superconduction temperature": "1.70 K", + "Thermal conductivity": "48 W m-1 K-1", + "Van der waals radius": 2.16, + "Velocity of sound": "4700 m s-1", + "Vickers hardness": "2450 MN m-2", + "X": 1.9, + "Youngs modulus": "463 GPa", + "Metallic radius": 1.375, + "iupac_ordering": 59, + "IUPAC ordering": 59, + "Ground level": "6S5/2", + "Ionization energies": [ + 7.83352, + 16.6, + 27, + 39.1, + 51.9, + 67, + 82.71, + 144.4, + 165, + 187, + 208, + 236, + 268, + 291, + 330, + 377, + 403, + 429, + 476, + 520, + 570, + 620, + 670, + 720, + 760, + 810, + 860, + 910, + 953, + 1194, + 1242, + 1294, + 1349, + 1402, + 1454, + 1530, + 1583, + 1641, + 1696, + 1912, + 1966, + 2025, + 2080, + 2240, + 2302, + 2450, + 2514.5, + 4214, + 4335, + 4468, + 4609, + 4745, + 4877, + 5099, + 5236, + 5388, + 5528, + 5919, + 6042, + 6176, + 6300, + 6810, + 6952, + 7230, + 7366, + 16080, + 16410, + 16780, + 17120, + 19000, + 19420, + 19950, + 20297.4, + 81556.9, + 83162.3 + ], + "Electron affinity": 0.06039663 + }, + "Rh": { + "Atomic mass": 102.9055, + "Atomic no": 45, + "Atomic orbitals": { + "1s": -821.136773, + "2p": -108.357665, + "2s": -116.80695, + "3d": -11.21725, + "3p": -17.415299, + "3s": -20.765603, + "4d": -0.239422, + "4p": -1.806456, + "4s": -2.825505, + "5s": -0.154624 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.73, + "Boiling point": "3968 K", + "Brinell hardness": "1100 MN m-2", + "Bulk modulus": "380 GPa", + "Coefficient of linear thermal expansion": "8.2 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "12450 kg m-3", + "Electrical resistivity": "4.3 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d8.5s1", + "3": "[Kr].4d6" + }, + "ICSD oxidation states": [ + 3, + 4 + ], + "Ionic radii": { + "3": 0.805, + "4": 0.74, + "5": 0.69 + }, + "Liquid range": "1731 K", + "Melting point": "2237 K", + "Mendeleev no": 65, + "Mineral hardness": "6.0", + "Molar volume": "8.28 cm3", + "Name": "Rhodium", + "Oxidation states": [ + -1, + 1, + 2, + 3, + 4, + 5, + 6 + ], + "Poissons ratio": "0.26", + "Reflectivity": "84 %", + "Refractive index": "no data", + "Rigidity modulus": "150 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.805, + "ionic_radius": 0.665 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.74, + "ionic_radius": 0.6 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.69, + "ionic_radius": 0.55 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "150 W m-1 K-1", + "Van der waals radius": 2.1, + "Velocity of sound": "4700 m s-1", + "Vickers hardness": "1246 MN m-2", + "X": 2.28, + "Youngs modulus": "275 GPa", + "Metallic radius": 1.345, + "iupac_ordering": 66, + "IUPAC ordering": 66, + "Ground level": "4F9/2", + "Ionization energies": [ + 7.4589, + 18.08, + 31.06, + 42, + 63, + 80, + 97, + 115.1, + 135, + 207.51, + 228, + 252.1, + 277, + 306, + 331.58, + 389.3, + 415.97, + 739, + 794, + 857, + 921, + 984, + 1061, + 1131, + 1202, + 1274, + 1344, + 1544, + 1604.9, + 1677.6, + 1763, + 1851, + 1903, + 2063, + 2129.22, + 5018, + 5203, + 5406, + 5600, + 5940, + 6161, + 6444, + 6623.262, + 27486.983, + 28311.965 + ], + "Electron affinity": 1.142892 + }, + "Rn": { + "Atomic mass": 220, + "Atomic no": 86, + "Atomic orbitals": { + "1s": -3204.756288, + "2p": -527.533025, + "2s": -546.57796, + "3d": -106.945006, + "3p": -124.172862, + "3s": -133.369144, + "4d": -19.449994, + "4f": -8.953318, + "4p": -27.108985, + "4s": -31.230804, + "5d": -1.911329, + "5p": -4.408702, + "5s": -5.889683, + "6p": -0.29318, + "6s": -0.62657 + }, + "Atomic radius": "no data", + "Atomic radius calculated": 1.2, + "Boiling point": "211.3 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Critical temperature": "377 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d10.6s2.6p6" + }, + "Liquid range": "9.3 K", + "Max oxidation state": 0, + "Melting point": "202 K", + "Mendeleev no": 6, + "Min oxidation state": 0, + "Mineral hardness": "no data", + "Molar volume": "50.50 cm3", + "Name": "Radon", + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.00361 W m-1 K-1", + "Van der waals radius": 2.2, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.2, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 0, + "IUPAC ordering": 0, + "Ground level": "1S0", + "Ionization energies": [ + 10.7485, + 21.4, + 29.4, + 36.9, + 52.9, + 64, + 88, + 102, + 154, + 173.9, + 195, + 218, + 240, + 264, + 293, + 317, + 342, + 367, + 488, + 520, + 550, + 580, + 640, + 680, + 760, + 800, + 850, + 920, + 980, + 1050, + 1110, + 1180, + 1250, + 1310, + 1390, + 1460, + 1520, + 1590, + 1660, + 1720, + 2033, + 2094, + 2158, + 2227, + 2293, + 2357, + 2467, + 2535, + 2606, + 2674, + 2944, + 3010, + 3082, + 3149, + 3433, + 3510, + 3699, + 3777, + 6169, + 6318, + 6476, + 6646, + 6807, + 6964, + 7283, + 7450, + 7630, + 7800, + 8260, + 8410, + 8570, + 8710, + 9610, + 9780, + 10120, + 10290, + 21770, + 22160, + 22600, + 22990, + 26310, + 26830, + 27490, + 27903.1, + 110842, + 112843.7 + ], + "Electron affinity": -0.72 + }, + "Ru": { + "Atomic mass": 101.07, + "Atomic no": 44, + "Atomic orbitals": { + "1s": -782.918621, + "2p": -102.333649, + "2s": -110.536054, + "3d": -10.195668, + "3p": -16.145217, + "3s": -19.366692, + "4d": -0.210375, + "4p": -1.667549, + "4s": -2.628363, + "5s": -0.152834 + }, + "Atomic radius": 1.3, + "Atomic radius calculated": 1.78, + "Boiling point": "4423 K", + "Brinell hardness": "2160 MN m-2", + "Bulk modulus": "220 GPa", + "Coefficient of linear thermal expansion": "6.4 x10-6K-1", + "Common oxidation states": [ + 3, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "12370 kg m-3", + "Electrical resistivity": "7.1 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d7.5s1", + "3": "[Kr].4d5", + "4": "[Kr].4d4" + }, + "ICSD oxidation states": [ + 2, + 3, + 4, + 5, + 6 + ], + "Ionic radii": { + "3": 0.82, + "4": 0.76, + "5": 0.705, + "7": 0.52, + "8": 0.5 + }, + "Liquid range": "1816 K", + "Melting point": "2607 K", + "Mendeleev no": 62, + "Mineral hardness": "6.5", + "Molar volume": "8.17 cm3", + "Name": "Ruthenium", + "Oxidation states": [ + -2, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8 + ], + "Poissons ratio": "0.30", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "173 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.82, + "ionic_radius": 0.68 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.76, + "ionic_radius": 0.62 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.705, + "ionic_radius": 0.565 + } + } + }, + "7": { + "IV": { + "": { + "crystal_radius": 0.52, + "ionic_radius": 0.38 + } + } + }, + "8": { + "IV": { + "": { + "crystal_radius": 0.5, + "ionic_radius": 0.36 + } + } + } + }, + "Superconduction temperature": "0.49 K", + "Thermal conductivity": "120 W m-1 K-1", + "Van der waals radius": 2.13, + "Velocity of sound": "5970 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.2, + "Youngs modulus": "447 GPa", + "Metallic radius": 1.339, + "iupac_ordering": 63, + "IUPAC ordering": 63, + "Ground level": "5F5", + "Ionization energies": [ + 7.3605, + 16.76, + 28.47, + 45, + 59, + 76, + 93, + 110, + 178.41, + 198, + 219.9, + 245, + 271, + 295.9, + 348, + 376.25, + 670, + 723, + 784, + 845, + 905, + 981, + 1048, + 1115, + 1187, + 1253, + 1447, + 1506.7, + 1577, + 1659, + 1743, + 1794, + 1949, + 2013.04, + 4758, + 4939, + 5136, + 5330, + 5647, + 5861, + 6137, + 6311.721, + 26229.895, + 27033.502 + ], + "Electron affinity": 1.0463825 + }, + "S": { + "Atomic mass": 32.065, + "Atomic no": 16, + "Atomic orbitals": { + "1s": -87.789937, + "2p": -5.751257, + "2s": -7.69994, + "3p": -0.261676, + "3s": -0.630912 + }, + "Atomic radius": 1, + "Atomic radius calculated": 0.88, + "Boiling point": "717.87 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "7.7 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -2, + 2, + 4, + 6 + ], + "Critical temperature": "1314 K", + "Density of solid": "1960 kg m-3", + "Electrical resistivity": "> 102310-8 Ω m", + "Electronic structure": { + "0": "[Ne].3s2.3p4", + "-2": "[Ne].3s2.3p6", + "2": "[Ne].3s2.3p2", + "4": "[Ne].3s2", + "6": "1s2.2s2.2p6" + }, + "ICSD oxidation states": [ + -1, + 2, + 4, + -2, + 6 + ], + "Ionic radii": { + "4": 0.51, + "6": 0.43, + "-2": 1.7 + }, + "Liquid range": "329.51 K", + "Melting point": "388.36 K", + "Mendeleev no": 94, + "Mineral hardness": "2.0", + "Molar volume": "15.53 cm3", + "Name": "Sulfur", + "Oxidation states": [ + -2, + -1, + 1, + 2, + 3, + 4, + 5, + 6 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.001111", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "4": { + "VI": { + "": { + "crystal_radius": 0.51, + "ionic_radius": 0.37 + } + } + }, + "6": { + "IV": { + "": { + "crystal_radius": 0.26, + "ionic_radius": 0.12 + } + }, + "VI": { + "": { + "crystal_radius": 0.43, + "ionic_radius": 0.29 + } + } + }, + "-2": { + "VI": { + "": { + "crystal_radius": 1.7, + "ionic_radius": 1.84 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.205 W m-1 K-1", + "Van der waals radius": 1.8, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.58, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "S-33": -67.8, + "S-35": 47.1 + }, + "Metallic radius": "no data", + "iupac_ordering": 96, + "IUPAC ordering": 96, + "Ground level": "3P2", + "Ionization energies": [ + 10.36001, + 23.33788, + 34.86, + 47.222, + 72.5945, + 88.0529, + 280.954, + 328.794, + 379.84, + 447.7, + 504.55, + 564.41, + 651.96, + 706.994, + 3223.7807, + 3494.1879 + ], + "Electron affinity": 2.077104512 + }, + "Sb": { + "Atomic mass": 121.76, + "Atomic no": 51, + "Atomic orbitals": { + "1s": -1070.823495, + "2p": -149.214271, + "2s": -159.171745, + "3d": -19.239895, + "3p": -26.956184, + "3s": -31.098242, + "4d": -1.297338, + "4p": -3.646579, + "4s": -5.04964, + "5p": -0.185623, + "5s": -0.445605 + }, + "Atomic radius": 1.45, + "Atomic radius calculated": 1.33, + "Boiling point": "1860 K", + "Brinell hardness": "294 MN m-2", + "Bulk modulus": "42 GPa", + "Coefficient of linear thermal expansion": "11 x10-6K-1", + "Common oxidation states": [ + -3, + 3, + 5 + ], + "Critical temperature": "no data K", + "Density of solid": "6697 kg m-3", + "Electrical resistivity": "40 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d10.5s2.5p3", + "-3": "[Kr].4d10.5s2.5p6", + "3": "[Kr].4d10.5s2", + "5": "[Kr].4d10" + }, + "ICSD oxidation states": [ + -2, + 3, + 5, + -1, + -3 + ], + "Ionic radii": { + "3": 0.9, + "5": 0.76 + }, + "Liquid range": "956.22 K", + "Melting point": "903.78 K", + "Mendeleev no": 88, + "Mineral hardness": "3.0", + "Molar volume": "18.19 cm3", + "Name": "Antimony", + "Oxidation states": [ + -3, + 3, + 5 + ], + "Poissons ratio": "no data", + "Reflectivity": "55 %", + "Refractive index": "no data", + "Rigidity modulus": "20 GPa", + "Shannon radii": { + "3": { + "IVPY": { + "": { + "crystal_radius": 0.9, + "ionic_radius": 0.76 + } + }, + "V": { + "": { + "crystal_radius": 0.94, + "ionic_radius": 0.8 + } + }, + "VI": { + "": { + "crystal_radius": 0.9, + "ionic_radius": 0.76 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.74, + "ionic_radius": 0.6 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "24 W m-1 K-1", + "Van der waals radius": 2.06, + "Velocity of sound": "3420 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.05, + "Youngs modulus": "55 GPa", + "NMR Quadrupole Moment": { + "Sb-121": -543.11, + "Sb-123": -692.14 + }, + "Metallic radius": 1.61, + "iupac_ordering": 88, + "IUPAC ordering": 88, + "Ground level": "4S°3/2", + "Ionization energies": [ + 8.608389, + 16.626, + 25.3235, + 43.804, + 55, + 99.51, + 117, + 139, + 162, + 185, + 214, + 238, + 265, + 292, + 317, + 420, + 447, + 479, + 510, + 552, + 584, + 657, + 693.26, + 1214, + 1285, + 1360, + 1441, + 1518, + 1606, + 1698, + 1781, + 1869, + 1954, + 2190, + 2266, + 2349, + 2428, + 2567, + 2654, + 2815, + 2900, + 6714, + 6929, + 7167, + 7390, + 7887, + 8140, + 8455, + 8669.48, + 35710.028, + 36668.05 + ], + "Electron affinity": 1.04740119 + }, + "Sc": { + "Atomic mass": 44.955912, + "Atomic no": 21, + "Atomic orbitals": { + "1s": -160.184109, + "2p": -14.240006, + "2s": -17.206464, + "3d": -0.13108, + "3p": -1.233165, + "3s": -1.988378, + "4s": -0.156478 + }, + "Atomic radius": 1.6, + "Atomic radius calculated": 1.84, + "Boiling point": "3103 K", + "Brinell hardness": "750 MN m-2", + "Bulk modulus": "57 GPa", + "Coefficient of linear thermal expansion": "10.2 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "2985 kg m-3", + "Electrical resistivity": "about 55 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d1.4s2", + "3": "[Ne].3s2.3p6" + }, + "ICSD oxidation states": [ + 2, + 3 + ], + "Ionic radii": { + "3": 0.885 + }, + "Liquid range": "1289 K", + "Melting point": "1814 K", + "Mendeleev no": 19, + "Mineral hardness": "no data", + "Molar volume": "15.00 cm3", + "Name": "Scandium", + "Oxidation states": [ + 1, + 2, + 3 + ], + "Poissons ratio": "0.28", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "29 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.885, + "ionic_radius": 0.745 + } + }, + "VIII": { + "": { + "crystal_radius": 1.01, + "ionic_radius": 0.87 + } + } + } + }, + "Superconduction temperature": "0.05 (under pressure)K", + "Thermal conductivity": "16 W m-1 K-1", + "Van der waals radius": 2.15, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.36, + "Youngs modulus": "74 GPa", + "NMR Quadrupole Moment": { + "Sc-45": -220.2 + }, + "Metallic radius": 1.641, + "iupac_ordering": 49, + "IUPAC ordering": 49, + "Ground level": "2D3/2", + "Ionization energies": [ + 6.56149, + 12.79977, + 24.756839, + 73.4894, + 91.95, + 110.68, + 137.99, + 158.08, + 180.03, + 225.18, + 249.798, + 687.36, + 757.7, + 833.2, + 926.5, + 1008.6, + 1093.5, + 1213.1, + 1287.957, + 5674.9037, + 6033.7542 + ], + "Electron affinity": 0.1882 + }, + "Se": { + "Atomic mass": 78.96, + "Atomic no": 34, + "Atomic orbitals": { + "1s": -451.300258, + "2p": -51.514388, + "2s": -57.311948, + "3d": -2.011392, + "3p": -5.553517, + "3s": -7.547186, + "4p": -0.245806, + "4s": -0.621248 + }, + "Atomic radius": 1.15, + "Atomic radius calculated": 1.03, + "Boiling point": "958 K", + "Brinell hardness": "736 MN m-2", + "Bulk modulus": "8.3 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -2, + 2, + 4, + 6 + ], + "Critical temperature": "1766 K", + "Density of solid": "4819 kg m-3", + "Electrical resistivity": "high 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d10.4s2.4p4", + "-2": "[Ar].3d10.4s2.4p6", + "2": "[Ar].3d10.4s2.4p2", + "4": "[Ar].3d10.4s2", + "6": "[Ar].3d10" + }, + "ICSD oxidation states": [ + -1, + 4, + -2, + 6 + ], + "Ionic radii": { + "4": 0.64, + "6": 0.56, + "-2": 1.84 + }, + "Liquid range": "464 K", + "Melting point": "494 K", + "Mendeleev no": 93, + "Mineral hardness": "2.0", + "Molar volume": "16.42 cm3", + "Name": "Selenium", + "Oxidation states": [ + -2, + 2, + 4, + 6 + ], + "Poissons ratio": "0.33", + "Reflectivity": "no data %", + "Refractive index": "1.000895", + "Rigidity modulus": "3.7 GPa", + "Shannon radii": { + "4": { + "VI": { + "": { + "crystal_radius": 0.64, + "ionic_radius": 0.5 + } + } + }, + "6": { + "IV": { + "": { + "crystal_radius": 0.42, + "ionic_radius": 0.28 + } + }, + "VI": { + "": { + "crystal_radius": 0.56, + "ionic_radius": 0.42 + } + } + }, + "-2": { + "VI": { + "": { + "crystal_radius": 1.84, + "ionic_radius": 1.98 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.52 W m-1 K-1", + "Van der waals radius": 1.9, + "Velocity of sound": "3350 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.55, + "Youngs modulus": "10 GPa", + "Metallic radius": "no data", + "iupac_ordering": 95, + "IUPAC ordering": 95, + "Ground level": "3P2", + "Ionization energies": [ + 9.752392, + 21.196, + 31.697, + 42.947, + 68.3, + 81.83, + 155.327, + 184, + 219, + 255, + 291, + 342.9, + 383, + 426, + 473, + 517, + 650.5, + 693.4, + 739.8, + 798, + 845.8, + 887, + 989.6, + 1036.36, + 2540.7, + 2674, + 2820, + 2964, + 3146, + 3301.8, + 3507, + 3636.526, + 15367.491, + 15968.084 + ], + "Electron affinity": 2.020604712 + }, + "Si": { + "Atomic mass": 28.0855, + "Atomic no": 14, + "Atomic orbitals": { + "1s": -65.184426, + "2p": -3.514938, + "2s": -5.075056, + "3p": -0.153293, + "3s": -0.398139 + }, + "Atomic radius": 1.1, + "Atomic radius calculated": 1.11, + "Boiling point": "3173 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "100 GPa", + "Coefficient of linear thermal expansion": "2.6 x10-6K-1", + "Common oxidation states": [ + -4, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "2330 kg m-3", + "Electrical resistivity": "about 100000 10-8 Ω m", + "Electronic structure": { + "0": "[Ne].3s2.3p2", + "-4": "[Ne].3s2.3p6", + "4": "1s2.2s2.2p6" + }, + "ICSD oxidation states": [ + -4, + 4 + ], + "Ionic radii": { + "4": 0.54 + }, + "Liquid range": "1486 K", + "Melting point": "1687 K", + "Mendeleev no": 85, + "Mineral hardness": "6.5", + "Molar volume": "12.06 cm3", + "Name": "Silicon", + "Oxidation states": [ + -4, + -3, + -2, + -1, + 1, + 2, + 3, + 4 + ], + "Poissons ratio": "no data", + "Reflectivity": "28 %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "4": { + "IV": { + "": { + "crystal_radius": 0.4, + "ionic_radius": 0.26 + } + }, + "VI": { + "": { + "crystal_radius": 0.54, + "ionic_radius": 0.4 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "150 W m-1 K-1", + "Van der waals radius": 2.1, + "Velocity of sound": "2200 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.9, + "Youngs modulus": "47 GPa", + "Metallic radius": "no data", + "iupac_ordering": 85, + "IUPAC ordering": 85, + "Ground level": "3P0", + "Ionization energies": [ + 8.15168, + 16.34585, + 33.493, + 45.14179, + 166.767, + 205.279, + 246.57, + 303.59, + 351.28, + 401.38, + 476.273, + 523.415, + 2437.65815, + 2673.17755 + ], + "Electron affinity": 1.38952128 + }, + "Sm": { + "Atomic mass": 150.36, + "Atomic no": 62, + "Atomic orbitals": { + "1s": -1617.183426, + "2p": -242.729726, + "2s": -255.498846, + "3d": -39.528656, + "3p": -50.08426, + "3s": -55.731133, + "4d": -4.814978, + "4f": -0.21776, + "4p": -8.672685, + "4s": -10.844667, + "5p": -0.835987, + "5s": -1.408552, + "6s": -0.128259 + }, + "Atomic radius": 1.85, + "Atomic radius calculated": 2.38, + "Boiling point": "2076 K", + "Brinell hardness": "441 MN m-2", + "Bulk modulus": "38 GPa", + "Coefficient of linear thermal expansion": "12.7 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "7353 kg m-3", + "Electrical resistivity": "94 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f6.6s2", + "3": "[Xe].4f5" + }, + "ICSD oxidation states": [ + 2, + 3 + ], + "Ionic radii": { + "2": 1.36, + "3": 1.0979999999999999 + }, + "Liquid range": "731 K", + "Melting point": "1345 K", + "Mendeleev no": 28, + "Mineral hardness": "no data", + "Molar volume": "19.98 cm3", + "Name": "Samarium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "0.27", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "20 GPa", + "Shannon radii": { + "2": { + "VII": { + "": { + "crystal_radius": 1.36, + "ionic_radius": 1.22 + } + }, + "VIII": { + "": { + "crystal_radius": 1.41, + "ionic_radius": 1.27 + } + }, + "IX": { + "": { + "crystal_radius": 1.46, + "ionic_radius": 1.32 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 1.098, + "ionic_radius": 0.958 + } + }, + "VII": { + "": { + "crystal_radius": 1.16, + "ionic_radius": 1.02 + } + }, + "VIII": { + "": { + "crystal_radius": 1.219, + "ionic_radius": 1.079 + } + }, + "IX": { + "": { + "crystal_radius": 1.272, + "ionic_radius": 1.132 + } + }, + "XII": { + "": { + "crystal_radius": 1.38, + "ionic_radius": 1.24 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "13 W m-1 K-1", + "Van der waals radius": 2.36, + "Velocity of sound": "2130 m s-1", + "Vickers hardness": "412 MN m-2", + "X": 1.17, + "Youngs modulus": "50 GPa", + "Metallic radius": 1.804, + "iupac_ordering": 42, + "IUPAC ordering": 42, + "Ground level": "7F0", + "Ionization energies": [ + 5.64371, + 11.078, + 23.55, + 41.64, + 62.7, + 87, + 103, + 118, + 141, + 158, + 179, + 208, + 237, + 257, + 276, + 306.5, + 474, + 506, + 543, + 581, + 617, + 658, + 702, + 742, + 782, + 822, + 976, + 1016, + 1060, + 1103, + 1180, + 1226, + 1332, + 1381.56, + 2371, + 2466, + 2569, + 2676, + 2782, + 2887, + 3028, + 3137, + 3253, + 3363, + 3669, + 3766, + 3873, + 3971, + 4227, + 4337, + 4548, + 4655, + 10494, + 10762, + 11060, + 11337, + 12264, + 12588, + 12992, + 13262.85, + 53986.12, + 55214.23 + ], + "Electron affinity": 0.162 + }, + "Sn": { + "Atomic mass": 118.71, + "Atomic no": 50, + "Atomic orbitals": { + "1s": -1026.762169, + "2p": -141.821093, + "2s": -151.523991, + "3d": -17.657276, + "3p": -25.117913, + "3s": -29.125969, + "4d": -1.004952, + "4p": -3.211998, + "4s": -4.546335, + "5p": -0.14445, + "5s": -0.369349 + }, + "Atomic radius": 1.45, + "Atomic radius calculated": 1.45, + "Boiling point": "2875 K", + "Brinell hardness": "51 MN m-2", + "Bulk modulus": "58 GPa", + "Coefficient of linear thermal expansion": "22 x10-6K-1", + "Common oxidation states": [ + -4, + 2, + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "7310 kg m-3", + "Electrical resistivity": "11.5 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d10.5s2.5p2", + "-4": "[Kr].4d10.5s2.5p6", + "2": "[Kr].4d10.5s2", + "4": "[Kr].4d10" + }, + "ICSD oxidation states": [ + 2, + 3, + 4 + ], + "Ionic radii": { + "4": 0.83 + }, + "Liquid range": "2369.92 K", + "Melting point": "505.08 K", + "Mendeleev no": 83, + "Mineral hardness": "1.5", + "Molar volume": "16.29 cm3", + "Name": "Tin", + "Oxidation states": [ + -4, + 2, + 4 + ], + "Poissons ratio": "0.36", + "Reflectivity": "54 %", + "Refractive index": "no data", + "Rigidity modulus": "18 GPa", + "Shannon radii": { + "4": { + "IV": { + "": { + "crystal_radius": 0.69, + "ionic_radius": 0.55 + } + }, + "V": { + "": { + "crystal_radius": 0.76, + "ionic_radius": 0.62 + } + }, + "VI": { + "": { + "crystal_radius": 0.83, + "ionic_radius": 0.69 + } + }, + "VII": { + "": { + "crystal_radius": 0.89, + "ionic_radius": 0.75 + } + }, + "VIII": { + "": { + "crystal_radius": 0.95, + "ionic_radius": 0.81 + } + } + } + }, + "Superconduction temperature": "3.72 K", + "Thermal conductivity": "67 W m-1 K-1", + "Van der waals radius": 2.17, + "Velocity of sound": "2500 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.96, + "Youngs modulus": "50 GPa", + "NMR Quadrupole Moment": { + "Sn-119": -132.1 + }, + "Metallic radius": 1.58, + "iupac_ordering": 83, + "IUPAC ordering": 83, + "Ground level": "3P0", + "Ionization energies": [ + 7.343918, + 14.63307, + 30.506, + 40.74, + 77.03, + 94, + 112.9, + 135, + 156, + 184, + 208, + 232, + 258, + 282, + 379, + 407, + 437, + 466, + 506, + 537, + 608, + 642.35, + 1127, + 1195, + 1269, + 1347, + 1421, + 1508, + 1596, + 1676, + 1763, + 1844, + 2074, + 2142.1, + 2227, + 2326, + 2443, + 2499, + 2687, + 2762.49, + 6421, + 6631, + 6859, + 7080, + 7531, + 7790, + 8103, + 8306.95, + 34257.143, + 35192.39 + ], + "Electron affinity": 1.1120702 + }, + "Sr": { + "Atomic mass": 87.62, + "Atomic no": 38, + "Atomic orbitals": { + "1s": -572.870169, + "2p": -69.745941, + "2s": -76.491823, + "3d": -4.813498, + "3p": -9.301863, + "3s": -11.771585, + "4p": -0.844489, + "4s": -1.455317, + "5s": -0.131793 + }, + "Atomic radius": 2, + "Atomic radius calculated": 2.19, + "Boiling point": "1655 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "22.5 x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "2630 kg m-3", + "Electrical resistivity": "13.5 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].5s2", + "2": "[Ar].3d10.4s2.4p6" + }, + "ICSD oxidation states": [ + 2 + ], + "Ionic radii": { + "2": 1.32 + }, + "Liquid range": "605 K", + "Melting point": "1050 K", + "Mendeleev no": 15, + "Mineral hardness": "1.5", + "Molar volume": "33.94 cm3", + "Name": "Strontium", + "Oxidation states": [ + 2 + ], + "Poissons ratio": "0.28", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "6.1 GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1.32, + "ionic_radius": 1.18 + } + }, + "VII": { + "": { + "crystal_radius": 1.35, + "ionic_radius": 1.21 + } + }, + "VIII": { + "": { + "crystal_radius": 1.4, + "ionic_radius": 1.26 + } + }, + "IX": { + "": { + "crystal_radius": 1.45, + "ionic_radius": 1.31 + } + }, + "X": { + "": { + "crystal_radius": 1.5, + "ionic_radius": 1.36 + } + }, + "XII": { + "": { + "crystal_radius": 1.58, + "ionic_radius": 1.44 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "35 W m-1 K-1", + "Van der waals radius": 2.49, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 0.95, + "Youngs modulus": "no data GPa", + "NMR Quadrupole Moment": { + "Sr-87": 305.2 + }, + "Metallic radius": 2.151, + "iupac_ordering": 14, + "IUPAC ordering": 14, + "Ground level": "1S0", + "Ionization energies": [ + 5.69486745, + 11.0302765, + 42.88353, + 56.28, + 70.7, + 88, + 104, + 121.21, + 158.33, + 177.3, + 324.07, + 362, + 408, + 454, + 499, + 562, + 612, + 665, + 722, + 774, + 932, + 982.1, + 1038, + 1105, + 1165, + 1211, + 1333.4, + 1387.19, + 3344.7, + 3497, + 3664, + 3830, + 4053, + 4232, + 4465, + 4612.397, + 19345.588, + 20025.233 + ], + "Electron affinity": 0.052066 + }, + "Ta": { + "Atomic mass": 180.94788, + "Atomic no": 73, + "Atomic orbitals": { + "1s": -2275.371387, + "2p": -357.248334, + "2s": -372.828724, + "3d": -63.942521, + "3p": -77.440942, + "3s": -84.658467, + "4d": -8.265848, + "4f": -1.199347, + "4p": -13.71981, + "4s": -16.713337, + "5d": -0.182464, + "5p": -1.37653, + "5s": -2.223807, + "6s": -0.174814 + }, + "Atomic radius": 1.45, + "Atomic radius calculated": 2, + "Boiling point": "5731 K", + "Brinell hardness": "800 MN m-2", + "Bulk modulus": "200 GPa", + "Coefficient of linear thermal expansion": "6.3 x10-6K-1", + "Common oxidation states": [ + 5 + ], + "Critical temperature": "no data K", + "Density of solid": "16650 kg m-3", + "Electrical resistivity": "13.5 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d3.6s2", + "5": "[Xe].4f14" + }, + "ICSD oxidation states": [ + 3, + 4, + 5 + ], + "Ionic radii": { + "3": 0.86, + "4": 0.82, + "5": 0.78 + }, + "Liquid range": "2441 K", + "Melting point": "3290 K", + "Mendeleev no": 52, + "Mineral hardness": "6.5", + "Molar volume": "10.85 cm3", + "Name": "Tantalum", + "Oxidation states": [ + -1, + 2, + 3, + 4, + 5 + ], + "Poissons ratio": "0.34", + "Reflectivity": "78 %", + "Refractive index": "no data", + "Rigidity modulus": "69 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 0.86, + "ionic_radius": 0.72 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.82, + "ionic_radius": 0.68 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.78, + "ionic_radius": 0.64 + } + }, + "VII": { + "": { + "crystal_radius": 0.83, + "ionic_radius": 0.69 + } + }, + "VIII": { + "": { + "crystal_radius": 0.88, + "ionic_radius": 0.74 + } + } + } + }, + "Superconduction temperature": "4.47 K", + "Thermal conductivity": "57 W m-1 K-1", + "Van der waals radius": 2.22, + "Velocity of sound": "3400 m s-1", + "Vickers hardness": "873 MN m-2", + "X": 1.5, + "Youngs modulus": "186 GPa", + "Metallic radius": 1.47, + "iupac_ordering": 53, + "IUPAC ordering": 53, + "Ground level": "4F3/2", + "Ionization energies": [ + 7.549571, + 16.2, + 23.1, + 35, + 48.272, + 94.01, + 119, + 139, + 159, + 180, + 213, + 235, + 262, + 304, + 338, + 363, + 396, + 439, + 482, + 530, + 570, + 610, + 660, + 700, + 750, + 790, + 832, + 1064, + 1110, + 1160, + 1211, + 1262, + 1313, + 1382, + 1434, + 1490, + 1542, + 1748, + 1799, + 1857, + 1910, + 2053, + 2113, + 2254, + 2314.7, + 3898.7, + 4014, + 4143, + 4278, + 4410, + 4537, + 4745, + 4877, + 5024, + 5159, + 5537, + 5655, + 5785, + 5907, + 6364, + 6502, + 6769, + 6900, + 15137, + 15461, + 15820, + 16150, + 17840, + 18250, + 18760, + 19088.51, + 76852.03, + 78394.7 + ], + "Electron affinity": 0.32312 + }, + "Tb": { + "Atomic mass": 158.92535, + "Atomic no": 65, + "Atomic orbitals": { + "1s": -1785.331942, + "2p": -271.590585, + "2s": -285.121013, + "3d": -45.443863, + "3p": -56.785113, + "3s": -62.851563, + "4d": -5.467662, + "4f": -0.256311, + "4p": -9.735637, + "4s": -12.120486, + "5p": -0.88723, + "5s": -1.513669, + "6s": -0.131677 + }, + "Atomic radius": 1.75, + "Atomic radius calculated": 2.25, + "Boiling point": "3503 K", + "Brinell hardness": "677 MN m-2", + "Bulk modulus": "38.7 GPa", + "Coefficient of linear thermal expansion": "10.3 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "8219 kg m-3", + "Electrical resistivity": "115 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f9.6s2", + "3": "[Xe].4f8" + }, + "ICSD oxidation states": [ + 3, + 4 + ], + "Ionic radii": { + "3": 1.063, + "4": 0.9 + }, + "Liquid range": "1874 K", + "Melting point": "1629 K", + "Mendeleev no": 26, + "Mineral hardness": "no data", + "Molar volume": "19.30 cm3", + "Name": "Terbium", + "Oxidation states": [ + 1, + 3, + 4 + ], + "Poissons ratio": "0.26", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "22 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.063, + "ionic_radius": 0.923 + } + }, + "VII": { + "": { + "crystal_radius": 1.12, + "ionic_radius": 0.98 + } + }, + "VIII": { + "": { + "crystal_radius": 1.18, + "ionic_radius": 1.04 + } + }, + "IX": { + "": { + "crystal_radius": 1.235, + "ionic_radius": 1.095 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 0.9, + "ionic_radius": 0.76 + } + }, + "VIII": { + "": { + "crystal_radius": 1.02, + "ionic_radius": 0.88 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "11 W m-1 K-1", + "Van der waals radius": 2.33, + "Velocity of sound": "2620 m s-1", + "Vickers hardness": "863 MN m-2", + "X": 1.1, + "Youngs modulus": "56 GPa", + "Metallic radius": 1.781, + "iupac_ordering": 39, + "IUPAC ordering": 39, + "Ground level": "6H°15/2", + "Ionization energies": [ + 5.8638, + 11.513, + 21.82, + 39.33, + 66.5, + 90, + 108, + 125, + 143, + 168, + 186, + 216, + 250, + 273, + 294, + 325, + 358, + 393, + 426.6, + 613, + 651, + 690, + 732, + 772, + 816, + 866, + 909, + 954, + 997, + 1165, + 1208, + 1256, + 1301, + 1393, + 1443, + 1559, + 1610.4, + 2750, + 2852, + 2961, + 3078, + 3189, + 3300, + 3458, + 3573, + 3698, + 3814, + 4139, + 4242, + 4355, + 4460, + 4760, + 4877, + 5103, + 5217, + 11673, + 11957, + 12272, + 12563, + 13658, + 14003, + 14434, + 14721.02, + 59739.3, + 61049.65 + ], + "Electron affinity": 0.131318 + }, + "Tc": { + "Atomic mass": 98, + "Atomic no": 43, + "Atomic orbitals": { + "1s": -745.742024, + "2p": -96.61021, + "2s": -104.567508, + "3d": -9.33986, + "3p": -15.041738, + "3s": -18.135303, + "4d": -0.270262, + "4p": -1.64323, + "4s": -2.550712, + "5s": -0.183636 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.83, + "Boiling point": "4538 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + 4, + 7 + ], + "Critical temperature": "no data K", + "Density of solid": "11500 kg m-3", + "Electrical resistivity": "about 22 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d5.5s2", + "4": "[Kr].4d3", + "7": "[Ar].3d10.4s2.4p6" + }, + "Ionic radii": { + "4": 0.785, + "5": 0.74, + "7": 0.7 + }, + "Liquid range": "2108 K", + "Melting point": "2430 K", + "Mendeleev no": 59, + "Mineral hardness": "no data", + "Molar volume": "8.63 cm3", + "Name": "Technetium", + "Oxidation states": [ + -3, + -1, + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "4": { + "VI": { + "": { + "crystal_radius": 0.785, + "ionic_radius": 0.645 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.74, + "ionic_radius": 0.6 + } + } + }, + "7": { + "IV": { + "": { + "crystal_radius": 0.51, + "ionic_radius": 0.37 + } + }, + "VI": { + "": { + "crystal_radius": 0.7, + "ionic_radius": 0.56 + } + } + } + }, + "Superconduction temperature": "7.8 K", + "Thermal conductivity": "51 W m-1 K-1", + "Van der waals radius": 2.16, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.9, + "Youngs modulus": "no data GPa", + "Metallic radius": 1.363, + "iupac_ordering": 60, + "IUPAC ordering": 60, + "Ground level": "6S5/2", + "Ionization energies": [ + 7.11938, + 15.26, + 29.55, + 41, + 57, + 72, + 88, + 150, + 169, + 189.9, + 214, + 239, + 262.08, + 311, + 338.55, + 604, + 655, + 713, + 773, + 829, + 904, + 968, + 1032, + 1102, + 1166, + 1354, + 1411.6, + 1479.5, + 1559, + 1638, + 1689, + 1838, + 1900.28, + 4505, + 4681, + 4874, + 5060, + 5361, + 5570, + 5838, + 6008.391, + 25004.533, + 25786.99 + ], + "Electron affinity": 0.552 + }, + "Te": { + "Atomic mass": 127.6, + "Atomic no": 52, + "Atomic orbitals": { + "1s": -1115.831819, + "2p": -156.808583, + "2s": -167.021776, + "3d": -20.887801, + "3p": -28.860685, + "3s": -33.137485, + "4d": -1.608381, + "4p": -4.100084, + "4s": -5.572846, + "5p": -0.226594, + "5s": -0.520997 + }, + "Atomic radius": 1.4, + "Atomic radius calculated": 1.23, + "Boiling point": "1261 K", + "Brinell hardness": "180 MN m-2", + "Bulk modulus": "65 GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Common oxidation states": [ + -2, + 2, + 4, + 6 + ], + "Critical temperature": "no data K", + "Density of solid": "6240 kg m-3", + "Electrical resistivity": "about 10000 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d10.5s2.5p4", + "-2": "[Kr].4d10.5s2.5p6", + "2": "[Kr].4d10.5s2.5p2", + "4": "[Kr].4d10.5s2", + "6": "[Kr].4d10" + }, + "ICSD oxidation states": [ + -2, + 4, + -1, + 6 + ], + "Ionic radii": { + "4": 1.11, + "6": 0.7, + "-2": 2.07 + }, + "Liquid range": "538.34 K", + "Melting point": "722.66 K", + "Mendeleev no": 92, + "Mineral hardness": "2.25", + "Molar volume": "20.46 cm3", + "Name": "Tellurium", + "Oxidation states": [ + -2, + 2, + 4, + 5, + 6 + ], + "Poissons ratio": "no data", + "Reflectivity": "50 %", + "Refractive index": "1.000991", + "Rigidity modulus": "16 GPa", + "Shannon radii": { + "4": { + "III": { + "": { + "crystal_radius": 0.66, + "ionic_radius": 0.52 + } + }, + "IV": { + "": { + "crystal_radius": 0.8, + "ionic_radius": 0.66 + } + }, + "VI": { + "": { + "crystal_radius": 1.11, + "ionic_radius": 0.97 + } + } + }, + "6": { + "IV": { + "": { + "crystal_radius": 0.57, + "ionic_radius": 0.43 + } + }, + "VI": { + "": { + "crystal_radius": 0.7, + "ionic_radius": 0.56 + } + } + }, + "-2": { + "VI": { + "": { + "crystal_radius": 2.07, + "ionic_radius": 2.21 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "3 W m-1 K-1", + "Van der waals radius": 2.06, + "Velocity of sound": "2610 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.1, + "Youngs modulus": "43 GPa", + "Metallic radius": "no data", + "iupac_ordering": 94, + "IUPAC ordering": 94, + "Ground level": "3P2", + "Ionization energies": [ + 9.009808, + 18.6, + 27.84, + 37.4155, + 59.3, + 69.1, + 124.2, + 143, + 167, + 191.1, + 215, + 245, + 272, + 299, + 328, + 354, + 461, + 491, + 522, + 555, + 599, + 633, + 709, + 746.12, + 1304, + 1377, + 1455, + 1538, + 1618, + 1707, + 1803, + 1889, + 1979, + 2066, + 2309, + 2386, + 2472, + 2552, + 2700, + 2788, + 2954, + 3041, + 7022, + 7243, + 7485, + 7714, + 8240, + 8499, + 8821, + 9040.83, + 37196.522, + 38177.56 + ], + "Electron affinity": 1.9708757 + }, + "Th": { + "Atomic mass": 232.03806, + "Atomic no": 90, + "Atomic orbitals": { + "1s": -3524.439052, + "2p": -588.218112, + "2s": -608.350958, + "3d": -123.846396, + "3p": -142.25581, + "3s": -152.079741, + "4d": -24.955184, + "4f": -13.397389, + "4p": -33.325252, + "4s": -37.814094, + "5d": -3.625729, + "5p": -6.58281, + "5s": -8.287057, + "6d": -0.172896, + "6p": -0.846921, + "6s": -1.333769, + "7s": -0.135872 + }, + "Atomic radius": 1.8, + "Atomic radius calculated": "no data", + "Boiling point": "5093 K", + "Brinell hardness": "400 MN m-2", + "Bulk modulus": "54 GPa", + "Coefficient of linear thermal expansion": "11.0 x10-6K-1", + "Common oxidation states": [ + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "11724 kg m-3", + "Electrical resistivity": "15 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].6d2.7s2", + "4": "[Hg].6p6" + }, + "ICSD oxidation states": [ + 4 + ], + "Ionic radii": { + "4": 1.08 + }, + "Liquid range": "2978 K", + "Melting point": "2115 K", + "Mendeleev no": 47, + "Mineral hardness": "3.0", + "Molar volume": "19.80 cm3", + "Name": "Thorium", + "Oxidation states": [ + 2, + 3, + 4 + ], + "Poissons ratio": "0.27", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "31 GPa", + "Shannon radii": { + "4": { + "VI": { + "": { + "crystal_radius": 1.08, + "ionic_radius": 0.94 + } + }, + "VIII": { + "": { + "crystal_radius": 1.19, + "ionic_radius": 1.05 + } + }, + "IX": { + "": { + "crystal_radius": 1.23, + "ionic_radius": 1.09 + } + }, + "X": { + "": { + "crystal_radius": 1.27, + "ionic_radius": 1.13 + } + }, + "XI": { + "": { + "crystal_radius": 1.32, + "ionic_radius": 1.18 + } + }, + "XII": { + "": { + "crystal_radius": 1.35, + "ionic_radius": 1.21 + } + } + } + }, + "Superconduction temperature": "1.38 K", + "Thermal conductivity": "54 W m-1 K-1", + "Van der waals radius": 2.45, + "Velocity of sound": "2490 m s-1", + "Vickers hardness": "350 MN m-2", + "X": 1.3, + "Youngs modulus": "79 GPa", + "Metallic radius": 1.798, + "iupac_ordering": 31, + "IUPAC ordering": 31, + "Ground level": "3F2", + "Ionization energies": [ + 6.3067, + 12.1, + 18.32, + 28.648, + 58, + 69.1, + 82, + 95, + 118, + 133, + 165, + 181, + 262, + 285, + 310, + 336, + 362, + 389, + 424, + 451, + 480, + 508, + 650, + 680, + 720, + 750, + 830, + 870, + 970, + 1010, + 1090, + 1160, + 1240, + 1310, + 1380, + 1460, + 1530, + 1600, + 1680, + 1760, + 1830, + 1910, + 1980, + 2060, + 2390, + 2455, + 2524, + 2598, + 2669, + 2737, + 2864, + 2935, + 3013, + 3086, + 3375, + 3445, + 3522, + 3593, + 3943, + 4025, + 4230, + 4313, + 6972, + 7130, + 7299, + 7480, + 7650, + 7810, + 8180, + 8350, + 8550, + 8720, + 9220, + 9370, + 9540, + 9690, + 10790, + 10970, + 11340, + 11510, + 24060, + 24480, + 24940, + 25360, + 29410, + 29970, + 30680, + 31122.8, + 123086.4, + 125253.4 + ], + "Electron affinity": 1.17 + }, + "Ti": { + "Atomic mass": 47.867, + "Atomic no": 22, + "Atomic orbitals": { + "1s": -177.276643, + "2p": -16.285339, + "2s": -19.457901, + "3d": -0.17001, + "3p": -1.422947, + "3s": -2.258007, + "4s": -0.167106 + }, + "Atomic radius": 1.4, + "Atomic radius calculated": 1.76, + "Boiling point": "3560 K", + "Brinell hardness": "716 MN m-2", + "Bulk modulus": "110 GPa", + "Coefficient of linear thermal expansion": "8.6 x10-6K-1", + "Common oxidation states": [ + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "4507 kg m-3", + "Electrical resistivity": "about 40 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d2.4s2", + "4": "[Ne].3s2.3p6" + }, + "ICSD oxidation states": [ + 2, + 3, + 4 + ], + "Ionic radii": { + "2": 1, + "3": 0.81, + "4": 0.745 + }, + "Liquid range": "1619 K", + "Melting point": "1941 K", + "Mendeleev no": 51, + "Mineral hardness": "6.0", + "Molar volume": "10.64 cm3", + "Name": "Titanium", + "Oxidation states": [ + -1, + 2, + 3, + 4 + ], + "Poissons ratio": "0.32", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "44 GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1, + "ionic_radius": 0.86 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 0.81, + "ionic_radius": 0.67 + } + } + }, + "4": { + "IV": { + "": { + "crystal_radius": 0.56, + "ionic_radius": 0.42 + } + }, + "V": { + "": { + "crystal_radius": 0.65, + "ionic_radius": 0.51 + } + }, + "VI": { + "": { + "crystal_radius": 0.745, + "ionic_radius": 0.605 + } + }, + "VIII": { + "": { + "crystal_radius": 0.88, + "ionic_radius": 0.74 + } + } + } + }, + "Superconduction temperature": "0.40 K", + "Thermal conductivity": "22 W m-1 K-1", + "Van der waals radius": 2.11, + "Velocity of sound": "4140 m s-1", + "Vickers hardness": "970 MN m-2", + "X": 1.54, + "Youngs modulus": "116 GPa", + "NMR Quadrupole Moment": { + "Ti-47": 302.1, + "Ti-49": 247.11 + }, + "Metallic radius": 1.462, + "iupac_ordering": 52, + "IUPAC ordering": 52, + "Ground level": "3F2", + "Ionization energies": [ + 6.82812, + 13.5755, + 27.49171, + 43.26717, + 99.299, + 119.533, + 140.68, + 170.5, + 192.1, + 215.92, + 265.07, + 291.5, + 787.67, + 864, + 944.5, + 1042.5, + 1130.2, + 1220.3, + 1346.3, + 1425.257, + 6249.0226, + 6625.8073 + ], + "Electron affinity": 0.075545 + }, + "Tl": { + "Atomic mass": 204.3833, + "Atomic no": 81, + "Atomic orbitals": { + "1s": -2827.569408, + "2p": -457.255971, + "2s": -474.953368, + "3d": -88.328299, + "3p": -104.099296, + "3s": -112.52218, + "4d": -14.008848, + "4f": -4.835747, + "4p": -20.797078, + "4s": -24.471512, + "5d": -0.674544, + "5p": -2.59873, + "5s": -3.811512, + "6p": -0.101507, + "6s": -0.28502 + }, + "Atomic radius": 1.9, + "Atomic radius calculated": 1.56, + "Boiling point": "1746 K", + "Brinell hardness": "26.4 MN m-2", + "Bulk modulus": "43 GPa", + "Coefficient of linear thermal expansion": "29.9 x10-6K-1", + "Common oxidation states": [ + 1, + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "11850 kg m-3", + "Electrical resistivity": "15 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d10.6s2.6p1", + "1": "[Xe].4f14.5d10.6s2", + "3": "[Xe].4f14.5d10" + }, + "ICSD oxidation states": [ + 1, + 3 + ], + "Ionic radii": { + "1": 1.64, + "3": 1.025 + }, + "Liquid range": "1169 K", + "Melting point": "577 K", + "Mendeleev no": 78, + "Mineral hardness": "1.2", + "Molar volume": "17.22 cm3", + "Name": "Thallium", + "Oxidation states": [ + 1, + 3 + ], + "Poissons ratio": "0.45", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "2.8 GPa", + "Shannon radii": { + "1": { + "VI": { + "": { + "crystal_radius": 1.64, + "ionic_radius": 1.5 + } + }, + "VIII": { + "": { + "crystal_radius": 1.73, + "ionic_radius": 1.59 + } + }, + "XII": { + "": { + "crystal_radius": 1.84, + "ionic_radius": 1.7 + } + } + }, + "3": { + "IV": { + "": { + "crystal_radius": 0.89, + "ionic_radius": 0.75 + } + }, + "VI": { + "": { + "crystal_radius": 1.025, + "ionic_radius": 0.885 + } + }, + "VIII": { + "": { + "crystal_radius": 1.12, + "ionic_radius": 0.98 + } + } + } + }, + "Superconduction temperature": "2.38 K", + "Thermal conductivity": "46 W m-1 K-1", + "Van der waals radius": 1.96, + "Velocity of sound": "818 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.62, + "Youngs modulus": "8 GPa", + "Metallic radius": 1.7, + "iupac_ordering": 77, + "IUPAC ordering": 77, + "Ground level": "2P°1/2", + "Ionization energies": [ + 6.1082873, + 20.4283, + 29.852, + 51.14, + 62.6, + 80, + 97.9, + 116, + 135, + 158, + 177, + 198, + 218.3, + 306.9, + 340, + 366, + 392, + 439, + 467, + 520, + 570, + 600, + 640, + 700, + 760, + 820, + 880, + 930, + 990, + 1060, + 1110, + 1170, + 1230, + 1290, + 1350, + 1625, + 1681, + 1740, + 1802, + 1862, + 1920, + 2014, + 2075, + 2140, + 2202, + 2447, + 2508, + 2574, + 2635, + 2854, + 2925, + 3094, + 3164.7, + 5234, + 5371, + 5518, + 5674, + 5824, + 5969, + 6241, + 6392, + 6560, + 6714, + 7146, + 7281, + 7430, + 7570, + 8260, + 8420, + 8730, + 8880, + 19070, + 19440, + 19840, + 20210, + 22780, + 23250, + 23850, + 24234.1, + 96783.21, + 98591.6 + ], + "Electron affinity": 0.32005319 + }, + "Tm": { + "Atomic mass": 168.93421, + "Atomic no": 69, + "Atomic orbitals": { + "1s": -2022.471608, + "2p": -312.510608, + "2s": -327.05712, + "3d": -53.835494, + "3p": -66.239338, + "3s": -72.873753, + "4d": -6.350307, + "4f": -0.28312, + "4p": -11.187151, + "4s": -13.865665, + "5p": -0.950748, + "5s": -1.64999, + "6s": -0.135953 + }, + "Atomic radius": 1.75, + "Atomic radius calculated": 2.22, + "Boiling point": "2223 K", + "Brinell hardness": "471 MN m-2", + "Bulk modulus": "45 GPa", + "Coefficient of linear thermal expansion": "13.3 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "9321 kg m-3", + "Electrical resistivity": "67.6 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f13.6s2", + "3": "[Xe].4f12" + }, + "ICSD oxidation states": [ + 3 + ], + "Ionic radii": { + "2": 1.17, + "3": 1.02 + }, + "Liquid range": "405 K", + "Melting point": "1818 K", + "Mendeleev no": 21, + "Mineral hardness": "no data", + "Molar volume": "19.1 cm3", + "Name": "Thulium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "0.21", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "31 GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1.17, + "ionic_radius": 1.03 + } + }, + "VII": { + "": { + "crystal_radius": 1.23, + "ionic_radius": 1.09 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 1.02, + "ionic_radius": 0.88 + } + }, + "VIII": { + "": { + "crystal_radius": 1.134, + "ionic_radius": 0.994 + } + }, + "IX": { + "": { + "crystal_radius": 1.192, + "ionic_radius": 1.052 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "17 W m-1 K-1", + "Van der waals radius": 2.27, + "Velocity of sound": "no data m s-1", + "Vickers hardness": "520 MN m-2", + "X": 1.25, + "Youngs modulus": "74 GPa", + "Metallic radius": 1.747, + "iupac_ordering": 35, + "IUPAC ordering": 35, + "Ground level": "2F°7/2", + "Ionization energies": [ + 6.18431, + 12.065, + 23.66, + 42.41, + 65.4, + 98, + 116, + 133, + 160, + 180, + 205, + 239, + 274, + 295, + 317, + 352, + 387, + 424, + 460, + 496, + 530, + 570, + 603, + 825, + 866, + 911, + 958, + 1004, + 1050, + 1110, + 1157, + 1207, + 1255, + 1442, + 1490, + 1542, + 1591, + 1706, + 1761, + 1889, + 1945.2, + 3298, + 3409, + 3528, + 3653, + 3775, + 3895, + 4075, + 4199, + 4335, + 4461, + 4812, + 4922, + 5044, + 5157, + 5527, + 5656, + 5901, + 6023, + 13347, + 13651, + 13988, + 14300, + 15663, + 16036, + 16510, + 16814.34, + 67965.26, + 69387.3 + ], + "Electron affinity": 1.02922 + }, + "U": { + "Atomic mass": 238.02891, + "Atomic no": 92, + "Atomic orbitals": { + "1s": -3689.355141, + "2p": -619.10855, + "2s": -639.778728, + "3d": -131.977358, + "3p": -150.97898, + "3s": -161.118073, + "4d": -27.123212, + "4f": -15.02746, + "4p": -35.853321, + "4s": -40.528084, + "5d": -3.866175, + "5f": -0.366543, + "5p": -7.018092, + "5s": -8.824089, + "6d": -0.14319, + "6p": -0.822538, + "6s": -1.325976, + "7s": -0.130948 + }, + "Atomic radius": 1.75, + "Atomic radius calculated": "no data", + "Boiling point": "4200 K", + "Brinell hardness": "2400 MN m-2", + "Bulk modulus": "100 GPa", + "Coefficient of linear thermal expansion": "13.9 x10-6K-1", + "Common oxidation states": [ + 6 + ], + "Critical temperature": "no data K", + "Density of solid": "19050 kg m-3", + "Electrical resistivity": "28 10-8 Ω m", + "Electronic structure": { + "0": "[Rn].5f3.6d1.7s2", + "6": "[Hg].6p6" + }, + "ICSD oxidation states": [ + 3, + 4, + 5, + 6 + ], + "Ionic radii": { + "3": 1.165, + "4": 1.03, + "5": 0.9, + "6": 0.87 + }, + "Liquid range": "2794.7 K", + "Melting point": "1405.3 K", + "Mendeleev no": 45, + "Mineral hardness": "6.0", + "Molar volume": "12.49 cm3", + "Name": "Uranium", + "Oxidation states": [ + 3, + 4, + 5, + 6 + ], + "Poissons ratio": "0.23", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "111 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.165, + "ionic_radius": 1.025 + } + } + }, + "4": { + "VI": { + "": { + "crystal_radius": 1.03, + "ionic_radius": 0.89 + } + }, + "VII": { + "": { + "crystal_radius": 1.09, + "ionic_radius": 0.95 + } + }, + "VIII": { + "": { + "crystal_radius": 1.14, + "ionic_radius": 1 + } + }, + "IX": { + "": { + "crystal_radius": 1.19, + "ionic_radius": 1.05 + } + }, + "XII": { + "": { + "crystal_radius": 1.31, + "ionic_radius": 1.17 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.9, + "ionic_radius": 0.76 + } + }, + "VII": { + "": { + "crystal_radius": 0.98, + "ionic_radius": 0.84 + } + } + }, + "6": { + "II": { + "": { + "crystal_radius": 0.59, + "ionic_radius": 0.45 + } + }, + "IV": { + "": { + "crystal_radius": 0.66, + "ionic_radius": 0.52 + } + }, + "VI": { + "": { + "crystal_radius": 0.87, + "ionic_radius": 0.73 + } + }, + "VII": { + "": { + "crystal_radius": 0.95, + "ionic_radius": 0.81 + } + }, + "VIII": { + "": { + "crystal_radius": 1, + "ionic_radius": 0.86 + } + } + } + }, + "Superconduction temperature": "0.2 K", + "Thermal conductivity": "27 W m-1 K-1", + "Van der waals radius": 2.41, + "Velocity of sound": "3155 m s-1", + "Vickers hardness": "1960 MN m-2", + "X": 1.38, + "Youngs modulus": "208 GPa", + "Metallic radius": 1.542, + "iupac_ordering": 29, + "IUPAC ordering": 29, + "Ground level": "5L°6", + "Ionization energies": [ + 6.19405, + 11.6, + 19.8, + 36.7, + 46, + 62, + 89, + 101, + 116, + 128.9, + 158, + 173, + 210, + 227, + 323, + 348, + 375, + 402, + 431, + 458, + 497, + 525, + 557, + 585, + 730, + 770, + 800, + 840, + 930, + 970, + 1070, + 1110, + 1210, + 1290, + 1370, + 1440, + 1520, + 1590, + 1670, + 1750, + 1830, + 1910, + 1990, + 2070, + 2140, + 2220, + 2578, + 2646, + 2718, + 2794, + 2867, + 2938, + 3073, + 3147, + 3228, + 3301, + 3602, + 3675, + 3753, + 3827, + 4214, + 4299, + 4513, + 4598, + 7393, + 7550, + 7730, + 7910, + 8090, + 8260, + 8650, + 8830, + 9030, + 9210, + 9720, + 9870, + 10040, + 10200, + 11410, + 11600, + 11990, + 12160, + 25260, + 25680, + 26150, + 26590, + 31060, + 31640, + 32400, + 32836.5, + 129570.3, + 131821 + ], + "Electron affinity": 0.53 + }, + "V": { + "Atomic mass": 50.9415, + "Atomic no": 23, + "Atomic orbitals": { + "1s": -195.224014, + "2p": -18.435189, + "2s": -21.815346, + "3d": -0.204634, + "3p": -1.610516, + "3s": -2.526904, + "4s": -0.175968 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.71, + "Boiling point": "3680 K", + "Brinell hardness": "628 MN m-2", + "Bulk modulus": "160 GPa", + "Coefficient of linear thermal expansion": "8.4 x10-6K-1", + "Common oxidation states": [ + 5 + ], + "Critical temperature": "no data K", + "Density of solid": "6110 kg m-3", + "Electrical resistivity": "20 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d3.4s2", + "2": "[Ar].3d3", + "3": "[Ar].3d2", + "4": "[Ar].3d1", + "5": "[Ne].3s2.3p6" + }, + "ICSD oxidation states": [ + 2, + 3, + 4, + 5 + ], + "Ionic radii": { + "2": 0.93, + "3": 0.78, + "4": 0.72, + "5": 0.68 + }, + "Liquid range": "1497 K", + "Melting point": "2183 K", + "Mendeleev no": 54, + "Mineral hardness": "7.0", + "Molar volume": "8.32 cm3", + "Name": "Vanadium", + "Oxidation states": [ + -1, + 1, + 2, + 3, + 4, + 5 + ], + "Poissons ratio": "0.37", + "Reflectivity": "61 %", + "Refractive index": "no data", + "Rigidity modulus": "47 GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 0.93, + "ionic_radius": 0.79 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 0.78, + "ionic_radius": 0.64 + } + } + }, + "4": { + "V": { + "": { + "crystal_radius": 0.67, + "ionic_radius": 0.53 + } + }, + "VI": { + "": { + "crystal_radius": 0.72, + "ionic_radius": 0.58 + } + }, + "VIII": { + "": { + "crystal_radius": 0.86, + "ionic_radius": 0.72 + } + } + }, + "5": { + "IV": { + "": { + "crystal_radius": 0.495, + "ionic_radius": 0.355 + } + }, + "V": { + "": { + "crystal_radius": 0.6, + "ionic_radius": 0.46 + } + }, + "VI": { + "": { + "crystal_radius": 0.68, + "ionic_radius": 0.54 + } + } + } + }, + "Superconduction temperature": "5.40 K", + "Thermal conductivity": "31 W m-1 K-1", + "Van der waals radius": 2.07, + "Velocity of sound": "4560 m s-1", + "Vickers hardness": "628 MN m-2", + "X": 1.63, + "Youngs modulus": "128 GPa", + "NMR Quadrupole Moment": { + "V-50": 210.4, + "V-51": -52.1 + }, + "Metallic radius": 1.347, + "iupac_ordering": 55, + "IUPAC ordering": 55, + "Ground level": "4F3/2", + "Ionization energies": [ + 6.746187, + 14.634, + 29.3111, + 46.709, + 65.28165, + 128.125, + 150.72, + 173.55, + 206, + 230.5, + 254.8, + 308.5, + 336.274, + 896, + 977.2, + 1062.9, + 1165.2, + 1258.9, + 1354.2, + 1486.7, + 1569.656, + 6851.3109, + 7246.1226 + ], + "Electron affinity": 0.527662 + }, + "W": { + "Atomic mass": 183.84, + "Atomic no": 74, + "Atomic orbitals": { + "1s": -2341.042887, + "2p": -369.013973, + "2s": -384.856157, + "3d": -66.724787, + "3p": -80.502102, + "3s": -87.867792, + "4d": -8.879693, + "4f": -1.550835, + "4p": -14.495102, + "4s": -17.570797, + "5d": -0.220603, + "5p": -1.504457, + "5s": -2.396018, + "6s": -0.181413 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.93, + "Boiling point": "5828 K", + "Brinell hardness": "2570 MN m-2", + "Bulk modulus": "310 GPa", + "Coefficient of linear thermal expansion": "4.5 x10-6K-1", + "Common oxidation states": [ + 4, + 6 + ], + "Critical temperature": "no data K", + "Density of solid": "19250 kg m-3", + "Electrical resistivity": "5.4 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.5d4.6s2", + "4": "[Xe].4f14.5d2", + "6": "[Xe].4f14" + }, + "ICSD oxidation states": [ + 2, + 3, + 4, + 5, + 6 + ], + "Ionic radii": { + "4": 0.8, + "5": 0.76, + "6": 0.74 + }, + "Liquid range": "2133 K", + "Melting point": "3695 K", + "Mendeleev no": 55, + "Mineral hardness": "7.5", + "Molar volume": "9.47 cm3", + "Name": "Tungsten", + "Oxidation states": [ + -2, + -1, + 1, + 2, + 3, + 4, + 5, + 6 + ], + "Poissons ratio": "0.28", + "Reflectivity": "62 %", + "Refractive index": "no data", + "Rigidity modulus": "161 GPa", + "Shannon radii": { + "4": { + "VI": { + "": { + "crystal_radius": 0.8, + "ionic_radius": 0.66 + } + } + }, + "5": { + "VI": { + "": { + "crystal_radius": 0.76, + "ionic_radius": 0.62 + } + } + }, + "6": { + "IV": { + "": { + "crystal_radius": 0.56, + "ionic_radius": 0.42 + } + }, + "V": { + "": { + "crystal_radius": 0.65, + "ionic_radius": 0.51 + } + }, + "VI": { + "": { + "crystal_radius": 0.74, + "ionic_radius": 0.6 + } + } + } + }, + "Superconduction temperature": "0.015 K", + "Thermal conductivity": "170 W m-1 K-1", + "Van der waals radius": 2.18, + "Velocity of sound": "5174 m s-1", + "Vickers hardness": "3430 MN m-2", + "X": 2.36, + "Youngs modulus": "411 GPa", + "Metallic radius": 1.41, + "iupac_ordering": 56, + "IUPAC ordering": 56, + "Ground level": "5D0", + "Ionization energies": [ + 7.86403, + 16.37, + 26, + 38.2, + 51.6, + 64.77, + 122.01, + 141.2, + 160.2, + 179, + 208.9, + 231.6, + 258.3, + 290.7, + 325.3, + 361.9, + 387.9, + 420.7, + 462.1, + 502.6, + 543.4, + 594.5, + 640.6, + 685.6, + 734.1, + 784.4, + 833.4, + 881.4, + 1132.2, + 1180, + 1230.4, + 1283.4, + 1335.1, + 1386.8, + 1459.9, + 1512.4, + 1569.1, + 1621.7, + 1829.8, + 1882.9, + 1940.6, + 1994.8, + 2149.1, + 2210, + 2354.5, + 2414.1, + 4057, + 4180, + 4309, + 4446, + 4578, + 4709, + 4927, + 5063, + 5209, + 5348, + 5719, + 5840, + 5970, + 6093, + 6596, + 6735, + 7000, + 7130, + 15566, + 15896, + 16252, + 16588, + 18476, + 18872, + 19362, + 19686.74, + 79181.94, + 80755.6 + ], + "Electron affinity": 0.816268 + }, + "Xe": { + "Atomic mass": 131.293, + "Atomic no": 54, + "Atomic orbitals": { + "1s": -1208.688993, + "2p": -172.599583, + "2s": -183.327495, + "3d": -24.37823, + "3p": -32.867042, + "3s": -37.415454, + "4d": -2.286666, + "4p": -5.063802, + "4s": -6.67834, + "5p": -0.309835, + "5s": -0.672086 + }, + "Atomic radius": "no data", + "Atomic radius calculated": 1.08, + "Boiling point": "165.1 K", + "Brinell hardness": "no data MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "no data x10-6K-1", + "Critical temperature": "289.7 K", + "Density of solid": "no data kg m-3", + "Electrical resistivity": "no data 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d10.5s2.5p6" + }, + "Ionic radii": { + "8": 0.62 + }, + "Liquid range": "3.7 K", + "Max oxidation state": 8, + "Melting point": "161.4 K", + "Mendeleev no": 5, + "Min oxidation state": 2, + "Mineral hardness": "no data", + "Molar volume": "35.92 cm3", + "Name": "Xenon", + "Poissons ratio": "no data", + "Reflectivity": "no data %", + "Refractive index": "1.000702", + "Rigidity modulus": "no data GPa", + "Shannon radii": { + "8": { + "IV": { + "": { + "crystal_radius": 0.54, + "ionic_radius": 0.4 + } + }, + "VI": { + "": { + "crystal_radius": 0.62, + "ionic_radius": 0.48 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "0.00565 W m-1 K-1", + "Van der waals radius": 2.16, + "Velocity of sound": "1090 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 2.6, + "Youngs modulus": "no data GPa", + "Metallic radius": "no data", + "iupac_ordering": 1, + "IUPAC ordering": 1, + "Ground level": "1S0", + "Ionization energies": [ + 12.1298437, + 20.975, + 31.05, + 42.2, + 54.1, + 66.703, + 91.6, + 105.9778, + 179.84, + 202, + 229.02, + 255, + 281, + 314, + 343, + 374, + 404, + 434, + 549, + 582, + 616, + 650, + 700, + 736, + 818, + 857, + 1493, + 1571, + 1653, + 1742, + 1826, + 1919, + 2023, + 2113, + 2209, + 2300, + 2556, + 2637, + 2726, + 2811, + 2975, + 3068, + 3243, + 3333.8, + 7660, + 7889, + 8144, + 8382, + 8971, + 9243, + 9581, + 9810.37, + 40271.724, + 41299.71 + ], + "Electron affinity": -0.82 + }, + "Y": { + "Atomic mass": 88.90585, + "Atomic no": 39, + "Atomic orbitals": { + "1s": -605.631981, + "2p": -74.803201, + "2s": -81.789102, + "3d": -5.671499, + "3p": -10.399926, + "3s": -12.992217, + "4d": -0.108691, + "4p": -1.02449, + "4s": -1.697124, + "5s": -0.150727 + }, + "Atomic radius": 1.8, + "Atomic radius calculated": 2.12, + "Boiling point": "3609 K", + "Brinell hardness": "589 MN m-2", + "Bulk modulus": "41 GPa", + "Coefficient of linear thermal expansion": "10.6 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "4472 kg m-3", + "Electrical resistivity": "about 60 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d1.5s2", + "3": "[Ar].3d10.4s2.4p6" + }, + "ICSD oxidation states": [ + 3 + ], + "Ionic radii": { + "3": 1.04 + }, + "Liquid range": "1810 K", + "Melting point": "1799 K", + "Mendeleev no": 25, + "Mineral hardness": "no data", + "Molar volume": "19.88 cm3", + "Name": "Yttrium", + "Oxidation states": [ + 1, + 2, + 3 + ], + "Poissons ratio": "0.24", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "26 GPa", + "Shannon radii": { + "3": { + "VI": { + "": { + "crystal_radius": 1.04, + "ionic_radius": 0.9 + } + }, + "VII": { + "": { + "crystal_radius": 1.1, + "ionic_radius": 0.96 + } + }, + "VIII": { + "": { + "crystal_radius": 1.159, + "ionic_radius": 1.019 + } + }, + "IX": { + "": { + "crystal_radius": 1.215, + "ionic_radius": 1.075 + } + } + } + }, + "Superconduction temperature": "1.3 (under pressure)K", + "Thermal conductivity": "17 W m-1 K-1", + "Van der waals radius": 2.32, + "Velocity of sound": "3300 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.22, + "Youngs modulus": "64 GPa", + "Metallic radius": 1.8, + "iupac_ordering": 48, + "IUPAC ordering": 48, + "Ground level": "2D3/2", + "Ionization energies": [ + 6.21726, + 12.2236, + 20.52441, + 60.6072, + 75.35, + 91.39, + 110.02, + 128.12, + 145.64, + 185.7, + 205.814, + 374.04, + 414, + 463, + 512, + 559, + 624, + 677, + 733, + 790, + 847, + 1010, + 1061.9, + 1120.2, + 1190, + 1253, + 1300, + 1427.6, + 1483.12, + 3562.9, + 3720, + 3892, + 4060, + 4299, + 4484, + 4724, + 4875.731, + 20415.717, + 21115.55 + ], + "Electron affinity": 0.30712 + }, + "Yb": { + "Atomic mass": 173.04, + "Atomic no": 70, + "Atomic orbitals": { + "1s": -2084.069389, + "2p": -323.178219, + "2s": -337.978976, + "3d": -56.026315, + "3p": -68.698655, + "3s": -75.47663, + "4d": -6.574963, + "4f": -0.286408, + "4p": -11.558246, + "4s": -14.312076, + "5p": -0.966137, + "5s": -1.683886, + "6s": -0.136989 + }, + "Atomic radius": 1.75, + "Atomic radius calculated": 2.22, + "Boiling point": "1469 K", + "Brinell hardness": "343 MN m-2", + "Bulk modulus": "31 GPa", + "Coefficient of linear thermal expansion": "26.3 x10-6K-1", + "Common oxidation states": [ + 3 + ], + "Critical temperature": "no data K", + "Density of solid": "6570 kg m-3", + "Electrical resistivity": "25.0 10-8 Ω m", + "Electronic structure": { + "0": "[Xe].4f14.6s2", + "3": "[Xe].4f13" + }, + "ICSD oxidation states": [ + 2, + 3 + ], + "Ionic radii": { + "2": 1.16, + "3": 1.008 + }, + "Liquid range": "372 K", + "Melting point": "1097 K", + "Mendeleev no": 17, + "Mineral hardness": "no data", + "Molar volume": "24.84 cm3", + "Name": "Ytterbium", + "Oxidation states": [ + 2, + 3 + ], + "Poissons ratio": "0.21", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "9.9 GPa", + "Shannon radii": { + "2": { + "VI": { + "": { + "crystal_radius": 1.16, + "ionic_radius": 1.02 + } + }, + "VII": { + "": { + "crystal_radius": 1.22, + "ionic_radius": 1.08 + } + }, + "VIII": { + "": { + "crystal_radius": 1.28, + "ionic_radius": 1.14 + } + } + }, + "3": { + "VI": { + "": { + "crystal_radius": 1.008, + "ionic_radius": 0.868 + } + }, + "VII": { + "": { + "crystal_radius": 1.065, + "ionic_radius": 0.925 + } + }, + "VIII": { + "": { + "crystal_radius": 1.125, + "ionic_radius": 0.985 + } + }, + "IX": { + "": { + "crystal_radius": 1.182, + "ionic_radius": 1.042 + } + } + } + }, + "Superconduction temperature": "no data K", + "Thermal conductivity": "39 W m-1 K-1", + "Van der waals radius": 2.26, + "Velocity of sound": "1590 m s-1", + "Vickers hardness": "206 MN m-2", + "X": 1.1, + "Youngs modulus": "24 GPa", + "Metallic radius": 1.94, + "iupac_ordering": 34, + "IUPAC ordering": 34, + "Ground level": "1S0", + "Ionization energies": [ + 6.25416, + 12.179185, + 25.053, + 43.61, + 65.6, + 99, + 117, + 135, + 163, + 182, + 209, + 244, + 279, + 301, + 324, + 360, + 396, + 431, + 469, + 505, + 540, + 580, + 610, + 651, + 882, + 924, + 971, + 1019, + 1065, + 1114, + 1175, + 1224, + 1275, + 1324, + 1516, + 1564, + 1618, + 1668, + 1789, + 1845, + 1978, + 2036.4, + 3443, + 3555, + 3677, + 3805, + 3929, + 4051, + 4238, + 4364, + 4502, + 4630, + 4988, + 5101, + 5224, + 5339, + 5731, + 5860, + 6111, + 6236, + 13784, + 14093, + 14435, + 14752, + 16191, + 16570, + 17050, + 17365.44, + 70123.04, + 71574.8 + ], + "Electron affinity": -0.02 + }, + "Zn": { + "Atomic mass": 65.409, + "Atomic no": 30, + "Atomic orbitals": { + "1s": -344.969756, + "2p": -36.648765, + "2s": -41.531323, + "3d": -0.398944, + "3p": -3.022363, + "3s": -4.573041, + "4s": -0.222725 + }, + "Atomic radius": 1.35, + "Atomic radius calculated": 1.42, + "Boiling point": "1180 K", + "Brinell hardness": "412 MN m-2", + "Bulk modulus": "70 GPa", + "Coefficient of linear thermal expansion": "30.2 x10-6K-1", + "Common oxidation states": [ + 2 + ], + "Critical temperature": "no data K", + "Density of solid": "7140 kg m-3", + "Electrical resistivity": "6.0 10-8 Ω m", + "Electronic structure": { + "0": "[Ar].3d10.4s2", + "2": "[Ar].3d10" + }, + "ICSD oxidation states": [ + 2 + ], + "Ionic radii": { + "2": 0.88 + }, + "Liquid range": "487.32 K", + "Melting point": "692.68 K", + "Mendeleev no": 76, + "Mineral hardness": "2.5", + "Molar volume": "9.16 cm3", + "Name": "Zinc", + "Oxidation states": [ + 1, + 2 + ], + "Poissons ratio": "0.25", + "Reflectivity": "80 %", + "Refractive index": "1.002050", + "Rigidity modulus": "43 GPa", + "Shannon radii": { + "2": { + "IV": { + "": { + "crystal_radius": 0.74, + "ionic_radius": 0.6 + } + }, + "V": { + "": { + "crystal_radius": 0.82, + "ionic_radius": 0.68 + } + }, + "VI": { + "": { + "crystal_radius": 0.88, + "ionic_radius": 0.74 + } + }, + "VIII": { + "": { + "crystal_radius": 1.04, + "ionic_radius": 0.9 + } + } + } + }, + "Superconduction temperature": "0.85 K", + "Thermal conductivity": "120 W m-1 K-1", + "Van der waals radius": 2.01, + "Velocity of sound": "3700 m s-1", + "Vickers hardness": "no data MN m-2", + "X": 1.65, + "Youngs modulus": "108 GPa", + "NMR Quadrupole Moment": { + "Zn-67": 150.15 + }, + "Metallic radius": 1.34, + "iupac_ordering": 76, + "IUPAC ordering": 76, + "Ground level": "1S0", + "Ionization energies": [ + 9.394197, + 17.96439, + 39.7233, + 59.573, + 82.6, + 108, + 133.9, + 173.9, + 203, + 238, + 274.4, + 310.8, + 417.6, + 453.4, + 490.6, + 540, + 577.8, + 613.3, + 697.5, + 737.366, + 1846.8, + 1961, + 2085, + 2214, + 2358, + 2491.5, + 2669.9, + 2781.996, + 11864.9399, + 12388.929 + ], + "Electron affinity": -0.62 + }, + "Zr": { + "Atomic mass": 91.224, + "Atomic no": 40, + "Atomic orbitals": { + "1s": -639.292236, + "2p": -80.010043, + "2s": -87.237062, + "3d": -6.544643, + "3p": -11.514415, + "3s": -14.230432, + "4d": -0.150673, + "4p": -1.186597, + "4s": -1.918971, + "5s": -0.162391 + }, + "Atomic radius": 1.55, + "Atomic radius calculated": 2.06, + "Boiling point": "4682 K", + "Brinell hardness": "650 MN m-2", + "Bulk modulus": "no data GPa", + "Coefficient of linear thermal expansion": "5.7 x10-6K-1", + "Common oxidation states": [ + 4 + ], + "Critical temperature": "no data K", + "Density of solid": "6511 kg m-3", + "Electrical resistivity": "43.3 10-8 Ω m", + "Electronic structure": { + "0": "[Kr].4d2.5s2", + "4": "[Ar].3d10.4s2.4p6" + }, + "ICSD oxidation states": [ + 2, + 3, + 4 + ], + "Ionic radii": { + "4": 0.86 + }, + "Liquid range": "2554 K", + "Melting point": "2128 K", + "Mendeleev no": 49, + "Mineral hardness": "5.0", + "Molar volume": "14.02 cm3", + "Name": "Zirconium", + "Oxidation states": [ + 1, + 2, + 3, + 4 + ], + "Poissons ratio": "0.34", + "Reflectivity": "no data %", + "Refractive index": "no data", + "Rigidity modulus": "33 GPa", + "Shannon radii": { + "4": { + "IV": { + "": { + "crystal_radius": 0.73, + "ionic_radius": 0.59 + } + }, + "V": { + "": { + "crystal_radius": 0.8, + "ionic_radius": 0.66 + } + }, + "VI": { + "": { + "crystal_radius": 0.86, + "ionic_radius": 0.72 + } + }, + "VII": { + "": { + "crystal_radius": 0.92, + "ionic_radius": 0.78 + } + }, + "VIII": { + "": { + "crystal_radius": 0.98, + "ionic_radius": 0.84 + } + }, + "IX": { + "": { + "crystal_radius": 1.03, + "ionic_radius": 0.89 + } + } + } + }, + "Superconduction temperature": "0.61 K", + "Thermal conductivity": "23 W m-1 K-1", + "Van der waals radius": 2.23, + "Velocity of sound": "3800 m s-1", + "Vickers hardness": "903 MN m-2", + "X": 1.33, + "Youngs modulus": "68 GPa", + "Metallic radius": 1.602, + "iupac_ordering": 51, + "IUPAC ordering": 51, + "Ground level": "3F2", + "Ionization energies": [ + 6.634126, + 13.13, + 23.17, + 34.41836, + 80.348, + 96.38, + 112, + 133.7, + 153, + 172.02, + 214.9, + 236.252, + 426, + 470, + 520, + 573, + 622, + 690, + 745, + 803, + 863, + 922, + 1092, + 1144.7, + 1205.4, + 1277, + 1344, + 1392, + 1525.1, + 1582.37, + 3788, + 3950, + 4127, + 4300, + 4553, + 4744, + 4991, + 5146.935, + 21516.469, + 22236.678 + ], + "Electron affinity": 0.433289 + }, + "Rf": { + "Atomic mass": 267, + "Atomic no": 104, + "Name": "Rutherfordium", + "Ground level": "3F2", + "Ionization energies": [ + 6.02, + 14.35, + 23.84, + 31.87, + 64, + 77, + 102, + 119, + 146.1, + 169, + 193, + 225, + 244, + 275, + null, + 791, + 825, + 860, + 899, + 936, + 972, + 1036, + 1073, + 1114, + 1151, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + 3857, + 3938, + 4025, + 4116, + 4203, + 4287, + 4489, + 4580, + 4670, + 4760, + 5130, + 5210, + 5300, + 5390, + 6100, + 6200, + 6470, + 6570, + 10170, + 10360, + 10560, + 10780, + 10980, + 11180, + 11750, + 11960, + 12200, + 12410, + 13010, + 13190, + 13400, + 13600, + 15800, + 16000, + 16400, + 16700, + 33100, + 33600, + 34100, + 34600, + 42700, + 43400, + 44300, + null, + null, + 177148 + ], + "Electron affinity": null, + "Van der waals radius": "no data" + }, + "Db": { + "Atomic mass": 268, + "Atomic no": 105, + "Name": "Dubnium", + "Ground level": "4F3/2", + "Ionization energies": [ + 6.8, + 14, + 23.1, + 33, + 43, + 86, + 98.9, + 126, + 145.1, + 172, + 196, + 220.9, + 254, + 274, + 307, + null, + 838, + 872, + 908, + 948, + 985, + 1022, + 1089, + 1126, + 1168, + 1207, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + 3975, + 4057, + 4145, + 4237, + 4326, + 4411, + 4620, + 4710, + 4810, + 4900, + 5260, + 5350, + 5450, + 5530, + 6280, + 6380, + 6650, + 6760, + 10420, + 10610, + 10820, + 11040, + 11240, + 11440, + 12040, + 12250, + 12480, + 12700, + 13300, + 13500, + 13700, + 13900, + 16200, + 16400, + 16900, + 17100, + 33800, + 34300, + 34800, + 35300, + 43800, + 44500, + 45400, + null, + null, + 181444 + ], + "Electron affinity": null, + "Van der waals radius": "no data" + }, + "Sg": { + "Atomic mass": 269, + "Atomic no": 106, + "Name": "Seaborgium", + "Ground level": "0", + "Ionization energies": [ + 7.8, + 17.1, + 25.8, + 35.5, + 47.2, + 59.3, + 109, + 122, + 152, + 170, + 200, + 224, + 251, + 285, + 306, + 339, + null, + 885, + 921, + 958, + 998, + 1036, + 1073, + 1143, + 1181, + 1223, + 1263, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + 4095, + 4178, + 4267, + 4360, + 4450, + 4540, + 4750, + 4840, + 4940, + 5030, + 5410, + 5490, + 5590, + 5680, + 6460, + 6570, + 6840, + 6950, + 10680, + 10870, + 11080, + 11300, + 11510, + 11710, + 12320, + 12540, + 12780, + 12990, + 13600, + 13800, + 14000, + 14200, + 16600, + 16800, + 17300, + 17500, + 34500, + 35000, + 35600, + 36100, + 44900, + 45700, + 46600, + null, + null, + 185839 + ], + "Electron affinity": null, + "Van der waals radius": "no data" + }, + "Bh": { + "Atomic mass": 270, + "Atomic no": 107, + "Name": "Bohrium", + "Ground level": "5/2", + "Ionization energies": [ + 7.7, + 17.5, + 26.7, + 37.3, + 49, + 62.1, + 74.9, + 134, + 148, + 178, + 198, + 228, + 255, + 281, + 318, + 337, + 374, + null, + 934, + 969, + 1008, + 1049, + 1088, + 1126, + 1197, + 1237, + 1280, + 1320, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + 4216, + 4301, + 4390, + 4486, + 4580, + 4660, + 4890, + 4980, + 5080, + 5170, + 5550, + 5640, + 5740, + 5830, + 6650, + 6760, + 7040, + 7140, + 10930, + 11130, + 11340, + 11560, + 11780, + 11980, + 12610, + 12830, + 13070, + 13300, + 13900, + 14100, + 14300, + 14500, + 17000, + 17300, + 17700, + 18000, + 35200, + 35700, + 36300, + 36800, + 46100, + 46900, + 47800, + null, + null, + 190331 + ], + "Electron affinity": null, + "Van der waals radius": "no data" + }, + "Hs": { + "Atomic mass": 270, + "Atomic no": 108, + "Name": "Hassium", + "Ground level": "4", + "Ionization energies": [ + 7.6, + 18.2, + 29.3, + 37.7, + 51.2, + 64, + 78.1, + 91.7, + 159.9, + 173.9, + 206.1, + 227, + 258, + 285, + 314, + 351, + 371, + 409, + null, + 984, + 1020, + 1060, + 1101, + 1140, + 1180, + 1253, + 1294, + 1338, + 1379, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + 4339, + 4425, + 4516, + 4610, + 4700, + 4790, + 5020, + 5110, + 5220, + 5310, + 5700, + 5780, + 5880, + 5980, + 6840, + 6950, + 7230, + 7340, + 11200, + 11390, + 11610, + 11830, + 12040, + 12250, + 12910, + 13130, + 13400, + 13600, + 14200, + 14400, + 14600, + 14800, + 17500, + 17700, + 18200, + 18400, + 35900, + 36400, + 37000, + 37500, + 47300, + 48100, + 49000, + null, + null, + 194917 + ], + "Electron affinity": null, + "Van der waals radius": "no data" + }, + "Mt": { + "Atomic mass": 278, + "Atomic no": 109, + "Name": "Meitnerium", + "Ground level": null, + "Ionization energies": [ + 50, + null, + null, + 94, + 109, + 187, + 202, + 235.9, + 257, + 289, + 318, + 346, + 386, + 406, + 445, + null, + 1035, + 1072, + 1112, + 1154, + 1195, + 1234, + 1311, + 1352, + 1397, + 1439, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + 4464, + 4551, + 4640, + 4740, + 4830, + 4920, + 5160, + 5250, + 5360, + 5450, + 5840, + 5930, + 6030, + 6130, + 7030, + 7150, + 7430, + 7550, + 11460, + 11660, + 11870, + 12100, + 12320, + 12530, + 13200, + 13400, + 13700, + 13900, + 14500, + 14700, + 14900, + 15100, + 17900, + 18200, + 18700, + 18900, + 36700, + 37200, + 37800, + 38300, + 48500, + 49400, + 50300, + null, + null, + 199606 + ], + "Electron affinity": null, + "Van der waals radius": "no data" + }, + "Ds": { + "Atomic mass": 281, + "Atomic no": 110, + "Name": "Darmstadtium", + "Ground level": null, + "Ionization energies": [ + 65, + null, + null, + 112.9, + 128, + 216, + 231, + 266, + 288, + 322, + 352, + 380, + 422, + 442, + 483, + null, + 1087, + 1125, + 1165, + 1208, + 1250, + 1290, + 1369, + 1412, + 1457, + 1500, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + 4590, + 4680, + 4770, + 4870, + 4960, + 5060, + 5300, + 5400, + 5500, + 5600, + 5990, + 6080, + 6190, + 6280, + 7230, + 7350, + 7640, + 7750, + 11730, + 11930, + 12140, + 12380, + 12600, + 12810, + 13500, + 13700, + 14000, + 14200, + 14800, + 15000, + 15300, + 15500, + 18400, + 18600, + 19100, + 19400, + 37400, + 37900, + 38500, + 39100, + 49800, + 50700, + 51600, + null, + null, + 204400 + ], + "Electron affinity": null, + "Van der waals radius": "no data" + }, + "Rg": { + "Atomic mass": 282, + "Atomic no": 111, + "Name": "Roentgenium", + "Ground level": null, + "Ionization energies": [], + "Electron affinity": 1.565, + "Van der waals radius": "no data" + }, + "Cn": { + "Atomic mass": 285, + "Atomic no": 112, + "Name": "Copernicium", + "Ground level": null, + "Ionization energies": [], + "Electron affinity": null, + "Van der waals radius": "no data" + }, + "Nh": { + "Atomic mass": 286, + "Atomic no": 113, + "Name": "Nihonium", + "Ground level": null, + "Ionization energies": [], + "Electron affinity": 0.69, + "Van der waals radius": "no data" + }, + "Fl": { + "Atomic mass": 289, + "Atomic no": 114, + "Name": "Flerovium", + "Ground level": null, + "Ionization energies": [], + "Electron affinity": null, + "Van der waals radius": "no data" + }, + "Mc": { + "Atomic mass": 290, + "Atomic no": 115, + "Name": "Moscovium", + "Ground level": null, + "Ionization energies": [], + "Electron affinity": 0.366, + "Van der waals radius": "no data" + }, + "Lv": { + "Atomic mass": 293, + "Atomic no": 116, + "Name": "Livermorium", + "Ground level": null, + "Ionization energies": [], + "Electron affinity": 0.776, + "Van der waals radius": "no data" + }, + "Ts": { + "Atomic mass": 294, + "Atomic no": 117, + "Name": "Tennessine", + "Ground level": null, + "Ionization energies": [], + "Electron affinity": 1.719, + "Van der waals radius": "no data" + }, + "Og": { + "Atomic mass": 294, + "Atomic no": 118, + "Name": "Oganesson", + "Ground level": null, + "Ionization energies": [], + "Electron affinity": 0.0561, + "Van der waals radius": "no data" + }, + "D": { + "Atomic no": 1, + "Atomic mass": 2.013553212712, + "Atomic mass no": 2, + "Common oxidation states": [ + -1, + 1 + ], + "Is named isotope": true, + "Name": "Deuterium", + "Oxidation states": [ + -1, + 1 + ], + "Shannon radii": { + "1": { + "II": { + "": { + "crystal_radius": 0.04, + "ionic_radius": -0.1 + } + } + } + }, + "Electron affinity": 0.754674 + }, + "T": { + "Atomic no": 1, + "Atomic mass": 3.0155007134, + "Atomic mass no": 3, + "Common oxidation states": [ + -1, + 1 + ], + "Is named isotope": true, + "Name": "Tritium", + "Oxidation states": [ + -1, + 1 + ], + "Electron affinity": null + } +} diff --git a/pymatgen/core/periodic_table.py b/src/pymatgen/core/periodic_table.py similarity index 91% rename from pymatgen/core/periodic_table.py rename to src/pymatgen/core/periodic_table.py index 285d0bb5a3e..9e346e987b8 100644 --- a/pymatgen/core/periodic_table.py +++ b/src/pymatgen/core/periodic_table.py @@ -17,7 +17,6 @@ import numpy as np from monty.dev import deprecated from monty.json import MSONable - from pymatgen.core.units import SUPPORTED_UNIT_NAMES, FloatWithUnit, Ha_to_eV, Length, Mass, Unit from pymatgen.io.core import ParseError from pymatgen.util.string import Stringify, formula_double_format @@ -25,9 +24,8 @@ if TYPE_CHECKING: from typing import Any, Callable, Literal - from typing_extensions import Self - from pymatgen.util.typing import SpeciesLike + from typing_extensions import Self # Load element data from JSON file with open(Path(__file__).absolute().parent / "periodic_table.json", encoding="utf-8") as ptable_json: @@ -326,10 +324,19 @@ def electron_affinity(self) -> float: @property def electronic_structure(self) -> str: - """Electronic structure as string, with only valence electrons. - e.g. The electronic structure for Fe is represented as '[Ar].3d6.4s2'. + """Electronic structure as string, with only valence electrons. The + electrons are listed in order of increasing prinicpal quantum number + (orbital number), irrespective of the actual energy level, + e.g., The electronic structure for Fe is represented as '[Ar].3d6.4s2' + even though the 3d electrons are higher in energy than the 4s. + + References: + Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2023). NIST + Atomic Spectra Database (ver. 5.11). https://physics.nist.gov/asd [2024, + June 3]. National Institute of Standards and Technology, Gaithersburg, + MD. DOI: https://doi.org/10.18434/T4W30F """ - return re.sub("", "", self._data["Electronic structure"]) + return re.sub("", "", self._data["Electronic structure"]["0"]) @property def average_ionic_radius(self) -> FloatWithUnit: @@ -414,10 +421,18 @@ def icsd_oxidation_states(self) -> tuple[int, ...]: @property def full_electronic_structure(self) -> list[tuple[int, str, int]]: - """Full electronic structure as tuple. - e.g. The electronic structure for Fe is represented as: + """Full electronic structure as list of tuples, in order of increasing + principal (n) and angular momentum (l) quantum numbers. + + For example, the electronic structure for Fe is represented as: [(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6), (3, "d", 6), (4, "s", 2)]. + + References: + Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2023). NIST + Atomic Spectra Database (ver. 5.11). https://physics.nist.gov/asd [2024, + June 3]. National Institute of Standards and Technology, Gaithersburg, + MD. DOI: https://doi.org/10.18434/T4W30F """ e_str = self.electronic_structure @@ -435,7 +450,8 @@ def parse_orbital(orb_str): @property def valence(self) -> tuple[int | np.nan, int]: """Valence subshell angular moment (L) and number of valence e- (v_e), - obtained from full electron config. + obtained from full electron config, where L=0, 1, 2, or 3 for s, p, d, + and f orbitals, respectively. """ if self.group == 18: return np.nan, 0 # The number of valence of noble gas is 0 @@ -1080,21 +1096,79 @@ def spin(self) -> float | None: return self._spin @property - def full_electronic_structure(self) -> list[tuple[int, str, int]]: - """Full electronic structure as tuple. Not implemented for Species as of now.""" - raise NotImplementedError + def electronic_structure(self) -> str: + """Electronic structure as string, with only valence electrons. The + electrons are listed in order of increasing prinicpal quantum number + (orbital number), irrespective of the actual energy level, + e.g., The electronic structure for Fe is represented as '[Ar].3d6.4s2' + even though the 3d electrons are higher in energy than the 4s. + + References: + Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2023). NIST + Atomic Spectra Database (ver. 5.11). https://physics.nist.gov/asd [2024, + June 3]. National Institute of Standards and Technology, Gaithersburg, + MD. DOI: https://doi.org/10.18434/T4W30F + """ + if self._data["Electronic structure"].get(str(self._oxi_state)) is not None: + return re.sub("", "", self._data["Electronic structure"][str(self._oxi_state)]) + raise ValueError(f"No electronic structure data for oxidation state {self.oxi_state}") + + # NOTE - copied exactly from Element. Refactoring / inheritance may improve + # robustness @property - def electronic_structure(self) -> list[tuple[int, str, int]]: - """Electronic structure as tuple. Not implemented for Species as of now.""" - raise NotImplementedError + def full_electronic_structure(self) -> list[tuple[int, str, int]]: + """Full electronic structure as list of tuples, in order of increasing + principal (n) and angular momentum (l) quantum numbers. + + For example, the electronic structure for Fe+2 is represented as: + [(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6), + (3, "d", 6)]. + + References: + Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2023). NIST + Atomic Spectra Database (ver. 5.11). https://physics.nist.gov/asd [2024, + June 3]. National Institute of Standards and Technology, Gaithersburg, + MD. DOI: https://doi.org/10.18434/T4W30F + """ + e_str = self.electronic_structure + + def parse_orbital(orb_str): + if match := re.match(r"(\d+)([spdfg]+)(\d+)", orb_str): + return int(match[1]), match[2], int(match[3]) + return orb_str + + data = [parse_orbital(s) for s in e_str.split(".")] + if data[0][0] == "[": + sym = data[0].replace("[", "").replace("]", "") + data = list(Element(sym).full_electronic_structure) + data[1:] + return data + # NOTE - copied exactly from Element. Refactoring / inheritance may improve + # robustness @property def valence(self) -> tuple[int | np.nan, int]: """Valence subshell angular moment (L) and number of valence e- (v_e), - obtained from full electron config. Not implemented for Species as of now. + obtained from full electron config, where L=0, 1, 2, or 3 for s, p, d, + and f orbitals, respectively. """ - raise NotImplementedError + if self.group == 18: + return np.nan, 0 # The number of valence of noble gas is 0 + + L_symbols = "SPDFGHIKLMNOQRTUVWXYZ" + valence: list[tuple[int, int]] = [] + full_electron_config = self.full_electronic_structure + last_orbital = full_electron_config[-1] + for n, l_symbol, ne in full_electron_config: + idx = L_symbols.lower().index(l_symbol) + if ne < (2 * idx + 1) * 2 or ( + (n, l_symbol, ne) == last_orbital and ne == (2 * idx + 1) * 2 and len(valence) == 0 + ): # check for full last shell (e.g. column 2) + valence.append((idx, ne)) + if len(valence) > 1: + raise ValueError(f"{self} has ambiguous valence") + + return valence[0] @property def ionic_radius(self) -> float | None: @@ -1210,7 +1284,8 @@ def get_shannon_radius( Shannon radius for specie in the specified environment. """ radii = self._el.data["Shannon radii"] - radii = radii[str(int(self._oxi_state))][cn] # type: ignore + assert self._oxi_state is not None + radii = radii[str(int(self._oxi_state))][cn] if len(radii) == 1: key, data = next(iter(radii.items())) if key != spin: @@ -1249,7 +1324,8 @@ def get_crystal_field_spin( if len(elec) < 4 or elec[-1][1] != "s" or elec[-2][1] != "d": raise AttributeError(f"Invalid element {self.symbol} for crystal field calculation") - n_electrons = elec[-1][2] + elec[-2][2] - self.oxi_state # type: ignore + assert self.oxi_state is not None + n_electrons = elec[-1][2] + elec[-2][2] - self.oxi_state if n_electrons < 0 or n_electrons > 10: raise AttributeError(f"Invalid oxidation state {self.oxi_state} for element {self.symbol}") @@ -1506,13 +1582,13 @@ def get_el_sp(obj: int | SpeciesLike) -> Element | Species | DummySpecies: Species | Element: with a bias for the maximum number of properties that can be determined. """ - # if obj is already an Element or Species, return as is + # If obj is already an Element or Species, return as is if isinstance(obj, (Element, Species, DummySpecies)): if getattr(obj, "_is_named_isotope", None): return Element(obj.name) if isinstance(obj, Element) else Species(str(obj)) return obj - # if obj is an integer, return the Element with atomic number obj + # If obj is an integer, return the Element with atomic number obj try: flt = float(obj) assert flt == int(flt) @@ -1520,22 +1596,22 @@ def get_el_sp(obj: int | SpeciesLike) -> Element | Species | DummySpecies: except (AssertionError, ValueError, TypeError, KeyError): pass - # if obj is a string, attempt to parse it as a Species + # If obj is a string, attempt to parse it as a Species try: - return Species.from_str(obj) # type: ignore + return Species.from_str(obj) # type: ignore[arg-type] except (ValueError, TypeError, KeyError): pass - # if Species parsing failed, try Element + # If Species parsing failed, try Element try: - return Element(obj) # type: ignore + return Element(obj) # type: ignore[arg-type] except (ValueError, TypeError, KeyError): pass - # if Element parsing failed, try DummySpecies + # If Element parsing failed, try DummySpecies try: - return DummySpecies.from_str(obj) # type: ignore - except Exception: - raise ValueError(f"Can't parse Element or Species from {obj!r}") + return DummySpecies.from_str(obj) # type: ignore[arg-type] + except Exception as exc: + raise ValueError(f"Can't parse Element or Species from {obj!r}") from exc @unique diff --git a/pymatgen/core/quad_data.json b/src/pymatgen/core/quad_data.json similarity index 100% rename from pymatgen/core/quad_data.json rename to src/pymatgen/core/quad_data.json diff --git a/pymatgen/core/reconstructions_archive.json b/src/pymatgen/core/reconstructions_archive.json similarity index 100% rename from pymatgen/core/reconstructions_archive.json rename to src/pymatgen/core/reconstructions_archive.json diff --git a/pymatgen/core/sites.py b/src/pymatgen/core/sites.py similarity index 99% rename from pymatgen/core/sites.py rename to src/pymatgen/core/sites.py index a703c79a335..fd8a61118ef 100644 --- a/pymatgen/core/sites.py +++ b/src/pymatgen/core/sites.py @@ -8,7 +8,6 @@ import numpy as np from monty.json import MontyDecoder, MontyEncoder, MSONable - from pymatgen.core.composition import Composition from pymatgen.core.lattice import Lattice from pymatgen.core.periodic_table import DummySpecies, Element, Species, get_el_sp @@ -18,9 +17,8 @@ from typing import Any from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.util.typing import CompositionLike, SpeciesLike, Vector3D + from typing_extensions import Self class Site(collections.abc.Hashable, MSONable): diff --git a/pymatgen/core/spectrum.py b/src/pymatgen/core/spectrum.py similarity index 99% rename from pymatgen/core/spectrum.py rename to src/pymatgen/core/spectrum.py index 6567f3a63a2..94ade3ce43e 100644 --- a/pymatgen/core/spectrum.py +++ b/src/pymatgen/core/spectrum.py @@ -8,11 +8,10 @@ import numpy as np from monty.json import MSONable +from pymatgen.util.coord import get_linear_interpolated_value from scipy import stats from scipy.ndimage import convolve1d -from pymatgen.util.coord import get_linear_interpolated_value - if TYPE_CHECKING: from typing import Callable, Literal diff --git a/pymatgen/core/structure.py b/src/pymatgen/core/structure.py similarity index 99% rename from pymatgen/core/structure.py rename to src/pymatgen/core/structure.py index b82f2076f12..f0d7d477ad6 100644 --- a/pymatgen/core/structure.py +++ b/src/pymatgen/core/structure.py @@ -31,12 +31,6 @@ from monty.json import MSONable from numpy import cross, eye from numpy.linalg import norm -from ruamel.yaml import YAML -from scipy.cluster.hierarchy import fcluster, linkage -from scipy.linalg import expm, polar -from scipy.spatial.distance import squareform -from tabulate import tabulate - from pymatgen.core.bonds import CovalentBond, get_bond_length from pymatgen.core.composition import Composition from pymatgen.core.lattice import Lattice, get_points_in_spheres @@ -47,6 +41,11 @@ from pymatgen.electronic_structure.core import Magmom from pymatgen.symmetry.maggroups import MagneticSpaceGroup from pymatgen.util.coord import all_distances, get_angle, lattice_points_in_supercell +from ruamel.yaml import YAML +from scipy.cluster.hierarchy import fcluster, linkage +from scipy.linalg import expm, polar +from scipy.spatial.distance import squareform +from tabulate import tabulate if TYPE_CHECKING: from collections.abc import Iterable, Iterator, Sequence @@ -59,11 +58,11 @@ from ase.optimize.optimize import Optimizer from matgl.ext.ase import TrajectoryObserver from numpy.typing import ArrayLike, NDArray - from typing_extensions import Self - from pymatgen.util.typing import CompositionLike, MillerIndex, PathLike, PbcLike, SpeciesLike + from typing_extensions import Self FileFormats = Literal["cif", "poscar", "cssr", "json", "yaml", "yml", "xsf", "mcsqs", "res", "pwmat", ""] +StructureSources = Literal["Materials Project", "COD"] class Neighbor(Site): @@ -828,7 +827,6 @@ def _relax( from ase.constraints import ExpCellFilter from ase.io import read from ase.optimize.optimize import Optimizer - from pymatgen.io.ase import AseAtomsAdaptor opt_kwargs = opt_kwargs or {} @@ -2937,6 +2935,28 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str: writer.write_file(filename) return str(writer) + @classmethod + def from_id(cls, id_: str, source: StructureSources = "Materials Project", **kwargs) -> Structure: + """ + Load a structure file based on an id, usually from an online source. + + Args: + id_: The id associated with the structure. E.g., the Materials Project id. + source: Source of the data. Defaults to "Materials Project". + **kwargs: Pass-through to any API calls. + """ + if source == "Materials Project": + from pymatgen.ext.matproj import MPRester + + mpr = MPRester(**kwargs) + return mpr.get_structure_by_material_id(id_) # type: ignore[attr-defined] + if source == "COD": + from pymatgen.ext.cod import COD + + cod = COD() + return cod.get_structure_by_id(int(id_)) + raise ValueError(f"Invalid source: {source}") + @classmethod def from_str( # type: ignore[override] cls, @@ -3440,25 +3460,26 @@ def find_nn_pos_before_site(site_idx: int): output = [] output_var = [] for idx, site in enumerate(self): + sp = site.specie if idx == 0: - output.append(f"{site.specie}") + output.append(f"{sp}") elif idx == 1: nn = find_nn_pos_before_site(idx) bond_length = self.get_distance(idx, nn[0]) - output.append(f"{self[idx].specie} {nn[0] + 1} B{idx}") + output.append(f"{sp} {nn[0] + 1} B{idx}") output_var.append(f"B{idx}={bond_length:.6f}") elif idx == 2: nn = find_nn_pos_before_site(idx) bond_length = self.get_distance(idx, nn[0]) angle = self.get_angle(idx, nn[0], nn[1]) - output.append(f"{self[idx].specie} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx}") + output.append(f"{site.specie} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx}") output_var.extend((f"B{idx}={bond_length:.6f}", f"A{idx}={angle:.6f}")) else: nn = find_nn_pos_before_site(idx) bond_length = self.get_distance(idx, nn[0]) angle = self.get_angle(idx, nn[0], nn[1]) dih = self.get_dihedral(idx, nn[0], nn[1], nn[2]) - output.append(f"{self[idx].specie} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx} {nn[2] + 1} D{idx}") + output.append(f"{sp} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx} {nn[2] + 1} D{idx}") output_var.extend((f"B{idx}={bond_length:.6f}", f"A{idx}={angle:.6f}", f"D{idx}={dih:.6f}")) return "\n".join(output) + "\n\n" + "\n".join(output_var) @@ -3938,7 +3959,7 @@ def __setitem__( # type: ignore[override] structure[(0, 2, 3)] = "Fe" Replaces sites 0, 2 and 3 with Fe. - structure[0::2] = "Fe" + structure[::2] = "Fe" Replaces all even index sites with Fe. structure["Mn"] = "Fe" diff --git a/pymatgen/core/surface.py b/src/pymatgen/core/surface.py similarity index 99% rename from pymatgen/core/surface.py rename to src/pymatgen/core/surface.py index 7e8e969e405..f59d3a3cbc0 100644 --- a/pymatgen/core/surface.py +++ b/src/pymatgen/core/surface.py @@ -27,26 +27,24 @@ import numpy as np from monty.fractions import lcm -from scipy.cluster.hierarchy import fcluster, linkage -from scipy.spatial.distance import squareform - from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core import Lattice, PeriodicSite, Structure, get_el_sp from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.coord import in_coord_list from pymatgen.util.due import Doi, due from pymatgen.util.typing import Tuple3Ints +from scipy.cluster.hierarchy import fcluster, linkage +from scipy.spatial.distance import squareform if TYPE_CHECKING: from collections.abc import Sequence from typing import Any from numpy.typing import ArrayLike, NDArray - from typing_extensions import Self - from pymatgen.core.composition import Element, Species from pymatgen.symmetry.groups import CrystalSystem from pymatgen.util.typing import MillerIndex + from typing_extensions import Self __author__ = "Richard Tran, Wenhao Sun, Zihan Xu, Shyue Ping Ong" diff --git a/pymatgen/core/tensors.py b/src/pymatgen/core/tensors.py similarity index 99% rename from pymatgen/core/tensors.py rename to src/pymatgen/core/tensors.py index 35152d195bf..feacea08c43 100644 --- a/pymatgen/core/tensors.py +++ b/src/pymatgen/core/tensors.py @@ -15,21 +15,19 @@ import numpy as np from monty.json import MSONable from monty.serialization import loadfn -from scipy.linalg import polar - from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core.lattice import Lattice from pymatgen.core.operations import SymmOp from pymatgen.symmetry.analyzer import SpacegroupAnalyzer +from scipy.linalg import polar if TYPE_CHECKING: from collections.abc import Sequence from typing import Any from numpy.typing import NDArray - from typing_extensions import Self - from pymatgen.core import Structure + from typing_extensions import Self __author__ = "Joseph Montoya" __credits__ = "Maarten de Jong, Shyam Dwaraknath, Wei Chen, Mark Asta, Anubhav Jain, Terence Lew" @@ -139,7 +137,7 @@ def einsum_sequence( ) -> NDArray: """Calculate the result of an einstein summation expression.""" if not isinstance(other_arrays, list): - raise ValueError("other tensors must be list of tensors or tensor input") + raise TypeError("other tensors must be list of tensors or tensor input") other_arrays = [np.array(a) for a in other_arrays] if not einsum_string: @@ -356,7 +354,7 @@ def is_voigt_symmetric(self, tol: float = 1e-6) -> bool: transpose_pieces[n] += [transpose_pieces[n][0][::-1]] for trans_seq in itertools.product(*transpose_pieces): transpose_seq = list(itertools.chain(*trans_seq)) - if (self - self.transpose(transpose_seq) > tol).any(): # type: ignore + if (self - self.transpose(transpose_seq) > tol).any(): return False return True diff --git a/pymatgen/core/trajectory.py b/src/pymatgen/core/trajectory.py similarity index 99% rename from pymatgen/core/trajectory.py rename to src/pymatgen/core/trajectory.py index ad595bb0e45..1d50e2a8df5 100644 --- a/pymatgen/core/trajectory.py +++ b/src/pymatgen/core/trajectory.py @@ -13,7 +13,6 @@ import numpy as np from monty.io import zopen from monty.json import MSONable - from pymatgen.core.structure import Composition, DummySpecies, Element, Lattice, Molecule, Species, Structure from pymatgen.io.ase import AseAtomsAdaptor @@ -21,9 +20,8 @@ from collections.abc import Iterator from typing import Any - from typing_extensions import Self - from pymatgen.util.typing import Matrix3D, PathLike, SitePropsType, Vector3D + from typing_extensions import Self __author__ = "Eric Sivonxay, Shyam Dwaraknath, Mingjian Wen, Evan Spotte-Smith" diff --git a/pymatgen/core/units.py b/src/pymatgen/core/units.py similarity index 97% rename from pymatgen/core/units.py rename to src/pymatgen/core/units.py index 6b0d8071b27..9e6b44b9de3 100644 --- a/pymatgen/core/units.py +++ b/src/pymatgen/core/units.py @@ -12,6 +12,7 @@ import collections import re +import warnings from collections import defaultdict from functools import partial from numbers import Number @@ -78,16 +79,13 @@ "intensity": {"cd": 1}, "memory": { "byte": 1, - "Kb": 1024, - "Mb": 1024**2, - "Gb": 1024**3, - "Tb": 1024**4, + "KB": 1024, + "MB": 1024**2, + "GB": 1024**3, + "TB": 1024**4, }, } -# Accept kb, mb, gb ... as well. -BASE_UNITS["memory"].update({k.lower(): v for k, v in BASE_UNITS["memory"].items()}) - # This current list are supported derived units defined in terms of powers of # SI base units and constants. DERIVED_UNITS: dict[str, dict] = { @@ -312,6 +310,14 @@ def __init__( unit (str | Unit): A unit. e.g. "C". unit_type (str): A type of unit. e.g. "charge" """ + # Check deprecated memory unit + # TODO: remove after 2025-01-01 + if unit_type == "memory" and str(unit) in {"Kb", "kb", "Mb", "mb", "Gb", "gb", "Tb", "tb"}: + warnings.warn( + f"Unit {unit!s} is deprecated, please use {str(unit).upper()} instead", DeprecationWarning, stacklevel=2 + ) + unit = str(unit).upper() + if unit_type is not None and str(unit) not in ALL_UNITS[unit_type]: raise UnitError(f"{unit} is not a supported unit for {unit_type}") @@ -440,16 +446,16 @@ def from_str(cls, string: str) -> Self: """Convert string to FloatWithUnit. Example usage: - Memory.from_str("1. Mb"). + Memory.from_str("1. MB"). """ - # Extract num and unit string. + # Extract num and unit string string = string.strip() for _idx, char in enumerate(string): if char.isalpha() or char.isspace(): break else: raise ValueError(f"Unit is missing in string {string}") - num, unit = float(string[:_idx]), string[_idx:] + num, unit = float(string[:_idx]), string[_idx:].strip() # Find unit type (set it to None if it cannot be detected) for unit_type, dct in BASE_UNITS.items(): @@ -763,7 +769,7 @@ def _my_partial(func, *args, **kwargs): Args: val (float): Value - unit (Unit): e.g. Kb, Mb, Gb, Tb. Must be valid unit or UnitError + unit (Unit): e.g. KB, MB, GB, TB. Must be valid unit or UnitError is raised. """ diff --git a/pymatgen/core/xcfunc.py b/src/pymatgen/core/xcfunc.py similarity index 99% rename from pymatgen/core/xcfunc.py rename to src/pymatgen/core/xcfunc.py index a17d9c939fb..4b2e46d7376 100644 --- a/pymatgen/core/xcfunc.py +++ b/src/pymatgen/core/xcfunc.py @@ -6,7 +6,6 @@ from monty.functools import lazy_property from monty.json import MSONable - from pymatgen.core.libxcfunc import LibxcFunc if TYPE_CHECKING: diff --git a/pymatgen/dao.py b/src/pymatgen/dao.py similarity index 100% rename from pymatgen/dao.py rename to src/pymatgen/dao.py diff --git a/pymatgen/electronic_structure/__init__.py b/src/pymatgen/electronic_structure/__init__.py similarity index 100% rename from pymatgen/electronic_structure/__init__.py rename to src/pymatgen/electronic_structure/__init__.py diff --git a/pymatgen/electronic_structure/bandstructure.py b/src/pymatgen/electronic_structure/bandstructure.py similarity index 99% rename from pymatgen/electronic_structure/bandstructure.py rename to src/pymatgen/electronic_structure/bandstructure.py index f844674be2b..f03160bb9ea 100644 --- a/pymatgen/electronic_structure/bandstructure.py +++ b/src/pymatgen/electronic_structure/bandstructure.py @@ -11,7 +11,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.core import Element, Lattice, Structure, get_el_sp from pymatgen.electronic_structure.core import Orbital, Spin from pymatgen.symmetry.analyzer import SpacegroupAnalyzer diff --git a/pymatgen/electronic_structure/boltztrap.py b/src/pymatgen/electronic_structure/boltztrap.py similarity index 99% rename from pymatgen/electronic_structure/boltztrap.py rename to src/pymatgen/electronic_structure/boltztrap.py index a0de391a7d5..980ccb4f1a7 100644 --- a/pymatgen/electronic_structure/boltztrap.py +++ b/src/pymatgen/electronic_structure/boltztrap.py @@ -31,10 +31,6 @@ from monty.dev import requires from monty.json import MSONable, jsanitize from monty.os import cd -from scipy import constants -from scipy.optimize import fsolve -from scipy.spatial import distance - from pymatgen.core.lattice import Lattice from pymatgen.core.units import Energy, Length from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine, Kpoint @@ -42,15 +38,17 @@ from pymatgen.electronic_structure.dos import CompleteDos, Dos, Spin from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.symmetry.bandstructure import HighSymmKpath +from scipy import constants +from scipy.optimize import fsolve +from scipy.spatial import distance if TYPE_CHECKING: from typing import Literal from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.core.sites import PeriodicSite from pymatgen.core.structure import Structure + from typing_extensions import Self __author__ = "Geoffroy Hautier, Zachary Gibbs, Francesco Ricci, Anubhav Jain" __copyright__ = "Copyright 2013, The Materials Project" @@ -611,14 +609,11 @@ def run( bt_exe.append("-so") with subprocess.Popen( - bt_exe, - stdout=subprocess.PIPE, - stdin=subprocess.PIPE, - stderr=subprocess.PIPE, - ) as p: - p.wait() - - for c in p.communicate(): + bt_exe, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE + ) as process: + process.wait() + + for c in process.communicate(): logging.info(c.decode()) if "error in factorization" in c.decode(): raise BoltztrapError("error in factorization") @@ -870,7 +865,7 @@ def get_symm_bands(self, structure: Structure, efermi, kpt_line=None, labels_dic w: list[bool] = [] prec = 1e-5 while len(w) == 0: - w = np.where(np.all(np.abs(kp - self._bz_kpoints) < [prec] * 3, axis=1))[0] # type: ignore + w = np.where(np.all(np.abs(kp - self._bz_kpoints) < [prec] * 3, axis=1))[0] prec *= 10 _idx_list.append((idx, w[0])) @@ -878,7 +873,7 @@ def get_symm_bands(self, structure: Structure, efermi, kpt_line=None, labels_dic idx_list = np.array(_idx_list) bz_bands_in_eV = (self._bz_bands * Energy(1, "Ry").to("eV") + efermi).T - bands_dict = {Spin.up: bz_bands_in_eV[:, idx_list[:, 1]].tolist()} # type: ignore + bands_dict = {Spin.up: bz_bands_in_eV[:, idx_list[:, 1]].tolist()} return BandStructureSymmLine( kpt_line, bands_dict, structure.lattice.reciprocal_lattice, efermi, labels_dict=labels_dict diff --git a/pymatgen/electronic_structure/boltztrap2.py b/src/pymatgen/electronic_structure/boltztrap2.py similarity index 99% rename from pymatgen/electronic_structure/boltztrap2.py rename to src/pymatgen/electronic_structure/boltztrap2.py index d3ed99d5167..d84df06e2a9 100644 --- a/pymatgen/electronic_structure/boltztrap2.py +++ b/src/pymatgen/electronic_structure/boltztrap2.py @@ -34,8 +34,6 @@ import matplotlib.pyplot as plt import numpy as np from monty.serialization import dumpfn, loadfn -from tqdm import tqdm - from pymatgen.electronic_structure.bandstructure import BandStructure, BandStructureSymmLine, Spin from pymatgen.electronic_structure.boltztrap import BoltztrapError from pymatgen.electronic_structure.dos import CompleteDos, Dos, Orbital @@ -43,6 +41,7 @@ from pymatgen.io.ase import AseAtomsAdaptor from pymatgen.io.vasp import Vasprun from pymatgen.symmetry.bandstructure import HighSymmKpath +from tqdm import tqdm if TYPE_CHECKING: from pathlib import Path diff --git a/pymatgen/electronic_structure/cohp.py b/src/pymatgen/electronic_structure/cohp.py similarity index 99% rename from pymatgen/electronic_structure/cohp.py rename to src/pymatgen/electronic_structure/cohp.py index bd1fa4b794f..17bcdce0be5 100644 --- a/pymatgen/electronic_structure/cohp.py +++ b/src/pymatgen/electronic_structure/cohp.py @@ -17,8 +17,6 @@ import numpy as np from monty.json import MSONable -from scipy.interpolate import InterpolatedUnivariateSpline - from pymatgen.core.sites import PeriodicSite from pymatgen.core.structure import Structure from pymatgen.electronic_structure.core import Orbital, Spin @@ -27,6 +25,7 @@ from pymatgen.util.coord import get_linear_interpolated_value from pymatgen.util.due import Doi, due from pymatgen.util.num import round_to_sigfigs +from scipy.interpolate import InterpolatedUnivariateSpline if TYPE_CHECKING: from typing import Any @@ -172,7 +171,7 @@ def has_antibnd_states_below_efermi(self, spin=None, limit=0.01): if spin is None: dict_to_return = {} for sp, cohp_vals in populations.items(): - if (max(cohp_vals[0:n_energies_below_efermi])) > limit: + if (max(cohp_vals[:n_energies_below_efermi])) > limit: dict_to_return[sp] = True else: dict_to_return[sp] = False @@ -182,7 +181,7 @@ def has_antibnd_states_below_efermi(self, spin=None, limit=0.01): spin = Spin(spin) elif isinstance(spin, str): spin = Spin({"up": 1, "down": -1}[spin.lower()]) - if (max(populations[spin][0:n_energies_below_efermi])) > limit: + if (max(populations[spin][:n_energies_below_efermi])) > limit: dict_to_return[spin] = True else: dict_to_return[spin] = False diff --git a/pymatgen/electronic_structure/core.py b/src/pymatgen/electronic_structure/core.py similarity index 99% rename from pymatgen/electronic_structure/core.py rename to src/pymatgen/electronic_structure/core.py index c10ee208137..1297c8495aa 100644 --- a/pymatgen/electronic_structure/core.py +++ b/src/pymatgen/electronic_structure/core.py @@ -13,9 +13,8 @@ if TYPE_CHECKING: from collections.abc import Sequence - from typing_extensions import Self - from pymatgen.core import Lattice + from typing_extensions import Self @unique diff --git a/pymatgen/electronic_structure/dos.py b/src/pymatgen/electronic_structure/dos.py similarity index 98% rename from pymatgen/electronic_structure/dos.py rename to src/pymatgen/electronic_structure/dos.py index be074213ca6..26662562e7c 100644 --- a/pymatgen/electronic_structure/dos.py +++ b/src/pymatgen/electronic_structure/dos.py @@ -8,23 +8,21 @@ import numpy as np from monty.json import MSONable -from scipy.constants import value as _cd -from scipy.ndimage import gaussian_filter1d -from scipy.signal import hilbert - from pymatgen.core import Structure, get_el_sp from pymatgen.core.spectrum import Spectrum from pymatgen.electronic_structure.core import Orbital, OrbitalType, Spin from pymatgen.util.coord import get_linear_interpolated_value +from scipy.constants import value as _cd +from scipy.ndimage import gaussian_filter1d +from scipy.signal import hilbert if TYPE_CHECKING: from collections.abc import Mapping from numpy.typing import ArrayLike, NDArray - from typing_extensions import Self - from pymatgen.core.sites import PeriodicSite from pymatgen.util.typing import SpeciesLike, Tuple3Floats + from typing_extensions import Self class DOS(Spectrum): @@ -558,7 +556,7 @@ def get_fermi( for _ in range(precision): fermi_range = np.arange(-nstep, nstep + 1) * step + fermi calc_doping = np.array([self.get_doping(fermi_lvl, temperature) for fermi_lvl in fermi_range]) - relative_error = np.abs(calc_doping / concentration - 1.0) # type: ignore + relative_error = np.abs(calc_doping / concentration - 1.0) fermi = fermi_range[np.argmin(relative_error)] step /= 10.0 @@ -809,16 +807,12 @@ def get_band_filling( if elements: for idx, el in enumerate(elements): spd_dos = self.get_element_spd_dos(el)[band] - densities = ( - spd_dos.densities if idx == 0 else add_densities(densities, spd_dos.densities) # type: ignore - ) + densities = spd_dos.densities if idx == 0 else add_densities(densities, spd_dos.densities) dos = Dos(self.efermi, self.energies, densities) elif sites: for idx, site in enumerate(sites): spd_dos = self.get_site_spd_dos(site)[band] - densities = ( - spd_dos.densities if idx == 0 else add_densities(densities, spd_dos.densities) # type: ignore - ) + densities = spd_dos.densities if idx == 0 else add_densities(densities, spd_dos.densities) dos = Dos(self.efermi, self.energies, densities) else: dos = self.get_spd_dos()[band] @@ -1092,7 +1086,7 @@ def get_upper_band_edge( def get_dos_fp( self, - type: str = "summed_pdos", + type: str = "summed_pdos", # noqa: A002 binning: bool = True, min_e: float | None = None, max_e: float | None = None, @@ -1169,7 +1163,7 @@ class fingerprint(NamedTuple): dos_rebin = np.zeros(ener.shape) - for ii, e1, e2 in zip(range(len(ener)), ener_bounds[0:-1], ener_bounds[1:]): + for ii, e1, e2 in zip(range(len(ener)), ener_bounds[:-1], ener_bounds[1:]): inds = np.where((energies >= e1) & (energies < e2)) dos_rebin[ii] = np.sum(densities[inds]) if normalize: # scale DOS bins to make area under histogram equal 1 @@ -1283,9 +1277,7 @@ def as_dict(self) -> dict: for at in self.structure: dd = {} for orb, pdos in self.pdos[at].items(): - dd[str(orb)] = { - "densities": {str(int(spin)): list(dens) for spin, dens in pdos.items()} # type: ignore - } + dd[str(orb)] = {"densities": {str(int(spin)): list(dens) for spin, dens in pdos.items()}} dct["pdos"].append(dd) dct["atom_dos"] = {str(at): dos.as_dict() for at, dos in self.get_element_dos().items()} dct["spd_dos"] = {str(orb): dos.as_dict() for orb, dos in self.get_spd_dos().items()} @@ -1298,7 +1290,7 @@ def __str__(self) -> str: class LobsterCompleteDos(CompleteDos): """Extended CompleteDOS for Lobster.""" - def get_site_orbital_dos(self, site: PeriodicSite, orbital: str) -> Dos: # type: ignore + def get_site_orbital_dos(self, site: PeriodicSite, orbital: str) -> Dos: # type: ignore[override] """Get the Dos for a particular orbital of a particular site. Args: @@ -1312,7 +1304,7 @@ def get_site_orbital_dos(self, site: PeriodicSite, orbital: str) -> Dos: # type Returns: Dos containing densities of an orbital of a specific site. """ - if orbital[1:] not in [ + if orbital[1:] not in { "s", "p_y", "p_z", @@ -1329,9 +1321,9 @@ def get_site_orbital_dos(self, site: PeriodicSite, orbital: str) -> Dos: # type "f_xz^2", "f_z(x^2-y^2)", "f_x(x^2-3y^2)", - ]: + }: raise ValueError("orbital is not correct") - return Dos(self.efermi, self.energies, self.pdos[site][orbital]) # type: ignore + return Dos(self.efermi, self.energies, self.pdos[site][orbital]) # type: ignore[index] def get_site_t2g_eg_resolved_dos(self, site: PeriodicSite) -> dict[str, Dos]: """Get the t2g, eg projected DOS for a particular site. @@ -1358,7 +1350,7 @@ def get_site_t2g_eg_resolved_dos(self, site: PeriodicSite) -> dict[str, Dos]: "e_g": Dos(self.efermi, self.energies, functools.reduce(add_densities, eg_dos)), } - def get_spd_dos(self) -> dict[str, Dos]: # type: ignore + def get_spd_dos(self) -> dict[OrbitalType, Dos]: """Get orbital projected Dos. For example, if 3s and 4s are included in the basis of some element, they will be both summed in the orbital projected DOS. @@ -1367,6 +1359,7 @@ def get_spd_dos(self) -> dict[str, Dos]: # type: ignore dict of {orbital: Dos}, e.g. {"s": Dos object, ...} """ spd_dos = {} + orb = None for atom_dos in self.pdos.values(): for orb, pdos in atom_dos.items(): orbital_type = _get_orb_type_lobster(orb) @@ -1375,9 +1368,9 @@ def get_spd_dos(self) -> dict[str, Dos]: # type: ignore else: spd_dos[orbital_type] = add_densities(spd_dos[orbital_type], pdos) - return {orb: Dos(self.efermi, self.energies, densities) for orb, densities in spd_dos.items()} # type: ignore + return {orb: Dos(self.efermi, self.energies, densities) for orb, densities in spd_dos.items()} # type: ignore[misc] - def get_element_spd_dos(self, el: SpeciesLike) -> dict[str, Dos]: # type: ignore + def get_element_spd_dos(self, el: SpeciesLike) -> dict[OrbitalType, Dos]: """Get element and spd projected Dos. Args: @@ -1397,7 +1390,7 @@ def get_element_spd_dos(self, el: SpeciesLike) -> dict[str, Dos]: # type: ignor else: el_dos[orbital_type] = add_densities(el_dos[orbital_type], pdos) - return {orb: Dos(self.efermi, self.energies, densities) for orb, densities in el_dos.items()} # type: ignore + return {orb: Dos(self.efermi, self.energies, densities) for orb, densities in el_dos.items()} # type: ignore[misc] @classmethod def from_dict(cls, dct: dict) -> Self: diff --git a/pymatgen/electronic_structure/plotter.py b/src/pymatgen/electronic_structure/plotter.py similarity index 99% rename from pymatgen/electronic_structure/plotter.py rename to src/pymatgen/electronic_structure/plotter.py index 29dae3e718d..b11a7c264ad 100644 --- a/pymatgen/electronic_structure/plotter.py +++ b/src/pymatgen/electronic_structure/plotter.py @@ -20,7 +20,6 @@ from matplotlib.gridspec import GridSpec from monty.dev import requires from monty.json import jsanitize - from pymatgen.core import Element from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine from pymatgen.electronic_structure.boltztrap import BoltztrapError @@ -37,7 +36,6 @@ from typing import Literal from numpy.typing import ArrayLike - from pymatgen.electronic_structure.dos import CompleteDos, Dos logger = logging.getLogger(__name__) @@ -289,7 +287,7 @@ def _check_bs_kpath(self, band_structs: list[BandStructureSymmLine]) -> Literal[ # check obj type for bs in band_structs: if not isinstance(bs, BandStructureSymmLine): - raise ValueError( + raise TypeError( "BSPlotter only works with BandStructureSymmLine objects. " "A BandStructure object (on a uniform grid for instance and " "not along symmetry lines won't work)" @@ -1290,7 +1288,7 @@ def _get_projections_by_branches_patom_pmorb(self, dictio, dictpa, sum_atoms, su raise ValueError("The 'selected_branches' is empty. We cannot do anything.") for index in selected_branches: if not isinstance(index, int): - raise ValueError( + raise TypeError( "You do not give a correct type of index of symmetry lines. It should be 'int' type" ) if index > n_branches or index < 1: @@ -1777,7 +1775,7 @@ def _Orbitals_SumOrbitals(cls, dictio, sum_morbs): raise ValueError(f"The dictio[{elt}] is empty. We cannot do anything") for orb in dictio[elt]: if not isinstance(orb, str): - raise ValueError( + raise TypeError( f"The invalid format of orbitals is in 'dictio[{elt}]': {orb}. They should be string." ) if orb not in all_orbitals: @@ -1902,8 +1900,8 @@ def _number_of_subfigures(self, dictio, dictpa, sum_atoms, sum_morbs): raise ValueError(f"The dictpa[{elt}] is empty. We cannot do anything") _sites = self._bs.structure.sites indices = [] - for site_idx in range(len(_sites)): - if next(iter(_sites[site_idx]._species)) == Element(elt): + for site_idx, site in enumerate(_sites): + if next(iter(site._species)) == Element(elt): indices.append(site_idx + 1) for number in dictpa[elt]: if isinstance(number, str): @@ -1917,7 +1915,7 @@ def _number_of_subfigures(self, dictio, dictpa, sum_atoms, sum_morbs): if number not in indices: raise ValueError(f"You put wrong site numbers in 'dictpa[{elt}]': {number}.") else: - raise ValueError(f"You put wrong site numbers in 'dictpa[{elt}]': {number}.") + raise TypeError(f"You put wrong site numbers in 'dictpa[{elt}]': {number}.") nelems = Counter(dictpa[elt]).values() if sum(nelems) > len(nelems): raise ValueError(f"You put at least two similar site numbers into 'dictpa[{elt}]'.") @@ -1949,8 +1947,8 @@ def _number_of_subfigures(self, dictio, dictpa, sum_atoms, sum_morbs): raise ValueError(f"The sum_atoms[{elt}] is empty. We cannot do anything") _sites = self._bs.structure.sites indices = [] - for site_idx in range(len(_sites)): - if next(iter(_sites[site_idx]._species)) == Element(elt): + for site_idx, site in enumerate(_sites): + if next(iter(site._species)) == Element(elt): indices.append(site_idx + 1) for number in sum_atoms[elt]: if isinstance(number, str): @@ -1968,7 +1966,8 @@ def _number_of_subfigures(self, dictio, dictpa, sum_atoms, sum_morbs): f"mentioned in dicpta[{elt}]" ) else: - raise ValueError(f"You put wrong site numbers in 'sum_atoms[{elt}]'.") + raise TypeError(f"You put wrong site numbers in 'sum_atoms[{elt}]'.") + nelems = Counter(sum_atoms[elt]).values() if sum(nelems) > len(nelems): raise ValueError(f"You put at least two similar site numbers into 'sum_atoms[{elt}]'.") @@ -2363,7 +2362,7 @@ def get_plot( left_kpoint = bs.kpoints[branch["start_index"]].cart_coords right_kpoint = bs.kpoints[branch["end_index"]].cart_coords distance = np.linalg.norm(right_kpoint - left_kpoint) - xlabel_distances.append(xlabel_distances[-1] + distance) # type: ignore + xlabel_distances.append(xlabel_distances[-1] + distance) # add x-coordinates for kpoint data npts = branch["end_index"] - branch["start_index"] @@ -2411,7 +2410,7 @@ def get_plot( band_energies[spin] = [] for band in bs.bands[spin]: band = cast(list[float], band) - band_energies[spin].append([e - bs.efermi for e in band]) # type: ignore + band_energies[spin].append([e - bs.efermi for e in band]) # type: ignore[arg-type] # renormalize the DOS energies to Fermi level dos_energies = [e - dos.efermi for e in dos.energies] if dos else [] @@ -2446,7 +2445,7 @@ def get_plot( if spin in dos.densities: # plot the total DOS dos_densities = dos.densities[spin] * int(spin) - label = "total" if spin == Spin.up else None + label: str | None = "total" if spin == Spin.up else None dos_ax.plot(dos_densities, dos_energies, color=(0.6, 0.6, 0.6), label=label) dos_ax.fill_betweenx( dos_energies, @@ -2480,7 +2479,7 @@ def get_plot( for idx, orb in enumerate([OrbitalType.s, OrbitalType.p, OrbitalType.d, OrbitalType.f]): if orb in spd_dos: dos_densities = spd_dos[orb].densities[spin] * int(spin) - label = orb if spin == Spin.up else None # type: ignore + label = orb if spin == Spin.up else None # type: ignore[assignment] dos_ax.plot( dos_densities, dos_energies, @@ -2671,7 +2670,7 @@ def _cmyk_triangle(ax, c_label, m_label, y_label, k_label, loc) -> None: inset_ax.set_ylim([-0.35, 1.00]) # add the labels - common = dict(fontsize=13, family="Times New Roman") + common = {"fontsize": 13, "family": "Times New Roman"} inset_ax.text(0.70, -0.2, m_label, **common, color=(0, 0, 0), horizontalalignment="left") inset_ax.text(0.325, 0.70, c_label, **common, color=(0, 0, 0), horizontalalignment="center") inset_ax.text(-0.05, -0.2, y_label, **common, color=(0, 0, 0), horizontalalignment="right") diff --git a/pymatgen/entries/MITCompatibility.yaml b/src/pymatgen/entries/MITCompatibility.yaml similarity index 100% rename from pymatgen/entries/MITCompatibility.yaml rename to src/pymatgen/entries/MITCompatibility.yaml diff --git a/pymatgen/entries/MP2020Compatibility.yaml b/src/pymatgen/entries/MP2020Compatibility.yaml similarity index 100% rename from pymatgen/entries/MP2020Compatibility.yaml rename to src/pymatgen/entries/MP2020Compatibility.yaml diff --git a/pymatgen/entries/MPCompatibility.yaml b/src/pymatgen/entries/MPCompatibility.yaml similarity index 100% rename from pymatgen/entries/MPCompatibility.yaml rename to src/pymatgen/entries/MPCompatibility.yaml diff --git a/pymatgen/entries/__init__.py b/src/pymatgen/entries/__init__.py similarity index 99% rename from pymatgen/entries/__init__.py rename to src/pymatgen/entries/__init__.py index 51e6d6cee5a..fd0471b8416 100644 --- a/pymatgen/entries/__init__.py +++ b/src/pymatgen/entries/__init__.py @@ -12,7 +12,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.core.composition import Composition if TYPE_CHECKING: diff --git a/pymatgen/entries/calc_compounds.json.gz b/src/pymatgen/entries/calc_compounds.json.gz similarity index 100% rename from pymatgen/entries/calc_compounds.json.gz rename to src/pymatgen/entries/calc_compounds.json.gz diff --git a/pymatgen/entries/compatibility.py b/src/pymatgen/entries/compatibility.py similarity index 99% rename from pymatgen/entries/compatibility.py rename to src/pymatgen/entries/compatibility.py index fcfc8982d51..ba2ef68dd07 100644 --- a/pymatgen/entries/compatibility.py +++ b/src/pymatgen/entries/compatibility.py @@ -9,15 +9,12 @@ import os import warnings from collections import defaultdict -from typing import TYPE_CHECKING, Union +from typing import TYPE_CHECKING, Union, cast import numpy as np from monty.design_patterns import cached_class from monty.json import MSONable from monty.serialization import loadfn -from tqdm import tqdm -from uncertainties import ufloat - from pymatgen.analysis.structure_analyzer import oxide_type, sulfide_type from pymatgen.core import SETTINGS, Composition, Element from pymatgen.entries.computed_entries import ( @@ -30,6 +27,8 @@ ) from pymatgen.io.vasp.sets import MITRelaxSet, MPRelaxSet, VaspInputSet from pymatgen.util.due import Doi, due +from tqdm import tqdm +from uncertainties import ufloat if TYPE_CHECKING: from collections.abc import Sequence @@ -306,7 +305,7 @@ def get_correction(self, entry) -> ufloat: correction += ox_corr * comp["O"] elif hasattr(entry, "structure"): - ox_type, n_bonds = oxide_type(entry.structure, 1.05, return_nbonds=True) # type: ignore + ox_type, n_bonds = cast(tuple[str, int], oxide_type(entry.structure, 1.05, return_nbonds=True)) if ox_type in self.oxide_correction: correction += self.oxide_correction[ox_type] * n_bonds elif ox_type == "hydroxide": @@ -603,7 +602,7 @@ def process_entries( adjustments = self.get_adjustments(entry) except CompatibilityError as exc: if on_error == "raise": - raise exc + raise if on_error == "warn": warnings.warn(str(exc)) continue diff --git a/pymatgen/entries/computed_entries.py b/src/pymatgen/entries/computed_entries.py similarity index 97% rename from pymatgen/entries/computed_entries.py rename to src/pymatgen/entries/computed_entries.py index 494619d1caa..b80a45f8b29 100644 --- a/pymatgen/entries/computed_entries.py +++ b/src/pymatgen/entries/computed_entries.py @@ -17,19 +17,17 @@ import numpy as np from monty.json import MontyDecoder, MontyEncoder, MSONable -from scipy.interpolate import interp1d -from uncertainties import ufloat - from pymatgen.core.composition import Composition from pymatgen.entries import Entry from pymatgen.util.due import Doi, due +from scipy.interpolate import interp1d +from uncertainties import ufloat if TYPE_CHECKING: from typing import Literal - from typing_extensions import Self - from pymatgen.core import Structure + from typing_extensions import Self __author__ = "Ryan Kingsbury, Matt McDermott, Shyue Ping Ong, Anubhav Jain" __copyright__ = "Copyright 2011-2020, The Materials Project" @@ -482,27 +480,26 @@ def from_dict(cls, dct: dict) -> Self: Returns: ComputedEntry """ - # the first block here is for legacy ComputedEntry that were - # serialized before we had the energy_adjustments attribute. - if dct["correction"] != 0 and not dct.get("energy_adjustments"): - return cls( - dct["composition"], - dct["energy"], - dct["correction"], - parameters={k: MontyDecoder().process_decoded(v) for k, v in dct.get("parameters", {}).items()}, - data={k: MontyDecoder().process_decoded(v) for k, v in dct.get("data", {}).items()}, - entry_id=dct.get("entry_id"), - ) + # Must handle cases where some kwargs exist in `dct` but are None + # include extra logic to ensure these get properly treated + energy_adj = [MontyDecoder().process_decoded(e) for e in (dct.get("energy_adjustments", []) or [])] + # this is the preferred / modern way of instantiating ComputedEntry # we don't pass correction explicitly because it will be calculated # on the fly from energy_adjustments + correction = 0 + if dct["correction"] != 0 and len(energy_adj) == 0: + # this block is for legacy ComputedEntry that were + # serialized before we had the energy_adjustments attribute. + correction = dct["correction"] + return cls( dct["composition"], dct["energy"], - correction=0, - energy_adjustments=[MontyDecoder().process_decoded(e) for e in dct.get("energy_adjustments", {})], - parameters={k: MontyDecoder().process_decoded(v) for k, v in dct.get("parameters", {}).items()}, - data={k: MontyDecoder().process_decoded(v) for k, v in dct.get("data", {}).items()}, + correction=correction, + energy_adjustments=energy_adj, + parameters={k: MontyDecoder().process_decoded(v) for k, v in (dct.get("parameters", {}) or {}).items()}, + data={k: MontyDecoder().process_decoded(v) for k, v in (dct.get("data", {}) or {}).items()}, entry_id=dct.get("entry_id"), ) diff --git a/pymatgen/entries/correction_calculator.py b/src/pymatgen/entries/correction_calculator.py similarity index 99% rename from pymatgen/entries/correction_calculator.py rename to src/pymatgen/entries/correction_calculator.py index 153c71a4b59..778c3885752 100644 --- a/pymatgen/entries/correction_calculator.py +++ b/src/pymatgen/entries/correction_calculator.py @@ -10,12 +10,11 @@ import numpy as np import plotly.graph_objects as go from monty.serialization import loadfn -from ruamel import yaml -from scipy.optimize import curve_fit - from pymatgen.analysis.reaction_calculator import ComputedReaction from pymatgen.analysis.structure_analyzer import sulfide_type from pymatgen.core import Composition, Element +from ruamel import yaml +from scipy.optimize import curve_fit class CorrectionCalculator: @@ -359,7 +358,7 @@ def graph_residual_error_per_species(self, specie: str) -> go.Figure: return fig - def make_yaml(self, name: str = "MP2020", dir: str | None = None) -> None: + def make_yaml(self, name: str = "MP2020", dir: str | None = None) -> None: # noqa: A002 """Create the _name_Compatibility.yaml that stores corrections as well as _name_CompatibilityUncertainties.yaml for correction uncertainties. diff --git a/pymatgen/entries/data/g_els.json b/src/pymatgen/entries/data/g_els.json similarity index 100% rename from pymatgen/entries/data/g_els.json rename to src/pymatgen/entries/data/g_els.json diff --git a/pymatgen/entries/data/nist_gas_gf.json b/src/pymatgen/entries/data/nist_gas_gf.json similarity index 100% rename from pymatgen/entries/data/nist_gas_gf.json rename to src/pymatgen/entries/data/nist_gas_gf.json diff --git a/pymatgen/entries/entry_tools.py b/src/pymatgen/entries/entry_tools.py similarity index 97% rename from pymatgen/entries/entry_tools.py rename to src/pymatgen/entries/entry_tools.py index da2903f0d20..fc6eb821891 100644 --- a/pymatgen/entries/entry_tools.py +++ b/src/pymatgen/entries/entry_tools.py @@ -16,7 +16,6 @@ from typing import TYPE_CHECKING from monty.json import MontyDecoder, MontyEncoder, MSONable - from pymatgen.analysis.phase_diagram import PDEntry from pymatgen.analysis.structure_matcher import SpeciesComparator, StructureMatcher from pymatgen.core import Composition, Element @@ -25,10 +24,9 @@ from collections.abc import Iterable from typing import Literal - from typing_extensions import Self - from pymatgen.entries import Entry from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry + from typing_extensions import Self logger = logging.getLogger(__name__) @@ -112,7 +110,7 @@ def group_entries_by_structure( """ if comparator is None: comparator = SpeciesComparator() - start = datetime.datetime.now() + start = datetime.datetime.now(tz=datetime.timezone.utc) logger.info(f"Started at {start}") entries_host = [(entry, _get_host(entry.structure, species_to_remove)) for entry in entries] if ncpus: @@ -123,9 +121,9 @@ def group_entries_by_structure( logging.info(f"Using {ncpus} cpus") manager = mp.Manager() groups = manager.list() - with mp.Pool(ncpus) as p: + with mp.Pool(ncpus) as pool: # Parallel processing only supports Python primitives and not objects. - p.map( + pool.map( _perform_grouping, [ ( @@ -161,8 +159,8 @@ def group_entries_by_structure( entry_groups = [] for g in groups: entry_groups.append(json.loads(g, cls=MontyDecoder)) - logging.info(f"Finished at {datetime.datetime.now()}") - logging.info(f"Took {datetime.datetime.now() - start}") + logging.info(f"Finished at {datetime.datetime.now(tz=datetime.timezone.utc)}") + logging.info(f"Took {datetime.datetime.now(tz=datetime.timezone.utc) - start}") return entry_groups diff --git a/pymatgen/entries/exp_compounds.json.gz b/src/pymatgen/entries/exp_compounds.json.gz similarity index 100% rename from pymatgen/entries/exp_compounds.json.gz rename to src/pymatgen/entries/exp_compounds.json.gz diff --git a/pymatgen/entries/exp_entries.py b/src/pymatgen/entries/exp_entries.py similarity index 99% rename from pymatgen/entries/exp_entries.py rename to src/pymatgen/entries/exp_entries.py index e012ed7a9fb..78adad7a6ef 100644 --- a/pymatgen/entries/exp_entries.py +++ b/src/pymatgen/entries/exp_entries.py @@ -5,7 +5,6 @@ from typing import TYPE_CHECKING from monty.json import MSONable - from pymatgen.analysis.phase_diagram import PDEntry from pymatgen.analysis.thermochemistry import ThermoData from pymatgen.core.composition import Composition diff --git a/pymatgen/entries/mixing_scheme.py b/src/pymatgen/entries/mixing_scheme.py similarity index 99% rename from pymatgen/entries/mixing_scheme.py rename to src/pymatgen/entries/mixing_scheme.py index 8f8fb637ab5..8a4a50fb214 100644 --- a/pymatgen/entries/mixing_scheme.py +++ b/src/pymatgen/entries/mixing_scheme.py @@ -11,7 +11,6 @@ import numpy as np import pandas as pd - from pymatgen.analysis.phase_diagram import PhaseDiagram from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.entries.compatibility import ( diff --git a/pymatgen/ext/cod.py b/src/pymatgen/ext/cod.py similarity index 98% rename from pymatgen/ext/cod.py rename to src/pymatgen/ext/cod.py index e695a56a4d7..0bc9966c2dc 100644 --- a/pymatgen/ext/cod.py +++ b/src/pymatgen/ext/cod.py @@ -34,7 +34,6 @@ import requests from monty.dev import requires - from pymatgen.core.composition import Composition from pymatgen.core.structure import Structure @@ -76,7 +75,7 @@ def get_cod_ids(self, formula) -> list[int]: cod_ids = [] for line in text: if match := re.search(r"(\d+)", line): - cod_ids.append(int(match.group(1))) + cod_ids.append(int(match[1])) return cod_ids def get_structure_by_id(self, cod_id: int, timeout: int = 600, **kwargs) -> Structure: diff --git a/pymatgen/ext/matproj.py b/src/pymatgen/ext/matproj.py similarity index 99% rename from pymatgen/ext/matproj.py rename to src/pymatgen/ext/matproj.py index 79654f68da9..71a4cff7a7a 100644 --- a/pymatgen/ext/matproj.py +++ b/src/pymatgen/ext/matproj.py @@ -20,7 +20,6 @@ import requests from monty.json import MontyDecoder - from pymatgen.core import SETTINGS from pymatgen.core import __version__ as PMG_VERSION from pymatgen.symmetry.analyzer import SpacegroupAnalyzer @@ -29,11 +28,10 @@ from typing import Callable from mp_api.client import MPRester as _MPResterNew - from typing_extensions import Self - from pymatgen.core.structure import Structure from pymatgen.entries.computed_entries import ComputedStructureEntry from pymatgen.ext.matproj_legacy import _MPResterLegacy + from typing_extensions import Self logger = logging.getLogger(__name__) @@ -229,7 +227,7 @@ def get_structure_by_material_id(self, material_id: str, conventional_unit_cell: Structure object. """ prop = "structure" - response = self.request(f"materials/summary/{material_id}/?_fields={prop}") + response = self.request(f"materials/summary?material_ids={material_id}&_fields={prop}") structure = response[0][prop] if conventional_unit_cell: return SpacegroupAnalyzer(structure).get_conventional_standard_structure() @@ -253,7 +251,7 @@ def get_initial_structures_by_material_id( response = self.request(f"materials/summary/{material_id}/?_fields={prop}") structures = response[0][prop] if conventional_unit_cell: - return [SpacegroupAnalyzer(s).get_conventional_standard_structure() for s in structures] # type: ignore + return [SpacegroupAnalyzer(s).get_conventional_standard_structure() for s in structures] return structures def get_entries( diff --git a/pymatgen/ext/matproj_legacy.py b/src/pymatgen/ext/matproj_legacy.py similarity index 99% rename from pymatgen/ext/matproj_legacy.py rename to src/pymatgen/ext/matproj_legacy.py index 62fc26dd9b0..ff3ea075ec3 100644 --- a/pymatgen/ext/matproj_legacy.py +++ b/src/pymatgen/ext/matproj_legacy.py @@ -20,9 +20,6 @@ import requests from monty.json import MontyDecoder, MontyEncoder -from ruamel.yaml import YAML -from tqdm import tqdm - from pymatgen.core import SETTINGS, Composition, Element, Structure from pymatgen.core import __version__ as PMG_VERSION from pymatgen.core.surface import get_symmetrically_equivalent_miller_indices @@ -31,15 +28,16 @@ from pymatgen.entries.exp_entries import ExpEntry from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.due import Doi, due +from ruamel.yaml import YAML +from tqdm import tqdm if TYPE_CHECKING: from collections.abc import Sequence from typing import Any, Literal - from typing_extensions import Self - from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine from pymatgen.phonon.dos import CompletePhononDos + from typing_extensions import Self logger = logging.getLogger(__name__) MP_LOG_FILE = os.path.join(os.path.expanduser("~"), ".mprester.log.yaml") @@ -1014,8 +1012,8 @@ def query( break except MPRestError as exc: if match := re.search(r"error status code (\d+)", str(exc)): - if not match.group(1).startswith("5"): - raise exc + if not match[1].startswith("5"): + raise n_tries += 1 print( "Unknown server error. Trying again in five " @@ -1606,7 +1604,7 @@ def parse_sym(sym): return [el.symbol for el in Element] if match := re.match(r"\{(.*)\}", sym): - return [s.strip() for s in match.group(1).split(",")] + return [s.strip() for s in match[1].split(",")] return [sym] def parse_tok(t): diff --git a/pymatgen/ext/optimade.py b/src/pymatgen/ext/optimade.py similarity index 98% rename from pymatgen/ext/optimade.py rename to src/pymatgen/ext/optimade.py index 6fbd1d18a05..fa7e9fb3d3c 100644 --- a/pymatgen/ext/optimade.py +++ b/src/pymatgen/ext/optimade.py @@ -8,11 +8,10 @@ from urllib.parse import urljoin, urlparse import requests -from tqdm import tqdm - from pymatgen.core import DummySpecies, Structure from pymatgen.util.due import Doi, due from pymatgen.util.provenance import StructureNL +from tqdm import tqdm if TYPE_CHECKING: from typing import ClassVar @@ -356,10 +355,10 @@ def get_snls_with_filter( if structures: all_snls[identifier] = structures - except Exception as exc: + except Exception: # TODO: manually inspect failures to either (a) correct a bug or (b) raise more appropriate error - _logger.error(f"Could not retrieve required information from provider {identifier} and {url=}: {exc}") + _logger.exception(f"Could not retrieve required information from provider {identifier} and {url=}") return all_snls @@ -520,8 +519,8 @@ def _parse_provider(self, provider: str, provider_url: str) -> dict[str, Provide try: url = urljoin(provider_url, "v1/links") provider_link_json = self._get_json(url) - except Exception as exc: - _logger.error(f"Failed to parse {url} when following links: {exc}") + except Exception: + _logger.exception(f"Failed to parse {url} when following links") return {} def _parse_provider_link(provider, provider_link_json): diff --git a/pymatgen/io/abinit/__init__.py b/src/pymatgen/io/abinit/__init__.py similarity index 100% rename from pymatgen/io/abinit/__init__.py rename to src/pymatgen/io/abinit/__init__.py diff --git a/pymatgen/io/abinit/abiobjects.py b/src/pymatgen/io/abinit/abiobjects.py similarity index 96% rename from pymatgen/io/abinit/abiobjects.py rename to src/pymatgen/io/abinit/abiobjects.py index 4e6a8d1d4f7..b7733a58db2 100644 --- a/pymatgen/io/abinit/abiobjects.py +++ b/src/pymatgen/io/abinit/abiobjects.py @@ -284,7 +284,7 @@ def structure_to_abivars( def contract(string): """ assert contract("1 1 1 2 2 3") == "3*1 2*2 1*3" - assert contract("1 1 3 2 3") == "2*1 1*3 1*2 1*3" + assert contract("1 1 3 2 3") == "2*1 1*3 1*2 1*3". """ if not string: return string @@ -304,9 +304,7 @@ def contract(string): class AbivarAble(abc.ABC): - """ - An AbivarAble object provides a method to_abivars that returns a dictionary with the abinit variables. - """ + """An AbivarAble object provides a method to_abivars that returns a dictionary with the abinit variables.""" @abc.abstractmethod def to_abivars(self) -> dict: @@ -403,14 +401,14 @@ class Smearing(AbivarAble, MSONable): """ # Map string_mode to occopt - _mode2occopt: ClassVar[dict[str, int]] = dict( - nosmearing=1, - fermi_dirac=3, - marzari4=4, - marzari5=5, - methfessel=6, - gaussian=7, - ) + _mode2occopt: ClassVar[dict[str, int]] = { + "nosmearing": 1, + "fermi_dirac": 3, + "marzari4": 4, + "marzari5": 5, + "methfessel": 6, + "gaussian": 7, + } def __init__(self, occopt: int, tsmear: float): """ @@ -509,18 +507,18 @@ class ElectronsAlgorithm(dict, AbivarAble, MSONable): """Variables controlling the SCF/NSCF algorithm.""" # None indicates that we use abinit defaults - _DEFAULT: ClassVar[dict[str, int | None]] = dict( - iprcell=None, - iscf=None, - diemac=None, - diemix=None, - diemixmag=None, - dielam=None, - diegap=None, - dielng=None, - diecut=None, - nstep=50, - ) + _DEFAULT: ClassVar[dict[str, int | None]] = { + "iprcell": None, + "iscf": None, + "diemac": None, + "diemix": None, + "diemixmag": None, + "dielam": None, + "diegap": None, + "dielng": None, + "diecut": None, + "nstep": 50, + } def __init__(self, *args, **kwargs): """ @@ -1036,17 +1034,17 @@ class RelaxationMethod(AbivarAble, MSONable): The set of variables are constructed in to_abivars depending on ionmov and optcell. """ - _default_vars: ClassVar[dict[str, Any]] = dict( - ionmov=MANDATORY, - optcell=MANDATORY, - ntime=80, - dilatmx=1.05, - ecutsm=0.5, - strfact=None, - tolmxf=None, - strtarget=None, - atoms_constraints={}, # Constraints are stored in a dictionary. {} means if no constraint is enforced. - ) + _default_vars: ClassVar[dict[str, Any]] = { + "ionmov": MANDATORY, + "optcell": MANDATORY, + "ntime": 80, + "dilatmx": 1.05, + "ecutsm": 0.5, + "strfact": None, + "tolmxf": None, + "strtarget": None, + "atoms_constraints": {}, # Constraints are stored in a dictionary. {} means if no constraint is enforced. + } IONMOV_DEFAULT = 3 OPTCELL_DEFAULT = 2 @@ -1338,14 +1336,14 @@ class Screening(AbivarAble): """ # Approximations used for W - _WTYPES: ClassVar[dict[str, int]] = dict(RPA=0) + _WTYPES: ClassVar[dict[str, int]] = {"RPA": 0} # Self-consistency modes - _SC_MODES: ClassVar[dict[str, int]] = dict( - one_shot=0, - energy_only=1, - wavefunctions=2, - ) + _SC_MODES: ClassVar[dict[str, int]] = { + "one_shot": 0, + "energy_only": 1, + "wavefunctions": 2, + } def __init__( self, @@ -1429,20 +1427,20 @@ def to_abivars(self): class SelfEnergy(AbivarAble): """Define the parameters used for the computation of the self-energy.""" - _SIGMA_TYPES: ClassVar[dict[str, int]] = dict( - gw=0, - hartree_fock=5, - sex=6, - cohsex=7, - model_gw_ppm=8, - model_gw_cd=9, - ) + _SIGMA_TYPES: ClassVar[dict[str, int]] = { + "gw": 0, + "hartree_fock": 5, + "sex": 6, + "cohsex": 7, + "model_gw_ppm": 8, + "model_gw_cd": 9, + } - _SC_MODES: ClassVar[dict[str, int]] = dict( - one_shot=0, - energy_only=1, - wavefunctions=2, - ) + _SC_MODES: ClassVar[dict[str, int]] = { + "one_shot": 0, + "energy_only": 1, + "wavefunctions": 2, + } def __init__( self, @@ -1554,7 +1552,7 @@ def to_abivars(self): # ppmodel variables if self.use_ppmodel: - abivars.update(self.ppmodel.to_abivars()) + abivars |= self.ppmodel.to_abivars() return abivars @@ -1563,18 +1561,18 @@ class ExcHamiltonian(AbivarAble): """Contain parameters for the solution of the Bethe-Salpeter equation.""" # Types of excitonic Hamiltonian. - _EXC_TYPES: ClassVar[dict[str, int]] = dict( - TDA=0, # Tamm-Dancoff approximation. - coupling=1, # Calculation with coupling. - ) + _EXC_TYPES: ClassVar[dict[str, int]] = { + "TDA": 0, # Tamm-Dancoff approximation. + "coupling": 1, # Calculation with coupling. + } # Algorithms used to compute the macroscopic dielectric function # and/or the exciton wavefunctions. - _ALGO2VAR: ClassVar[dict[str, int]] = dict( - direct_diago=1, - haydock=2, - cg=3, - ) + _ALGO2VAR: ClassVar[dict[str, int]] = { + "direct_diago": 1, + "haydock": 2, + "cg": 3, + } # Options specifying the treatment of the Coulomb term. _COULOMB_MODES = ("diago", "full", "model_df") diff --git a/pymatgen/io/abinit/abitimer.py b/src/pymatgen/io/abinit/abitimer.py similarity index 99% rename from pymatgen/io/abinit/abitimer.py rename to src/pymatgen/io/abinit/abitimer.py index 258a7b53a52..daf0f6cdbd1 100644 --- a/pymatgen/io/abinit/abitimer.py +++ b/src/pymatgen/io/abinit/abitimer.py @@ -14,7 +14,6 @@ import numpy as np import pandas as pd from matplotlib.gridspec import GridSpec - from typing import TYPE_CHECKING from monty.string import is_string, list_strings from pymatgen.io.core import ParseError @@ -302,7 +301,6 @@ def pefficiency(self) -> ParallelEfficiency: def summarize(self, **kwargs) -> pd.DataFrame: """Return pandas DataFrame with the most important results stored in the timers.""" - col_names = ["fname", "wall_time", "cpu_time", "mpi_nprocs", "omp_nthreads", "mpi_rank"] frame = pd.DataFrame(columns=col_names) @@ -656,11 +654,8 @@ def ncpus(self) -> int: return self.mpi_nprocs * self.omp_nthreads def get_section(self, section_name: str): - """Return the section associated to `section_name`.""" - try: - idx = self.section_names.index(section_name) - except Exception: - raise + """Return section associated to `section_name`.""" + idx = self.section_names.index(section_name) sect = self.sections[idx] assert sect.name == section_name return sect @@ -698,7 +693,6 @@ def to_table(self, sort_key="wall_time", stop=None) -> list[list[str]]: def get_dataframe(self, sort_key="wall_time", **kwargs) -> pd.DataFrame: """Return a pandas DataFrame with entries sorted according to `sort_key`.""" - frame = pd.DataFrame(columns=AbinitTimerSection.FIELDS) for osect in self.order_sections(sort_key): @@ -725,7 +719,7 @@ def get_values(self, keys): values.append([sec.__dict__[key] for sec in self.sections]) return values - def names_and_values(self, key, minval=None, minfract=None, sorted=True): + def names_and_values(self, key, minval=None, minfract=None, sorted=True): # noqa: A002 """Select the entries whose value[key] is >= minval or whose fraction[key] is >= minfract Return the names of the sections and the corresponding values. """ diff --git a/pymatgen/io/abinit/inputs.py b/src/pymatgen/io/abinit/inputs.py similarity index 99% rename from pymatgen/io/abinit/inputs.py rename to src/pymatgen/io/abinit/inputs.py index cce399da66e..1382f819d7a 100644 --- a/pymatgen/io/abinit/inputs.py +++ b/src/pymatgen/io/abinit/inputs.py @@ -18,7 +18,6 @@ import numpy as np from monty.collections import AttrDict from monty.json import MSONable - from pymatgen.core.structure import Structure from pymatgen.io.abinit import abiobjects as aobj from pymatgen.io.abinit.pseudos import Pseudo, PseudoTable @@ -163,7 +162,6 @@ def from_object(cls, obj) -> Self: def _stopping_criterion(run_level, accuracy): """Return the stopping criterion for this run_level with the given accuracy.""" - # Name of the (default) tolerance used by the run levels. _run_level_tolname_map = { "scf": "tolvrs", @@ -1097,7 +1095,7 @@ def from_inputs(cls, inputs: list[BasicAbinitInput]) -> Self: return multi @classmethod - def replicate_input(cls, input, ndtset): + def replicate_input(cls, input, ndtset): # noqa: A002 """Construct a multidataset with ndtset from the BasicAbinitInput input.""" multi = cls(input.structure, input.pseudos, ndtset=ndtset) diff --git a/pymatgen/io/abinit/netcdf.py b/src/pymatgen/io/abinit/netcdf.py similarity index 95% rename from pymatgen/io/abinit/netcdf.py rename to src/pymatgen/io/abinit/netcdf.py index b2c453f5dff..9ddf82eb097 100644 --- a/pymatgen/io/abinit/netcdf.py +++ b/src/pymatgen/io/abinit/netcdf.py @@ -1,5 +1,3 @@ -# - """Wrapper for netCDF readers.""" from __future__ import annotations @@ -14,10 +12,10 @@ from monty.dev import requires from monty.functools import lazy_property from monty.string import marquee - -from pymatgen.core.units import ArrayWithUnit -#from pymatgen.core.xcfunc import XcFunc from pymatgen.core.structure import Structure +from pymatgen.core.units import ArrayWithUnit +from pymatgen.core.xcfunc import XcFunc +from pymatgen.electronic_structure.core import Magmom if TYPE_CHECKING: from typing_extensions import Self @@ -101,7 +99,7 @@ def __enter__(self) -> Self: """Activated when used in the with statement.""" return self - def __exit__(self, type, value, traceback): + def __exit__(self, type, value, traceback): # noqa: A002 """Activated at the end of the with statement. It automatically closes the file.""" self.rootgrp.close() @@ -322,9 +320,26 @@ def structure_from_ncdata(ncdata, site_properties=None, cls=None): znucl_type = ncdata.read_value("atomic_numbers") - # type_atom[0:natom] --> index Between 1 and number of atom species + # type_atom[:natom] --> index Between 1 and number of atom species type_atom = ncdata.read_value("atom_species") + try: + intgden = ncdata.read_value("intgden") + nspden = intgden.shape[1] + except NetcdfReaderError: + intgden = None + nspden = None + + if intgden is not None: + if nspden == 2: + magmoms = Magmom(intgden[:, 1] - intgden[:, 0]) + elif nspden == 4: + magmoms = [Magmom([intg_at[1], intg_at[2], intg_at[3]]) for intg_at in intgden] + else: + magmoms = None + else: + magmoms = None + # Fortran to C index and float --> int conversion. species = n_atom * [None] for atom in range(n_atom): @@ -336,6 +351,9 @@ def structure_from_ncdata(ncdata, site_properties=None, cls=None): for prop in site_properties: dct[prop] = ncdata.read_value(prop) + if magmoms is not None and "magmom" not in dct: + dct["magmom"] = magmoms + structure = cls(lattice, species, red_coords, site_properties=dct) # Quick and dirty hack. @@ -453,7 +471,7 @@ def __init__(self, name, doc, etsf_name=None): ), # _H(type(pawrhoij_type), allocatable :: pawrhoij(:) ! EVOLVING variable, only for paw ) -_HDR_VARIABLES = {h.name: h for h in _HDR_VARIABLES} # type: ignore +_HDR_VARIABLES = {h.name: h for h in _HDR_VARIABLES} # type: ignore[assignment] class AbinitHeader(AttrDict): diff --git a/pymatgen/io/abinit/pseudos.py b/src/pymatgen/io/abinit/pseudos.py similarity index 98% rename from pymatgen/io/abinit/pseudos.py rename to src/pymatgen/io/abinit/pseudos.py index 7dd1a3d4244..05bbb3a6454 100644 --- a/pymatgen/io/abinit/pseudos.py +++ b/src/pymatgen/io/abinit/pseudos.py @@ -26,12 +26,11 @@ from monty.itertools import iterator_from_slice from monty.json import MontyDecoder, MSONable from monty.os.path import find_exts -from tabulate import tabulate - from pymatgen.core import Element from pymatgen.core.xcfunc import XcFunc from pymatgen.io.core import ParseError from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig +from tabulate import tabulate if TYPE_CHECKING: from collections.abc import Iterator, Sequence @@ -138,7 +137,6 @@ def __str__(self) -> str: def to_str(self, verbose=0) -> str: """String representation.""" - lines: list[str] = [] lines += ( f"<{type(self).__name__}: {self.basename}>", @@ -307,13 +305,11 @@ def as_tmpfile(self, tmpdir=None): @property def has_dojo_report(self) -> bool: """True if the pseudo has an associated `DOJO_REPORT` section.""" - return hasattr(self, "dojo_report") and self.dojo_report @property def djrepo_path(self) -> str: """The path of the djrepo file. None if file does not exist.""" - root, _ext = os.path.splitext(self.filepath) return f"{root}.djrepo" # if os.path.isfile(path): return path @@ -327,7 +323,6 @@ def hint_for_accuracy(self, accuracy: str = "normal") -> Hint: Args: accuracy: ["low", "normal", "high"] """ - if not self.has_dojo_report: return Hint(ecut=0.0, pawecutdg=0.0) @@ -533,7 +528,6 @@ def Z(self): @property def Z_val(self): """Number of valence electrons.""" - return self._zion @property @@ -677,20 +671,20 @@ def _int_from_str(string: str) -> int: class NcAbinitHeader(AbinitHeader): """The abinit header found in the NC pseudopotential files.""" - _VARS: ClassVar[dict[str, tuple]] = dict( - zatom=(None, _int_from_str), - zion=(None, float), - pspdat=(None, float), - pspcod=(None, int), - pspxc=(None, int), - lmax=(None, int), - lloc=(None, int), - r2well=(None, float), - mmax=(None, float), - rchrg=(0.0, float), - fchrg=(0.0, float), - qchrg=(0.0, float), - ) + _VARS: ClassVar[dict[str, tuple]] = { + "zatom": (None, _int_from_str), + "zion": (None, float), + "pspdat": (None, float), + "pspcod": (None, int), + "pspxc": (None, int), + "lmax": (None, int), + "lloc": (None, int), + "r2well": (None, float), + "mmax": (None, float), + "rchrg": (0.0, float), + "fchrg": (0.0, float), + "qchrg": (0.0, float), + } def __init__(self, summary, **kwargs): super().__init__() @@ -868,26 +862,26 @@ def tm_header(filename, ppdesc) -> NcAbinitHeader: class PawAbinitHeader(AbinitHeader): """The abinit header found in the PAW pseudopotential files.""" - _VARS: ClassVar[dict[str, tuple]] = dict( - zatom=(None, _int_from_str), - zion=(None, float), - pspdat=(None, float), - pspcod=(None, int), - pspxc=(None, int), - lmax=(None, int), - lloc=(None, int), - mmax=(None, int), - r2well=(None, float), - pspfmt=(None, str), - creatorID=(None, int), - basis_size=(None, int), - lmn_size=(None, int), - orbitals=(None, list), - number_of_meshes=(None, int), - r_cut=(None, float), # r_cut(PAW) in the header - shape_type=(None, int), - rshape=(None, float), - ) + _VARS: ClassVar[dict[str, tuple]] = { + "zatom": (None, _int_from_str), + "zion": (None, float), + "pspdat": (None, float), + "pspcod": (None, int), + "pspxc": (None, int), + "lmax": (None, int), + "lloc": (None, int), + "mmax": (None, int), + "r2well": (None, float), + "pspfmt": (None, str), + "creatorID": (None, int), + "basis_size": (None, int), + "lmn_size": (None, int), + "orbitals": (None, list), + "number_of_meshes": (None, int), + "r_cut": (None, float), # r_cut(PAW) in the header + "shape_type": (None, int), + "rshape": (None, float), + } def __init__(self, summary, **kwargs): super().__init__() @@ -1096,8 +1090,8 @@ def read_ppdesc(self, filename: str): # Assume file with the abinit header. lines = _read_nlines(filename, 80) - for lineno, line in enumerate(lines, start=1): - if lineno == 3: + for lineno, line in enumerate(lines): + if lineno == 2: try: tokens = line.split() pspcod, _pspxc = map(int, tokens[:2]) @@ -1113,7 +1107,7 @@ def read_ppdesc(self, filename: str): if pspcod == 7: # PAW -> need to know the format pspfmt - tokens = lines[lineno].split() + tokens = lines[lineno + 1].split() pspfmt, _creatorID = tokens[:2] ppdesc = ppdesc._replace(format=pspfmt) @@ -1193,7 +1187,6 @@ def __init__(self, filepath: str): Args: filepath: path to pseudopotential file """ - self.path = os.path.abspath(filepath) # Get the XML root (this trick is used to that the object is pickleable). @@ -1336,7 +1329,6 @@ def _eval_grid(grid_params): def _parse_radfunc(self, func_name): """Parse the first occurrence of func_name in the XML file.""" - node = self.root.find(func_name) grid = node.attrib["grid"] values = np.array([float(s) for s in node.text.split()]) @@ -1345,7 +1337,6 @@ def _parse_radfunc(self, func_name): def _parse_all_radfuncs(self, func_name): """Parse all the nodes with tag func_name in the XML file.""" - for node in self.root.findall(func_name): grid = node.attrib["grid"] values = np.array([float(s) for s in node.text.split()]) @@ -1442,7 +1433,6 @@ def plot_waves(self, ax: plt.Axes = None, fontsize=8, **kwargs): Returns: plt.Figure: matplotlib figure """ - ax, fig = get_ax_fig(ax) ax.set_xlabel("r [Bohr]") @@ -1472,7 +1462,6 @@ def plot_projectors(self, ax: plt.Axes = None, fontsize=8, **kwargs): Returns: plt.Figure: matplotlib figure """ - ax, fig = get_ax_fig(ax) ax.grid(visible=True) ax.set_xlabel("r [Bohr]") diff --git a/pymatgen/io/abinit/variable.py b/src/pymatgen/io/abinit/variable.py similarity index 100% rename from pymatgen/io/abinit/variable.py rename to src/pymatgen/io/abinit/variable.py diff --git a/pymatgen/io/adf.py b/src/pymatgen/io/adf.py similarity index 94% rename from pymatgen/io/adf.py rename to src/pymatgen/io/adf.py index e302530505c..59a3d8bfabc 100644 --- a/pymatgen/io/adf.py +++ b/src/pymatgen/io/adf.py @@ -10,7 +10,6 @@ from monty.itertools import chunks from monty.json import MSONable from monty.serialization import zopen - from pymatgen.core.structure import Molecule if TYPE_CHECKING: @@ -93,7 +92,7 @@ def __init__(self, name, options=None, subkeys=None): if len(self.subkeys) > 0: for k in subkeys: if not isinstance(k, AdfKey): - raise ValueError("Not all subkeys are ``AdfKey`` objects!") + raise TypeError("Not all subkeys are ``AdfKey`` objects!") self._sized_op = None if len(self.options) > 0: self._sized_op = isinstance(self.options[0], (list, tuple)) @@ -168,7 +167,7 @@ def has_subkey(self, subkey: str | AdfKey) -> bool: elif isinstance(subkey, AdfKey): key = subkey.key else: - raise ValueError("The subkey should be an AdfKey or a string!") + raise TypeError("The subkey should be an AdfKey or a string!") return len(self.subkeys) > 0 and key in (k.key for k in self.subkeys) def add_subkey(self, subkey): @@ -193,8 +192,8 @@ def remove_subkey(self, subkey): """ if len(self.subkeys) > 0: key = subkey if isinstance(subkey, str) else subkey.key - for idx, subkey in enumerate(self.subkeys): - if subkey.key == key: + for idx, sk in enumerate(self.subkeys): + if sk.key == key: self.subkeys.pop(idx) break @@ -370,13 +369,13 @@ class AdfTask(MSONable): ADF does not support calculating force/gradient. """ - operations: ClassVar[dict[str, str]] = dict( - energy="Evaluate the single point energy.", - optimize="Minimize the energy by varying the molecular structure.", - frequencies="Compute second derivatives and print out an analysis of molecular vibrations.", - freq="Same as frequencies.", - numerical_frequencies="Compute molecular frequencies using numerical method.", - ) + operations: ClassVar[dict[str, str]] = { + "energy": "Evaluate the single point energy.", + "optimize": "Minimize the energy by varying the molecular structure.", + "frequencies": "Compute second derivatives and print out an analysis of molecular vibrations.", + "freq": "Same as frequencies.", + "numerical_frequencies": "Compute molecular frequencies using numerical method.", + } def __init__( self, @@ -474,7 +473,7 @@ def __str__(self): out += "\n" for block_key in self.other_directives: if not isinstance(block_key, AdfKey): - raise ValueError(f"{block_key} is not an AdfKey!") + raise TypeError(f"{block_key} is not an AdfKey!") out += str(block_key) + "\n" return out @@ -663,19 +662,19 @@ def _parse_logfile(self, logfile): for line in file: if match := error_patt.search(line): self.is_failed = True - self.error = match.group(1) + self.error = match[1] break if self.run_type is None: if match := run_type_patt.search(line): - if match.group(1) == "FREQUENCIES": + if match[1] == "FREQUENCIES": self.freq_type = "Numerical" self.run_type = "NumericalFreq" - elif match.group(1) == "GEOMETRY OPTIMIZATION": + elif match[1] == "GEOMETRY OPTIMIZATION": self.run_type = "GeometryOptimization" - elif match.group(1) == "CREATE": + elif match[1] == "CREATE": self.run_type = None - elif match.group(1) == "SINGLE POINT": + elif match[1] == "SINGLE POINT": self.run_type = "SinglePoint" else: raise AdfOutputError("Undefined Runtype!") @@ -684,12 +683,12 @@ def _parse_logfile(self, logfile): if match := coord_patt.search(line): sites.append([match.groups()[0], list(map(float, match.groups()[2:]))]) elif match := final_energy_patt.search(line): - self.final_energy = float(match.group(1)) + self.final_energy = float(match[1]) self.final_structure = self._sites_to_mol(sites) elif self.run_type == "GeometryOptimization": if match := cycle_patt.search(line): - cycle = int(match.group(1)) + cycle = int(match[1]) if cycle <= 0: raise AdfOutputError(f"Wrong {cycle=}") if cycle > last_cycle: @@ -701,14 +700,14 @@ def _parse_logfile(self, logfile): if match := coord_patt.search(line): sites.append([match.groups()[1], list(map(float, match.groups()[2:]))]) elif match := energy_patt.search(line): - self.energies.append(float(match.group(1))) + self.energies.append(float(match[1])) mol = self._sites_to_mol(sites) self.structures.append(mol) parse_cycle = False sites = [] elif parse_final: if match := final_energy_patt.search(line): - self.final_energy = float(match.group(1)) + self.final_energy = float(match[1]) elif self.run_type == "NumericalFreq": break @@ -759,7 +758,7 @@ def _parse_adf_output(self): if match := coord_on_patt.search(line): parse_coord = True elif match := coord_patt.search(line): - sites.append([match.group(2), list(map(float, match.groups()[2:5]))]) + sites.append([match[2], list(map(float, match.groups()[2:5]))]) n_strike += 1 elif n_strike > 0: find_structure = False @@ -789,12 +788,12 @@ def _parse_adf_output(self): self.normal_modes.append([]) elif parse_mode and (match := mode_patt.search(line)): - v = list(chunks(map(float, match.group(3).split()), 3)) + v = list(chunks(map(float, match[3].split()), 3)) if len(v) != n_next: raise AdfOutputError("Odd Error!") for i, k in enumerate(range(-n_next, 0)): self.normal_modes[k].extend(v[i]) - if int(match.group(1)) == n_atoms: + if int(match[1]) == n_atoms: parse_freq = True parse_mode = False if isinstance(self.final_structure, list): diff --git a/pymatgen/io/aims/__init__.py b/src/pymatgen/io/aims/__init__.py similarity index 100% rename from pymatgen/io/aims/__init__.py rename to src/pymatgen/io/aims/__init__.py diff --git a/pymatgen/io/aims/inputs.py b/src/pymatgen/io/aims/inputs.py similarity index 68% rename from pymatgen/io/aims/inputs.py rename to src/pymatgen/io/aims/inputs.py index fda6aba8a75..e03d0355f75 100644 --- a/pymatgen/io/aims/inputs.py +++ b/src/pymatgen/io/aims/inputs.py @@ -5,8 +5,8 @@ from __future__ import annotations -import gzip import os +import re import time from copy import deepcopy from dataclasses import dataclass, field @@ -16,16 +16,15 @@ import numpy as np from monty.io import zopen from monty.json import MontyDecoder, MSONable - -from pymatgen.core import Lattice, Molecule, Structure +from monty.os.path import zpath +from pymatgen.core import SETTINGS, Element, Lattice, Molecule, Structure if TYPE_CHECKING: from collections.abc import Sequence from typing import Any - from typing_extensions import Self - from pymatgen.util.typing import Tuple3Floats, Tuple3Ints + from typing_extensions import Self __author__ = "Thomas A. R. Purcell" __version__ = "1.0" @@ -35,7 +34,7 @@ @dataclass class AimsGeometryIn(MSONable): - """Representation of an aims geometry.in file + """Representation of an aims geometry.in file. Attributes: _content (str): The content of the input file @@ -48,7 +47,7 @@ class AimsGeometryIn(MSONable): @classmethod def from_str(cls, contents: str) -> Self: - """Create an input from the content of an input file + """Create an input from the content of an input file. Args: contents (str): The content of the file @@ -61,7 +60,7 @@ def from_str(cls, contents: str) -> Self: ] species, coords, is_frac, lattice_vectors = [], [], [], [] - charges_dct, moments_dct = {}, {} + charges_dct, moments_dct, velocities_dct = {}, {}, {} for line in content_lines: inp = line.split() @@ -75,6 +74,8 @@ def from_str(cls, contents: str) -> Self: moments_dct[len(coords) - 1] = float(inp[1]) if inp[0] == "initial_charge": charges_dct[len(coords) - 1] = float(inp[1]) + if inp[0] == "velocity": + velocities_dct[len(coords) - 1] = [float(x) for x in inp[1:]] charge = np.zeros(len(coords)) for key, val in charges_dct.items(): @@ -84,6 +85,10 @@ def from_str(cls, contents: str) -> Self: for key, val in moments_dct.items(): magmom[key] = val + velocity: list[None | list[float]] = [None for _ in coords] + for key, v in velocities_dct.items(): + velocity[key] = v + if len(lattice_vectors) == 3: lattice = Lattice(lattice_vectors) for cc in range(len(coords)): @@ -97,6 +102,9 @@ def from_str(cls, contents: str) -> Self: raise ValueError("Incorrect number of lattice vectors passed.") site_props = {"magmom": magmom, "charge": charge} + if velocities_dct: + site_props["velocity"] = velocity + if lattice is None: structure = Molecule(species, coords, np.sum(charge), site_properties=site_props) else: @@ -138,27 +146,31 @@ def from_structure(cls, structure: Structure | Molecule) -> Self: charges = structure.site_properties.get("charge", np.zeros(len(structure.species))) magmoms = structure.site_properties.get("magmom", np.zeros(len(structure.species))) - for species, coord, charge, magmom in zip(structure.species, structure.cart_coords, charges, magmoms): + velocities = structure.site_properties.get("velocity", [None for _ in structure.species]) + for species, coord, charge, magmom, v in zip( + structure.species, structure.cart_coords, charges, magmoms, velocities + ): content_lines.append(f"atom {coord[0]: .12e} {coord[1]: .12e} {coord[2]: .12e} {species}") if charge != 0: content_lines.append(f" initial_charge {charge:.12e}") if magmom != 0: content_lines.append(f" initial_moment {magmom:.12e}") - + if v is not None and any(v_i != 0.0 for v_i in v): + content_lines.append(f" velocity {' '.join([f'{v_i:.12e}' for v_i in v])}") return cls(_content="\n".join(content_lines), _structure=structure) @property def structure(self) -> Structure | Molecule: - """Access structure for the file""" + """Access structure for the file.""" return self._structure @property def content(self) -> str: - """Access the contents of the file""" + """Access the contents of the file.""" return self._content def write_file(self, directory: str | Path | None = None, overwrite: bool = False) -> None: - """Write the geometry.in file + """Write the geometry.in file. Args: directory (str | Path | None): The directory to write the geometry.in file @@ -233,7 +245,7 @@ def from_dict(cls, dct: dict[str, Any]) -> Self: @dataclass class AimsCube(MSONable): - """The FHI-aims cubes + """The FHI-aims cubes. Attributes: type (str): The value to be outputted as a cube file @@ -264,7 +276,7 @@ class AimsCube(MSONable): elf_type: int | None = None def __eq__(self, other: object) -> bool: - """Check if two cubes are equal to each other""" + """Check if two cubes are equal to each other.""" if not isinstance(other, AimsCube): return NotImplemented @@ -295,7 +307,7 @@ def __eq__(self, other: object) -> bool: return self.elf_type == other.elf_type def __post_init__(self) -> None: - """Check the inputted variables to make sure they are correct + """Check the inputted variables to make sure they are correct. Raises: ValueError: If any of the inputs is invalid @@ -336,7 +348,7 @@ def __post_init__(self) -> None: @property def control_block(self) -> str: - """The block of text for the control.in file of the Cube""" + """The block of text for the control.in file of the Cube.""" cb = f"output cube {self.type}\n" cb += f" cube origin {self.origin[0]: .12e} {self.origin[1]: .12e} {self.origin[2]: .12e}\n" for idx in range(3): @@ -400,11 +412,11 @@ class AimsControlIn(MSONable): _parameters: dict[str, Any] = field(default_factory=dict) def __post_init__(self) -> None: - """Initialize the output list of _parameters""" + """Initialize the output list of _parameters.""" self._parameters.setdefault("output", []) def __getitem__(self, key: str) -> Any: - """Get an input parameter + """Get an input parameter. Args: key (str): The parameter to get @@ -420,7 +432,7 @@ def __getitem__(self, key: str) -> Any: return self._parameters[key] def __setitem__(self, key: str, value: Any) -> None: - """Set an attribute of the class + """Set an attribute of the class. Args: key (str): The parameter to get @@ -434,7 +446,7 @@ def __setitem__(self, key: str, value: Any) -> None: self._parameters[key] = value def __delitem__(self, key: str) -> Any: - """Delete a parameter from the input object + """Delete a parameter from the input object. Args: key (str): The key in the parameter to remove @@ -447,12 +459,12 @@ def __delitem__(self, key: str) -> Any: @property def parameters(self) -> dict[str, Any]: - """The dictionary of input parameters for control.in""" + """The dictionary of input parameters for control.in.""" return self._parameters @parameters.setter def parameters(self, parameters: dict[str, Any]) -> None: - """Reset a control.in inputs from a parameters dictionary + """Reset a control.in inputs from a parameters dictionary. Args: parameters (dict[str, Any]): The new set of parameters to use @@ -461,7 +473,7 @@ def parameters(self, parameters: dict[str, Any]) -> None: self._parameters.setdefault("output", []) def get_aims_control_parameter_str(self, key: str, value: Any, fmt: str) -> str: - """Get the string needed to add a parameter to the control.in file + """Get the string needed to add a parameter to the control.in file. Args: key (str): The name of the input flag @@ -478,7 +490,7 @@ def get_aims_control_parameter_str(self, key: str, value: Any, fmt: str) -> str: def get_content( self, structure: Structure | Molecule, verbose_header: bool = False, directory: str | Path | None = None ) -> str: - """Get the content of the file + """Get the content of the file. Args: structure (Structure | Molecule): The structure to write the input @@ -544,8 +556,10 @@ def get_content( content += cube.control_block content += f"{lim}\n\n" - species_dir = self._parameters.get("species_dir", os.environ.get("AIMS_SPECIES_DIR")) - content += self.get_species_block(structure, species_dir) + species_defaults = self._parameters.get("species_dir", "") + if not species_defaults: + raise KeyError("Species' defaults not specified in the parameters") + content += self.get_species_block(structure, species_defaults) return content @@ -556,7 +570,7 @@ def write_file( verbose_header: bool = False, overwrite: bool = False, ) -> None: - """Write the control.in file + """Write the control.in file. Args: structure (Structure | Molecule): The structure to write the input @@ -591,12 +605,15 @@ def write_file( file.write(content) - def get_species_block(self, structure: Structure | Molecule, species_dir: str | Path) -> str: - """Get the basis set information for a structure + def get_species_block(self, structure: Structure | Molecule, basis_set: str | dict[str, str]) -> str: + """Get the basis set information for a structure. Args: structure (Molecule or Structure): The structure to get the basis set information for - species_dir (str or Pat:): The directory to find the species files in + basis_set (str | dict[str, str]): + a name of a basis set (`light`, `tight`...) or a mapping from site labels to basis set names. + The name of a basis set can either correspond to the subfolder in `defaults_2020` folder + or be a full path from the `FHI-aims/species_defaults` directory. Returns: The block to add to the control.in file for the species @@ -604,20 +621,8 @@ def get_species_block(self, structure: Structure | Molecule, species_dir: str | Raises: ValueError: If a file for the species is not found """ - block = "" - species = np.unique(structure.species) - for sp in species: - filename = f"{species_dir}/{sp.Z:02d}_{sp.symbol}_default" - if Path(filename).exists(): - with open(filename) as sf: - block += "".join(sf.readlines()) - elif Path(f"{filename}.gz").exists(): - with gzip.open(f"{filename}.gz", mode="rt") as sf: - block += "".join(sf.readlines()) - else: - raise ValueError(f"Species file for {sp.symbol} not found.") - - return block + species_defaults = SpeciesDefaults.from_structure(structure, basis_set) + return str(species_defaults) def as_dict(self) -> dict[str, Any]: """Get a dictionary representation of the geometry.in file.""" @@ -640,3 +645,179 @@ def from_dict(cls, dct: dict[str, Any]) -> Self: decoded = {key: MontyDecoder().process_decoded(val) for key, val in dct.items() if not key.startswith("@")} return cls(_parameters=decoded["parameters"]) + + +class AimsSpeciesFile: + """An FHI-aims single species' defaults file.""" + + def __init__(self, data: str, label: str | None = None) -> None: + """ + Args: + data (str): A string of the complete species defaults file + label (str): A string representing the name of species. + """ + self.data = data + self.label = label + if self.label is None: + for line in data.splitlines(): + if "species" in line: + self.label = line.split()[1] + + @classmethod + def from_file(cls, filename: str, label: str | None = None) -> AimsSpeciesFile: + """Initialize from file. + + Args: + filename (str): The filename of the species' defaults file + label (str): A string representing the name of species + + Returns: + The AimsSpeciesFile instance + """ + with zopen(filename, mode="rt") as file: + return cls(file.read(), label) + + @classmethod + def from_element_and_basis_name(cls, element: str, basis: str, *, label: str | None = None) -> AimsSpeciesFile: + """Initialize from element and basis names. + + Args: + element (str): the element name (not to confuse with the species) + basis (str): the directory in which the species' defaults file is located relative to the + root `species_defaults` (or `species_defaults/defaults_2020`) directory.`. + label (str): A string representing the name of species. If not specified, + then equal to element + + Returns: + an AimsSpeciesFile instance + """ + # check if element is in the Periodic Table (+ Emptium) + if element != "Emptium": + if not hasattr(Element, element): + raise ValueError(f"{element} is not a valid element name.") + el_obj = Element(element) + species_file_name = f"{el_obj.Z:02}_{element}_default" + else: + species_file_name = "00_Emptium_default" + + aims_species_dir = SETTINGS.get("AIMS_SPECIES_DIR") + if aims_species_dir is None: + raise ValueError( + "No AIMS_SPECIES_DIR variable found in the config file. " + "Please set the variable in ~/.config/.pmgrc.yaml to the root of `species_defaults` " + "folder in FHIaims/ directory." + ) + paths_to_try = [ + (Path(aims_species_dir) / basis / species_file_name).expanduser().as_posix(), + (Path(aims_species_dir) / "defaults_2020" / basis / species_file_name).expanduser().as_posix(), + ] + for path in paths_to_try: + path = zpath(path) + if os.path.isfile(path): + return cls.from_file(path, label) + + raise RuntimeError( + f"Can't find the species' defaults file for {element} in {basis} basis set. Paths tried: {paths_to_try}" + ) + + def __str__(self): + """String representation of the species' defaults file.""" + return re.sub(r"^ *species +\w+", f" species {self.label}", self.data, flags=re.MULTILINE) + + @property + def element(self) -> str: + match = re.search(r"^ *species +(\w+)", self.data, flags=re.MULTILINE) + if match is None: + raise ValueError("Can't find element in species' defaults file") + return match.group(1) + + def as_dict(self) -> dict[str, Any]: + """Dictionary representation of the species' defaults file.""" + return {"label": self.label, "data": self.data, "@module": type(self).__module__, "@class": type(self).__name__} + + @classmethod + def from_dict(cls, dct: dict[str, Any]) -> AimsSpeciesFile: + """Deserialization of the AimsSpeciesFile object.""" + return AimsSpeciesFile(data=dct["data"], label=dct["label"]) + + +class SpeciesDefaults(list, MSONable): + """A list containing a set of species' defaults objects with + methods to read and write them to files. + """ + + def __init__( + self, + labels: Sequence[str], + basis_set: str | dict[str, str], + *, + elements: dict[str, str] | None = None, + ) -> None: + """ + Args: + labels (list[str]): a list of labels, for which to build species' defaults + basis_set (str | dict[str, str]): + a name of a basis set (`light`, `tight`...) or a mapping from site labels to basis set names. + The name of a basis set can either correspond to the subfolder in `defaults_2020` folder + or be a full path from the `FHI-aims/species_defaults` directory. + elements (dict[str, str] | None): + a mapping from site labels to elements. If some label is not in this mapping, + it coincides with an element. + """ + super().__init__() + self.labels = labels + self.basis_set = basis_set + if elements is None: + elements = {} + self.elements = {} + for label in self.labels: + self.elements[label] = elements.get(label, label) + self._set_species() + + def _set_species(self) -> None: + """Initialize species defaults from the instance data.""" + del self[:] + + for label in self.labels: + el = self.elements[label] + if isinstance(self.basis_set, dict): + basis_set = self.basis_set.get(label, None) + if basis_set is None: + raise ValueError(f"Basis set not found for specie {label} (represented by element {el})") + else: + basis_set = self.basis_set + self.append(AimsSpeciesFile.from_element_and_basis_name(el, basis_set, label=label)) + + def __str__(self): + """String representation of the species' defaults.""" + return "".join([str(x) for x in self]) + + @classmethod + def from_structure(cls, struct: Structure | Molecule, basis_set: str | dict[str, str]): + """Initialize species defaults from a structure.""" + labels = [] + elements = {} + for label, el in sorted(zip(struct.labels, struct.species)): + if not isinstance(el, Element): + raise TypeError("FHI-aims does not support fractional compositions") + if (label is None) or (el is None): + raise ValueError("Something is terribly wrong with the structure") + if label not in labels: + labels.append(label) + elements[label] = el.name + return SpeciesDefaults(labels, basis_set, elements=elements) + + def to_dict(self): + """Dictionary representation of the species' defaults.""" + return { + "labels": self.labels, + "elements": self.elements, + "basis_set": self.basis_set, + "@module": type(self).__module__, + "@class": type(self).__name__, + } + + @classmethod + def from_dict(cls, dct: dict[str, Any]) -> SpeciesDefaults: + """Deserialization of the SpeciesDefaults object.""" + return SpeciesDefaults(dct["labels"], dct["basis_set"], elements=dct["elements"]) diff --git a/pymatgen/io/aims/outputs.py b/src/pymatgen/io/aims/outputs.py similarity index 99% rename from pymatgen/io/aims/outputs.py rename to src/pymatgen/io/aims/outputs.py index ae4b8d3aca7..f6012472ac5 100644 --- a/pymatgen/io/aims/outputs.py +++ b/src/pymatgen/io/aims/outputs.py @@ -6,7 +6,6 @@ import numpy as np from monty.json import MontyDecoder, MSONable - from pymatgen.io.aims.parsers import ( read_aims_header_info, read_aims_header_info_from_content, @@ -19,10 +18,9 @@ from pathlib import Path from typing import Any - from typing_extensions import Self - from pymatgen.core import Molecule, Structure from pymatgen.util.typing import Matrix3D, Vector3D + from typing_extensions import Self __author__ = "Andrey Sobolev and Thomas A. R. Purcell" __version__ = "1.0" @@ -46,7 +44,7 @@ def __init__( metadata (Dict[str, Any]): The metadata of the executable used to perform the calculation structure_summary (Dict[str, Any]): The summary of the starting - atomic structure + atomic structure. """ self._results = results self._metadata = metadata diff --git a/pymatgen/io/aims/parsers.py b/src/pymatgen/io/aims/parsers.py similarity index 96% rename from pymatgen/io/aims/parsers.py rename to src/pymatgen/io/aims/parsers.py index f06f1307893..3021c49279c 100644 --- a/pymatgen/io/aims/parsers.py +++ b/src/pymatgen/io/aims/parsers.py @@ -8,7 +8,6 @@ from typing import TYPE_CHECKING, cast import numpy as np - from pymatgen.core import Lattice, Molecule, Structure from pymatgen.core.tensors import Tensor from pymatgen.util.typing import Tuple3Floats @@ -31,14 +30,14 @@ class ParseError(Exception): - """Parse error during reading of a file""" + """Parse error during reading of a file.""" class AimsParseError(Exception): """Exception raised if an error occurs when parsing an Aims output file.""" def __init__(self, message: str) -> None: - """Initialize the error with the message, message""" + """Initialize the error with the message, message.""" self.message = message super().__init__(self.message) @@ -105,7 +104,7 @@ def search_for_all(self, key: str, line_start: int = 0, line_end: int = -1) -> l line_index.append(ll + line_start) return line_index - def parse_scalar(self, property: str) -> float | None: + def parse_scalar(self, property: str) -> float | None: # noqa: A002 """Parse a scalar property from the chunk. Args: @@ -231,7 +230,7 @@ def initial_lattice(self) -> Lattice | None: @property def initial_structure(self) -> Structure | Molecule: - """The initial structure + """The initial structure. Using the FHI-aims output file recreate the initial structure for the calculation. @@ -274,20 +273,20 @@ def initial_structure(self) -> Structure | Molecule: @property def initial_charges(self) -> Sequence[float]: - """The initial charges for the structure""" + """The initial charges for the structure.""" if "initial_charges" not in self._cache: self._parse_initial_charges_and_moments() return self._cache["initial_charges"] @property def initial_magnetic_moments(self) -> Sequence[float]: - """The initial magnetic Moments""" + """The initial magnetic Moments.""" if "initial_magnetic_moments" not in self._cache: self._parse_initial_charges_and_moments() return self._cache["initial_magnetic_moments"] def _parse_initial_charges_and_moments(self) -> None: - """Parse the initial charges and magnetic moments from a file""" + """Parse the initial charges and magnetic moments from a file.""" charges = np.zeros(self.n_atoms) magmoms = None line_start = self.reverse_search_for(["Initial charges", "Initial moments and charges"]) @@ -526,7 +525,7 @@ def _parse_structure(self) -> Structure | Molecule: def _parse_lattice_atom_pos( self, ) -> tuple[list[str], list[Vector3D], list[Vector3D], Lattice | None]: - """Parse the lattice and atomic positions of the structure + """Parse the lattice and atomic positions of the structure. Returns: list[str]: The species symbols for the atoms in the structure @@ -577,7 +576,7 @@ def _parse_lattice_atom_pos( @property def species(self) -> list[str]: - """The list of atomic symbols for all atoms in the structure""" + """The list of atomic symbols for all atoms in the structure.""" if "species" not in self._cache: self._cache["species"], self._cache["coords"], self._cache["velocities"], self._cache["lattice"] = ( self._parse_lattice_atom_pos() @@ -586,7 +585,7 @@ def species(self) -> list[str]: @property def coords(self) -> list[Vector3D]: - """The cartesian coordinates of the atoms""" + """The cartesian coordinates of the atoms.""" if "coords" not in self._cache: self._cache["species"], self._cache["coords"], self._cache["velocities"], self._cache["lattice"] = ( self._parse_lattice_atom_pos() @@ -595,7 +594,7 @@ def coords(self) -> list[Vector3D]: @property def velocities(self) -> list[Vector3D]: - """The velocities of the atoms""" + """The velocities of the atoms.""" if "velocities" not in self._cache: self._cache["species"], self._cache["coords"], self._cache["velocities"], self._cache["lattice"] = ( self._parse_lattice_atom_pos() @@ -604,7 +603,7 @@ def velocities(self) -> list[Vector3D]: @property def lattice(self) -> Lattice: - """The Lattice object for the structure""" + """The Lattice object for the structure.""" if "lattice" not in self._cache: self._cache["species"], self._cache["coords"], self._cache["velocities"], self._cache["lattice"] = ( self._parse_lattice_atom_pos() @@ -814,17 +813,17 @@ def results(self) -> dict[str, Any]: # Properties from the aims.out header @property def initial_structure(self) -> Structure | Molecule: - """The initial structure for the calculation""" + """The initial structure for the calculation.""" return self._header["initial_structure"] @property def initial_lattice(self) -> Lattice | None: - """The initial Lattice of the structure""" + """The initial Lattice of the structure.""" return self._header["initial_lattice"] @property def n_atoms(self) -> int: - """The number of atoms in the structure""" + """The number of atoms in the structure.""" return self._header["n_atoms"] @property @@ -864,7 +863,7 @@ def k_point_weights(self) -> Sequence[float]: @property def free_energy(self) -> float | None: - """The free energy of the calculation""" + """The free energy of the calculation.""" return self.parse_scalar("free_energy") @property @@ -877,43 +876,43 @@ def n_iter(self) -> int | None: @property def magmom(self) -> float | None: - """The magnetic moment of the structure""" + """The magnetic moment of the structure.""" return self.parse_scalar("magnetic_moment") @property def E_f(self) -> float | None: - """The Fermi energy""" + """The Fermi energy.""" return self.parse_scalar("fermi_energy") @property def converged(self) -> bool: - """True if the calculation is converged""" + """True if the calculation is converged.""" return (len(self.lines) > 0) and ("Have a nice day." in self.lines[-5:]) @property def hirshfeld_charges(self) -> Sequence[float] | None: - """The Hirshfeld charges of the system""" + """The Hirshfeld charges of the system.""" if "hirshfeld_charges" not in self._cache: self._parse_hirshfeld() return self._cache["hirshfeld_charges"] @property def hirshfeld_atomic_dipoles(self) -> Sequence[Vector3D] | None: - """The Hirshfeld atomic dipoles of the system""" + """The Hirshfeld atomic dipoles of the system.""" if "hirshfeld_atomic_dipoles" not in self._cache: self._parse_hirshfeld() return self._cache["hirshfeld_atomic_dipoles"] @property def hirshfeld_volumes(self) -> Sequence[float] | None: - """The Hirshfeld atomic dipoles of the system""" + """The Hirshfeld atomic dipoles of the system.""" if "hirshfeld_volumes" not in self._cache: self._parse_hirshfeld() return self._cache["hirshfeld_volumes"] @property def hirshfeld_dipole(self) -> None | Vector3D: - """The Hirshfeld dipole of the system""" + """The Hirshfeld dipole of the system.""" if "hirshfeld_dipole" not in self._cache: self._parse_hirshfeld() @@ -921,27 +920,27 @@ def hirshfeld_dipole(self) -> None | Vector3D: @property def vbm(self) -> float: - """The valance band maximum""" + """The valance band maximum.""" return self._parse_homo_lumo()["vbm"] @property def cbm(self) -> float: - """The conduction band minimnum""" + """The conduction band minimnum.""" return self._parse_homo_lumo()["cbm"] @property def gap(self) -> float: - """The band gap""" + """The band gap.""" return self._parse_homo_lumo()["gap"] @property def direct_gap(self) -> float: - """The direct bandgap""" + """The direct bandgap.""" return self._parse_homo_lumo()["direct_gap"] def get_lines(content: str | TextIOWrapper) -> list[str]: - """Get a list of lines from a str or file of content + """Get a list of lines from a str or file of content. Args: content: the content of the file to parse @@ -955,7 +954,7 @@ def get_lines(content: str | TextIOWrapper) -> list[str]: def get_header_chunk(content: str | TextIOWrapper) -> AimsOutHeaderChunk: - """Get the header chunk for an output + """Get the header chunk for an output. Args: content (str or TextIOWrapper): the content to parse @@ -1101,7 +1100,7 @@ def read_aims_header_info( def read_aims_output_from_content( content: str, index: int | slice = -1, non_convergence_ok: bool = False ) -> Structure | Molecule | Sequence[Structure | Molecule]: - """Read and aims output file from the content of a file + """Read and aims output file from the content of a file. Args: content (str): The content of the file to read diff --git a/pymatgen/io/aims/sets/__init__.py b/src/pymatgen/io/aims/sets/__init__.py similarity index 100% rename from pymatgen/io/aims/sets/__init__.py rename to src/pymatgen/io/aims/sets/__init__.py diff --git a/pymatgen/io/aims/sets/base.py b/src/pymatgen/io/aims/sets/base.py similarity index 96% rename from pymatgen/io/aims/sets/base.py rename to src/pymatgen/io/aims/sets/base.py index b868a8621d8..c15385d9a2e 100644 --- a/pymatgen/io/aims/sets/base.py +++ b/src/pymatgen/io/aims/sets/base.py @@ -12,7 +12,6 @@ import numpy as np from monty.json import MontyDecoder, MontyEncoder - from pymatgen.core import Molecule, Structure from pymatgen.io.aims.inputs import AimsControlIn, AimsGeometryIn from pymatgen.io.aims.parsers import AimsParseError, read_aims_output @@ -20,7 +19,8 @@ if TYPE_CHECKING: from collections.abc import Sequence - from pathlib import Path + + from pymatgen.util.typing import PathLike TMPDIR_NAME: str = "tmpdir" OUTPUT_FILE_NAME: str = "aims.out" @@ -133,7 +133,11 @@ def set_parameters(self, *args, **kwargs) -> dict[str, Any]: return self._parameters - def remove_parameters(self, keys: Iterable[str] | str, strict: bool = True) -> dict[str, Any]: + def remove_parameters( + self, + keys: Iterable[str] | str, + strict: bool = True, + ) -> dict[str, Any]: """Remove the aims parameters listed in keys. This removes the aims variables from the parameters object. @@ -190,10 +194,10 @@ class AimsInputGenerator(InputGenerator): user_params: dict[str, Any] = field(default_factory=dict) user_kpoints_settings: dict[str, Any] = field(default_factory=dict) - def get_input_set( # type: ignore + def get_input_set( self, structure: Structure | Molecule | None = None, - prev_dir: str | Path | None = None, + prev_dir: PathLike | None = None, properties: list[str] | None = None, ) -> AimsInputSet: """Generate an AimsInputSet object. @@ -221,7 +225,7 @@ def get_input_set( # type: ignore @staticmethod def _read_previous( - prev_dir: str | Path | None = None, + prev_dir: PathLike | None = None, ) -> tuple[Structure | Molecule | None, dict[str, Any], dict[str, Any]]: """Read in previous results. @@ -288,7 +292,9 @@ def _get_properties( return properties def _get_input_parameters( - self, structure: Structure | Molecule, prev_parameters: dict[str, Any] | None = None + self, + structure: Structure | Molecule, + prev_parameters: dict[str, Any] | None = None, ) -> dict[str, Any]: """Create the input parameters. @@ -340,7 +346,11 @@ def _get_input_parameters( return parameters - def get_parameter_updates(self, structure: Structure | Molecule, prev_parameters: dict[str, Any]) -> dict[str, Any]: + def get_parameter_updates( + self, + structure: Structure | Molecule, + prev_parameters: dict[str, Any], + ) -> dict[str, Any]: """Update the parameters for a given calculation type. Args: @@ -363,7 +373,6 @@ def d2k( inspired by [ase.calculators.calculator.kptdensity2monkhorstpack] Args: - structure (Structure): Contains unit cell and information about boundary conditions. kptdensity (float | list[float]): Required k-point diff --git a/pymatgen/io/aims/sets/bs.py b/src/pymatgen/io/aims/sets/bs.py similarity index 99% rename from pymatgen/io/aims/sets/bs.py rename to src/pymatgen/io/aims/sets/bs.py index 7c1cafaa7ef..d59c4abc71a 100644 --- a/pymatgen/io/aims/sets/bs.py +++ b/src/pymatgen/io/aims/sets/bs.py @@ -83,7 +83,7 @@ def get_parameter_updates( dict: The updated for the parameters for the output section of FHI-aims """ if isinstance(structure, Molecule): - raise ValueError("BandStructures can not be made for non-periodic systems") + raise ValueError("BandStructures can not be made for non-periodic systems") # noqa: TRY004 updated_outputs = prev_parameters.get("output", []) updated_outputs += prepare_band_input(structure, self.k_point_density) diff --git a/src/pymatgen/io/aims/sets/core.py b/src/pymatgen/io/aims/sets/core.py new file mode 100644 index 00000000000..c858b2f1236 --- /dev/null +++ b/src/pymatgen/io/aims/sets/core.py @@ -0,0 +1,198 @@ +"""Module defining core FHI-aims input set generators.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from pymatgen.core import Structure +from pymatgen.io.aims.sets.base import AimsInputGenerator + +if TYPE_CHECKING: + from typing import Any + + from pymatgen.core import Molecule + + +_valid_dynamics: dict[str, tuple[str, ...]] = { + "nve": ("", "4th_order", "damped"), + "nvt": ("andersen", "berendsen", "parrinello", "nose-hoover"), + "gle": ("thermostat",), +} + + +@dataclass +class StaticSetGenerator(AimsInputGenerator): + """Common class for ground-state generators. + + Attributes: + calc_type (str): The type of calculation + """ + + calc_type: str = "static" + + def get_parameter_updates(self, structure: Structure | Molecule, prev_parameters: dict[str, Any]) -> dict[str, Any]: + """Get the parameter updates for the calculation. + + Args: + structure (Structure or Molecule): The structure to calculate the bands for + prev_parameters (Dict[str, Any]): The previous parameters + + Returns: + dict: The updated for the parameters for the output section of FHI-aims + """ + return prev_parameters + + +@dataclass +class RelaxSetGenerator(AimsInputGenerator): + """Generate FHI-aims relax sets for optimizing internal coordinates and lattice params. + + Attributes: + calc_type (str): The type of calculation + relax_cell (bool): If True then relax the unit cell from the structure + max_force (float): Maximum allowed force in the calculation + method (str): Method used for the geometry optimization + """ + + calc_type: str = "relaxation" + relax_cell: bool = True + max_force: float = 1e-3 + method: str = "trm" + + def get_parameter_updates(self, structure: Structure | Molecule, prev_parameters: dict[str, Any]) -> dict: + """Get the parameter updates for the calculation. + + Args: + structure (Structure or Molecule): The structure to calculate the bands for + prev_parameters (Dict[str, Any]): The previous parameters + + Returns: + dict: The updated for the parameters for the output section of FHI-aims + """ + updates = {"relax_geometry": f"{self.method} {self.max_force:e}"} + if isinstance(structure, Structure) and self.relax_cell: + updates["relax_unit_cell"] = "full" + elif isinstance(structure, Structure): + updates["relax_unit_cell"] = "none" + + return updates + + +@dataclass +class SocketIOSetGenerator(AimsInputGenerator): + """Generate FHI-aims input sets for running with the socket. + + Attributes: + calc_type (str): The type of calculation + host (str): The hostname for the server the socket is on + port (int): The port the socket server is listening on + """ + + calc_type: str = "multi_scf" + host: str = "localhost" + port: int = 12345 + + def get_parameter_updates(self, structure: Structure | Molecule, prev_parameters: dict[str, Any]) -> dict: + """Get the parameter updates for the calculation. + + Args: + structure (Structure or Molecule): The structure to calculate the bands for + prev_parameters (Dict[str, Any]): The previous parameters + + Returns: + dict: The updated for the parameters for the output section of FHI-aims + """ + return {"use_pimd_wrapper": (self.host, self.port)} + + +@dataclass +class MDSetGenerator(AimsInputGenerator): + """ + A class for generating FHI-aims input sets for molecular dynamics calculations. + + Parameters + ---------- + ensemble + Molecular dynamics ensemble to run. Options include `nvt`, `nve`, and `gle`. + Default: `nve` + ensemble_specs + A dictionary containing the specifications of the molecular dynamics ensemble. + Valid keys are `type` (the ensemble type, valid types are defined in + `_valid_dynamics` dict), and `parameter` - the control parameter for the thermostat + (not used for `nve` and `nve_4th_order`). + temp + Thermostat temperature. Default: None + time + Simulation time (in picoseconds). Negative value stands for indefinite run. + Default: 5 ps + time_step + The time step (in picoseconds) for the simulation. default: 1 fs + **kwargs + Other keyword arguments that will be passed to :obj:`AimsInputGenerator`. + """ + + calc_type: str = "md" + ensemble: str = "nve" + ensemble_specs: dict[str, Any] = field(default_factory=dict) + temp: float | None = None + time: float = 5.0 + time_step: float = 0.001 + init_velocities: bool = True + + def get_parameter_updates(self, structure: Structure | Molecule, prev_parameters: dict[str, Any]) -> dict: + """Get the parameter updates for the calculation. + + Parameters + ---------- + structure (Structure or Molecule): + The structure to calculate the bands for + prev_parameters (Dict[str, Any]): + The previous parameters + + Returns + ------- + dict + A dictionary of updates to apply. + """ + updates: dict[str, Any] = {"MD_run": [self.time], "MD_time_step": self.time_step} + + # check for ensemble type validity + default_ensemble_types = {"nve": "", "nvt": "parrinello", "gle": "thermostat"} + if self.ensemble not in _valid_dynamics: + raise ValueError(f"Ensemble {self.ensemble} not valid") + ensemble_type = self.ensemble_specs.get("type", default_ensemble_types[self.ensemble]) + if ensemble_type not in _valid_dynamics[self.ensemble]: + raise ValueError( + f"Type {ensemble_type} is not valid for {self.ensemble} ensemble. " + f"Valid types are: {' ,'.join(_valid_dynamics[self.ensemble])}" + ) + ensemble_name = f"{self.ensemble.upper()}_{ensemble_type}" if ensemble_type else self.ensemble.upper() + updates["MD_run"].append(ensemble_name) + + # add temperature + if self.ensemble == "nve": + if not self.init_velocities and "velocity" not in structure.site_properties: + raise ValueError("Velocities must be initialized for NVE ensemble") + else: + if self.temp is None: + raise ValueError(f"Temperature must be set for {ensemble_name} ensemble") + updates["MD_run"].append(self.temp) + + # check for ensemble control parameter + ensemble_parameter = self.ensemble_specs.get("parameter", None) + if ensemble_name not in ("NVE", "NVE_4th_order"): + if ensemble_parameter is None: + raise ValueError(f"Ensemble {ensemble_name} parameter is not defined") + updates["MD_run"].append(ensemble_parameter) + + # ...and put everything in the string + updates["MD_run"] = " ".join(map(str, updates["MD_run"])) + + # initialize velocities + if self.init_velocities: + if self.temp is None: + raise ValueError("Temperature must be set for velocity initialisation") + updates["MD_MB_init"] = self.temp + + return updates diff --git a/pymatgen/io/ase.py b/src/pymatgen/io/ase.py similarity index 99% rename from pymatgen/io/ase.py rename to src/pymatgen/io/ase.py index 7058a9d2eee..bae2dbc5a62 100644 --- a/pymatgen/io/ase.py +++ b/src/pymatgen/io/ase.py @@ -12,7 +12,6 @@ import numpy as np from monty.json import MontyDecoder, MSONable, jsanitize - from pymatgen.core.structure import Molecule, Structure try: @@ -36,9 +35,8 @@ def __init__(self, *args, **kwargs): from typing import Any from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.core.structure import SiteCollection + from typing_extensions import Self __author__ = "Shyue Ping Ong, Andrew S. Rosen" __copyright__ = "Copyright 2012, The Materials Project" diff --git a/pymatgen/io/atat.py b/src/pymatgen/io/atat.py similarity index 99% rename from pymatgen/io/atat.py rename to src/pymatgen/io/atat.py index 7badcab828c..98660051d6b 100644 --- a/pymatgen/io/atat.py +++ b/src/pymatgen/io/atat.py @@ -3,7 +3,6 @@ from __future__ import annotations import numpy as np - from pymatgen.core import Lattice, Structure, get_el_sp __author__ = "Matthew Horton" diff --git a/pymatgen/io/babel.py b/src/pymatgen/io/babel.py similarity index 99% rename from pymatgen/io/babel.py rename to src/pymatgen/io/babel.py index b8326bd01e6..a648a783831 100644 --- a/pymatgen/io/babel.py +++ b/src/pymatgen/io/babel.py @@ -11,7 +11,6 @@ from typing import TYPE_CHECKING from monty.dev import requires - from pymatgen.core.structure import IMolecule, Molecule try: @@ -20,9 +19,8 @@ openbabel = pybel = None if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.analysis.graphs import MoleculeGraph + from typing_extensions import Self __author__ = "Shyue Ping Ong, Qi Wang" @@ -84,7 +82,7 @@ def __init__(self, mol: Molecule | openbabel.OBMol | pybel.Molecule) -> None: elif isinstance(mol, pybel.Molecule): self._ob_mol = mol.OBMol else: - raise ValueError(f"Unsupported input type {type(mol)}, must be Molecule, openbabel.OBMol or pybel.Molecule") + raise TypeError(f"Unsupported input type {type(mol)}, must be Molecule, openbabel.OBMol or pybel.Molecule") @property def pymatgen_mol(self) -> Molecule: diff --git a/pymatgen/io/cif.py b/src/pymatgen/io/cif.py similarity index 98% rename from pymatgen/io/cif.py rename to src/pymatgen/io/cif.py index 728abf7967d..5020d66d83b 100644 --- a/pymatgen/io/cif.py +++ b/src/pymatgen/io/cif.py @@ -19,7 +19,6 @@ from monty.dev import deprecated from monty.io import zopen from monty.serialization import loadfn - from pymatgen.core import Composition, DummySpecies, Element, Lattice, PeriodicSite, Species, Structure, get_el_sp from pymatgen.core.operations import MagSymmOp, SymmOp from pymatgen.electronic_structure.core import Magmom @@ -33,16 +32,15 @@ from typing import Any from numpy.typing import NDArray - from typing_extensions import Self - from pymatgen.util.typing import PathLike, Vector3D + from typing_extensions import Self __author__ = "Shyue Ping Ong, Will Richards, Matthew Horton" class CifBlock: """ - Object for storing cif data. All data is stored in a single dictionary. + Object for storing CIF data. All data is stored in a single dictionary. Data inside loops are stored in lists in the data dictionary, and information on which keys are grouped together are stored in the loops attribute. @@ -58,7 +56,7 @@ def __init__( ) -> None: """ Args: - data: dict of data to go into the cif. Values should be convertible to string, + data: dict of data to go into the CIF. Values should be convertible to string, or lists of these if the key is in a loop loops: list of lists of keys, grouped by which loop they should appear in header: name of the block (appears after the data_ on the first line). @@ -77,7 +75,7 @@ def __getitem__(self, key: str) -> Any: return self.data[key] def __str__(self) -> str: - """Get the cif string for the data block.""" + """Get the CIF string for the data block.""" out = [f"data_{self.header}"] keys = list(self.data) written = [] @@ -199,7 +197,7 @@ def from_str(cls, string: str) -> Self: while deq: _str = deq.popleft() - # cif keys aren't in quotes, so show up as _str[0] + # CIF keys aren't in quotes, so show up as _str[0] if _str[0] == "_eof": break @@ -249,7 +247,7 @@ def __init__( """ Args: data (dict): Of CifBlock objects. - orig_string (str): The original cif. + orig_string (str): The original CIF. comment (str): Comment. """ self.data = data @@ -372,13 +370,13 @@ def is_magcif_incommensurate() -> bool: self._site_tolerance = site_tolerance self._frac_tolerance = frac_tolerance - # Read cif file + # Read CIF file if isinstance(filename, (str, Path)): self._cif = CifFile.from_file(filename) elif isinstance(filename, StringIO): self._cif = CifFile.from_str(filename.read()) else: - raise RuntimeError("Unsupported file format.") + raise TypeError("Unsupported file format.") # Options related to checking CIFs for missing elements # or incorrect stoichiometries @@ -915,7 +913,7 @@ def _parse_symbol(self, sym: str) -> str | None: Returns: A string for the parsed symbol. None if no parsing was possible. """ - # Common representations for elements/water in cif files + # Common representations for elements/water in CIF files # TODO: fix inconsistent handling of water special_syms = { "Hw": "H", @@ -955,7 +953,7 @@ def _get_structure( symmetrized: bool, check_occu: bool = False, ) -> Structure | None: - """Generate structure from part of the cif.""" + """Generate structure from part of the CIF.""" def get_num_implicit_hydrogens(symbol: str) -> int: """Get number of implicit hydrogens.""" @@ -1142,7 +1140,7 @@ def get_matching_coord( all_coords.extend(coords) all_species.extend(len(coords) * [species]) all_magmoms.extend(_magmoms) - all_labels.extend(new_labels) # type: ignore + all_labels.extend(new_labels) # Scale occupancies if necessary all_species_noedit = all_species.copy() # save copy before scaling in case of check_occu=False, used below @@ -1312,7 +1310,7 @@ def get_structures(self, *args, **kwargs) -> list[Structure]: def get_bibtex_string(self) -> str: """Get BibTeX reference from CIF file. - args: + Args: data: Returns: @@ -1346,7 +1344,7 @@ def get_bibtex_string(self) -> str: # TODO: CIF specification supports multiple citations. for idx, data in enumerate(self._cif.data.values()): - # Convert to lower-case keys, some cif files inconsistent + # Convert to lower-case keys, some CIF files inconsistent _data = {k.lower(): v for k, v in data.data.items()} bibtex_entry = {} @@ -1380,7 +1378,7 @@ def get_bibtex_string(self) -> str: return BibliographyData(entries).to_string(bib_format="bibtex") def as_dict(self) -> dict: - """MSONable dict""" + """MSONable dict.""" dct: dict = {} for key, val in self._cif.data.items(): dct[key] = {} @@ -1484,10 +1482,10 @@ def str2float(text: str) -> float: if isinstance(text, list) and len(text) == 1: return float(re.sub(r"\(.+\)*", "", text[0])) - except ValueError as exc: + except ValueError: if text.strip() == ".": return 0 - raise exc + raise raise ValueError(f"{text!s} cannot be converted to float") @@ -1508,7 +1506,7 @@ def __init__( Args: struct (Structure): structure to write. symprec (float): If not none, finds the symmetry of the structure - and writes the cif with symmetry information. Passes symprec + and writes the CIF with symmetry information. Passes symprec to the SpacegroupAnalyzer. See also refine_struct. write_magmoms (bool): If True, will write magCIF file. Incompatible with symprec diff --git a/pymatgen/io/common.py b/src/pymatgen/io/common.py similarity index 99% rename from pymatgen/io/common.py rename to src/pymatgen/io/common.py index 073f26b7935..0949bf08306 100644 --- a/pymatgen/io/common.py +++ b/src/pymatgen/io/common.py @@ -11,11 +11,10 @@ import numpy as np from monty.io import zopen from monty.json import MSONable -from scipy.interpolate import RegularGridInterpolator - from pymatgen.core import Element, Site, Structure from pymatgen.core.units import ang_to_bohr, bohr_to_angstrom from pymatgen.electronic_structure.core import Spin +from scipy.interpolate import RegularGridInterpolator if TYPE_CHECKING: from pathlib import Path @@ -113,7 +112,7 @@ def __sub__(self, other): return self.linear_add(other, -1.0) def copy(self) -> Self: - """Make a copy of VolumetricData object""" + """Make a copy of VolumetricData object.""" return VolumetricData( self.structure, {k: v.copy() for k, v in self.data.items()}, diff --git a/pymatgen/io/core.py b/src/pymatgen/io/core.py similarity index 87% rename from pymatgen/io/core.py rename to src/pymatgen/io/core.py index 4d723c138ed..c4c944706eb 100644 --- a/pymatgen/io/core.py +++ b/src/pymatgen/io/core.py @@ -37,7 +37,8 @@ from monty.json import MSONable if TYPE_CHECKING: - from os import PathLike + from pymatgen.util.typing import PathLike + from typing_extensions import Self __author__ = "Ryan Kingsbury" @@ -59,18 +60,20 @@ class InputFile(MSONable): to __init__ as attributes. """ + def __str__(self) -> str: + return self.get_str() + @abc.abstractmethod def get_str(self) -> str: """Return a string representation of an entire input file.""" - def write_file(self, filename: str | PathLike) -> None: + def write_file(self, filename: PathLike) -> None: """Write the input file. Args: filename: The filename to output to, including path. """ - filename = filename if isinstance(filename, Path) else Path(filename) - with zopen(filename, mode="wt") as file: + with zopen(Path(filename), mode="wt") as file: file.write(self.get_str()) @classmethod @@ -88,7 +91,7 @@ def from_str(cls, contents: str) -> None: raise NotImplementedError(f"from_str has not been implemented in {cls.__name__}") @classmethod - def from_file(cls, path: str | Path) -> None: + def from_file(cls, path: PathLike) -> None: """ Creates an InputFile object from a file. @@ -98,13 +101,9 @@ def from_file(cls, path: str | Path) -> None: Returns: InputFile """ - filename = path if isinstance(path, Path) else Path(path) - with zopen(filename, mode="rt") as file: + with zopen(Path(path), mode="rt") as file: return cls.from_str(file.read()) # from_str not implemented - def __str__(self) -> str: - return self.get_str() - class InputSet(MSONable, MutableMapping): """ @@ -120,9 +119,8 @@ class InputSet(MSONable, MutableMapping): is optional. """ - def __init__(self, inputs: dict[str | Path, str | InputFile] | None = None, **kwargs): - """ - Instantiate an InputSet. + def __init__(self, inputs: dict[PathLike, str | InputFile] | None = None, **kwargs) -> None: + """Instantiate an InputSet. Args: inputs: The core mapping of filename: file contents that defines the InputSet data. @@ -139,12 +137,12 @@ def __init__(self, inputs: dict[str | Path, str | InputFile] | None = None, **kw self.__dict__.update(**kwargs) def __getattr__(self, key): - # allow accessing keys as attributes + """Allow accessing keys as attributes.""" if key in self._kwargs: return self.get(key) raise AttributeError(f"'{type(self).__name__}' object has no attribute {key!r}") - def __copy__(self) -> InputSet: + def __copy__(self) -> Self: cls = type(self) new_instance = cls.__new__(cls) @@ -153,7 +151,7 @@ def __copy__(self) -> InputSet: return new_instance - def __deepcopy__(self, memo: dict[int, InputSet]) -> InputSet: + def __deepcopy__(self, memo: dict[int, InputSet]) -> Self: cls = type(self) new_instance = cls.__new__(cls) memo[id(self)] = new_instance @@ -166,26 +164,26 @@ def __deepcopy__(self, memo: dict[int, InputSet]) -> InputSet: def __len__(self) -> int: return len(self.inputs) - def __iter__(self) -> Iterator[str | Path]: + def __iter__(self) -> Iterator[PathLike]: return iter(self.inputs) - def __getitem__(self, key: str | Path) -> str | InputFile | slice: + def __getitem__(self, key: PathLike) -> str | InputFile | slice: return self.inputs[key] - def __setitem__(self, key: str | Path, value: str | InputFile) -> None: + def __setitem__(self, key: PathLike, value: str | InputFile) -> None: self.inputs[key] = value - def __delitem__(self, key: str | Path) -> None: + def __delitem__(self, key: PathLike) -> None: del self.inputs[key] def write_input( self, - directory: str | Path, + directory: PathLike, make_dir: bool = True, overwrite: bool = True, zip_inputs: bool = False, - ): - """Write Inputs to one or more files. + ) -> None: + """Write inputs to one or more files. Args: directory: Directory to write input files to @@ -226,7 +224,7 @@ def write_input( pass @classmethod - def from_directory(cls, directory: str | Path) -> None: + def from_directory(cls, directory: PathLike) -> None: """ Construct an InputSet from a directory of one or more files. @@ -261,4 +259,4 @@ def get_input_set(self, *args, **kwargs): class ParseError(SyntaxError): - """This exception indicates a problem was encountered during parsing due to unexpected formatting.""" + """Indicate a problem was encountered during parsing due to unexpected formatting.""" diff --git a/pymatgen/io/cp2k/__init__.py b/src/pymatgen/io/cp2k/__init__.py similarity index 100% rename from pymatgen/io/cp2k/__init__.py rename to src/pymatgen/io/cp2k/__init__.py diff --git a/pymatgen/io/cp2k/inputs.py b/src/pymatgen/io/cp2k/inputs.py similarity index 99% rename from pymatgen/io/cp2k/inputs.py rename to src/pymatgen/io/cp2k/inputs.py index 95ec03833ae..83054d4380b 100644 --- a/pymatgen/io/cp2k/inputs.py +++ b/src/pymatgen/io/cp2k/inputs.py @@ -37,7 +37,6 @@ from monty.dev import deprecated from monty.io import zopen from monty.json import MSONable - from pymatgen.core import Element from pymatgen.io.cp2k.utils import chunk, postprocessor, preprocessor from pymatgen.io.vasp.inputs import Kpoints as VaspKpoints @@ -48,11 +47,10 @@ from collections.abc import Sequence from typing import Any, Literal - from typing_extensions import Self - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Molecule, Structure from pymatgen.util.typing import Kpoint, Tuple3Ints + from typing_extensions import Self __author__ = "Nicholas Winner" __version__ = "2.0" @@ -2532,9 +2530,9 @@ def from_str(cls, string: str) -> Self: data["nlcc"] = True if "GTH" in string: data["potential_type"] = "GTH" - for idx, char in enumerate(string, start=1): - if char == "Q" and string[idx].isnumeric(): - data["electrons"] = int("".join(_ for _ in string[idx:] if _.isnumeric())) + for idx, char in enumerate(string): + if char == "Q" and string[idx + 1].isnumeric(): + data["electrons"] = int("".join(_ for _ in string[(idx + 1) :] if _.isnumeric())) for x in ("LDA", "PADA", "MGGA", "GGA", "HF", "PBE0", "PBE", "BP", "BLYP", "B3LYP", "SCAN"): if x in string: diff --git a/pymatgen/io/cp2k/outputs.py b/src/pymatgen/io/cp2k/outputs.py similarity index 99% rename from pymatgen/io/cp2k/outputs.py rename to src/pymatgen/io/cp2k/outputs.py index 83ffea0998b..0fecc2bd98b 100644 --- a/pymatgen/io/cp2k/outputs.py +++ b/src/pymatgen/io/cp2k/outputs.py @@ -17,7 +17,6 @@ from monty.io import zopen from monty.json import MSONable, jsanitize from monty.re import regrep - from pymatgen.core.structure import Molecule, Structure from pymatgen.core.units import Ha_to_eV from pymatgen.electronic_structure.bandstructure import BandStructure, BandStructureSymmLine @@ -662,9 +661,7 @@ def parse_qs_params(self): self.data["QS"]["Multi_grid_cutoffs_[a.u.]"] = tmp def parse_overlap_condition(self): - """ - Retrieve the overlap condition number - """ + """Retrieve the overlap condition number.""" overlap_condition = re.compile(r"\|A\|\*\|A\^-1\|.+=\s+(-?\d+\.\d+E[+\-]?\d+)\s+Log") self.read_pattern( {"overlap_condition_number": overlap_condition}, @@ -929,7 +926,7 @@ def parse_opt_steps(self): ) def parse_mulliken(self): - """Parse the mulliken population analysis info for each step""" + """Parse the mulliken population analysis info for each step.""" header = r"Mulliken Population Analysis.+Net charge" pattern = r"\s+(\d)\s+(\w+)\s+(\d+)\s+(-?\d+\.\d+)\s+(-?\d+\.\d+)" footer = r".+Total charge" @@ -1461,7 +1458,7 @@ def parse_raman(self): @staticmethod def _gauss_smear(densities, energies, npts, width): - """Return a gaussian smeared DOS""" + """Return a gaussian smeared DOS.""" if not width: return densities diff --git a/pymatgen/io/cp2k/sets.py b/src/pymatgen/io/cp2k/sets.py similarity index 99% rename from pymatgen/io/cp2k/sets.py rename to src/pymatgen/io/cp2k/sets.py index 0e9130c48b0..9af72d01594 100644 --- a/pymatgen/io/cp2k/sets.py +++ b/src/pymatgen/io/cp2k/sets.py @@ -24,8 +24,6 @@ import warnings import numpy as np -from ruamel.yaml import YAML - from pymatgen.core import SETTINGS from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Element, Molecule, Structure @@ -67,6 +65,7 @@ from pymatgen.io.cp2k.utils import get_truncated_coulomb_cutoff, get_unique_site_indices from pymatgen.io.vasp.inputs import Kpoints as VaspKpoints from pymatgen.io.vasp.inputs import KpointsSupportedModes +from ruamel.yaml import YAML __author__ = "Nicholas Winner" __version__ = "2.0" @@ -1199,9 +1198,7 @@ def activate_robust_minimization(self) -> None: self.update({"FORCE_EVAL": {"DFT": {"SCF": {"OT": ot}}}}) def activate_very_strict_minimization(self) -> None: - """ - Method to modify the set to use very strict SCF minimization scheme - """ + """Method to modify the set to use very strict SCF minimization scheme.""" ot = OrbitalTransformation( minimizer="CG", preconditioner="FULL_ALL", diff --git a/pymatgen/io/cp2k/utils.py b/src/pymatgen/io/cp2k/utils.py similarity index 98% rename from pymatgen/io/cp2k/utils.py rename to src/pymatgen/io/cp2k/utils.py index 6fd1f7f33e2..d82beca9c64 100644 --- a/pymatgen/io/cp2k/utils.py +++ b/src/pymatgen/io/cp2k/utils.py @@ -50,7 +50,7 @@ def postprocessor(data: str) -> str | float | bool | None: return data -def preprocessor(data: str, dir: str = ".") -> str: +def preprocessor(data: str, dir: str = ".") -> str: # noqa: A002 """ Cp2k contains internal preprocessor flags that are evaluated before execution. This helper function recognizes those preprocessor flags and replaces them with an equivalent cp2k input diff --git a/pymatgen/io/cssr.py b/src/pymatgen/io/cssr.py similarity index 96% rename from pymatgen/io/cssr.py rename to src/pymatgen/io/cssr.py index 2db58b08a3d..52d02996815 100644 --- a/pymatgen/io/cssr.py +++ b/src/pymatgen/io/cssr.py @@ -6,7 +6,6 @@ from typing import TYPE_CHECKING from monty.io import zopen - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure @@ -80,8 +79,8 @@ def from_str(cls, string: str) -> Self: sp, coords = [], [] for line in lines[4:]: if match := re.match(r"\d+\s+(\w+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)", line.strip()): - sp.append(match.group(1)) - coords.append([float(match.group(i)) for i in range(2, 5)]) + sp.append(match[1]) + coords.append([float(match[i]) for i in range(2, 5)]) return cls(Structure(lattice, sp, coords)) @classmethod diff --git a/pymatgen/io/exciting/__init__.py b/src/pymatgen/io/exciting/__init__.py similarity index 100% rename from pymatgen/io/exciting/__init__.py rename to src/pymatgen/io/exciting/__init__.py diff --git a/pymatgen/io/exciting/inputs.py b/src/pymatgen/io/exciting/inputs.py similarity index 99% rename from pymatgen/io/exciting/inputs.py rename to src/pymatgen/io/exciting/inputs.py index 95f1db0391d..2a61fa77184 100644 --- a/pymatgen/io/exciting/inputs.py +++ b/src/pymatgen/io/exciting/inputs.py @@ -10,7 +10,6 @@ import scipy.constants as const from monty.io import zopen from monty.json import MSONable - from pymatgen.core import Element, Lattice, Structure from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.symmetry.bandstructure import HighSymmKpath @@ -161,7 +160,7 @@ def from_str(cls, data: str) -> Self: def from_file(cls, filename: str | Path) -> Self: """ Args: - filename: Filename + filename: Filename. Returns: ExcitingInput diff --git a/pymatgen/io/feff/MPELNESSet.yaml b/src/pymatgen/io/feff/MPELNESSet.yaml similarity index 100% rename from pymatgen/io/feff/MPELNESSet.yaml rename to src/pymatgen/io/feff/MPELNESSet.yaml diff --git a/pymatgen/io/feff/MPEXAFSSet.yaml b/src/pymatgen/io/feff/MPEXAFSSet.yaml similarity index 100% rename from pymatgen/io/feff/MPEXAFSSet.yaml rename to src/pymatgen/io/feff/MPEXAFSSet.yaml diff --git a/pymatgen/io/feff/MPEXELFSSet.yaml b/src/pymatgen/io/feff/MPEXELFSSet.yaml similarity index 100% rename from pymatgen/io/feff/MPEXELFSSet.yaml rename to src/pymatgen/io/feff/MPEXELFSSet.yaml diff --git a/pymatgen/io/feff/MPXANESSet.yaml b/src/pymatgen/io/feff/MPXANESSet.yaml similarity index 100% rename from pymatgen/io/feff/MPXANESSet.yaml rename to src/pymatgen/io/feff/MPXANESSet.yaml diff --git a/pymatgen/io/feff/__init__.py b/src/pymatgen/io/feff/__init__.py similarity index 100% rename from pymatgen/io/feff/__init__.py rename to src/pymatgen/io/feff/__init__.py diff --git a/pymatgen/io/feff/inputs.py b/src/pymatgen/io/feff/inputs.py similarity index 99% rename from pymatgen/io/feff/inputs.py rename to src/pymatgen/io/feff/inputs.py index 5ec7be0b45b..52e95a14521 100644 --- a/pymatgen/io/feff/inputs.py +++ b/src/pymatgen/io/feff/inputs.py @@ -15,14 +15,13 @@ import numpy as np from monty.io import zopen from monty.json import MSONable -from tabulate import tabulate - from pymatgen.core import Element, Lattice, Molecule, Structure from pymatgen.io.cif import CifParser from pymatgen.io.core import ParseError from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.io_utils import clean_lines from pymatgen.util.string import str_delimited +from tabulate import tabulate if TYPE_CHECKING: from typing_extensions import Self @@ -193,7 +192,7 @@ def __init__( self.periodic = False self.space_number = self.space_group = None else: - raise ValueError("'struct' argument must be a Structure or Molecule!") + raise TypeError("'struct' argument must be a Structure or Molecule!") self.comment = comment or "None given" @classmethod @@ -331,7 +330,6 @@ def from_str(cls, header_str: str) -> Self: def __str__(self): """String representation of Header.""" - output = [ "* This FEFF.inp file generated by pymatgen", f"TITLE comment: {self.comment}", diff --git a/pymatgen/io/feff/outputs.py b/src/pymatgen/io/feff/outputs.py similarity index 99% rename from pymatgen/io/feff/outputs.py rename to src/pymatgen/io/feff/outputs.py index 133a28c7821..4337ee78741 100644 --- a/pymatgen/io/feff/outputs.py +++ b/src/pymatgen/io/feff/outputs.py @@ -13,7 +13,6 @@ import numpy as np from monty.io import zopen from monty.json import MSONable - from pymatgen.core import Element from pymatgen.electronic_structure.core import Orbital, Spin from pymatgen.electronic_structure.dos import CompleteDos, Dos diff --git a/pymatgen/io/feff/sets.py b/src/pymatgen/io/feff/sets.py similarity index 99% rename from pymatgen/io/feff/sets.py rename to src/pymatgen/io/feff/sets.py index 55ddd7fd588..4231f1772ad 100644 --- a/pymatgen/io/feff/sets.py +++ b/src/pymatgen/io/feff/sets.py @@ -20,7 +20,6 @@ from monty.json import MSONable from monty.os.path import zpath from monty.serialization import loadfn - from pymatgen.core.structure import Molecule, Structure from pymatgen.io.feff.inputs import Atoms, Header, Potential, Tags diff --git a/pymatgen/io/fiesta.py b/src/pymatgen/io/fiesta.py similarity index 98% rename from pymatgen/io/fiesta.py rename to src/pymatgen/io/fiesta.py index c98b3590f34..dc75893c37a 100644 --- a/pymatgen/io/fiesta.py +++ b/src/pymatgen/io/fiesta.py @@ -17,15 +17,13 @@ from monty.io import zopen from monty.json import MSONable - from pymatgen.core.structure import Molecule if TYPE_CHECKING: from pathlib import Path - from typing_extensions import Self - from pymatgen.util.typing import Tuple3Ints + from typing_extensions import Self __author__ = "ndardenne" __copyright__ = "Copyright 2012, The Materials Project" @@ -77,7 +75,7 @@ def run(self): os.chdir(init_folder) def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "@module": type(self).__module__, "@class": type(self).__name__, @@ -173,7 +171,7 @@ def bse_run(self): os.chdir(init_folder) def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "@module": type(self).__module__, "@class": type(self).__name__, @@ -186,7 +184,7 @@ def as_dict(self): def from_dict(cls, dct: dict) -> Self: """ Args: - dct (dict): Dict representation + dct (dict): Dict representation. Returns: FiestaRun @@ -265,7 +263,7 @@ def _parse_file(lines): return basis_set def set_n_nlmo(self): - """the number of nlm orbitals for the basis set""" + """The number of nlm orbitals for the basis set.""" n_nlm_orbs = 0 data_tmp = self.data @@ -311,7 +309,7 @@ def __init__( Exc_DFT_option: dict COHSEX_options: dict GW_options: dict - BSE_TDDFT_options: dict + BSE_TDDFT_options: dict. """ self._mol = mol self.correlation_grid = correlation_grid or {"dE_grid": "0.500", "n_grid": "14"} @@ -352,7 +350,7 @@ def set_auxiliary_basis_set(self, folder, auxiliary_folder, auxiliary_basis_set_ shutil.copyfile(f"{auxiliary_folder}/{file}", f"{folder}/{specie}2.ion") def set_gw_options(self, nv_band=10, nc_band=10, n_iteration=5, n_grid=6, dE_grid=0.5): - """Set parameters in cell.in for a GW computation + """Set parameters in cell.in for a GW computation. Args: nv__band: number of valence bands to correct with GW @@ -373,7 +371,7 @@ def make_full_bse_densities_folder(folder): return "makedirs FULL_BSE_Densities folder" def set_bse_options(self, n_excitations=10, nit_bse=200): - """Set parameters in cell.in for a BSE computation + """Set parameters in cell.in for a BSE computation. Args: nv_bse: number of valence bands @@ -386,7 +384,7 @@ def set_bse_options(self, n_excitations=10, nit_bse=200): def dump_bse_data_in_gw_run(self, BSE_dump=True): """ Args: - BSE_dump: bool + BSE_dump: bool. Returns: set the "do_bse" variable to one in cell.in @@ -399,7 +397,7 @@ def dump_bse_data_in_gw_run(self, BSE_dump=True): def dump_tddft_data_in_gw_run(self, tddft_dump: bool = True): """ Args: - TDDFT_dump: bool + TDDFT_dump: bool. Returns: set the do_tddft variable to one in cell.in @@ -528,7 +526,7 @@ def __str__(self): ) def write_file(self, filename: str | Path) -> None: - """Write FiestaInput to a file + """Write FiestaInput to a file. Args: filename: Filename. @@ -537,7 +535,7 @@ def write_file(self, filename: str | Path) -> None: file.write(str(self)) def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "mol": self._mol.as_dict(), "correlation_grid": self.correlation_grid, @@ -551,7 +549,7 @@ def as_dict(self): def from_dict(cls, dct: dict) -> Self: """ Args: - dct (dict): Dict representation + dct (dict): Dict representation. Returns: FiestaInput diff --git a/pymatgen/io/gaussian.py b/src/pymatgen/io/gaussian.py similarity index 96% rename from pymatgen/io/gaussian.py rename to src/pymatgen/io/gaussian.py index f423d218334..36102e6c334 100644 --- a/pymatgen/io/gaussian.py +++ b/src/pymatgen/io/gaussian.py @@ -9,14 +9,13 @@ import numpy as np import scipy.constants as cst from monty.io import zopen -from scipy.stats import norm - from pymatgen.core import Composition, Element, Molecule from pymatgen.core.operations import SymmOp from pymatgen.core.units import Ha_to_eV from pymatgen.electronic_structure.core import Spin from pymatgen.util.coord import get_angle from pymatgen.util.plotting import pretty_plot +from scipy.stats import norm if TYPE_CHECKING: from pathlib import Path @@ -62,17 +61,17 @@ def read_route_line(route): for tok in route.split(): if match := scrf_patt.match(tok): - route_params[match.group(1)] = match.group(2) + route_params[match[1]] = match[2] elif tok.upper() in ["#", "#N", "#P", "#T"]: # does not store # in route to avoid error in input dieze_tag = "#N" if tok == "#" else tok continue elif match := re.match(multi_params_patt, tok.strip("#")): pars = {} - for par in match.group(2).split(","): + for par in match[2].split(","): p = par.split("=") pars[p[0]] = None if len(p) == 1 else p[1] - route_params[match.group(1)] = pars + route_params[match[1]] = pars else: d = tok.strip("#").split("=") route_params[d[0]] = None if len(d) == 1 else d[1] @@ -178,7 +177,7 @@ def _parse_coords(coord_lines): var_pattern = re.compile(r"^([A-Za-z]+\S*)[\s=,]+([\d\-\.]+)$") for line in coord_lines: if match := var_pattern.match(line.strip()): - paras[match.group(1).strip("=")] = float(match.group(2)) + paras[match[1].strip("=")] = float(match[2]) species = [] coords = [] @@ -191,7 +190,7 @@ def _parse_coords(coord_lines): break if (not zmode) and GaussianInput._xyz_patt.match(line): match = GaussianInput._xyz_patt.match(line) - species.append(match.group(1)) + species.append(match[1]) tokens = re.split(r"[,\s]+", line.strip()) if len(tokens) > 4: coords.append([float(i) for i in tokens[2:5]]) @@ -295,7 +294,7 @@ def from_str(cls, contents: str) -> Self: if link0_patt.match(line): match = link0_patt.match(line) assert match is not None - link0_dict[match.group(1).strip("=")] = match.group(2) + link0_dict[match[1].strip("=")] = match[2] route_patt = re.compile(r"^#[sSpPnN]*.*") route = "" @@ -444,7 +443,7 @@ def write_file(self, filename, cart_coords=False): file.write(self.to_str(cart_coords)) def as_dict(self): - """MSONable dict""" + """MSONable dict.""" return { "@module": type(self).__module__, "@class": type(self).__name__, @@ -464,7 +463,7 @@ def as_dict(self): def from_dict(cls, dct: dict) -> Self: """ Args: - dct: dict + dct: dict. Returns: GaussianInput @@ -672,7 +671,7 @@ def _parse(self, filename): parse_stage = 1 elif link0_patt.match(line): match = link0_patt.match(line) - self.link0[match.group(1)] = match.group(2) + self.link0[match[1]] = match[2] elif route_patt.search(line) or route_line != "": if set(line.strip()) == {"-"}: params = read_route_line(route_line) @@ -692,8 +691,8 @@ def _parse(self, filename): self.title = line.strip() elif charge_mul_patt.search(line): match = charge_mul_patt.search(line) - self.charge = int(match.group(1)) - self.spin_multiplicity = int(match.group(2)) + self.charge = int(match[1]) + self.spin_multiplicity = int(match[2]) parse_stage = 2 elif parse_stage == 2: if self.is_pcm: @@ -701,11 +700,11 @@ def _parse(self, filename): if "freq" in route_lower and thermo_patt.search(line): match = thermo_patt.search(line) - if match.group(1) == "Zero-point": - self.corrections["Zero-point"] = float(match.group(3)) + if match[1] == "Zero-point": + self.corrections["Zero-point"] = float(match[3]) else: - key = match.group(2).replace(" to ", "") - self.corrections[key] = float(match.group(3)) + key = match[2].replace(" to ", "") + self.corrections[key] = float(match[3]) if read_coord: [file.readline() for i in range(3)] @@ -751,7 +750,7 @@ def _parse(self, filename): # read molecular orbital coefficients if (not num_basis_found) and num_basis_func_patt.search(line): match = num_basis_func_patt.search(line) - self.num_basis_func = int(match.group(1)) + self.num_basis_func = int(match[1]) num_basis_found = True elif read_mo: # build a matrix with all coefficients @@ -775,12 +774,12 @@ def _parse(self, filename): # identify atom and OA labels match = mo_coeff_name_patt.search(line) - if match.group(1).strip() != "": - atom_idx = int(match.group(2)) - 1 - # atname = m.group(3) - self.atom_basis_labels.append([match.group(4)]) + if match[1].strip() != "": + atom_idx = int(match[2]) - 1 + # atname = match[3] + self.atom_basis_labels.append([match[4]]) else: - self.atom_basis_labels[atom_idx].append(match.group(4)) + self.atom_basis_labels[atom_idx].append(match[4]) # MO coefficients coeffs = [float(c) for c in float_patt.findall(line)] @@ -892,7 +891,7 @@ def _parse(self, filename): elif termination_patt.search(line): match = termination_patt.search(line) - if match.group(1) == "Normal": + if match[1] == "Normal": self.properly_terminated = True terminated = True elif error_patt.search(line): @@ -901,10 +900,10 @@ def _parse(self, filename): "Convergence failure": "SCF convergence error", } match = error_patt.search(line) - self.errors.append(error_defs[match.group(1)]) + self.errors.append(error_defs[match[1]]) elif num_elec_patt.search(line): match = num_elec_patt.search(line) - self.electrons = (int(match.group(1)), int(match.group(2))) + self.electrons = (int(match[1]), int(match[2])) elif (not self.is_pcm) and pcm_patt.search(line): self.is_pcm = True self.pcm = {} @@ -912,13 +911,13 @@ def _parse(self, filename): self.stationary_type = "Saddle" elif mp2_patt.search(line): match = mp2_patt.search(line) - self.energies.append(float(match.group(1).replace("D", "E"))) + self.energies.append(float(match[1].replace("D", "E"))) elif oniom_patt.search(line): match = oniom_patt.matcher(line) - self.energies.append(float(match.group(1))) + self.energies.append(float(match[1])) elif scf_patt.search(line): match = scf_patt.search(line) - self.energies.append(float(match.group(1))) + self.energies.append(float(match[1])) elif std_orientation_patt.search(line): standard_orientation = True geom_orientation = "standard" @@ -945,7 +944,7 @@ def _parse(self, filename): parse_forces = True elif freq_on_patt.search(line): parse_freq = True - _ = [file.readline() for _i in range(3)] + _ = [file.readline() for _ in range(3)] elif mo_coeff_patt.search(line): if "Alpha" in line: self.is_spin = True @@ -976,7 +975,7 @@ def _parse(self, filename): for line in mulliken_txt: if mulliken_charge_patt.search(line): match = mulliken_charge_patt.search(line) - dic = {int(match.group(1)): [match.group(2), float(match.group(3))]} + dic = {int(match[1]): [match[2], float(match[3])]} mulliken_charges.update(dic) read_mulliken = False self.Mulliken_charges = mulliken_charges @@ -1031,13 +1030,13 @@ def _check_pcm(self, line): if energy_patt.search(line): match = energy_patt.search(line) - self.pcm[f"{match.group(1)} energy"] = float(match.group(2)) + self.pcm[f"{match[1]} energy"] = float(match[2]) elif total_patt.search(line): match = total_patt.search(line) - self.pcm["Total energy"] = float(match.group(1)) + self.pcm["Total energy"] = float(match[1]) elif parameter_patt.search(line): match = parameter_patt.search(line) - self.pcm[match.group(1)] = float(match.group(2)) + self.pcm[match[1]] = float(match[2]) def as_dict(self): """JSON-serializable dict representation.""" @@ -1151,7 +1150,6 @@ def get_scan_plot(self, coords=None): Args: coords: internal coordinate name to use as abscissa. """ - ax = pretty_plot(12, 8) dct = self.read_scan() diff --git a/pymatgen/io/icet.py b/src/pymatgen/io/icet.py similarity index 99% rename from pymatgen/io/icet.py rename to src/pymatgen/io/icet.py index 8c0bffaf90c..70620edef36 100644 --- a/pymatgen/io/icet.py +++ b/src/pymatgen/io/icet.py @@ -160,7 +160,6 @@ def run(self) -> Sqs: Returns: pymatgen Sqs object """ - sqs_structures = self.sqs_getter() for idx in range(len(sqs_structures)): sqs_structures[idx]["structure"] = AseAtomsAdaptor.get_structure(sqs_structures[idx]["structure"]) @@ -235,7 +234,6 @@ def enumerate_sqs_structures(self, cluster_space: _ClusterSpace | None = None) - "objective_function": SQS objective function, } """ - # Translate concentrations to the format required for concentration # restricted enumeration cr: dict[str, tuple] = {} diff --git a/pymatgen/io/jarvis.py b/src/pymatgen/io/jarvis.py similarity index 100% rename from pymatgen/io/jarvis.py rename to src/pymatgen/io/jarvis.py diff --git a/pymatgen/io/lammps/CoeffsDataType.yaml b/src/pymatgen/io/lammps/CoeffsDataType.yaml similarity index 100% rename from pymatgen/io/lammps/CoeffsDataType.yaml rename to src/pymatgen/io/lammps/CoeffsDataType.yaml diff --git a/pymatgen/io/lammps/__init__.py b/src/pymatgen/io/lammps/__init__.py similarity index 100% rename from pymatgen/io/lammps/__init__.py rename to src/pymatgen/io/lammps/__init__.py diff --git a/pymatgen/io/lammps/data.py b/src/pymatgen/io/lammps/data.py similarity index 99% rename from pymatgen/io/lammps/data.py rename to src/pymatgen/io/lammps/data.py index 72e248232f0..46ac9b97765 100644 --- a/pymatgen/io/lammps/data.py +++ b/src/pymatgen/io/lammps/data.py @@ -27,20 +27,18 @@ from monty.io import zopen from monty.json import MSONable from monty.serialization import loadfn -from ruamel.yaml import YAML - from pymatgen.core import Element, Lattice, Molecule, Structure from pymatgen.core.operations import SymmOp from pymatgen.util.io_utils import clean_lines +from ruamel.yaml import YAML if TYPE_CHECKING: from collections.abc import Sequence from typing import Any, Literal - from typing_extensions import Self - from pymatgen.core.sites import Site from pymatgen.core.structure import SiteCollection + from typing_extensions import Self __author__ = "Kiran Mathew, Zhi Deng, Tingzheng Hou" __copyright__ = "Copyright 2018, The Materials Virtual Lab" @@ -399,15 +397,15 @@ def map_charges(q) -> str: coeffs: dict[str, dict] = {} for style, types in coeffs_data_type.items(): coeffs[style] = {} - for type, formatter in types.items(): - coeffs[style][type] = {} - for coeff, datatype in formatter.items(): # type: ignore + for typ, formatter in types.items(): + coeffs[style][typ] = {} + for coeff, datatype in formatter.items(): # type: ignore[attr-defined] if datatype == "int_format": - coeffs[style][type][coeff] = int_format + coeffs[style][typ][coeff] = int_format elif datatype == "float_format_2": - coeffs[style][type][coeff] = float_format_2 + coeffs[style][typ][coeff] = float_format_2 else: - coeffs[style][type][coeff] = float_format + coeffs[style][typ][coeff] = float_format section_template = "{kw}\n\n{df}\n" parts = [] @@ -830,7 +828,7 @@ def from_structure( velos = np.array(struct.site_properties["velocities"]) rot = SymmOp.from_rotation_and_translation(symm_op.rotation_matrix) rot_velos = rot.operate_multi(velos) - site_properties["velocities"] = rot_velos # type: ignore + site_properties["velocities"] = rot_velos boxed_s = Structure( box.to_lattice(), struct.species, diff --git a/pymatgen/io/lammps/generators.py b/src/pymatgen/io/lammps/generators.py similarity index 99% rename from pymatgen/io/lammps/generators.py rename to src/pymatgen/io/lammps/generators.py index d4b0cbd1263..5e1c0a30950 100644 --- a/pymatgen/io/lammps/generators.py +++ b/src/pymatgen/io/lammps/generators.py @@ -15,7 +15,6 @@ from string import Template from monty.io import zopen - from pymatgen.core import Structure from pymatgen.io.core import InputGenerator from pymatgen.io.lammps.data import CombinedData, LammpsData @@ -111,7 +110,7 @@ def __init__( force_field: str = "Unspecified force field!", keep_stages: bool = False, ) -> None: - """ + r""" Args: template: Path (string) to the template file used to create the InputFile for LAMMPS. units: units to be used for the LAMMPS calculation (see LAMMPS docs). diff --git a/pymatgen/io/lammps/inputs.py b/src/pymatgen/io/lammps/inputs.py similarity index 99% rename from pymatgen/io/lammps/inputs.py rename to src/pymatgen/io/lammps/inputs.py index 9153321d152..5ea8477d5fd 100644 --- a/pymatgen/io/lammps/inputs.py +++ b/src/pymatgen/io/lammps/inputs.py @@ -19,7 +19,6 @@ from monty.dev import deprecated from monty.io import zopen from monty.json import MSONable - from pymatgen.core import __version__ as CURRENT_VER from pymatgen.io.core import InputFile from pymatgen.io.lammps.data import CombinedData, LammpsData @@ -28,9 +27,8 @@ if TYPE_CHECKING: from os import PathLike - from typing_extensions import Self - from pymatgen.io.core import InputSet + from typing_extensions import Self __author__ = "Kiran Mathew, Brandon Wood, Zhi Deng, Manas Likhit, Guillaume Brunin (Matgenix)" __copyright__ = "Copyright 2018, The Materials Virtual Lab" @@ -934,9 +932,9 @@ class LammpsTemplateGen(TemplateInputGen): See pymatgen.io.template.py for additional documentation of this method. """ - def get_input_set( # type: ignore + def get_input_set( # type: ignore[override] self, - script_template: str | Path, + script_template: PathLike, settings: dict | None = None, script_filename: str = "in.lammps", data: LammpsData | CombinedData | None = None, @@ -974,7 +972,7 @@ def write_lammps_inputs( **kwargs, ) -> None: """ - Writes input files for a LAMMPS run. Input script is constructed + Write input files for a LAMMPS run. Input script is constructed from a str template with placeholders to be filled by custom settings. Data file is either written from a LammpsData instance or copied from an existing file if read_data cmd is @@ -1051,7 +1049,7 @@ def write_lammps_inputs( input_script = template.safe_substitute(**variables) if make_dir_if_not_present: os.makedirs(output_dir, exist_ok=True) - with open(os.path.join(output_dir, script_filename), mode="w") as file: + with open(os.path.join(output_dir, script_filename), mode="w", encoding="utf-8") as file: file.write(input_script) if read_data := re.search(r"read_data\s+(.*)\n", input_script): diff --git a/pymatgen/io/lammps/outputs.py b/src/pymatgen/io/lammps/outputs.py similarity index 99% rename from pymatgen/io/lammps/outputs.py rename to src/pymatgen/io/lammps/outputs.py index 033a7d58b4a..b8e9688c06d 100644 --- a/pymatgen/io/lammps/outputs.py +++ b/src/pymatgen/io/lammps/outputs.py @@ -14,7 +14,6 @@ import pandas as pd from monty.io import zopen from monty.json import MSONable - from pymatgen.io.lammps.data import LammpsBox if TYPE_CHECKING: diff --git a/pymatgen/io/lammps/sets.py b/src/pymatgen/io/lammps/sets.py similarity index 93% rename from pymatgen/io/lammps/sets.py rename to src/pymatgen/io/lammps/sets.py index cb1cdb08e89..54e63afd5f2 100644 --- a/pymatgen/io/lammps/sets.py +++ b/src/pymatgen/io/lammps/sets.py @@ -18,8 +18,7 @@ from pymatgen.io.lammps.inputs import LammpsInputFile if TYPE_CHECKING: - from pathlib import Path - + from pymatgen.util.typing import PathLike from typing_extensions import Self __author__ = "Ryan Kingsbury, Guillaume Brunin (Matgenix)" @@ -50,7 +49,7 @@ def __init__( inputfile: LammpsInputFile | str, data: LammpsData | CombinedData, calc_type: str = "", - template_file: str = "", + template_file: PathLike = "", keep_stages: bool = False, ) -> None: """ @@ -75,9 +74,9 @@ def __init__( super().__init__(inputs={"in.lammps": self.inputfile, "system.data": self.data}) @classmethod - def from_directory(cls, directory: str | Path, keep_stages: bool = False) -> Self: # type: ignore[override] - """ - Construct a LammpsInputSet from a directory of two or more files. + def from_directory(cls, directory: PathLike, keep_stages: bool = False) -> Self: # type: ignore[override] + """Construct a LammpsInputSet from a directory of two or more files. + TODO: accept directories with only the input file, that should include the structure as well. Args: @@ -88,7 +87,7 @@ def from_directory(cls, directory: str | Path, keep_stages: bool = False) -> Sel input_file = LammpsInputFile.from_file(f"{directory}/in.lammps", keep_stages=keep_stages) atom_style = input_file.get_args("atom_style") if isinstance(atom_style, list): - raise ValueError("Variable atom_style is specified multiple times in the input file.") + raise ValueError("Variable atom_style is specified multiple times in the input file.") # noqa: TRY004 data_file = LammpsData.from_file(f"{directory}/system.data", atom_style=atom_style) return cls(inputfile=input_file, data=data_file, calc_type="read_from_dir") diff --git a/pymatgen/io/lammps/templates/md.template b/src/pymatgen/io/lammps/templates/md.template similarity index 100% rename from pymatgen/io/lammps/templates/md.template rename to src/pymatgen/io/lammps/templates/md.template diff --git a/pymatgen/io/lammps/templates/minimization.template b/src/pymatgen/io/lammps/templates/minimization.template similarity index 100% rename from pymatgen/io/lammps/templates/minimization.template rename to src/pymatgen/io/lammps/templates/minimization.template diff --git a/pymatgen/io/lammps/templates/msd.template b/src/pymatgen/io/lammps/templates/msd.template similarity index 100% rename from pymatgen/io/lammps/templates/msd.template rename to src/pymatgen/io/lammps/templates/msd.template diff --git a/pymatgen/io/lammps/templates/thermalization.template b/src/pymatgen/io/lammps/templates/thermalization.template similarity index 100% rename from pymatgen/io/lammps/templates/thermalization.template rename to src/pymatgen/io/lammps/templates/thermalization.template diff --git a/pymatgen/io/lammps/utils.py b/src/pymatgen/io/lammps/utils.py similarity index 98% rename from pymatgen/io/lammps/utils.py rename to src/pymatgen/io/lammps/utils.py index c7ae00f2f10..cc8537d8af6 100644 --- a/pymatgen/io/lammps/utils.py +++ b/src/pymatgen/io/lammps/utils.py @@ -11,7 +11,6 @@ import numpy as np from monty.dev import deprecated from monty.tempfile import ScratchDir - from pymatgen.core.operations import SymmOp from pymatgen.core.structure import Molecule from pymatgen.io.babel import BabelMolAdaptor @@ -190,7 +189,7 @@ def __init__( control_params: dict | None = None, auto_box: bool = True, output_file: str = "packed.xyz", - bin: str = "packmol", + bin: str = "packmol", # noqa: A002 ) -> None: """ Args: @@ -363,7 +362,6 @@ def convert_obatoms_to_molecule( Returns: Molecule object """ - if residue_name is not None and not hasattr(self, "map_residue_to_mol"): self._set_residue_map() @@ -430,7 +428,7 @@ def restore_site_properties(self, site_property: str = "ff_map", filename: str | class LammpsRunner: """LAMMPS wrapper.""" - def __init__(self, input_filename: str = "lammps.in", bin: str = "lammps") -> None: + def __init__(self, input_filename: str = "lammps.in", bin: str = "lammps") -> None: # noqa: A002 """ Args: input_filename (str): input file name @@ -450,8 +448,8 @@ def run(self) -> tuple[bytes, bytes]: """Write the input/data files and run LAMMPS.""" lammps_cmd = [*self.lammps_bin, "-in", self.input_filename] print(f"Running: {' '.join(lammps_cmd)}") - with Popen(lammps_cmd, stdout=PIPE, stderr=PIPE) as p: - stdout, stderr = p.communicate() + with Popen(lammps_cmd, stdout=PIPE, stderr=PIPE) as process: + stdout, stderr = process.communicate() return stdout, stderr diff --git a/pymatgen/io/lmto.py b/src/pymatgen/io/lmto.py similarity index 98% rename from pymatgen/io/lmto.py rename to src/pymatgen/io/lmto.py index 328821fea81..5c6057d8190 100644 --- a/pymatgen/io/lmto.py +++ b/src/pymatgen/io/lmto.py @@ -11,7 +11,6 @@ import numpy as np from monty.io import zopen - from pymatgen.core.structure import Structure from pymatgen.core.units import Ry_to_eV, bohr_to_angstrom from pymatgen.electronic_structure.core import Spin @@ -182,13 +181,13 @@ def from_str(cls, data: str, sigfigs: int = 8) -> Self: for cat in ["STRUC", "CLASS", "SITE"]: fields = struct_lines[cat].split("=") - for idx, field in enumerate(fields, start=1): + for idx, field in enumerate(fields): token = field.split()[-1] if token == "ALAT": - a_lat = round(float(fields[idx].split()[0]), sigfigs) + a_lat = round(float(fields[idx + 1].split()[0]), sigfigs) structure_tokens["ALAT"] = a_lat elif token == "ATOM": - atom = fields[idx].split()[0] + atom = fields[idx + 1].split()[0] if not bool(re.match("E[0-9]*$", atom)): if cat == "CLASS": structure_tokens["CLASS"].append(atom) @@ -198,9 +197,9 @@ def from_str(cls, data: str, sigfigs: int = 8) -> Self: pass elif token in ["PLAT", "POS"]: try: - arr = np.array([round(float(i), sigfigs) for i in fields[idx].split()]) + arr = np.array([round(float(i), sigfigs) for i in fields[idx + 1].split()]) except ValueError: - arr = np.array([round(float(i), sigfigs) for i in fields[idx].split()[:-1]]) + arr = np.array([round(float(i), sigfigs) for i in fields[idx + 1].split()[:-1]]) if token == "PLAT": structure_tokens["PLAT"] = arr.reshape([3, 3]) elif not bool(re.match("E[0-9]*$", atom)): @@ -362,6 +361,6 @@ def _get_bond_data(line): # Replacing "/" with "-" makes splitting easier sites = line[0].replace("/", "-").split("-") site_indices = tuple(int(ind) - 1 for ind in sites[1:4:2]) - species = tuple(re.split(r"\d+", spec)[0] for spec in sites[0:3:2]) + species = tuple(re.split(r"\d+", spec)[0] for spec in sites[:3:2]) label = f"{species[0]}{site_indices[0] + 1}-{species[1]}{site_indices[1] + 1}" return label, length, site_indices diff --git a/pymatgen/io/lobster/__init__.py b/src/pymatgen/io/lobster/__init__.py similarity index 100% rename from pymatgen/io/lobster/__init__.py rename to src/pymatgen/io/lobster/__init__.py diff --git a/pymatgen/io/lobster/inputs.py b/src/pymatgen/io/lobster/inputs.py similarity index 99% rename from pymatgen/io/lobster/inputs.py rename to src/pymatgen/io/lobster/inputs.py index bb57e4c4b9d..f3759a38b93 100644 --- a/pymatgen/io/lobster/inputs.py +++ b/src/pymatgen/io/lobster/inputs.py @@ -22,7 +22,6 @@ from monty.io import zopen from monty.json import MSONable from monty.serialization import loadfn - from pymatgen.core.structure import Structure from pymatgen.io.vasp import Vasprun from pymatgen.io.vasp.inputs import Incar, Kpoints, Potcar @@ -32,10 +31,9 @@ if TYPE_CHECKING: from typing import Any, ClassVar, Literal - from typing_extensions import Self - from pymatgen.core.composition import Composition from pymatgen.util.typing import PathLike, Tuple3Ints + from typing_extensions import Self MODULE_DIR = os.path.dirname(os.path.abspath(__file__)) @@ -264,7 +262,7 @@ def write_lobsterin( file.write(f"{type(self).LIST_KEYWORDS[key]} {value}\n") def as_dict(self) -> dict: - """MSONable dict""" + """MSONable dict.""" dct = dict(self) dct["@module"] = type(self).__module__ dct["@class"] = type(self).__name__ @@ -686,7 +684,6 @@ def standard_calculations_from_vasp_files( Returns: Lobsterin with standard settings """ - warnings.warn( "Always check and test the provided basis functions. The spilling of your Lobster calculation might help" ) diff --git a/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_max.yaml b/src/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_max.yaml similarity index 100% rename from pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_max.yaml rename to src/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_max.yaml diff --git a/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_min.yaml b/src/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_min.yaml similarity index 100% rename from pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_min.yaml rename to src/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_min.yaml diff --git a/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_standard.yaml b/src/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_standard.yaml similarity index 100% rename from pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_standard.yaml rename to src/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_standard.yaml diff --git a/pymatgen/io/lobster/lobsterenv.py b/src/pymatgen/io/lobster/lobsterenv.py similarity index 99% rename from pymatgen/io/lobster/lobsterenv.py rename to src/pymatgen/io/lobster/lobsterenv.py index 4f1a1cc56e9..7982b025c99 100644 --- a/pymatgen/io/lobster/lobsterenv.py +++ b/src/pymatgen/io/lobster/lobsterenv.py @@ -20,7 +20,6 @@ import numpy as np from monty.dev import deprecated - from pymatgen.analysis.bond_valence import BVAnalyzer from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments @@ -32,10 +31,9 @@ from pymatgen.util.due import Doi, due if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.core import Structure from pymatgen.core.periodic_table import Element + from typing_extensions import Self __author__ = "Janine George" __copyright__ = "Copyright 2021, The Materials Project" @@ -388,7 +386,7 @@ def get_light_structure_environment(self, only_cation_environments=False, only_i def get_info_icohps_to_neighbors(self, isites=None, onlycation_isites=True): """Get information on the icohps of neighbors for certain sites as identified by their site id. This is useful for plotting the relevant cohps of a site in the structure. - (could be ICOOPLIST.lobster or ICOHPLIST.lobster or ICOBILIST.lobster) + (could be ICOOPLIST.lobster or ICOHPLIST.lobster or ICOBILIST.lobster). Args: isites: list of site ids. If isite==None, all isites will be used to add the icohps of the neighbors @@ -1137,7 +1135,7 @@ def _determine_unit_cell(site): def _adapt_extremum_to_add_cond(self, list_icohps, percentage): """ - Convinicence method for returning the extremum of the given icohps or icoops or icobis list + Convinicence method for returning the extremum of the given icohps or icoops or icobis list. Args: list_icohps: can be a list of icohps or icobis or icobis @@ -1145,7 +1143,6 @@ def _adapt_extremum_to_add_cond(self, list_icohps, percentage): Returns: float: min value of input list of icohps / max value of input list of icobis or icobis """ - which_extr = min if not self.are_coops and not self.are_cobis else max return which_extr(list_icohps) * percentage diff --git a/pymatgen/io/lobster/outputs.py b/src/pymatgen/io/lobster/outputs.py similarity index 95% rename from pymatgen/io/lobster/outputs.py rename to src/pymatgen/io/lobster/outputs.py index e30308233db..d17c550ba9b 100644 --- a/pymatgen/io/lobster/outputs.py +++ b/src/pymatgen/io/lobster/outputs.py @@ -22,7 +22,6 @@ import numpy as np from monty.io import zopen from monty.json import MSONable - from pymatgen.core.structure import Structure from pymatgen.electronic_structure.bandstructure import LobsterBandStructureSymmLine from pymatgen.electronic_structure.core import Orbital, Spin @@ -35,6 +34,7 @@ from typing import Any from pymatgen.core.structure import IStructure + from pymatgen.util.typing import PathLike __author__ = "Janine George, Marco Esters" __copyright__ = "Copyright 2017, The Materials Project" @@ -80,7 +80,7 @@ def __init__( are_coops: bool = False, are_cobis: bool = False, are_multi_center_cobis: bool = False, - filename: str | None = None, + filename: PathLike | None = None, ) -> None: """ Args: @@ -278,7 +278,6 @@ def _get_bond_data(line: str, are_multi_center_cobis: bool = False) -> dict: indices, a tuple containing the orbitals (if orbital-resolved), and a label for the orbitals (if orbital-resolved). """ - if not are_multi_center_cobis: line_new = line.rsplit("(", 1) length = float(line_new[-1][:-1]) @@ -343,7 +342,7 @@ def __init__( self, are_coops: bool = False, are_cobis: bool = False, - filename: str | None = None, + filename: PathLike | None = None, is_spin_polarized: bool = False, orbitalwise: bool = False, icohpcollection=None, @@ -357,12 +356,9 @@ def __init__( filename: Name of the ICOHPLIST file. If it is None, the default file name will be chosen, depending on the value of are_coops is_spin_polarized: Boolean to indicate if the calculation is spin polarized - icohpcollection: IcohpCollection Object + icohpcollection: IcohpCollection Object. """ - # to avoid circular dependencies - from pymatgen.electronic_structure.cohp import IcohpCollection - self._filename = filename self.is_spin_polarized = is_spin_polarized self.orbitalwise = orbitalwise @@ -492,6 +488,9 @@ def __init__( else: list_orb_icohp[int(label) - 1][orb_label] = {"icohp": icohp, "orbitals": orbitals} + # Avoid circular import + from pymatgen.electronic_structure.cohp import IcohpCollection + self._icohpcollection = IcohpCollection( are_coops=are_coops, are_cobis=are_cobis, @@ -537,15 +536,19 @@ class NciCobiList: "interaction_type": type of the multi-center interaction """ - def __init__(self, filename: str | None = "NcICOBILIST.lobster"): # LOBSTER < 4.1.0: no COBI/ICOBI/NcICOBI + def __init__( + self, + filename: PathLike | None = "NcICOBILIST.lobster", + ) -> None: """ + LOBSTER < 4.1.0: no COBI/ICOBI/NcICOBI. + Args: filename: Name of the NcICOBILIST file. """ - # LOBSTER list files have an extra trailing blank line # and we don't need the header. - with zopen(filename, mode="rt") as file: # type:ignore + with zopen(filename, mode="rt") as file: data = file.read().split("\n")[1:-1] if len(data) == 0: raise RuntimeError("NcICOBILIST file contains no data.") @@ -611,9 +614,7 @@ def __init__(self, filename: str | None = "NcICOBILIST.lobster"): # LOBSTER < 4 @property def ncicobi_list(self) -> dict[Any, dict[str, Any]]: - """ - Returns: ncicobilist. - """ + """Returns: ncicobilist.""" ncicobi_list = {} for idx in range(len(self.list_labels)): ncicobi_list[str(idx + 1)] = { @@ -649,13 +650,13 @@ class Doscar: def __init__( self, - doscar: str = "DOSCAR.lobster", - structure_file: str | None = "POSCAR", + doscar: PathLike = "DOSCAR.lobster", + structure_file: PathLike | None = "POSCAR", structure: IStructure | Structure | None = None, ): """ Args: - doscar: DOSCAR filename, typically "DOSCAR.lobster" + doscar: DOSCAR file, typically "DOSCAR.lobster" structure_file: for vasp, this is typically "POSCAR" structure: instead of a structure file, the structure can be given directly. structure_file will be preferred. @@ -742,32 +743,32 @@ def _parse_doscar(self): @property def completedos(self) -> LobsterCompleteDos: - """LobsterCompleteDos""" + """LobsterCompleteDos.""" return self._completedos @property def pdos(self) -> list: - """Projected DOS""" + """Projected DOS.""" return self._pdos @property def tdos(self) -> Dos: - """Total DOS""" + """Total DOS.""" return self._tdos @property def energies(self) -> np.ndarray: - """Energies""" + """Energies.""" return self._energies @property def tdensities(self) -> dict[Spin, np.ndarray]: - """total densities as a np.ndarray""" + """Total densities as a np.ndarray.""" return self._tdensities @property def itdensities(self) -> dict[Spin, np.ndarray]: - """integrated total densities as a np.ndarray""" + """Integrated total densities as a np.ndarray.""" return self._itdensities @property @@ -789,7 +790,7 @@ class Charge(MSONable): def __init__( self, - filename: str = "CHARGE.lobster", + filename: PathLike = "CHARGE.lobster", num_atoms: int | None = None, atomlist: list[str] | None = None, types: list[str] | None = None, @@ -798,12 +799,12 @@ def __init__( ): """ Args: - filename: filename for the CHARGE file, typically "CHARGE.lobster". + filename: The CHARGE file, typically "CHARGE.lobster". num_atoms: number of atoms in the structure atomlist: list of atoms in the structure types: list of unique species in the structure mulliken: list of Mulliken charges - loewdin: list of Loewdin charges + loewdin: list of Loewdin charges. """ self._filename = filename self.num_atoms = num_atoms @@ -816,7 +817,7 @@ def __init__( with zopen(filename, mode="rt") as file: data = file.read().split("\n")[3:-3] if len(data) == 0: - raise RuntimeError("CHARGES file contains no data.") + raise RuntimeError("CHARGE file contains no data.") self.num_atoms = len(data) for atom in range(self.num_atoms): @@ -826,8 +827,8 @@ def __init__( self.mulliken += [float(line[2])] self.loewdin += [float(line[3])] - def get_structure_with_charges(self, structure_filename): - """Get a Structure with Mulliken and Loewdin charges as site properties + def get_structure_with_charges(self, structure_filename: PathLike) -> Structure: + """Get a Structure with Mulliken and Loewdin charges as site properties. Args: structure_filename: filename of POSCAR @@ -920,11 +921,11 @@ class Lobsterout(MSONable): # TODO: add tests for skipping COBI and madelung # TODO: add tests for including COBI and madelung - def __init__(self, filename: str | None, **kwargs) -> None: + def __init__(self, filename: PathLike | None, **kwargs) -> None: """ Args: - filename: filename of lobsterout. - **kwargs: dict to initialize Lobsterout instance + filename: The lobsterout file. + **kwargs: dict to initialize Lobsterout instance. """ self.filename = filename if kwargs: @@ -1007,46 +1008,38 @@ def __init__(self, filename: str | None, **kwargs) -> None: def get_doc(self) -> dict[str, Any]: """Get the LobsterDict with all the information stored in lobsterout.""" - lobster_dict: dict[str, Any] = {} - # check if Lobster starts from a projection - lobster_dict["restart_from_projection"] = self.is_restart_from_projection - lobster_dict["lobster_version"] = self.lobster_version - lobster_dict["threads"] = self.number_of_threads - lobster_dict["dft_program"] = self.dft_program - - lobster_dict["charge_spilling"] = self.charge_spilling - lobster_dict["total_spilling"] = self.total_spilling - - lobster_dict["elements"] = self.elements - lobster_dict["basis_type"] = self.basis_type - lobster_dict["basis_functions"] = self.basis_functions - - lobster_dict["timing"] = self.timing - - lobster_dict["warning_lines"] = self.warning_lines - - lobster_dict["info_orthonormalization"] = self.info_orthonormalization - - lobster_dict["info_lines"] = self.info_lines - - lobster_dict["has_doscar"] = self.has_doscar - lobster_dict["has_doscar_lso"] = self.has_doscar_lso - lobster_dict["has_cohpcar"] = self.has_cohpcar - lobster_dict["has_coopcar"] = self.has_coopcar - lobster_dict["has_cobicar"] = self.has_cobicar - lobster_dict["has_charge"] = self.has_charge - lobster_dict["has_madelung"] = self.has_madelung - lobster_dict["has_projection"] = self.has_projection - lobster_dict["has_bandoverlaps"] = self.has_bandoverlaps - lobster_dict["has_fatbands"] = self.has_fatbands - lobster_dict["has_grosspopulation"] = self.has_grosspopulation - lobster_dict["has_density_of_energies"] = self.has_density_of_energies - - return lobster_dict - - def as_dict(self): - """MSONable dict""" - dct = vars(self) + return { + # Check if LOBSTER starts from a projection + "restart_from_projection": self.is_restart_from_projection, + "lobster_version": self.lobster_version, + "threads": self.number_of_threads, + "dft_program": self.dft_program, + "charge_spilling": self.charge_spilling, + "total_spilling": self.total_spilling, + "elements": self.elements, + "basis_type": self.basis_type, + "basis_functions": self.basis_functions, + "timing": self.timing, + "warning_lines": self.warning_lines, + "info_orthonormalization": self.info_orthonormalization, + "info_lines": self.info_lines, + "has_doscar": self.has_doscar, + "has_doscar_lso": self.has_doscar_lso, + "has_cohpcar": self.has_cohpcar, + "has_coopcar": self.has_coopcar, + "has_cobicar": self.has_cobicar, + "has_charge": self.has_charge, + "has_madelung": self.has_madelung, + "has_projection": self.has_projection, + "has_bandoverlaps": self.has_bandoverlaps, + "has_fatbands": self.has_fatbands, + "has_grosspopulation": self.has_grosspopulation, + "has_density_of_energies": self.has_density_of_energies, + } + + def as_dict(self) -> dict: + """MSONable dict.""" + dct = dict(vars(self)) dct["@module"] = type(self).__module__ dct["@class"] = type(self).__name__ @@ -1137,7 +1130,7 @@ def _get_elements_basistype_basisfunctions(data): @staticmethod def _get_timing(data): - # will give back wall, user and sys time + # Will give back wall, user and sys time begin = False user_time, wall_time, sys_time = [], [], [] @@ -1212,9 +1205,9 @@ class Fatband: def __init__( self, - filenames: str | list = ".", - kpoints_file: str = "KPOINTS", - vasprun_file: str | None = "vasprun.xml", + filenames: PathLike | list = ".", + kpoints_file: PathLike = "KPOINTS", + vasprun_file: PathLike | None = "vasprun.xml", structure: Structure | IStructure | None = None, efermi: float | None = None, ): @@ -1222,12 +1215,12 @@ def __init__( Args: filenames (list or string): can be a list of file names or a path to a folder from which all "FATBAND_*" files will be read - kpoints_file (str): KPOINTS file for bandstructure calculation, typically "KPOINTS". - vasprun_file (str): Corresponding vasprun file. + kpoints_file (PathLike): KPOINTS file for bandstructure calculation, typically "KPOINTS". + vasprun_file (PathLike): Corresponding vasprun file. Instead, the Fermi energy from the DFT run can be provided. Then, this value should be set to None. structure (Structure): Structure object. - efermi (float): fermi energy in eV + efermi (float): fermi energy in eV. """ warnings.warn("Make sure all relevant FATBAND files were generated and read in!") warnings.warn("Use Lobster 3.2.0 or newer for fatband calculations!") @@ -1406,13 +1399,13 @@ def __init__( self.label_dict = label_dict - def get_bandstructure(self): + def get_bandstructure(self) -> LobsterBandStructureSymmLine: """Get a LobsterBandStructureSymmLine object which can be plotted with a normal BSPlotter.""" return LobsterBandStructureSymmLine( kpoints=self.kpoints_array, eigenvals=self.eigenvals, lattice=self.lattice, - efermi=self.efermi, # type: ignore + efermi=self.efermi, labels_dict=self.label_dict, structure=self.structure, projections=self.p_eigenvals, @@ -1421,6 +1414,7 @@ def get_bandstructure(self): class Bandoverlaps(MSONable): """Read in bandOverlaps.lobster files. These files are not created during every Lobster run. + Attributes: band_overlaps_dict (dict[Spin, Dict[str, Dict[str, Union[float, np.ndarray]]]]): A dictionary containing the band overlap data of the form: {spin: {"kpoint as string": {"maxDeviation": @@ -1460,7 +1454,7 @@ def __init__( def _read(self, contents: list, spin_numbers: list): """ - Will read in all contents of the file + Will read in all contents of the file. Args: contents: list of strings @@ -1508,7 +1502,7 @@ def _read(self, contents: list, spin_numbers: list): def has_good_quality_maxDeviation(self, limit_maxDeviation: float = 0.1) -> bool: """ - Will check if the maxDeviation from the ideal bandoverlap is smaller or equal to limit_maxDeviation + Will check if the maxDeviation from the ideal bandoverlap is smaller or equal to limit_maxDeviation. Args: limit_maxDeviation: limit of the maxDeviation @@ -1589,7 +1583,7 @@ def __init__(self, filename: str = "GROSSPOP.lobster", list_dict_grosspop: list[ """ Args: filename: filename of the "GROSSPOP.lobster" file - list_dict_grosspop: List of dictionaries including all information about the gross populations + list_dict_grosspop: List of dictionaries including all information about the gross populations. """ # opens file self._filename = filename @@ -1615,7 +1609,7 @@ def __init__(self, filename: str = "GROSSPOP.lobster", list_dict_grosspop: list[ self.list_dict_grosspop += [small_dict] def get_structure_with_total_grosspop(self, structure_filename: str) -> Structure: - """Get a Structure with Mulliken and Loewdin total grosspopulations as site properties + """Get a Structure with Mulliken and Loewdin total grosspopulations as site properties. Args: structure_filename (str): filename of POSCAR @@ -1890,7 +1884,7 @@ def __init__( sitepotentials_loewdin: Loewdin site potential sitepotentials_mulliken: Mulliken site potential madelungenergies_loewdin: Madelung energy based on the Loewdin approach - madelungenergies_mulliken: Madelung energy based on the Mulliken approach + madelungenergies_mulliken: Madelung energy based on the Mulliken approach. """ self._filename = filename self.ewald_splitting = [] if ewald_splitting is None else ewald_splitting @@ -1925,7 +1919,7 @@ def __init__( self.madelungenergies_loewdin = float(data[self.num_atoms + 1].split()[4]) def get_structure_with_site_potentials(self, structure_filename): - """Get a Structure with Mulliken and Loewdin charges as site properties + """Get a Structure with Mulliken and Loewdin charges as site properties. Args: structure_filename: filename of POSCAR @@ -2011,9 +2005,9 @@ def get_orb_from_str(orbs): orb_label = "" for iorb, orbital in enumerate(orbitals): if iorb == 0: - orb_label += f"{orbital[0]}{orbital[1].name}" # type: ignore + orb_label += f"{orbital[0]}{orbital[1].name}" else: - orb_label += f"-{orbital[0]}{orbital[1].name}" # type: ignore + orb_label += f"-{orbital[0]}{orbital[1].name}" return orb_label, orbitals @@ -2060,9 +2054,8 @@ def __init__(self, e_fermi=None, filename: str = "hamiltonMatrices.lobster"): Args: filename: filename for the hamiltonMatrices file, typically "hamiltonMatrices.lobster". e_fermi: fermi level in eV for the structure only - relevant if input file contains hamilton matrices data + relevant if input file contains hamilton matrices data. """ - self._filename = filename # hamiltonMatrices with zopen(self._filename, mode="rt") as file: diff --git a/pymatgen/io/nwchem.py b/src/pymatgen/io/nwchem.py similarity index 97% rename from pymatgen/io/nwchem.py rename to src/pymatgen/io/nwchem.py index e070934bcc5..8b39dcb40e3 100644 --- a/pymatgen/io/nwchem.py +++ b/src/pymatgen/io/nwchem.py @@ -29,7 +29,6 @@ import numpy as np from monty.io import zopen from monty.json import MSONable - from pymatgen.analysis.excitation import ExcitationSpectrum from pymatgen.core.structure import Molecule, Structure from pymatgen.core.units import Energy, FloatWithUnit @@ -732,7 +731,7 @@ def isfloatstring(in_str): if line.find(e) != -1: errors.append(v) if parse_time and (match := time_patt.search(line)): - time = match.group(1) + time = match[1] parse_time = False if parse_geom: if line.strip() == "Atomic Mass": @@ -746,11 +745,11 @@ def isfloatstring(in_str): parse_geom = False else: if match := coord_patt.search(line): - species.append(match.group(1).capitalize()) - coords.append([float(match.group(2)), float(match.group(3)), float(match.group(4))]) + species.append(match[1].capitalize()) + coords.append([float(match[2]), float(match[3]), float(match[4])]) if match := lat_vector_patt.search(line): - lattice.append([float(match.group(1)), float(match.group(2)), float(match.group(3))]) + lattice.append([float(match[1]), float(match[2]), float(match[3])]) if parse_force: if match := force_patt.search(line): @@ -836,7 +835,7 @@ def isfloatstring(in_str): else: if match := energy_patt.search(line): - energies.append(Energy(match.group(1), "Ha").to("eV")) + energies.append(Energy(match[1], "Ha").to("eV")) parse_time = True continue @@ -844,17 +843,17 @@ def isfloatstring(in_str): cosmo_scf_energy = energies[-1] energies[-1] = {} energies[-1]["cosmo scf"] = cosmo_scf_energy - energies[-1].update({"gas phase": Energy(match.group(1), "Ha").to("eV")}) + energies[-1].update({"gas phase": Energy(match[1], "Ha").to("eV")}) if match := energy_sol_patt.search(line): - energies[-1].update({"sol phase": Energy(match.group(1), "Ha").to("eV")}) + energies[-1].update({"sol phase": Energy(match[1], "Ha").to("eV")}) if match := preamble_patt.search(line): try: - val = int(match.group(2)) + val = int(match[2]) except ValueError: - val = match.group(2) - k = match.group(1).replace("No. of ", "n").replace(" ", "_") + val = match[2] + k = match[1].replace("No. of ", "n").replace(" ", "_") data[k.lower()] = val elif line.find('Geometry "geometry"') != -1: parse_geom = True @@ -892,7 +891,7 @@ def isfloatstring(in_str): if job_type == "NWChem DFT Module" and "COSMO solvation results" in output: job_type += " COSMO" elif match := corrections_patt.search(line): - corrections[match.group(1)] = FloatWithUnit(match.group(2), "kJ mol^-1").to("eV atom^-1") + corrections[match[1]] = FloatWithUnit(match[2], "kJ mol^-1").to("eV atom^-1") if frequencies: for _freq, mode in frequencies: diff --git a/pymatgen/io/openff.py b/src/pymatgen/io/openff.py similarity index 98% rename from pymatgen/io/openff.py rename to src/pymatgen/io/openff.py index 2eb016d7ab4..bef308811d5 100644 --- a/pymatgen/io/openff.py +++ b/src/pymatgen/io/openff.py @@ -6,7 +6,6 @@ from pathlib import Path import numpy as np - import pymatgen from pymatgen.analysis.graphs import MoleculeGraph from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender @@ -78,7 +77,7 @@ def mol_graph_to_openff_mol(mol_graph: MoleculeGraph) -> tk.Molecule: def mol_graph_from_openff_mol(molecule: tk.Molecule) -> MoleculeGraph: """ - This is designed to closely mirror the graph structure generated by tk.Molecule.to_networkx + This is designed to closely mirror the graph structure generated by tk.Molecule.to_networkx. Args: molecule (tk.Molecule): The OpenFF Molecule to convert. @@ -139,10 +138,10 @@ def get_atom_map(inferred_mol: tk.Molecule, openff_mol: tk.Molecule) -> tuple[bo isomorphism was found and a dictionary representing the atom mapping. """ # do not apply formal charge restrictions - kwargs = dict( - return_atom_map=True, - formal_charge_matching=False, - ) + kwargs = { + "return_atom_map": True, + "formal_charge_matching": False, + } isomorphic, atom_map = tk.topology.Molecule.are_isomorphic(openff_mol, inferred_mol, **kwargs) if isomorphic: return True, atom_map diff --git a/pymatgen/io/packmol.py b/src/pymatgen/io/packmol.py similarity index 92% rename from pymatgen/io/packmol.py rename to src/pymatgen/io/packmol.py index 70cce25c10e..d1f1f7f6c6a 100644 --- a/pymatgen/io/packmol.py +++ b/src/pymatgen/io/packmol.py @@ -23,12 +23,15 @@ class that provides a run() method for running packmol locally. import subprocess from pathlib import Path from shutil import which +from typing import TYPE_CHECKING import numpy as np - from pymatgen.core import Molecule from pymatgen.io.core import InputGenerator, InputSet +if TYPE_CHECKING: + from pymatgen.util.typing import PathLike + __author__ = "Tingzheng Hou, Ryan Kingsbury, Orion Cohen" __version__ = "1.0" __maintainer__ = "Ryan Kingsbury" @@ -37,11 +40,9 @@ class that provides a run() method for running packmol locally. class PackmolSet(InputSet): - """ - InputSet for the Packmol software. This class defines several attributes related to. - """ + """InputSet for the Packmol software. This class defines several attributes related to.""" - def run(self, path: str | Path, timeout=30): + def run(self, path: PathLike, timeout=30): """Run packmol and write out the packed structure. Args: @@ -88,12 +89,12 @@ def run(self, path: str | Path, timeout=30): os.chdir(wd) @classmethod - def from_directory(cls, directory: str | Path) -> None: + def from_directory(cls, directory: PathLike) -> None: """ Construct an InputSet from a directory of one or more files. Args: - directory (str | Path): Directory to read input files from. + directory (PathLike): Directory to read input files from. """ raise NotImplementedError(f"from_directory has not been implemented in {cls.__name__}") @@ -109,9 +110,9 @@ def __init__( tolerance: float = 2.0, seed: int = 1, control_params: dict | None = None, - inputfile: str | Path = "packmol.inp", - outputfile: str | Path = "packmol_out.xyz", - stdoutfile: str | Path = "packmol.stdout", + inputfile: PathLike = "packmol.inp", + outputfile: PathLike = "packmol_out.xyz", + stdoutfile: PathLike = "packmol.stdout", ) -> None: """ Instantiate a PackmolBoxGen class. The init method defines simulations parameters @@ -132,7 +133,7 @@ def __init__( self.tolerance = tolerance self.seed = seed - def get_input_set( # type: ignore + def get_input_set( self, molecules: list[dict], box: list[float] | None = None, @@ -182,7 +183,7 @@ def get_input_set( # type: ignore # estimate the total volume of all molecules in cubic Å net_volume = 0.0 for d in molecules: - mol = Molecule.from_file(d["coords"]) if not isinstance(d["coords"], Molecule) else d["coords"] + mol = d["coords"] if isinstance(d["coords"], Molecule) else Molecule.from_file(d["coords"]) if mol is None: raise ValueError("Molecule cannot be None.") @@ -222,10 +223,10 @@ def get_input_set( # type: ignore file_contents += f" inside box {box_list}\n" file_contents += "end structure\n\n" - mapping.update({str(self.inputfile): file_contents}) + mapping |= {str(self.inputfile): file_contents} return PackmolSet( - inputs=mapping, # type: ignore + inputs=mapping, # type: ignore[arg-type] seed=self.seed, inputfile=self.inputfile, outputfile=self.outputfile, diff --git a/pymatgen/io/phonopy.py b/src/pymatgen/io/phonopy.py similarity index 99% rename from pymatgen/io/phonopy.py rename to src/pymatgen/io/phonopy.py index e0fda1c8e33..6e156b2e2e5 100644 --- a/pymatgen/io/phonopy.py +++ b/src/pymatgen/io/phonopy.py @@ -5,14 +5,13 @@ import numpy as np from monty.dev import requires from monty.serialization import loadfn -from scipy.interpolate import InterpolatedUnivariateSpline - from pymatgen.core import Lattice, Structure from pymatgen.phonon.bandstructure import PhononBandStructure, PhononBandStructureSymmLine from pymatgen.phonon.dos import CompletePhononDos, PhononDos from pymatgen.phonon.gruneisen import GruneisenParameter, GruneisenPhononBandStructureSymmLine from pymatgen.phonon.thermal_displacements import ThermalDisplacementMatrices from pymatgen.symmetry.bandstructure import HighSymmKpath +from scipy.interpolate import InterpolatedUnivariateSpline try: from phonopy import Phonopy @@ -644,7 +643,7 @@ def get_thermal_displacement_matrices( thermal_displacements_yaml="thermal_displacement_matrices.yaml", structure_path="POSCAR" ): """Read "thermal_displacement_matrices.yaml" from phonopy and return a list of - ThermalDisplacementMatrices objects + ThermalDisplacementMatrices objects. Args: thermal_displacements_yaml: path to thermal_displacement_matrices.yaml diff --git a/pymatgen/io/prismatic.py b/src/pymatgen/io/prismatic.py similarity index 100% rename from pymatgen/io/prismatic.py rename to src/pymatgen/io/prismatic.py diff --git a/pymatgen/io/pwmat/__init__.py b/src/pymatgen/io/pwmat/__init__.py similarity index 100% rename from pymatgen/io/pwmat/__init__.py rename to src/pymatgen/io/pwmat/__init__.py diff --git a/pymatgen/io/pwmat/inputs.py b/src/pymatgen/io/pwmat/inputs.py similarity index 98% rename from pymatgen/io/pwmat/inputs.py rename to src/pymatgen/io/pwmat/inputs.py index 6475a6b195d..1051405ffe9 100644 --- a/pymatgen/io/pwmat/inputs.py +++ b/src/pymatgen/io/pwmat/inputs.py @@ -8,14 +8,12 @@ import numpy as np from monty.io import zopen from monty.json import MSONable - from pymatgen.core import Lattice, Structure from pymatgen.symmetry.kpath import KPathSeek if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.util.typing import PathLike + from typing_extensions import Self __author__ = "Hanyu Liu" __email__ = "domainofbuaa@gmail.com" @@ -27,7 +25,7 @@ class LineLocator(MSONable): @staticmethod def locate_all_lines(file_path: PathLike, content: str, exclusion: str = "") -> list[int]: - """Locate the line in file where a certain paragraph of text is located (return all indices) + """Locate the line in file where a certain paragraph of text is located (return all indices). Args: file_path (PathLike): Absolute path to file. @@ -51,7 +49,7 @@ class ListLocator(MSONable): @staticmethod def locate_all_lines(strs_lst: list[str], content: str, exclusion: str = "") -> list[int]: - """Locate the elements in list where a certain paragraph of text is located (return all indices) + """Locate the elements in list where a certain paragraph of text is located (return all indices). Args: strs_lst (list[str]): List of strings. @@ -68,7 +66,7 @@ def locate_all_lines(strs_lst: list[str], content: str, exclusion: str = "") -> class ACExtractorBase(ABC): - """A parent class of ACExtractor and ACstrExtractor, ensuring that they are as consistent as possible""" + """A parent class of ACExtractor and ACstrExtractor, ensuring that they are as consistent as possible.""" @abstractmethod def get_n_atoms(self) -> int: @@ -76,28 +74,28 @@ def get_n_atoms(self) -> int: @abstractmethod def get_lattice(self) -> np.ndarray: - """Get the lattice of structure defined by atom.config file""" + """Get the lattice of structure defined by atom.config file.""" @abstractmethod def get_types(self) -> np.ndarray: - """Get atomic number of atoms in structure defined by atom.config file""" + """Get atomic number of atoms in structure defined by atom.config file.""" @abstractmethod def get_coords(self) -> np.ndarray: - """Get fractional coordinates of atoms in structure defined by atom.config file""" + """Get fractional coordinates of atoms in structure defined by atom.config file.""" @abstractmethod def get_magmoms(self) -> np.ndarray: - """Get atomic magmoms of atoms in structure defined by atom.config file""" + """Get atomic magmoms of atoms in structure defined by atom.config file.""" class ACExtractor(ACExtractorBase): - """Extract information contained in atom.config : number of atoms, lattice, types, frac_coords, magmoms""" + """Extract information contained in atom.config : number of atoms, lattice, types, frac_coords, magmoms.""" def __init__(self, file_path: PathLike) -> None: - """Initialization function + """Initialization function. - Args + Args: file_path (str): The absolute path of atom.config file. """ self.atom_config_path = file_path @@ -405,7 +403,7 @@ def from_str(cls, data: str, mag: bool = False) -> Self: @classmethod def from_file(cls, filename: PathLike, mag: bool = False) -> Self: - """Get a AtomConfig from a file + """Get a AtomConfig from a file. Args: filename (PathLike): File name containing AtomConfig data @@ -468,7 +466,7 @@ def write_file(self, filename: PathLike, **kwargs): def as_dict(self): """ Returns: - dict + dict. """ return { "@module": type(self).__module__, diff --git a/pymatgen/io/pwmat/outputs.py b/src/pymatgen/io/pwmat/outputs.py similarity index 98% rename from pymatgen/io/pwmat/outputs.py rename to src/pymatgen/io/pwmat/outputs.py index 8013be25dc5..0ebd966efd2 100644 --- a/pymatgen/io/pwmat/outputs.py +++ b/src/pymatgen/io/pwmat/outputs.py @@ -8,7 +8,6 @@ import numpy as np from monty.io import zopen from monty.json import MSONable - from pymatgen.io.pwmat.inputs import ACstrExtractor, AtomConfig, LineLocator if TYPE_CHECKING: @@ -154,10 +153,10 @@ def _parse_sefv(self) -> list[dict]: class OutFermi(MSONable): - """Extract fermi energy (eV) from OUT.FERMI""" + """Extract fermi energy (eV) from OUT.FERMI.""" def __init__(self, filename: PathLike): - """Initialization function + """Initialization function. Args: filename (PathLike): The absolute path of OUT.FERMI file. @@ -318,7 +317,7 @@ class DosSpin(MSONable): """Extract information of DOS from DOS_SPIN file: - DOS.totalspin, DOS.totalspin_projected - DOS.spinup, DOS.spinup_projected - - DOS.spindown, DOS.spindown_projected + - DOS.spindown, DOS.spindown_projected. """ def __init__(self, filename: PathLike): @@ -343,7 +342,7 @@ def _parse(self): @property def labels(self) -> list[str]: - """The name of the partial density of states""" + """The name of the partial density of states.""" return self._labels @property diff --git a/pymatgen/io/pwscf.py b/src/pymatgen/io/pwscf.py similarity index 96% rename from pymatgen/io/pwscf.py rename to src/pymatgen/io/pwscf.py index 49f281569d2..2af861b9941 100644 --- a/pymatgen/io/pwscf.py +++ b/src/pymatgen/io/pwscf.py @@ -8,7 +8,6 @@ from monty.io import zopen from monty.re import regrep - from pymatgen.core import Element, Lattice, Structure from pymatgen.util.io_utils import clean_lines @@ -501,18 +500,18 @@ class PWInputError(BaseException): class PWOutput: """Parser for PWSCF output file.""" - patterns: ClassVar[dict[str, str]] = dict( - energies=r"total energy\s+=\s+([\d\.\-]+)\sRy", - ecut=r"kinetic\-energy cutoff\s+=\s+([\d\.\-]+)\s+Ry", - lattice_type=r"bravais\-lattice index\s+=\s+(\d+)", - celldm1=r"celldm\(1\)=\s+([\d\.]+)\s", - celldm2=r"celldm\(2\)=\s+([\d\.]+)\s", - celldm3=r"celldm\(3\)=\s+([\d\.]+)\s", - celldm4=r"celldm\(4\)=\s+([\d\.]+)\s", - celldm5=r"celldm\(5\)=\s+([\d\.]+)\s", - celldm6=r"celldm\(6\)=\s+([\d\.]+)\s", - nkpts=r"number of k points=\s+([\d]+)", - ) + patterns: ClassVar[dict[str, str]] = { + "energies": r"total energy\s+=\s+([\d\.\-]+)\sRy", + "ecut": r"kinetic\-energy cutoff\s+=\s+([\d\.\-]+)\s+Ry", + "lattice_type": r"bravais\-lattice index\s+=\s+(\d+)", + "celldm1": r"celldm\(1\)=\s+([\d\.]+)\s", + "celldm2": r"celldm\(2\)=\s+([\d\.]+)\s", + "celldm3": r"celldm\(3\)=\s+([\d\.]+)\s", + "celldm4": r"celldm\(4\)=\s+([\d\.]+)\s", + "celldm5": r"celldm\(5\)=\s+([\d\.]+)\s", + "celldm6": r"celldm\(6\)=\s+([\d\.]+)\s", + "nkpts": r"number of k points=\s+([\d]+)", + } def __init__(self, filename): """ diff --git a/pymatgen/io/qchem/__init__.py b/src/pymatgen/io/qchem/__init__.py similarity index 100% rename from pymatgen/io/qchem/__init__.py rename to src/pymatgen/io/qchem/__init__.py diff --git a/pymatgen/io/qchem/inputs.py b/src/pymatgen/io/qchem/inputs.py similarity index 99% rename from pymatgen/io/qchem/inputs.py rename to src/pymatgen/io/qchem/inputs.py index a960f2f24c1..bb20603c8bd 100644 --- a/pymatgen/io/qchem/inputs.py +++ b/src/pymatgen/io/qchem/inputs.py @@ -7,7 +7,6 @@ from typing import TYPE_CHECKING from monty.io import zopen - from pymatgen.core import Molecule from pymatgen.io.core import InputFile @@ -15,7 +14,7 @@ if TYPE_CHECKING: from pathlib import Path - from typing import Literal + from typing import Any, Literal from typing_extensions import Self @@ -240,10 +239,6 @@ def __init__( # - Validity checks specific to job type? # - Check OPT and PCM sections? - def get_str(self) -> str: - """Return a string representation of an entire input file.""" - return str(self) - def __str__(self) -> str: combined_list: list = [] # molecule section @@ -288,6 +283,10 @@ def __str__(self) -> str: combined_list.append(self.pcm_nonels_template(self.pcm_nonels)) return "\n".join(combined_list) + def get_str(self) -> str: + """Return a string representation of an entire input file.""" + return str(self) + @staticmethod def multi_job_string(job_list: list[QCInput]) -> str: """ @@ -1154,23 +1153,23 @@ def read_cdft(string: str) -> list[list[dict]]: if len(const_out) == 0: continue for const in const_out: - const_dict = { + const_dict: dict[str, Any] = { "value": float(const[0]), "coefficients": [], "first_atoms": [], "last_atoms": [], "types": [], - } # type: ignore + } sub_consts = const[1].strip().split("\n") for subconst in sub_consts: tokens = subconst.split() - const_dict["coefficients"].append(float(tokens[0])) # type: ignore - const_dict["first_atoms"].append(int(tokens[1])) # type: ignore - const_dict["last_atoms"].append(int(tokens[2])) # type: ignore + const_dict["coefficients"].append(float(tokens[0])) + const_dict["first_atoms"].append(int(tokens[1])) + const_dict["last_atoms"].append(int(tokens[2])) if len(tokens) > 3: - const_dict["types"].append(tokens[3]) # type: ignore + const_dict["types"].append(tokens[3]) else: - const_dict["types"].append(None) # type: ignore + const_dict["types"].append(None) state_list.append(const_dict) @@ -1202,7 +1201,7 @@ def read_almo(string: str) -> list[list[tuple[int, int]]]: section = section[0] - almo_coupling = [[], []] # type: ignore + almo_coupling: list[list] = [[], []] state_1 = section[0] for line in state_1.strip().split("\n"): diff --git a/pymatgen/io/qchem/outputs.py b/src/pymatgen/io/qchem/outputs.py similarity index 99% rename from pymatgen/io/qchem/outputs.py rename to src/pymatgen/io/qchem/outputs.py index 1bafe43d2fb..6db29b910ac 100644 --- a/pymatgen/io/qchem/outputs.py +++ b/src/pymatgen/io/qchem/outputs.py @@ -16,7 +16,6 @@ import pandas as pd from monty.io import zopen from monty.json import MSONable, jsanitize - from pymatgen.analysis.graphs import MoleculeGraph from pymatgen.analysis.local_env import OpenBabelNN from pymatgen.core import Molecule @@ -953,7 +952,6 @@ def _read_charges_and_dipoles(self): Parses associated dipole/multipole moments. Also parses spins given an unrestricted SCF. """ - self.data["dipoles"] = {} temp_dipole_total = read_pattern( self.text, {"key": r"X\s*[\d\-\.]+\s*Y\s*[\d\-\.]+\s*Z\s*[\d\-\.]+\s*Tot\s*([\d\-\.]+)"} @@ -2333,7 +2331,7 @@ def parse_natural_populations(lines: list[str]) -> list[pd.DataFrame]: # Extract the values values = line.split() if len(values[0]) > 2: - values.insert(0, values[0][0:-3]) + values.insert(0, values[0][:-3]) values[1] = values[1][-3:] data.append( [ diff --git a/pymatgen/io/qchem/sets.py b/src/pymatgen/io/qchem/sets.py similarity index 98% rename from pymatgen/io/qchem/sets.py rename to src/pymatgen/io/qchem/sets.py index 6b5f7661d99..7be1ddbc67a 100644 --- a/pymatgen/io/qchem/sets.py +++ b/src/pymatgen/io/qchem/sets.py @@ -8,14 +8,14 @@ from typing import TYPE_CHECKING from monty.io import zopen - from pymatgen.io.qchem.inputs import QCInput from pymatgen.io.qchem.utils import lower_and_check_unique if TYPE_CHECKING: - from typing import Literal + from typing import Any, Literal from pymatgen.core.structure import Molecule + from pymatgen.util.typing import PathLike __author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath, Evan Spotte-Smith, Ryan Kingsbury" __copyright__ = "Copyright 2018-2022, The Materials Project" @@ -25,12 +25,12 @@ logger = logging.getLogger(__name__) -# note that in addition to the solvent-specific parameters, this dict contains +# Note that in addition to the solvent-specific parameters, this dict contains # dielectric constants for use with each solvent. The dielectric constants # are used by the isodensity SS(V)PE electrostatic calculation part of CMIRS # they are not part of the parameters tabulated by Q-Chem # see https://manual.q-chem.com/latest/example_CMIRS-water.html -CMIRS_SETTINGS = { +CMIRS_SETTINGS: dict[str, Any] = { "water": { "0.001": { "a": "-0.006736", @@ -384,7 +384,7 @@ def __init__( "vdwscale": "1.1", } - svp_defaults = {"rhoiso": "0.001", "nptleb": "1202", "itrngr": "2", "irotgr": "2"} + svp_defaults: dict[str, Any] = {"rhoiso": "0.001", "nptleb": "1202", "itrngr": "2", "irotgr": "2"} plots_defaults = {"grid_spacing": "0.05", "total_density": "0"} @@ -397,20 +397,21 @@ def __init__( smx: dict = {} vdw: dict = {} plots: dict = {} - rem: dict = {} - svp: dict = {} - pcm_nonels: dict = {} - rem["job_type"] = job_type - rem["basis"] = self.basis_set - rem["max_scf_cycles"] = str(self.max_scf_cycles) - rem["gen_scfman"] = "true" - rem["xc_grid"] = "3" - rem["thresh"] = "14" - rem["s2thresh"] = "16" - rem["scf_algorithm"] = self.scf_algorithm - rem["resp_charges"] = "true" - rem["symmetry"] = "false" - rem["sym_ignore"] = "true" + svp: dict[str, Any] = {} + pcm_nonels: dict[str, Any] = {} + rem: dict[str, Any] = { + "job_type": job_type, + "basis": self.basis_set, + "max_scf_cycles": str(self.max_scf_cycles), + "gen_scfman": "true", + "xc_grid": "3", + "thresh": "14", + "s2thresh": "16", + "scf_algorithm": self.scf_algorithm, + "resp_charges": "true", + "symmetry": "false", + "sym_ignore": "true", + } if self.dft_rung == 1: rem["method"] = "spw92" @@ -476,10 +477,10 @@ def __init__( svp = svp_defaults rem["solvent_method"] = "isosvp" rem["gen_scfman"] = "false" - svp["dielst"] = CMIRS_SETTINGS[self.cmirs_solvent]["dielst"] # type: ignore + svp["dielst"] = CMIRS_SETTINGS[self.cmirs_solvent]["dielst"] svp["idefesr"] = "1" # this flag enables the CMIRS part svp["ipnrf"] = "1" # this flag is also required for some undocumented reason - pcm_nonels = CMIRS_SETTINGS[self.cmirs_solvent][svp["rhoiso"]] # type: ignore + pcm_nonels = CMIRS_SETTINGS[self.cmirs_solvent][svp["rhoiso"]] pcm_nonels["delta"] = "7" # as recommended by Q-Chem. See manual. pcm_nonels["gaulag_n"] = "40" # as recommended by Q-Chem. See manual. @@ -563,8 +564,8 @@ def __init__( "CMIRS is only parameterized for RHOISO values of 0.001 or 0.0005! Exiting..." ) for k2 in pcm_nonels: - if CMIRS_SETTINGS[self.cmirs_solvent][v].get(k2): # type: ignore - pcm_nonels[k2] = CMIRS_SETTINGS[self.cmirs_solvent][v].get(k2) # type: ignore + if CMIRS_SETTINGS[self.cmirs_solvent][v].get(k2): + pcm_nonels[k2] = CMIRS_SETTINGS[self.cmirs_solvent][v].get(k2) if k == "idefesr": if self.cmirs_solvent is not None and v == "0": warnings.warn( @@ -615,13 +616,13 @@ def __init__( pcm_nonels=pcm_nonels, ) - def write(self, input_file: str): + def write(self, input_file: PathLike) -> None: """ Args: - input_file (str): Filename. + input_file (PathLike): Filename. """ self.write_file(input_file) - if self.smd_solvent in ("custom", "other") and self.qchem_version == 5: + if self.smd_solvent in {"custom", "other"} and self.qchem_version == 5: with zopen(os.path.join(os.path.dirname(input_file), "solvent_data"), mode="wt") as file: file.write(self.custom_smd) diff --git a/pymatgen/io/qchem/utils.py b/src/pymatgen/io/qchem/utils.py similarity index 100% rename from pymatgen/io/qchem/utils.py rename to src/pymatgen/io/qchem/utils.py diff --git a/pymatgen/io/res.py b/src/pymatgen/io/res.py similarity index 99% rename from pymatgen/io/res.py rename to src/pymatgen/io/res.py index 0c0c2e38842..6218392ed1e 100644 --- a/pymatgen/io/res.py +++ b/src/pymatgen/io/res.py @@ -17,7 +17,6 @@ from monty.io import zopen from monty.json import MSONable - from pymatgen.core import Element, Lattice, PeriodicSite, Structure from pymatgen.entries.computed_entries import ComputedStructureEntry from pymatgen.io.core import ParseError @@ -28,9 +27,8 @@ from pathlib import Path from typing import Any, Callable, Literal - from typing_extensions import Self - from pymatgen.util.typing import Tuple3Ints, Vector3D + from typing_extensions import Self @dataclass(frozen=True) @@ -421,7 +419,7 @@ def _parse_date(cls, string: str) -> date: raise ResParseError(f"Could not parse the date from {string=}.") day, month, year, *_ = match.groups() - month_num = datetime.datetime.strptime(month, "%b").month + month_num = datetime.datetime.strptime(month, "%b").replace(tzinfo=datetime.timezone.utc).month return datetime.date(int(year), month_num, int(day)) diff --git a/pymatgen/io/shengbte.py b/src/pymatgen/io/shengbte.py similarity index 99% rename from pymatgen/io/shengbte.py rename to src/pymatgen/io/shengbte.py index d648c67a81f..7ccdee00c23 100644 --- a/pymatgen/io/shengbte.py +++ b/src/pymatgen/io/shengbte.py @@ -8,7 +8,6 @@ import numpy as np from monty.dev import requires from monty.json import MSONable - from pymatgen.core.structure import Structure from pymatgen.io.vasp import Kpoints @@ -103,7 +102,7 @@ def __init__(self, ngrid: list[int] | None = None, temperature: float | dict[str - positions (size natomx3 array): atomic positions in lattice coordinates - scell (size 3 list): supercell sizes along each crystal axis - used for the 2nd-order force constant calculation + used for the 2nd-order force constant calculation. """ super().__init__() if ngrid is None: @@ -119,7 +118,7 @@ def __init__(self, ngrid: list[int] | None = None, temperature: float | dict[str self["t_max"] = temperature["max"] self["t_step"] = temperature["step"] else: - raise ValueError("Unsupported temperature type, must be float or dict") + raise TypeError("Unsupported temperature type, must be float or dict") self.update(kwargs) diff --git a/pymatgen/io/template.py b/src/pymatgen/io/template.py similarity index 81% rename from pymatgen/io/template.py rename to src/pymatgen/io/template.py index de8aa33cbd4..6103f09d105 100644 --- a/pymatgen/io/template.py +++ b/src/pymatgen/io/template.py @@ -9,11 +9,10 @@ from typing import TYPE_CHECKING from monty.io import zopen - from pymatgen.io.core import InputGenerator, InputSet if TYPE_CHECKING: - from pathlib import Path + from pymatgen.util.typing import PathLike __author__ = "Ryan Kingsbury" __email__ = "RKingsbury@lbl.gov" @@ -31,9 +30,12 @@ class TemplateInputGen(InputGenerator): classes. """ - def get_input_set( # type: ignore - self, template: str | Path, variables: dict | None = None, filename: str = "input.txt" - ): + def get_input_set( + self, + template: PathLike, + variables: dict | None = None, + filename: PathLike = "input.txt", + ) -> InputSet: """ Args: template: the input file template containing variable strings to be @@ -42,16 +44,16 @@ def get_input_set( # type: ignore text to replaced with the values, e.g. {"TEMPERATURE": 298} will replace the text $TEMPERATURE in the template. See Python's Template.safe_substitute() method documentation for more details. - filename: name of the file to be written. + filename: the file to be written. """ self.template = template self.variables = variables or {} - self.filename = filename + self.filename = str(filename) - # load the template + # Load the template with zopen(self.template, mode="r") as file: template_str = file.read() - # replace all variables + # Replace all variables self.data = Template(template_str).safe_substitute(**self.variables) return InputSet({self.filename: self.data}) diff --git a/pymatgen/io/vasp/MITRelaxSet.yaml b/src/pymatgen/io/vasp/MITRelaxSet.yaml similarity index 100% rename from pymatgen/io/vasp/MITRelaxSet.yaml rename to src/pymatgen/io/vasp/MITRelaxSet.yaml diff --git a/pymatgen/io/vasp/MPAbsorptionSet.yaml b/src/pymatgen/io/vasp/MPAbsorptionSet.yaml similarity index 100% rename from pymatgen/io/vasp/MPAbsorptionSet.yaml rename to src/pymatgen/io/vasp/MPAbsorptionSet.yaml diff --git a/pymatgen/io/vasp/MPHSERelaxSet.yaml b/src/pymatgen/io/vasp/MPHSERelaxSet.yaml similarity index 100% rename from pymatgen/io/vasp/MPHSERelaxSet.yaml rename to src/pymatgen/io/vasp/MPHSERelaxSet.yaml diff --git a/pymatgen/io/vasp/MPRelaxSet.yaml b/src/pymatgen/io/vasp/MPRelaxSet.yaml similarity index 100% rename from pymatgen/io/vasp/MPRelaxSet.yaml rename to src/pymatgen/io/vasp/MPRelaxSet.yaml diff --git a/pymatgen/io/vasp/MPSCANRelaxSet.yaml b/src/pymatgen/io/vasp/MPSCANRelaxSet.yaml similarity index 100% rename from pymatgen/io/vasp/MPSCANRelaxSet.yaml rename to src/pymatgen/io/vasp/MPSCANRelaxSet.yaml diff --git a/pymatgen/io/vasp/MVLGWSet.yaml b/src/pymatgen/io/vasp/MVLGWSet.yaml similarity index 100% rename from pymatgen/io/vasp/MVLGWSet.yaml rename to src/pymatgen/io/vasp/MVLGWSet.yaml diff --git a/pymatgen/io/vasp/MVLRelax52Set.yaml b/src/pymatgen/io/vasp/MVLRelax52Set.yaml similarity index 100% rename from pymatgen/io/vasp/MVLRelax52Set.yaml rename to src/pymatgen/io/vasp/MVLRelax52Set.yaml diff --git a/pymatgen/io/vasp/MatPESStaticSet.yaml b/src/pymatgen/io/vasp/MatPESStaticSet.yaml similarity index 100% rename from pymatgen/io/vasp/MatPESStaticSet.yaml rename to src/pymatgen/io/vasp/MatPESStaticSet.yaml diff --git a/pymatgen/io/vasp/PBE54Base.yaml b/src/pymatgen/io/vasp/PBE54Base.yaml similarity index 100% rename from pymatgen/io/vasp/PBE54Base.yaml rename to src/pymatgen/io/vasp/PBE54Base.yaml diff --git a/pymatgen/io/vasp/PBE64Base.yaml b/src/pymatgen/io/vasp/PBE64Base.yaml similarity index 100% rename from pymatgen/io/vasp/PBE64Base.yaml rename to src/pymatgen/io/vasp/PBE64Base.yaml diff --git a/pymatgen/io/vasp/VASPIncarBase.yaml b/src/pymatgen/io/vasp/VASPIncarBase.yaml similarity index 100% rename from pymatgen/io/vasp/VASPIncarBase.yaml rename to src/pymatgen/io/vasp/VASPIncarBase.yaml diff --git a/pymatgen/io/vasp/__init__.py b/src/pymatgen/io/vasp/__init__.py similarity index 100% rename from pymatgen/io/vasp/__init__.py rename to src/pymatgen/io/vasp/__init__.py diff --git a/pymatgen/io/vasp/help.py b/src/pymatgen/io/vasp/help.py similarity index 100% rename from pymatgen/io/vasp/help.py rename to src/pymatgen/io/vasp/help.py diff --git a/pymatgen/io/vasp/incar_parameters.json b/src/pymatgen/io/vasp/incar_parameters.json similarity index 100% rename from pymatgen/io/vasp/incar_parameters.json rename to src/pymatgen/io/vasp/incar_parameters.json diff --git a/pymatgen/io/vasp/inputs.py b/src/pymatgen/io/vasp/inputs.py similarity index 99% rename from pymatgen/io/vasp/inputs.py rename to src/pymatgen/io/vasp/inputs.py index c8989160086..25572a2b1ab 100644 --- a/pymatgen/io/vasp/inputs.py +++ b/src/pymatgen/io/vasp/inputs.py @@ -31,23 +31,21 @@ from monty.os import cd from monty.os.path import zpath from monty.serialization import dumpfn, loadfn -from tabulate import tabulate - from pymatgen.core import SETTINGS, Element, Lattice, Structure, get_el_sp from pymatgen.electronic_structure.core import Magmom from pymatgen.util.io_utils import clean_lines from pymatgen.util.string import str_delimited from pymatgen.util.typing import Kpoint, Tuple3Floats, Tuple3Ints, Vector3D +from tabulate import tabulate if TYPE_CHECKING: from collections.abc import Iterator from typing import Any, ClassVar, Literal from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.symmetry.bandstructure import HighSymmKpath from pymatgen.util.typing import PathLike + from typing_extensions import Self __author__ = "Shyue Ping Ong, Geoffroy Hautier, Rickard Armiento, Vincent L Chevrier, Stephen Dacek" @@ -768,7 +766,7 @@ def as_dict(self) -> dict: def from_dict(cls, dct: dict[str, Any]) -> Self: """ Args: - dct (dict): Serialized Incar + dct (dict): Serialized Incar. Returns: Incar @@ -1062,7 +1060,7 @@ def __str__(self) -> str: def from_str(cls, mode: str) -> Self: """ Args: - mode: String + mode: String. Returns: Kpoints_supported_modes @@ -1187,9 +1185,7 @@ def __repr__(self) -> str: @property def kpts(self) -> Sequence[Kpoint]: - """ - A sequence of Kpoints, where each Kpoint is a tuple of 3 or 1. - """ + """A sequence of Kpoints, where each Kpoint is a tuple of 3 or 1.""" if all(isinstance(kpt, (list, tuple, np.ndarray)) and len(kpt) in {1, 3} for kpt in self._kpts): return cast(Sequence[Kpoint], list(map(tuple, self._kpts))) # type: ignore[arg-type] @@ -1202,7 +1198,7 @@ def kpts(self) -> Sequence[Kpoint]: def kpts(self, kpts: Sequence[float | int] | Sequence[Sequence[float | int]]) -> None: """ Args: - kpts: Sequence[float | int] | Sequence[Sequence[float | int]] + kpts: Sequence[float | int] | Sequence[Sequence[float | int]]. """ self._kpts = kpts @@ -1489,12 +1485,12 @@ def copy(self) -> Self: return self.from_dict(self.as_dict()) @classmethod - def from_file(cls, filename: str | Path) -> Self: + def from_file(cls, filename: PathLike) -> Self: """ Reads a Kpoints object from a KPOINTS file. Args: - filename (str): filename to read from. + filename (PathLike): filename to read from. Returns: Kpoints object @@ -2088,7 +2084,7 @@ def is_valid(self) -> bool: "header": dict[float], "data": dict[float], }, - } + }. Rationale: Each POTCAR is structured as @@ -2115,7 +2111,6 @@ def is_valid(self) -> bool: tol is then used to match statistical values within a tolerance """ - possible_potcar_matches = [] # Some POTCARs have an LEXCH (functional used to generate the POTCAR) # with the expected functional, e.g. the C_d POTCAR for PBE is actually an @@ -2618,7 +2613,7 @@ def __str__(self) -> str: def __iter__(self) -> Iterator[PotcarSingle]: """Boilerplate code. Only here to supply type hint so - `for psingle in Potcar()` is correctly inferred as PotcarSingle + `for psingle in Potcar()` is correctly inferred as PotcarSingle. """ return super().__iter__() diff --git a/pymatgen/io/vasp/optics.py b/src/pymatgen/io/vasp/optics.py similarity index 99% rename from pymatgen/io/vasp/optics.py rename to src/pymatgen/io/vasp/optics.py index 206b55816ef..bc52f8ec197 100644 --- a/pymatgen/io/vasp/optics.py +++ b/src/pymatgen/io/vasp/optics.py @@ -10,16 +10,14 @@ import scipy.constants import scipy.special from monty.json import MSONable -from tqdm import tqdm - from pymatgen.electronic_structure.core import Spin from pymatgen.io.vasp.outputs import Vasprun, Waveder +from tqdm import tqdm if TYPE_CHECKING: from numpy.typing import ArrayLike, NDArray - from typing_extensions import Self - from pymatgen.util.typing import PathLike + from typing_extensions import Self __author__ = "Jimmy-Xuan Shen" __copyright__ = "Copyright 2022, The Materials Project" @@ -130,7 +128,7 @@ def _try_reading(dtypes): except ValueError as exc: if "reshape" in str(exc): continue - raise exc + raise return None vrun = Vasprun(f"{directory}/vasprun.xml") @@ -414,7 +412,7 @@ def epsilon_imag( except ValueError as exc: if "zero-size array" in str(exc): return egrid, np.zeros_like(egrid, dtype=np.complex128) - raise exc + raise _, _, nk, nspin = cderm.shape[:4] iter_idx = [ range(min_band0, max_band0 + 1), diff --git a/pymatgen/io/vasp/outputs.py b/src/pymatgen/io/vasp/outputs.py similarity index 99% rename from pymatgen/io/vasp/outputs.py rename to src/pymatgen/io/vasp/outputs.py index 7eccca20661..9df9d6dadc9 100644 --- a/pymatgen/io/vasp/outputs.py +++ b/src/pymatgen/io/vasp/outputs.py @@ -2,6 +2,7 @@ from __future__ import annotations +import datetime import itertools import logging import math @@ -12,7 +13,6 @@ from collections import defaultdict from collections.abc import Iterable from dataclasses import dataclass -from datetime import datetime from glob import glob from io import StringIO from pathlib import Path @@ -24,7 +24,6 @@ from monty.os.path import zpath from monty.re import regrep from numpy.testing import assert_allclose - from pymatgen.core import Composition, Element, Lattice, Structure from pymatgen.core.trajectory import Trajectory from pymatgen.core.units import unitized @@ -51,9 +50,8 @@ from xml.etree.ElementTree import Element as XML_Element from numpy.typing import NDArray - from typing_extensions import Self - from pymatgen.util.typing import PathLike + from typing_extensions import Self logger = logging.getLogger(__name__) @@ -139,10 +137,10 @@ def _parse_vasp_array(elem) -> list[list[float]]: def _parse_from_incar(filename: PathLike, key: str) -> Any: """Helper function to parse a parameter from the INCAR.""" dirname = os.path.dirname(filename) - for filename in os.listdir(dirname): - if re.search("INCAR", filename): + for fn in os.listdir(dirname): + if re.search("INCAR", fn): warnings.warn(f"INCAR found. Using {key} from INCAR.") - incar = Incar.from_file(os.path.join(dirname, filename)) + incar = Incar.from_file(os.path.join(dirname, fn)) return incar.get(key, None) return None @@ -155,13 +153,13 @@ def _vasprun_float(flt: float | str) -> float: try: return float(flt) - except ValueError as exc: + except ValueError: flt = cast(str, flt) _flt: str = flt.strip() if _flt == "*" * len(_flt): warnings.warn("Float overflow (*******) encountered in vasprun") return np.nan - raise exc + raise @dataclass @@ -526,9 +524,9 @@ def _parse( if "kinetic" in d: md_data[-1]["energy"] = {i.attrib["name"]: float(i.text) for i in elem.findall("i")} - except ET.ParseError as exc: + except ET.ParseError: if self.exception_on_bad_xml: - raise exc + raise warnings.warn( "XML is malformed. Parsing has stopped but partial data is available.", UserWarning, @@ -722,7 +720,6 @@ def run_type(self) -> str: Hubbard U terms and vdW corrections are detected automatically as well. """ - # Care should be taken: if a GGA tag is not specified, VASP will default # to the functional specified by the POTCAR. It is not clear how # VASP handles the "--" value. @@ -846,7 +843,7 @@ def get_computed_entry( ComputedStructureEntry/ComputedEntry """ if entry_id is None: - entry_id = f"vasprun-{datetime.now()}" + entry_id = f"vasprun-{datetime.datetime.now(tz=datetime.timezone.utc)}" param_names = { "is_hubbard", "hubbards", @@ -1159,7 +1156,6 @@ def get_potcars(self, path: PathLike | bool) -> Potcar | None: Returns: Potcar | None: The POTCAR from the specified path or None if not found/no path specified. """ - if not path: return None @@ -1379,12 +1375,12 @@ def _parse_params(self, elem: XML_Element) -> dict: else: params[name] = _parse_v_parameters(ptype, val, self.filename, name) - except Exception as exc: + except Exception: if name == "RANDOM_SEED": # Handle the case where RANDOM_SEED > 99999, which results in ***** params[name] = None else: - raise exc + raise elem.clear() return Incar(params) @@ -1398,12 +1394,12 @@ def parse_atomic_symbol(symbol: str) -> str: return str(Element(symbol)) # vasprun.xml uses "X" instead of "Xe" for Xenon - except ValueError as exc: + except ValueError: if symbol == "X": return "Xe" if symbol == "r": return "Zr" - raise exc + raise atomic_symbols = [] potcar_symbols = [] @@ -2255,7 +2251,7 @@ def read_table_pattern( last_one_only: bool = True, first_one_only: bool = False, ) -> list: - """Parse table-like data. A table composes of three parts: header, + r"""Parse table-like data. A table composes of three parts: header, main body, footer. All the data matches "row pattern" in the main body will be returned. @@ -2348,7 +2344,7 @@ def _parse_sci_notation(line: str) -> list[float]: """ Parse lines with values in scientific notation and potentially without spaces in between the values. This assumes that the scientific - notation always lists two digits for the exponent, e.g. 3.535E-02 + notation always lists two digits for the exponent, e.g. 3.535E-02. Args: line: line to parse. @@ -3213,7 +3209,6 @@ def p_ion(results, match): def read_pseudo_zval(self) -> None: """Create a pseudopotential ZVAL dictionary.""" - try: def atom_symbols(results, match): @@ -3709,7 +3704,7 @@ def __init__( raise TypeError("Unsupported POSCAR type.") super().__init__(struct, data, data_aug=data_aug) - self._distance_matrix = {} + self._distance_matrix: dict = {} @classmethod def from_file(cls, filename: str) -> Self: diff --git a/pymatgen/io/vasp/potcar-summary-stats.json.bz2 b/src/pymatgen/io/vasp/potcar-summary-stats.json.bz2 similarity index 100% rename from pymatgen/io/vasp/potcar-summary-stats.json.bz2 rename to src/pymatgen/io/vasp/potcar-summary-stats.json.bz2 diff --git a/pymatgen/io/vasp/sets.py b/src/pymatgen/io/vasp/sets.py similarity index 99% rename from pymatgen/io/vasp/sets.py rename to src/pymatgen/io/vasp/sets.py index eaa8a93cb01..5bc09f6d46b 100644 --- a/pymatgen/io/vasp/sets.py +++ b/src/pymatgen/io/vasp/sets.py @@ -45,7 +45,6 @@ from monty.dev import deprecated from monty.json import MSONable from monty.serialization import loadfn - from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core import Element, PeriodicSite, SiteCollection, Species, Structure from pymatgen.io.core import InputGenerator @@ -59,9 +58,8 @@ if TYPE_CHECKING: from typing import Callable, Literal, Union - from typing_extensions import Self - from pymatgen.util.typing import PathLike, Tuple3Ints, Vector3D + from typing_extensions import Self UserPotcarFunctional = Union[ Literal["PBE", "PBE_52", "PBE_54", "LDA", "LDA_52", "LDA_54", "PW91", "LDA_US", "PW91_US"], None @@ -371,7 +369,7 @@ def as_dict(self, verbosity: int = 2) -> dict: return dct @property # type: ignore[no-redef] - def structure(self) -> Structure | None: + def structure(self) -> Structure | None: # noqa: F811 """Structure.""" return self._structure @@ -933,7 +931,6 @@ def potcar(self) -> Potcar: @property def potcar_symbols(self) -> list[str]: """List of POTCAR symbols.""" - elements = self.poscar.site_symbols potcar_symbols = [] settings = self._config_dict["POTCAR"] @@ -1404,14 +1401,20 @@ def kpoints_updates(self) -> dict | Kpoints: factor = self.small_gap_multiply[1] # prefer to use k-point scheme from previous run unless lepsilon = True is specified - if self.prev_kpoints and self.prev_kpoints.style == Kpoints.supported_modes.Monkhorst and not self.lepsilon: # type: ignore + if ( + self.prev_kpoints + and isinstance(self.prev_kpoints, Kpoints) + and self.prev_kpoints.style == Kpoints.supported_modes.Monkhorst + and not self.lepsilon + and self.structure is not None + ): kpoints = Kpoints.automatic_density_by_vol( - self.structure, # type: ignore + self.structure, int(self.reciprocal_density * factor), self.force_gamma, ) - k_div = [kp + 1 if kp % 2 == 1 else kp for kp in kpoints.kpts[0]] # type: ignore - return Kpoints.monkhorst_automatic(k_div) # type: ignore + k_div = cast(Kpoint, tuple(kp + 1 if kp % 2 == 1 else kp for kp in kpoints.kpts[0])) + return Kpoints.monkhorst_automatic(k_div) return {"reciprocal_density": self.reciprocal_density * factor} @@ -1919,11 +1922,11 @@ def incar_updates(self) -> dict[str, Any]: PREC="ACCURATE", SIGMA=0.01, ) - elif self.mode.lower() == "efg": + elif self.mode.lower() == "efg" and self.structure is not None: isotopes = {ist.split("-")[0]: ist for ist in self.isotopes} quad_efg = [ - float(Species(s.name).get_nmr_quadrupole_moment(isotopes.get(s.name))) - for s in self.structure.species # type: ignore + float(Species(sp.name).get_nmr_quadrupole_moment(isotopes.get(sp.name))) + for sp in self.structure.species ] updates.update( ALGO="FAST", @@ -2129,9 +2132,9 @@ def incar_updates(self) -> dict[str, Any]: updates |= {"ISIF": 2, "LVTOT": True, "NELMIN": 8} if self.set_mix: updates |= {"AMIN": 0.01, "AMIX": 0.2, "BMIX": 0.001} - if self.auto_dipole: - weights = [s.species.weight for s in self.structure] # type: ignore - center_of_mass = np.average(self.structure.frac_coords, weights=weights, axis=0) # type: ignore + if self.auto_dipole and self.structure is not None: + weights = [struct.species.weight for struct in self.structure] + center_of_mass = np.average(self.structure.frac_coords, weights=weights, axis=0) updates |= {"IDIPOL": 3, "LDIPOL": True, "DIPOL": center_of_mass} return updates @@ -2343,8 +2346,8 @@ def write_input( make_dir_if_not_present (bool): Set to True if you want the directory (and the whole path) to be created if it is not present. - write_cif (bool): If true, writes a cif along with each POSCAR. - write_path_cif (bool): If true, writes a cif for each image. + write_cif (bool): If true, writes a CIF along with each POSCAR. + write_path_cif (bool): If true, writes a CIF for each image. write_endpoint_inputs (bool): If true, writes input files for running endpoint calculations. """ @@ -3022,7 +3025,7 @@ class MPAbsorptionSet(VaspInputSet): SUPPORTED_MODES = ("IPA", "RPA") def __post_init__(self) -> None: - """Validate settings""" + """Validate settings.""" super().__post_init__() self.mode = self.mode.upper() if self.mode not in type(self).SUPPORTED_MODES: @@ -3102,7 +3105,7 @@ def _combine_kpoints(*kpoints_objects: Kpoints | None) -> Kpoints: _kpoints: list[Sequence[Kpoint]] = [] _weights = [] - for kpoints_object in filter(None, kpoints_objects): + for kpoints_object in filter(None, kpoints_objects): # type: ignore[var-annotated] if kpoints_object.style != Kpoints.supported_modes.Reciprocal: raise ValueError("Can only combine kpoints with style=Kpoints.supported_modes.Reciprocal") if kpoints_object.labels is None: @@ -3189,7 +3192,7 @@ def _get_nedos(vasprun: Vasprun | None, dedos: float) -> int: def auto_kspacing(bandgap: float | None, bandgap_tol: float) -> float: - """Set kspacing based on the bandgap""" + """Set kspacing based on the bandgap.""" if bandgap is None or bandgap <= bandgap_tol: # metallic return 0.22 diff --git a/pymatgen/io/vasp/vasp_potcar_file_hashes.json b/src/pymatgen/io/vasp/vasp_potcar_file_hashes.json similarity index 100% rename from pymatgen/io/vasp/vasp_potcar_file_hashes.json rename to src/pymatgen/io/vasp/vasp_potcar_file_hashes.json diff --git a/pymatgen/io/vasp/vasp_potcar_pymatgen_hashes.json b/src/pymatgen/io/vasp/vasp_potcar_pymatgen_hashes.json similarity index 100% rename from pymatgen/io/vasp/vasp_potcar_pymatgen_hashes.json rename to src/pymatgen/io/vasp/vasp_potcar_pymatgen_hashes.json diff --git a/pymatgen/io/vasp/vdW_parameters.yaml b/src/pymatgen/io/vasp/vdW_parameters.yaml similarity index 100% rename from pymatgen/io/vasp/vdW_parameters.yaml rename to src/pymatgen/io/vasp/vdW_parameters.yaml diff --git a/pymatgen/io/wannier90.py b/src/pymatgen/io/wannier90.py similarity index 100% rename from pymatgen/io/wannier90.py rename to src/pymatgen/io/wannier90.py diff --git a/pymatgen/io/xcrysden.py b/src/pymatgen/io/xcrysden.py similarity index 100% rename from pymatgen/io/xcrysden.py rename to src/pymatgen/io/xcrysden.py diff --git a/pymatgen/io/xr.py b/src/pymatgen/io/xr.py similarity index 97% rename from pymatgen/io/xr.py rename to src/pymatgen/io/xr.py index 60a9ac01975..3fb644c11bd 100644 --- a/pymatgen/io/xr.py +++ b/src/pymatgen/io/xr.py @@ -15,7 +15,6 @@ import numpy as np from monty.io import zopen - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure @@ -126,16 +125,16 @@ def from_str(cls, string: str, use_cores: bool = True, thresh: float = 1.0e-4) - r"\d+\s+(\w+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)", lines[4 + j].strip(), ): - tmp_sp = match.group(1) + tmp_sp = match[1] if use_cores and tmp_sp[len(tmp_sp) - 2 :] == "_s": continue if not use_cores and tmp_sp[len(tmp_sp) - 2 :] == "_c": continue if tmp_sp[len(tmp_sp) - 2] == "_": - sp.append(tmp_sp[0 : len(tmp_sp) - 2]) + sp.append(tmp_sp[: len(tmp_sp) - 2]) else: sp.append(tmp_sp) - coords.append([float(match.group(i)) for i in range(2, 5)]) + coords.append([float(match[i]) for i in range(2, 5)]) return cls(Structure(lattice, sp, coords, coords_are_cartesian=True)) @classmethod diff --git a/pymatgen/io/xtb/__init__.py b/src/pymatgen/io/xtb/__init__.py similarity index 100% rename from pymatgen/io/xtb/__init__.py rename to src/pymatgen/io/xtb/__init__.py diff --git a/pymatgen/io/xtb/inputs.py b/src/pymatgen/io/xtb/inputs.py similarity index 93% rename from pymatgen/io/xtb/inputs.py rename to src/pymatgen/io/xtb/inputs.py index d753885e08f..cbc6a413dbe 100644 --- a/pymatgen/io/xtb/inputs.py +++ b/src/pymatgen/io/xtb/inputs.py @@ -43,7 +43,7 @@ def __init__( coords_filename (str): Name of input coordinates file constraints (dict): Dictionary of common editable parameters for .constrains file. {"atoms": [List of 1-indexed atoms to fix], - "force_constant": float] + "force_constant": float]. """ self.molecule = molecule self.coords_filename = coords_filename @@ -69,7 +69,7 @@ def constrains_template(molecule, reference_fnm, constraints) -> str: molecule (Molecule): Molecule the constraints will be performed on reference_fnm (str): Name of file containing reference structure in same directory constraints (dict): Dictionary of common editable parameters for .constrains file. - {"atoms": [List of 1-indexed atoms to fix], "force_constant": float] + {"atoms": [List of 1-indexed atoms to fix], "force_constant": float]. Returns: str: for .constrains file @@ -80,11 +80,11 @@ def constrains_template(molecule, reference_fnm, constraints) -> str: atoms_for_mtd = [idx for idx in range(1, len(mol) + 1) if idx not in atoms_to_constrain] # Write as 1-3,5 instead of 1,2,3,5 interval_list = [atoms_for_mtd[0]] - for idx, val in enumerate(atoms_for_mtd, start=1): + for idx, val in enumerate(atoms_for_mtd): if val + 1 not in atoms_for_mtd: interval_list.append(val) - if idx != len(atoms_for_mtd): - interval_list.append(atoms_for_mtd[idx]) + if idx != len(atoms_for_mtd) - 1: + interval_list.append(atoms_for_mtd[idx + 1]) allowed_mtd_string = ",".join( [f"{interval_list[i]}-{interval_list[i + 1]}" for i in range(len(interval_list)) if i % 2 == 0] ) diff --git a/pymatgen/io/xtb/outputs.py b/src/pymatgen/io/xtb/outputs.py similarity index 98% rename from pymatgen/io/xtb/outputs.py rename to src/pymatgen/io/xtb/outputs.py index f7425b38535..60ca8c52834 100644 --- a/pymatgen/io/xtb/outputs.py +++ b/src/pymatgen/io/xtb/outputs.py @@ -7,7 +7,6 @@ import re from monty.json import MSONable - from pymatgen.core import Molecule from pymatgen.io.xyz import XYZ @@ -71,12 +70,12 @@ def _parse_crest_output(self): print(f"Input file {split_cmd[0]} not found") # Get CREST input flags - for i, entry in enumerate(split_cmd, start=1): + for i, entry in enumerate(split_cmd): value = None if entry and "-" in entry: option = entry[1:] - if i < len(split_cmd) and "-" not in split_cmd[i]: - value = split_cmd[i] + if i < len(split_cmd) and "-" not in split_cmd[i + 1]: + value = split_cmd[i + 1] self.cmd_options[option] = value # Get input charge for decorating parsed molecules chg = 0 diff --git a/pymatgen/io/xyz.py b/src/pymatgen/io/xyz.py similarity index 97% rename from pymatgen/io/xyz.py rename to src/pymatgen/io/xyz.py index d09c7a26edb..28914a47010 100644 --- a/pymatgen/io/xyz.py +++ b/src/pymatgen/io/xyz.py @@ -8,7 +8,6 @@ import pandas as pd from monty.io import zopen - from pymatgen.core import Molecule, Structure from pymatgen.core.structure import SiteCollection @@ -62,7 +61,7 @@ def _from_frame_str(contents) -> Molecule: coord_pattern = re.compile(r"(\w+)\s+([0-9\-\+\.*^eEdD]+)\s+([0-9\-\+\.*^eEdD]+)\s+([0-9\-\+\.*^eEdD]+)") for idx in range(2, 2 + n_sites): if match := coord_pattern.search(lines[idx]): - sp.append(match.group(1)) # this is 1-indexed + sp.append(match[1]) # this is 1-indexed # this is 0-indexed # in case of 0.0D+00 or 0.00d+01 old double precision writing # replace d or D by e for ten power exponent, @@ -92,7 +91,7 @@ def from_str(cls, contents: str) -> Self: pat = re.compile(frame_pattern_text, re.MULTILINE) mols = [] for xyz_match in pat.finditer(contents): - xyz_text = xyz_match.group(0) + xyz_text = xyz_match[0] mols.append(XYZ._from_frame_str(xyz_text)) return cls(mols) diff --git a/pymatgen/io/zeopp.py b/src/pymatgen/io/zeopp.py similarity index 97% rename from pymatgen/io/zeopp.py rename to src/pymatgen/io/zeopp.py index 70f8d13e141..5ebee530013 100644 --- a/pymatgen/io/zeopp.py +++ b/src/pymatgen/io/zeopp.py @@ -31,7 +31,6 @@ from monty.dev import requires from monty.io import zopen from monty.tempfile import ScratchDir - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Molecule, Structure from pymatgen.io.cssr import Cssr @@ -128,11 +127,11 @@ def from_str(cls, string: str) -> Self: r"\d+\s+(\w+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+(?:0\s+){8}([0-9\-\.]+)", line.strip(), ): - sp.append(match.group(1)) - # coords.append([float(m.group(i)) for i in xrange(2, 5)]) + sp.append(match[1]) + # coords.append([float(m[i]) for i in xrange(2, 5)]) # Zeo++ takes x-axis along a and pymatgen takes z-axis along c - coords.append([float(match.group(i)) for i in [3, 4, 2]]) - charge.append(match.group(5)) + coords.append([float(match[i]) for i in [3, 4, 2]]) + charge.append(match[5]) return cls(Structure(lattice, sp, coords, site_properties={"charge": charge})) @classmethod @@ -183,10 +182,10 @@ def from_str(cls, contents: str) -> Self: coord_patt = re.compile(r"(\w+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)") for idx in range(2, 2 + n_sites): if match := coord_patt.search(lines[idx]): - sp.append(match.group(1)) # this is 1-indexed + sp.append(match[1]) # this is 1-indexed # coords.append(map(float, m.groups()[1:4])) # this is 0-indexed - coords.append([float(j) for j in [match.group(i) for i in [3, 4, 2]]]) - prop.append(float(match.group(5))) + coords.append([float(j) for j in [match[i] for i in [3, 4, 2]]]) + prop.append(float(match[5])) return cls(Molecule(sp, coords, site_properties={"voronoi_radius": prop})) @classmethod diff --git a/pymatgen/optimization/__init__.py b/src/pymatgen/optimization/__init__.py similarity index 100% rename from pymatgen/optimization/__init__.py rename to src/pymatgen/optimization/__init__.py diff --git a/pymatgen/optimization/linear_assignment.pyx b/src/pymatgen/optimization/linear_assignment.pyx similarity index 99% rename from pymatgen/optimization/linear_assignment.pyx rename to src/pymatgen/optimization/linear_assignment.pyx index 9c7f28896ee..ae3e0a89125 100644 --- a/pymatgen/optimization/linear_assignment.pyx +++ b/src/pymatgen/optimization/linear_assignment.pyx @@ -12,6 +12,8 @@ cimport numpy as np from libc.math cimport fabs from libc.stdlib cimport free, malloc +np.import_array() + __author__ = "Will Richards" __copyright__ = "Copyright 2011, The Materials Project" __version__ = "1.0" diff --git a/pymatgen/optimization/neighbors.pyx b/src/pymatgen/optimization/neighbors.pyx similarity index 100% rename from pymatgen/optimization/neighbors.pyx rename to src/pymatgen/optimization/neighbors.pyx diff --git a/pymatgen/phonon/__init__.py b/src/pymatgen/phonon/__init__.py similarity index 100% rename from pymatgen/phonon/__init__.py rename to src/pymatgen/phonon/__init__.py diff --git a/pymatgen/phonon/bandstructure.py b/src/pymatgen/phonon/bandstructure.py similarity index 99% rename from pymatgen/phonon/bandstructure.py rename to src/pymatgen/phonon/bandstructure.py index d56ff99df89..17cb899b948 100644 --- a/pymatgen/phonon/bandstructure.py +++ b/src/pymatgen/phonon/bandstructure.py @@ -7,7 +7,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.electronic_structure.bandstructure import Kpoint @@ -18,9 +17,8 @@ from typing import Any from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.util.typing import Tuple3Ints + from typing_extensions import Self def get_reasonable_repetitions(n_atoms: int) -> Tuple3Ints: diff --git a/pymatgen/phonon/dos.py b/src/pymatgen/phonon/dos.py similarity index 99% rename from pymatgen/phonon/dos.py rename to src/pymatgen/phonon/dos.py index e4e26c192d4..0e3e0ea2296 100644 --- a/pymatgen/phonon/dos.py +++ b/src/pymatgen/phonon/dos.py @@ -8,10 +8,9 @@ import scipy.constants as const from monty.functools import lazy_property from monty.json import MSONable -from scipy.ndimage import gaussian_filter1d - from pymatgen.core.structure import Structure from pymatgen.util.coord import get_linear_interpolated_value +from scipy.ndimage import gaussian_filter1d if TYPE_CHECKING: from collections.abc import Sequence diff --git a/pymatgen/phonon/gruneisen.py b/src/pymatgen/phonon/gruneisen.py similarity index 99% rename from pymatgen/phonon/gruneisen.py rename to src/pymatgen/phonon/gruneisen.py index 1d309a81c75..67517b4faa7 100644 --- a/pymatgen/phonon/gruneisen.py +++ b/src/pymatgen/phonon/gruneisen.py @@ -8,13 +8,12 @@ import scipy.constants as const from monty.dev import requires from monty.json import MSONable -from scipy.interpolate import UnivariateSpline - from pymatgen.core import Structure from pymatgen.core.lattice import Lattice from pymatgen.core.units import amu_to_kg from pymatgen.phonon.bandstructure import PhononBandStructure, PhononBandStructureSymmLine from pymatgen.phonon.dos import PhononDos +from scipy.interpolate import UnivariateSpline try: import phonopy @@ -169,7 +168,7 @@ def thermal_conductivity_slack( return thermal_cond - @property # type: ignore + @property @requires(phonopy, "This method requires phonopy to be installed") def tdos(self): """The total DOS (re)constructed from the gruneisen.yaml file.""" diff --git a/pymatgen/phonon/ir_spectra.py b/src/pymatgen/phonon/ir_spectra.py similarity index 99% rename from pymatgen/phonon/ir_spectra.py rename to src/pymatgen/phonon/ir_spectra.py index 462f4fa94b9..9626e6c5726 100644 --- a/pymatgen/phonon/ir_spectra.py +++ b/src/pymatgen/phonon/ir_spectra.py @@ -11,7 +11,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.core.spectrum import Spectrum from pymatgen.core.structure import Structure from pymatgen.util.plotting import add_fig_kwargs diff --git a/pymatgen/phonon/plotter.py b/src/pymatgen/phonon/plotter.py similarity index 92% rename from pymatgen/phonon/plotter.py rename to src/pymatgen/phonon/plotter.py index ad4fb598cef..d5dd63bc2ec 100644 --- a/pymatgen/phonon/plotter.py +++ b/src/pymatgen/phonon/plotter.py @@ -8,9 +8,10 @@ import matplotlib.pyplot as plt import numpy as np import scipy.constants as const +from matplotlib import colors from matplotlib.collections import LineCollection +from matplotlib.colors import LinearSegmentedColormap from monty.json import jsanitize - from pymatgen.electronic_structure.plotter import BSDOSPlotter, plot_brillouin_zone from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine from pymatgen.phonon.gruneisen import GruneisenPhononBandStructureSymmLine @@ -23,7 +24,6 @@ from matplotlib.axes import Axes from matplotlib.figure import Figure - from pymatgen.core import Structure from pymatgen.phonon.dos import PhononDos from pymatgen.phonon.gruneisen import GruneisenParameter @@ -93,7 +93,7 @@ def __init__(self, stack: bool = False, sigma: float | None = None) -> None: # a likely user mistake is to try to pass a DOS as the first argument (similar to PhononBSPlotter) but # without the isinstance check, this would not raise an error and just silently cause a blank plot if not isinstance(stack, bool): - raise ValueError( + raise TypeError( "The first argument stack expects a boolean. If you are trying to add a DOS, use the add_dos() method." ) self.stack = stack @@ -293,7 +293,7 @@ def __init__(self, bs: PhononBandStructureSymmLine, label: str | None = None) -> the plot_compare method to distinguish the band structures. """ if not isinstance(bs, PhononBandStructureSymmLine): - raise ValueError( + raise TypeError( "PhononBSPlotter only works with PhononBandStructureSymmLine objects. " "A PhononBandStructure object (on a uniform grid for instance and " "not along symmetry lines won't work)" @@ -476,7 +476,7 @@ def get_proj_plot( assert 0 <= idx < len(all_sites), "one or more indices in site_comb does not exist" all_indices.remove(idx) if len(all_indices) != 0: - raise Exception(f"not all {len(all_sites)} indices are included in site_comb") + raise ValueError(f"not all {len(all_sites)} indices are included in site_comb") indices = site_comb # type: ignore[assignment] assert rgb_labels is None or len(rgb_labels) == len(indices), "wrong number of rgb_labels" @@ -1007,7 +1007,7 @@ def __init__(self, bs: GruneisenPhononBandStructureSymmLine) -> None: bs: A GruneisenPhononBandStructureSymmLine object. """ if not isinstance(bs, GruneisenPhononBandStructureSymmLine): - raise ValueError( + raise TypeError( "GruneisenPhononBSPlotter only works with GruneisenPhononBandStructureSymmLine objects. " "A GruneisenPhononBandStructure object (on a uniform grid for instance and " "not along symmetry lines won't work)" @@ -1054,26 +1054,58 @@ def bs_plot_data(self) -> dict[str, Any]: "lattice": self._bs.lattice_rec.as_dict(), } - def get_plot_gs(self, ylim: float | None = None, **kwargs) -> Axes: + def get_plot_gs(self, ylim: float | None = None, plot_ph_bs_with_gruneisen: bool = False, **kwargs) -> Axes: """Get a matplotlib object for the Gruneisen bandstructure plot. Args: ylim: Specify the y-axis (gruneisen) limits; by default None let the code choose. + plot_ph_bs_with_gruneisen (bool): Plot phonon band-structure with bands coloured + as per Gruneisen parameter values on a logarithmic scale **kwargs: additional keywords passed to ax.plot(). """ + u = freq_units(kwargs.get("units", "THz")) ax = pretty_plot(12, 8) + # Create a colormap (default is red to blue) + cmap = LinearSegmentedColormap.from_list("cmap", kwargs.get("cmap", ["red", "blue"])) + kwargs.setdefault("linewidth", 2) kwargs.setdefault("marker", "o") kwargs.setdefault("markersize", 2) data = self.bs_plot_data() - for dist_idx in range(len(data["distances"])): + + # extract min and max Grüneisen parameter values + max_gruneisen = np.array(data["gruneisen"]).max() + min_gruneisen = np.array(data["gruneisen"]).min() + + # LogNormalize colormap based on the min and max Grüneisen parameter values + norm = colors.SymLogNorm( + vmin=min_gruneisen, + vmax=max_gruneisen, + linthresh=1e-2, + linscale=1, + ) + + sc = None + for (dists_inx, dists), (_, freqs) in zip(enumerate(data["distances"]), enumerate(data["frequency"])): for band_idx in range(self.n_bands): - ys = [data["gruneisen"][dist_idx][band_idx][idx] for idx in range(len(data["distances"][dist_idx]))] + if plot_ph_bs_with_gruneisen: + ys = [freqs[band_idx][j] * u.factor for j in range(len(dists))] + ys_gru = [ + data["gruneisen"][dists_inx][band_idx][idx] for idx in range(len(data["distances"][dists_inx])) + ] + sc = ax.scatter(dists, ys, c=ys_gru, cmap=cmap, norm=norm, marker="o", s=1) + else: + keys_to_remove = ("units", "cmap") # needs to be removed before passing to line-plot + for k in keys_to_remove: + kwargs.pop(k, None) + ys = [ + data["gruneisen"][dists_inx][band_idx][idx] for idx in range(len(data["distances"][dists_inx])) + ] - ax.plot(data["distances"][dist_idx], ys, "b-", **kwargs) + ax.plot(data["distances"][dists_inx], ys, "b-", **kwargs) self._make_ticks(ax) @@ -1081,8 +1113,16 @@ def get_plot_gs(self, ylim: float | None = None, **kwargs) -> Axes: ax.axhline(0, linewidth=1, color="black") # Main X and Y Labels - ax.set_xlabel(r"$\mathrm{Wave\ Vector}$", fontsize=30) - ax.set_ylabel(r"$\mathrm{Grüneisen\ Parameter}$", fontsize=30) + if plot_ph_bs_with_gruneisen: + ax.set_xlabel(r"$\mathrm{Wave\ Vector}$", fontsize=30) + units = kwargs.get("units", "THz") + ax.set_ylabel(f"Frequencies ({units})", fontsize=30) + + cbar = plt.colorbar(sc, ax=ax) + cbar.set_label(r"$\gamma \ \mathrm{(logarithmized)}$", fontsize=30) + else: + ax.set_xlabel(r"$\mathrm{Wave\ Vector}$", fontsize=30) + ax.set_ylabel(r"$\mathrm{Grüneisen\ Parameter}$", fontsize=30) # X range (K) # last distance point @@ -1096,24 +1136,37 @@ def get_plot_gs(self, ylim: float | None = None, **kwargs) -> Axes: return ax - def show_gs(self, ylim: float | None = None) -> None: + def show_gs(self, ylim: float | None = None, plot_ph_bs_with_gruneisen: bool = False, **kwargs) -> None: """Show the plot using matplotlib. Args: ylim: Specifies the y-axis limits. + plot_ph_bs_with_gruneisen: Plot phonon band-structure with bands coloured + as per Gruneisen parameter values on a logarithmic scale + **kwargs: kwargs passed to get_plot_gs """ - self.get_plot_gs(ylim) + self.get_plot_gs(ylim=ylim, plot_ph_bs_with_gruneisen=plot_ph_bs_with_gruneisen, **kwargs) plt.show() - def save_plot_gs(self, filename: str | PathLike, img_format: str = "eps", ylim: float | None = None) -> None: + def save_plot_gs( + self, + filename: str | PathLike, + img_format: str = "eps", + ylim: float | None = None, + plot_ph_bs_with_gruneisen: bool = False, + **kwargs, + ) -> None: """Save matplotlib plot to a file. Args: filename: Filename to write to. img_format: Image format to use. Defaults to EPS. ylim: Specifies the y-axis limits. + plot_ph_bs_with_gruneisen: Plot phonon band-structure with bands coloured + as per Gruneisen parameter values on a logarithmic scale + **kwargs: kwargs passed to get_plot_gs """ - self.get_plot_gs(ylim=ylim) + self.get_plot_gs(ylim=ylim, plot_ph_bs_with_gruneisen=plot_ph_bs_with_gruneisen, **kwargs) plt.savefig(filename, format=img_format) plt.close() diff --git a/pymatgen/phonon/thermal_displacements.py b/src/pymatgen/phonon/thermal_displacements.py similarity index 96% rename from pymatgen/phonon/thermal_displacements.py rename to src/pymatgen/phonon/thermal_displacements.py index 3df4e1ff2e0..818b5f6f911 100644 --- a/pymatgen/phonon/thermal_displacements.py +++ b/src/pymatgen/phonon/thermal_displacements.py @@ -8,7 +8,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core.structure import Structure from pymatgen.io.cif import CifFile, CifParser, CifWriter, str2float @@ -37,7 +36,7 @@ sub_spgrp = partial(re.sub, r"[\s_]", "") -space_groups = {sub_spgrp(k): k for k in SYMM_DATA["space_group_encoding"]} # type: ignore +space_groups = {sub_spgrp(k): k for k in SYMM_DATA["space_group_encoding"]} class ThermalDisplacementMatrices(MSONable): @@ -97,19 +96,19 @@ def get_full_matrix(thermal_displacement: ArrayLike[ArrayLike]) -> np.ndarray[np Returns: 3d numpy array including thermal displacements, first dimensions are the atoms """ - matrixform = np.zeros((len(thermal_displacement), 3, 3)) - for imat, mat in enumerate(thermal_displacement): + matrix_form = np.zeros((len(thermal_displacement), 3, 3)) + for idx, mat in enumerate(thermal_displacement): # xx, yy, zz, yz, xz, xy - matrixform[imat][0][0] = mat[0] - matrixform[imat][1][1] = mat[1] - matrixform[imat][2][2] = mat[2] - matrixform[imat][1][2] = mat[3] - matrixform[imat][2][1] = mat[3] - matrixform[imat][0][2] = mat[4] - matrixform[imat][2][0] = mat[4] - matrixform[imat][0][1] = mat[5] - matrixform[imat][1][0] = mat[5] - return matrixform + matrix_form[idx][0][0] = mat[0] + matrix_form[idx][1][1] = mat[1] + matrix_form[idx][2][2] = mat[2] + matrix_form[idx][1][2] = mat[3] + matrix_form[idx][2][1] = mat[3] + matrix_form[idx][0][2] = mat[4] + matrix_form[idx][2][0] = mat[4] + matrix_form[idx][0][1] = mat[5] + matrix_form[idx][1][0] = mat[5] + return matrix_form @staticmethod def get_reduced_matrix(thermal_displacement: ArrayLike[ArrayLike]) -> np.ndarray[np.ndarray]: @@ -203,20 +202,20 @@ def U1U2U3(self) -> list: Returns: np.array: eigenvalues of Ucart. First dimension are the atoms in the structure. """ - U1U2U3 = [] + u1u2u3_eig_vals = [] for mat in self.thermal_displacement_matrix_cart_matrixform: - U1U2U3.append(np.linalg.eig(mat)[0]) - return U1U2U3 + u1u2u3_eig_vals.append(np.linalg.eig(mat)[0]) + return u1u2u3_eig_vals def write_cif(self, filename: str) -> None: - """Write a cif including thermal displacements. + """Write a CIF including thermal displacements. Args: - filename: name of the cif file + filename: name of the CIF file """ writer = CifWriter(self.structure) writer.write_file(filename) - # This will simply append the thermal displacement part to the cif from the CifWriter + # This will simply append the thermal displacement part to the CIF from the CifWriter # In the long run, CifWriter could be extended to handle thermal displacement matrices with open(filename, mode="a") as file: file.write("loop_ \n") @@ -333,7 +332,6 @@ def visualize_directionality_quality_criterion( raise ValueError("Illegal which_structure value.") with open(filename, mode="w", encoding="utf-8") as file: - # file.write("#VESTA_FORMAT_VERSION 3.5.4\n \n \n") file.write("CRYSTAL\n\n") file.write("TITLE\n") @@ -396,7 +394,7 @@ def visualize_directionality_quality_criterion( counter = 1 # two vectors per atom - for _i in range(len(result)): + for _ in range(len(result)): file.write(f"{counter} 0.2 255 0 0 1\n") counter += 1 file.write(f"{counter} 0.2 0 0 255 1\n") @@ -514,7 +512,7 @@ def from_structure_with_site_properties_Ucif(cls, structure: Structure, temperat @staticmethod def from_cif_P1(filename: str) -> list[ThermalDisplacementMatrices]: - """Reads a cif with P1 symmetry including positions and ADPs. + """Reads a CIF with P1 symmetry including positions and ADPs. Currently, no check of symmetry is performed as CifParser methods cannot be easily reused. Args: diff --git a/pymatgen/py.typed b/src/pymatgen/py.typed similarity index 100% rename from pymatgen/py.typed rename to src/pymatgen/py.typed diff --git a/pymatgen/symmetry/__init__.py b/src/pymatgen/symmetry/__init__.py similarity index 100% rename from pymatgen/symmetry/__init__.py rename to src/pymatgen/symmetry/__init__.py diff --git a/pymatgen/symmetry/analyzer.py b/src/pymatgen/symmetry/analyzer.py similarity index 87% rename from pymatgen/symmetry/analyzer.py rename to src/pymatgen/symmetry/analyzer.py index 1f08b8f6904..f404aa2170b 100644 --- a/pymatgen/symmetry/analyzer.py +++ b/src/pymatgen/symmetry/analyzer.py @@ -25,7 +25,6 @@ import numpy as np import scipy.cluster import spglib - from pymatgen.core.lattice import Lattice from pymatgen.core.operations import SymmOp from pymatgen.core.structure import Molecule, PeriodicSite, Structure @@ -36,9 +35,12 @@ if TYPE_CHECKING: from typing import Any, Literal + from numpy.typing import NDArray from pymatgen.core import Element, Species from pymatgen.core.sites import Site from pymatgen.symmetry.groups import CrystalSystem + from pymatgen.util.typing import Kpoint + from spglib import SpglibDataset LatticeType = Literal["cubic", "hexagonal", "monoclinic", "orthorhombic", "rhombohedral", "tetragonal", "triclinic"] @@ -75,7 +77,12 @@ class SpacegroupAnalyzer: Uses spglib to perform various symmetry finding operations. """ - def __init__(self, structure: Structure, symprec: float | None = 0.01, angle_tolerance: float = 5) -> None: + def __init__( + self, + structure: Structure, + symprec: float | None = 0.01, + angle_tolerance: float = 5, + ) -> None: """ Args: structure (Structure/IStructure): Structure to find symmetry @@ -94,7 +101,6 @@ def __init__(self, structure: Structure, symprec: float | None = 0.01, angle_tol self._site_props = structure.site_properties unique_species: list[Element | Species] = [] zs = [] - magmoms = [] for species, group in itertools.groupby(structure, key=lambda s: s.species): if species in unique_species: ind = unique_species.index(species) @@ -107,6 +113,7 @@ def __init__(self, structure: Structure, symprec: float | None = 0.01, angle_tol getattr(specie, "spin", None) is not None for specie in structure.types_of_species ) + magmoms = [] for site in structure: if hasattr(site, "magmom"): magmoms.append(site.magmom) @@ -140,7 +147,7 @@ def get_space_group_symbol(self) -> str: Returns: str: Spacegroup symbol for structure. """ - return self._space_group_data["international"] + return self._space_group_data.international def get_space_group_number(self) -> int: """Get the international spacegroup number (e.g., 62) for structure. @@ -148,7 +155,7 @@ def get_space_group_number(self) -> int: Returns: int: International spacegroup number for structure. """ - return int(self._space_group_data["number"]) + return int(self._space_group_data.number) def get_space_group_operations(self) -> SpacegroupOperations: """Get the SpacegroupOperations for the Structure. @@ -168,7 +175,7 @@ def get_hall(self) -> str: Returns: str: Hall symbol """ - return self._space_group_data["hall"] + return self._space_group_data.hall def get_point_group_symbol(self) -> str: """Get the point group associated with the structure. @@ -176,7 +183,7 @@ def get_point_group_symbol(self) -> str: Returns: Pointgroup: Point group for structure. """ - rotations = self._space_group_data["rotations"] + rotations = self._space_group_data.rotations # passing a 0-length rotations list to spglib can segfault if len(rotations) == 0: return "1" @@ -192,10 +199,10 @@ def get_crystal_system(self) -> CrystalSystem: Returns: str: Crystal system for structure """ - n = self._space_group_data["number"] + n = self._space_group_data.number - # not using isinstance(n, int) to allow 0-decimal floats - if not (n == int(n) and 0 < n < 231): + # Not using isinstance(n, int) to allow 0-decimal floats + if n != int(n) or not 0 < n < 231: raise ValueError(f"Received invalid space group {n}") if 0 < n < 3: @@ -223,33 +230,31 @@ def get_lattice_type(self) -> LatticeType: Returns: str: Lattice type for structure """ - spg_num = self._space_group_data["number"] + spg_num = self._space_group_data.number system = self.get_crystal_system() - if spg_num in (146, 148, 155, 160, 161, 166, 167): + if spg_num in {146, 148, 155, 160, 161, 166, 167}: return "rhombohedral" - if system == "trigonal": - return "hexagonal" - return system + return "hexagonal" if system == "trigonal" else system - def get_symmetry_dataset(self): - """Get the symmetry dataset as a dict. + def get_symmetry_dataset(self) -> SpglibDataset: + """Get the symmetry dataset as a SpglibDataset. Returns: - dict: With the following properties: + frozen dict: With the following properties: number: International space group number international: International symbol hall: Hall symbol transformation_matrix: Transformation matrix from lattice of - input cell to Bravais lattice L^bravais = L^original * Tmat - origin shift: Origin shift in the setting of "Bravais lattice" - rotations, translations: Rotation matrices and translation - vectors. Space group operations are obtained by - [(r,t) for r, t in zip(rotations, translations)] + input cell to Bravais lattice L^bravais = L^original * Tmat + origin shift: Origin shift in the setting of "Bravais lattice" + rotations, translations: Rotation matrices and translation + vectors. Space group operations are obtained by + [(r,t) for r, t in zip(rotations, translations)] wyckoffs: Wyckoff letters """ return self._space_group_data - def _get_symmetry(self): + def _get_symmetry(self) -> tuple[NDArray, NDArray]: """Get the symmetry operations associated with the structure. Returns: @@ -270,16 +275,16 @@ def _get_symmetry(self): # [1e-4, 2e-4, 1e-4] # (these are in fractional coordinates, so should be small denominator # fractions) - translations = [] - for t in dct["translations"]: - translations.append([float(Fraction(c).limit_denominator(1000)) for c in t]) - translations = np.array(translations) + _translations: list = [] + for trans in dct["translations"]: + _translations.append([float(Fraction(c).limit_denominator(1000)) for c in trans]) + translations: NDArray = np.array(_translations) - # fractional translations of 1 are more simply 0 + # Fractional translations of 1 are more simply 0 translations[np.abs(translations) == 1] = 0 return dct["rotations"], translations - def get_symmetry_operations(self, cartesian=False): + def get_symmetry_operations(self, cartesian: bool = False) -> list[SymmOp]: """Return symmetry operations as a list of SymmOp objects. By default returns fractional coord sym_ops. But Cartesian can be returned too. @@ -298,7 +303,7 @@ def get_symmetry_operations(self, cartesian=False): sym_ops.append(op) return sym_ops - def get_point_group_operations(self, cartesian=False): + def get_point_group_operations(self, cartesian: bool = False) -> list[SymmOp]: """Return symmetry operations as a list of SymmOp objects. By default returns fractional coord symm ops. But Cartesian can be returned too. @@ -325,7 +330,7 @@ def get_point_group_operations(self, cartesian=False): symm_ops.append(op) return symm_ops - def get_symmetrized_structure(self): + def get_symmetrized_structure(self) -> SymmetrizedStructure: """Get a symmetrized structure. A symmetrized structure is one where the sites have been grouped into symmetrically equivalent groups. @@ -338,9 +343,9 @@ def get_symmetrized_structure(self): self.get_space_group_number(), self.get_symmetry_operations(), ) - return SymmetrizedStructure(self._structure, spg_ops, sym_dataset["equivalent_atoms"], sym_dataset["wyckoffs"]) + return SymmetrizedStructure(self._structure, spg_ops, sym_dataset.equivalent_atoms, sym_dataset.wyckoffs) - def get_refined_structure(self, keep_site_properties=False): + def get_refined_structure(self, keep_site_properties: bool = False) -> Structure: """Get the refined structure based on detected symmetry. The refined structure is a *conventional* cell setting with atoms moved to the expected symmetry positions. @@ -369,7 +374,7 @@ def get_refined_structure(self, keep_site_properties=False): struct = Structure(lattice, species, scaled_positions, site_properties=site_properties) return struct.get_sorted_structure() - def find_primitive(self, keep_site_properties=False): + def find_primitive(self, keep_site_properties: bool = False) -> Structure: """Find a primitive version of the unit cell. Args: @@ -391,8 +396,8 @@ def find_primitive(self, keep_site_properties=False): species = [self._unique_species[i - 1] for i in numbers] if keep_site_properties: site_properties = {} - for k, v in self._site_props.items(): - site_properties[k] = [v[i - 1] for i in numbers] + for key, val in self._site_props.items(): + site_properties[key] = [val[i - 1] for i in numbers] else: site_properties = None @@ -400,9 +405,13 @@ def find_primitive(self, keep_site_properties=False): lattice, species, scaled_positions, to_unit_cell=True, site_properties=site_properties ).get_reduced_structure() - def get_ir_reciprocal_mesh(self, mesh=(10, 10, 10), is_shift=(0, 0, 0)): - """k-point mesh of the Brillouin zone generated taken into account symmetry.The - method returns the irreducible kpoints of the mesh and their weights. + def get_ir_reciprocal_mesh( + self, + mesh: tuple[int, int, int] = (10, 10, 10), + is_shift: tuple[float, float, float] = (0, 0, 0), + ) -> list[tuple[Kpoint, float]]: + """k-point mesh of the Brillouin zone generated taken into account symmetry. + The method returns the irreducible kpoints of the mesh and their weights. Args: mesh (3x1 array): The number of kpoint for the mesh needed in @@ -419,11 +428,15 @@ def get_ir_reciprocal_mesh(self, mesh=(10, 10, 10), is_shift=(0, 0, 0)): mapping, grid = spglib.get_ir_reciprocal_mesh(np.array(mesh), self._cell, is_shift=shift, symprec=self._symprec) results = [] - for i, count in zip(*np.unique(mapping, return_counts=True)): - results.append(((grid[i] + shift * (0.5, 0.5, 0.5)) / mesh, count)) + for idx, count in zip(*np.unique(mapping, return_counts=True)): + results.append(((grid[idx] + shift * (0.5, 0.5, 0.5)) / mesh, count)) return results - def get_ir_reciprocal_mesh_map(self, mesh=(10, 10, 10), is_shift=(0, 0, 0)): + def get_ir_reciprocal_mesh_map( + self, + mesh: tuple[int, int, int] = (10, 10, 10), + is_shift: tuple[float, float, float] = (0, 0, 0), + ) -> tuple[NDArray, NDArray]: """Same as 'get_ir_reciprocal_mesh' but the full grid together with the mapping that maps a reducible to an irreducible kpoint is returned. @@ -446,7 +459,10 @@ def get_ir_reciprocal_mesh_map(self, mesh=(10, 10, 10), is_shift=(0, 0, 0)): return grid_fractional_coords, mapping @cite_conventional_cell_algo - def get_conventional_to_primitive_transformation_matrix(self, international_monoclinic=True): + def get_conventional_to_primitive_transformation_matrix( + self, + international_monoclinic: bool = True, + ) -> NDArray: """Get the transformation matrix to transform a conventional unit cell to a primitive cell according to certain standards the standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure @@ -467,30 +483,32 @@ def get_conventional_to_primitive_transformation_matrix(self, international_mono return np.eye(3) if lattice == "rhombohedral": - # check if the conventional representation is hexagonal or + # Check if the conventional representation is hexagonal or # rhombohedral lengths = conv.lattice.lengths if abs(lengths[0] - lengths[2]) < 0.0001: - transf = np.eye - else: - transf = np.array([[-1, 1, 1], [2, 1, 1], [-1, -2, 1]], dtype=np.float64) / 3 + return np.eye + return np.array([[-1, 1, 1], [2, 1, 1], [-1, -2, 1]], dtype=np.float64) / 3 - elif "I" in self.get_space_group_symbol(): - transf = np.array([[-1, 1, 1], [1, -1, 1], [1, 1, -1]], dtype=np.float64) / 2 - elif "F" in self.get_space_group_symbol(): - transf = np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]], dtype=np.float64) / 2 - elif "C" in self.get_space_group_symbol() or "A" in self.get_space_group_symbol(): + if "I" in self.get_space_group_symbol(): + return np.array([[-1, 1, 1], [1, -1, 1], [1, 1, -1]], dtype=np.float64) / 2 + + if "F" in self.get_space_group_symbol(): + return np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]], dtype=np.float64) / 2 + + if "C" in self.get_space_group_symbol() or "A" in self.get_space_group_symbol(): if self.get_crystal_system() == "monoclinic": - transf = np.array([[1, 1, 0], [-1, 1, 0], [0, 0, 2]], dtype=np.float64) / 2 - else: - transf = np.array([[1, -1, 0], [1, 1, 0], [0, 0, 2]], dtype=np.float64) / 2 - else: - transf = np.eye(3) + return np.array([[1, 1, 0], [-1, 1, 0], [0, 0, 2]], dtype=np.float64) / 2 + return np.array([[1, -1, 0], [1, 1, 0], [0, 0, 2]], dtype=np.float64) / 2 - return transf + return np.eye(3) @cite_conventional_cell_algo - def get_primitive_standard_structure(self, international_monoclinic=True, keep_site_properties=False): + def get_primitive_standard_structure( + self, + international_monoclinic: bool = True, + keep_site_properties: bool = False, + ) -> Structure: """Get a structure with a primitive cell according to certain standards. The standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: Challenges and tools. Computational @@ -523,7 +541,7 @@ def get_primitive_standard_structure(self, international_monoclinic=True, keep_s international_monoclinic=international_monoclinic ) - new_sites = [] + new_sites: list[PeriodicSite] = [] lattice = Lattice(np.dot(transf, conv.lattice.matrix)) for site in conv: new_s = PeriodicSite( @@ -569,7 +587,11 @@ def get_primitive_standard_structure(self, international_monoclinic=True, keep_s return Structure.from_sites(new_sites) @cite_conventional_cell_algo - def get_conventional_standard_structure(self, international_monoclinic=True, keep_site_properties=False): + def get_conventional_standard_structure( + self, + international_monoclinic: bool = True, + keep_site_properties: bool = False, + ) -> Structure: """Get a structure with a conventional cell according to certain standards. The standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: Challenges and tools. Computational @@ -604,7 +626,7 @@ def get_conventional_standard_structure(self, international_monoclinic=True, kee key=lambda k: k["length"], ) - if latt_type in ("orthorhombic", "cubic"): + if latt_type in {"orthorhombic", "cubic"}: # you want to keep the c axis where it is # to keep the C- settings transf = np.zeros(shape=(3, 3)) @@ -612,7 +634,7 @@ def get_conventional_standard_structure(self, international_monoclinic=True, kee transf[2] = [0, 0, 1] a, b = sorted(lattice.abc[:2]) sorted_dic = sorted( - ({"vec": lattice.matrix[i], "length": lattice.abc[i], "orig_index": i} for i in [0, 1]), + ({"vec": lattice.matrix[i], "length": lattice.abc[i], "orig_index": i} for i in (0, 1)), key=lambda k: k["length"], ) for idx in range(2): @@ -624,7 +646,7 @@ def get_conventional_standard_structure(self, international_monoclinic=True, kee transf[2] = [1, 0, 0] a, b = sorted(lattice.abc[1:]) sorted_dic = sorted( - ({"vec": lattice.matrix[i], "length": lattice.abc[i], "orig_index": i} for i in [1, 2]), + ({"vec": lattice.matrix[i], "length": lattice.abc[i], "orig_index": i} for i in (1, 2)), key=lambda k: k["length"], ) for idx in range(2): @@ -648,7 +670,8 @@ def get_conventional_standard_structure(self, international_monoclinic=True, kee a, c = c, a transf = np.dot([[0, 0, 1], [0, 1, 0], [1, 0, 0]], transf) lattice = Lattice.tetragonal(a, c) - elif latt_type in ("hexagonal", "rhombohedral"): + + elif latt_type in {"hexagonal", "rhombohedral"}: # for the conventional cell representation, # we always show the rhombohedral lattices as hexagonal @@ -677,25 +700,25 @@ def get_conventional_standard_structure(self, international_monoclinic=True, kee transf = np.zeros(shape=(3, 3)) transf[2] = [0, 0, 1] sorted_dic = sorted( - ({"vec": lattice.matrix[i], "length": lattice.abc[i], "orig_index": i} for i in [0, 1]), + ({"vec": lattice.matrix[i], "length": lattice.abc[i], "orig_index": i} for i in (0, 1)), key=lambda k: k["length"], ) a = sorted_dic[0]["length"] b = sorted_dic[1]["length"] c = lattice.abc[2] new_matrix = None - for t in itertools.permutations(list(range(2)), 2): + for tp2 in itertools.permutations(list(range(2)), 2): m = lattice.matrix - latt2 = Lattice([m[t[0]], m[t[1]], m[2]]) + latt2 = Lattice([m[tp2[0]], m[tp2[1]], m[2]]) lengths = latt2.lengths angles = latt2.angles if angles[0] > 90: # if the angle is > 90 we invert a and b to get # an angle < 90 - a, b, c, alpha, beta, gamma = Lattice([-m[t[0]], -m[t[1]], m[2]]).parameters + a, b, c, alpha, beta, gamma = Lattice([-m[tp2[0]], -m[tp2[1]], m[2]]).parameters transf = np.zeros(shape=(3, 3)) - transf[0][t[0]] = -1 - transf[1][t[1]] = -1 + transf[0][tp2[0]] = -1 + transf[1][tp2[1]] = -1 transf[2][2] = 1 alpha = math.pi * alpha / 180 new_matrix = [ @@ -707,8 +730,8 @@ def get_conventional_standard_structure(self, international_monoclinic=True, kee if angles[0] < 90: transf = np.zeros(shape=(3, 3)) - transf[0][t[0]] = 1 - transf[1][t[1]] = 1 + transf[0][tp2[0]] = 1 + transf[1][tp2[1]] = 1 transf[2][2] = 1 a, b, c = lengths alpha = math.pi * angles[0] / 180 @@ -733,15 +756,15 @@ def get_conventional_standard_structure(self, international_monoclinic=True, kee # and b 90 and b < c: - a, b, c, alpha, beta, gamma = Lattice([-m[t[0]], -m[t[1]], m[t[2]]]).parameters + a, b, c, alpha, beta, gamma = Lattice([-m[tp3[0]], -m[tp3[1]], m[tp3[2]]]).parameters transf = np.zeros(shape=(3, 3)) - transf[0][t[0]] = -1 - transf[1][t[1]] = -1 - transf[2][t[2]] = 1 + transf[0][tp3[0]] = -1 + transf[1][tp3[1]] = -1 + transf[2][tp3[2]] = 1 alpha = math.pi * alpha / 180 new_matrix = [ [a, 0, 0], @@ -752,9 +775,9 @@ def get_conventional_standard_structure(self, international_monoclinic=True, kee if alpha < 90 and b < c: transf = np.zeros(shape=(3, 3)) - transf[0][t[0]] = 1 - transf[1][t[1]] = 1 - transf[2][t[2]] = 1 + transf[0][tp3[0]] = 1 + transf[1][tp3[1]] = 1 + transf[2][tp3[2]] = 1 alpha = math.pi * alpha / 180 new_matrix = [ [a, 0, 0], @@ -884,7 +907,7 @@ def is_all_acute_or_obtuse(matrix) -> bool: ) return new_struct.get_sorted_structure() - def get_kpoint_weights(self, kpoints, atol=1e-5): + def get_kpoint_weights(self, kpoints: Sequence[Kpoint], atol: float = 1e-5) -> list[float]: """Calculate the weights for a list of kpoints. Args: @@ -919,20 +942,20 @@ def get_kpoint_weights(self, kpoints, atol=1e-5): mapping = list(mapping) grid = (np.array(grid) + np.array(shift) * (0.5, 0.5, 0.5)) / mesh weights = [] - mapped = defaultdict(int) + mapped: dict[tuple, int] = defaultdict(int) for kpt in kpoints: for idx, g in enumerate(grid): if np.allclose(pbc_diff(kpt, g), (0, 0, 0), atol=atol): mapped[tuple(g)] += 1 weights.append(mapping.count(mapping[idx])) break - if (len(mapped) != len(set(mapping))) or (not all(v == 1 for v in mapped.values())): + if (len(mapped) != len(set(mapping))) or any(v != 1 for v in mapped.values()): raise ValueError("Unable to find 1:1 corresponding between input kpoints and irreducible grid!") return [w / sum(weights) for w in weights] def is_laue(self) -> bool: """Check if the point group of the structure has Laue symmetry (centrosymmetry).""" - laue = ("-1", "2/m", "mmm", "4/m", "4/mmm", "-3", "-3m", "6/m", "6/mmm", "m-3", "m-3m") + laue = {"-1", "2/m", "mmm", "4/m", "4/mmm", "-3", "-3m", "6/m", "6/mmm", "m-3", "m-3m"} return str(self.get_point_group_symbol()) in laue @@ -962,7 +985,13 @@ class PointGroupAnalyzer: inversion_op = SymmOp.inversion() - def __init__(self, mol, tolerance=0.3, eigen_tolerance=0.01, matrix_tolerance=0.1): + def __init__( + self, + mol: Molecule, + tolerance: float = 0.3, + eigen_tolerance: float = 0.01, + matrix_tolerance: float = 0.1, + ) -> None: """The default settings are usually sufficient. Args: @@ -980,10 +1009,10 @@ def __init__(self, mol, tolerance=0.3, eigen_tolerance=0.01, matrix_tolerance=0. self.eig_tol = eigen_tolerance self.mat_tol = matrix_tolerance self._analyze() - if self.sch_symbol in ["C1v", "C1h"]: - self.sch_symbol = "Cs" + if self.sch_symbol in {"C1v", "C1h"}: + self.sch_symbol: str = "Cs" - def _analyze(self): + def _analyze(self) -> None: if len(self.centered_mol) == 1: self.sch_symbol = "Kh" else: @@ -994,7 +1023,7 @@ def _analyze(self): wt = site.species.weight for i in range(3): inertia_tensor[i, i] += wt * (c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2) - for i, j in [(0, 1), (1, 2), (0, 2)]: + for i, j in ((0, 1), (1, 2), (0, 2)): inertia_tensor[i, j] += -wt * c[i] * c[j] inertia_tensor[j, i] += -wt * c[j] * c[i] total_inertia += wt * np.dot(c, c) @@ -1011,8 +1040,8 @@ def _analyze(self): eig_all_same = abs(v1 - v2) < self.eig_tol and abs(v1 - v3) < self.eig_tol eig_all_diff = abs(v1 - v2) > self.eig_tol and abs(v1 - v3) > self.eig_tol and abs(v2 - v3) > self.eig_tol - self.rot_sym = [] - self.symmops = [SymmOp(np.eye(4))] + self.rot_sym: list = [] + self.symmops: list[SymmOp] = [SymmOp(np.eye(4))] if eig_zero: logger.debug("Linear molecule detected") self._proc_linear() @@ -1026,14 +1055,14 @@ def _analyze(self): logger.debug("Symmetric top molecule detected") self._proc_sym_top() - def _proc_linear(self): + def _proc_linear(self) -> None: if self.is_valid_op(PointGroupAnalyzer.inversion_op): self.sch_symbol = "D*h" self.symmops.append(PointGroupAnalyzer.inversion_op) else: self.sch_symbol = "C*v" - def _proc_asym_top(self): + def _proc_asym_top(self) -> None: """Handles asymmetric top molecules, which cannot contain rotational symmetry larger than 2. """ @@ -1048,7 +1077,7 @@ def _proc_asym_top(self): logger.debug("Cyclic group detected.") self._proc_cyclic() - def _proc_sym_top(self): + def _proc_sym_top(self) -> None: """Handles symmetric top molecules which has one unique eigenvalue whose corresponding principal axis is a unique rotational axis. @@ -1075,7 +1104,7 @@ def _proc_sym_top(self): else: self._proc_no_rot_sym() - def _proc_no_rot_sym(self): + def _proc_no_rot_sym(self) -> None: """Handles molecules with no rotational symmetry. Only possible point groups are C1, Cs and Ci. @@ -1091,7 +1120,7 @@ def _proc_no_rot_sym(self): self.sch_symbol = "Cs" break - def _proc_cyclic(self): + def _proc_cyclic(self) -> None: """Handles cyclic group molecules.""" main_axis, rot = max(self.rot_sym, key=lambda v: v[1]) self.sch_symbol = f"C{rot}" @@ -1103,7 +1132,7 @@ def _proc_cyclic(self): elif mirror_type == "" and self.is_valid_op(SymmOp.rotoreflection(main_axis, angle=180 / rot)): self.sch_symbol = f"S{2 * rot}" - def _proc_dihedral(self): + def _proc_dihedral(self) -> None: """Handles dihedral group molecules, i.e those with intersecting R2 axes and a main axis. """ @@ -1115,7 +1144,7 @@ def _proc_dihedral(self): elif mirror_type != "": self.sch_symbol += "d" - def _check_R2_axes_asym(self): + def _check_R2_axes_asym(self) -> None: """Test for 2-fold rotation along the principal axes. Used to handle asymmetric top molecules. @@ -1126,14 +1155,14 @@ def _check_R2_axes_asym(self): self.symmops.append(op) self.rot_sym.append((v, 2)) - def _find_mirror(self, axis): + def _find_mirror(self, axis: NDArray) -> Literal["h", "d", "v", ""]: """Looks for mirror symmetry of specified type about axis. Possible types are "h" or "vd". Horizontal (h) mirrors are perpendicular to the axis while vertical (v) or diagonal (d) mirrors are parallel. v mirrors has atoms lying on the mirror plane while d mirrors do not. """ - mirror_type = "" + mirror_type: Literal["h", "d", "v", ""] = "" # First test whether the axis itself is the normal to a mirror plane. if self.is_valid_op(SymmOp.reflection(axis)): @@ -1160,7 +1189,7 @@ def _find_mirror(self, axis): return mirror_type - def _get_smallest_set_not_on_axis(self, axis): + def _get_smallest_set_not_on_axis(self, axis: NDArray) -> list: """Get the smallest list of atoms with the same species and distance from origin AND does not lie on the specified axis. @@ -1169,8 +1198,7 @@ def _get_smallest_set_not_on_axis(self, axis): """ def not_on_axis(site): - v = np.cross(site.coords, axis) - return np.linalg.norm(v) > self.tol + return np.linalg.norm(np.cross(site.coords, axis)) > self.tol valid_sets = [] _origin_site, dist_el_sites = cluster_sites(self.centered_mol, self.tol) @@ -1181,7 +1209,7 @@ def not_on_axis(site): return min(valid_sets, key=len) - def _check_rot_sym(self, axis): + def _check_rot_sym(self, axis: NDArray) -> int: """Determine the rotational symmetry about supplied axis. Used only for symmetric top molecules which has possible rotational symmetry @@ -1189,18 +1217,17 @@ def _check_rot_sym(self, axis): """ min_set = self._get_smallest_set_not_on_axis(axis) max_sym = len(min_set) - for i in range(max_sym, 0, -1): - if max_sym % i != 0: + for idx in range(max_sym, 0, -1): + if max_sym % idx != 0: continue - op = SymmOp.from_axis_angle_and_translation(axis, 360 / i) - rotvalid = self.is_valid_op(op) - if rotvalid: + op = SymmOp.from_axis_angle_and_translation(axis, 360 / idx) + if self.is_valid_op(op): self.symmops.append(op) - self.rot_sym.append((axis, i)) - return i + self.rot_sym.append((axis, idx)) + return idx return 1 - def _check_perpendicular_r2_axis(self, axis): + def _check_perpendicular_r2_axis(self, axis: NDArray) -> None | Literal[True]: """Check for R2 axes perpendicular to unique axis. For handling symmetric top molecules. @@ -1210,14 +1237,13 @@ def _check_perpendicular_r2_axis(self, axis): test_axis = np.cross(s1.coords - s2.coords, axis) if np.linalg.norm(test_axis) > self.tol: op = SymmOp.from_axis_angle_and_translation(test_axis, 180) - r2present = self.is_valid_op(op) - if r2present: + if self.is_valid_op(op): self.symmops.append(op) self.rot_sym.append((test_axis, 2)) return True return None - def _proc_sph_top(self): + def _proc_sph_top(self) -> None: """Handles Spherical Top Molecules, which belongs to the T, O or I point groups. """ @@ -1229,22 +1255,24 @@ def _proc_sph_top(self): if rot < 3: logger.debug("Accidental spherical top!") self._proc_sym_top() + elif rot == 3: mirror_type = self._find_mirror(main_axis) - if mirror_type != "": - if self.is_valid_op(PointGroupAnalyzer.inversion_op): - self.symmops.append(PointGroupAnalyzer.inversion_op) - self.sch_symbol = "Th" - else: - self.sch_symbol = "Td" - else: + if mirror_type == "": self.sch_symbol = "T" + elif self.is_valid_op(PointGroupAnalyzer.inversion_op): + self.symmops.append(PointGroupAnalyzer.inversion_op) + self.sch_symbol = "Th" + else: + self.sch_symbol = "Td" + elif rot == 4: if self.is_valid_op(PointGroupAnalyzer.inversion_op): self.symmops.append(PointGroupAnalyzer.inversion_op) self.sch_symbol = "Oh" else: self.sch_symbol = "O" + elif rot == 5: if self.is_valid_op(PointGroupAnalyzer.inversion_op): self.symmops.append(PointGroupAnalyzer.inversion_op) @@ -1252,14 +1280,14 @@ def _proc_sph_top(self): else: self.sch_symbol = "I" - def _find_spherical_axes(self): + def _find_spherical_axes(self) -> None: """Looks for R5, R4, R3 and R2 axes in spherical top molecules. Point group T molecules have only one unique 3-fold and one unique 2-fold axis. O molecules have one unique 4, 3 and 2-fold axes. I molecules have a unique 5-fold axis. """ - rot_present = defaultdict(bool) + rot_present: dict[int, bool] = defaultdict(bool) _origin_site, dist_el_sites = cluster_sites(self.centered_mol, self.tol) test_set = min(dist_el_sites.values(), key=len) coords = [s.coords for s in test_set] @@ -1287,21 +1315,20 @@ def _find_spherical_axes(self): if rot_present[2] and rot_present[3] and (rot_present[4] or rot_present[5]): break - def get_pointgroup(self): + def get_pointgroup(self) -> PointGroupOperations: """Get a PointGroup object for the molecule.""" return PointGroupOperations(self.sch_symbol, self.symmops, self.mat_tol) - def get_symmetry_operations(self): - """Return symmetry operations as a list of SymmOp objects. Returns Cartesian coord - symmops. + def get_symmetry_operations(self) -> Sequence[SymmOp]: + """Get symmetry operations. Returns: - list[SymmOp]: symmetry operations. + list[SymmOp]: symmetry operations in Cartesian coord. """ return generate_full_symmops(self.symmops, self.tol) - def get_rotational_symmetry_number(self): - """Return the rotational symmetry number.""" + def get_rotational_symmetry_number(self) -> int: + """Get the rotational symmetry number.""" symm_ops = self.get_symmetry_operations() symm_number = 0 for symm in symm_ops: @@ -1310,7 +1337,7 @@ def get_rotational_symmetry_number(self): symm_number += 1 return symm_number - def is_valid_op(self, symm_op) -> bool: + def is_valid_op(self, symm_op: SymmOp) -> bool: """Check if a particular symmetry operation is a valid symmetry operation for a molecule, i.e., the operation maps all atoms to another equivalent atom. @@ -1324,11 +1351,11 @@ def is_valid_op(self, symm_op) -> bool: for site in self.centered_mol: coord = symm_op.operate(site.coords) ind = find_in_coord_list(coords, coord, self.tol) - if not (len(ind) == 1 and self.centered_mol[ind[0]].species == site.species): + if len(ind) != 1 or self.centered_mol[ind[0]].species != site.species: return False return True - def _get_eq_sets(self): + def _get_eq_sets(self) -> dict[Literal["eq_sets", "sym_ops"], Any]: """Calculate the dictionary for mapping equivalent atoms onto each other. Returns: @@ -1339,7 +1366,8 @@ def _get_eq_sets(self): operation that maps atom i unto j. """ UNIT = np.eye(3) - eq_sets, operations = defaultdict(set), defaultdict(dict) + eq_sets: dict[int, set] = defaultdict(set) + operations: dict[int, dict] = defaultdict(dict) symm_ops = [op.rotation_matrix for op in generate_full_symmops(self.symmops, self.tol)] def get_clustered_indices(): @@ -1373,7 +1401,7 @@ def get_clustered_indices(): return {"eq_sets": eq_sets, "sym_ops": operations} @staticmethod - def _combine_eq_sets(equiv_sets, sym_ops): + def _combine_eq_sets(equiv_sets: dict, sym_ops: dict) -> dict: """Combines the dicts of _get_equivalent_atom_dicts into one. Args: @@ -1434,7 +1462,7 @@ def get_equivalent_atoms(self): eq = self._get_eq_sets() return self._combine_eq_sets(eq["eq_sets"], eq["sym_ops"]) - def symmetrize_molecule(self): + def symmetrize_molecule(self) -> dict: """Get a symmetrized molecule. The equivalent atoms obtained via @@ -1469,7 +1497,12 @@ def symmetrize_molecule(self): return {"sym_mol": molecule, "eq_sets": eq_sets, "sym_ops": ops} -def iterative_symmetrize(mol, max_n=10, tolerance=0.3, epsilon=1e-2): +def iterative_symmetrize( + mol: Molecule, + max_n: int = 10, + tolerance: float = 0.3, + epsilon: float = 1e-2, +) -> dict: """Get a symmetrized molecule. The equivalent atoms obtained via @@ -1490,7 +1523,6 @@ def iterative_symmetrize(mol, max_n=10, tolerance=0.3, epsilon=1e-2): subsequently symmetrized structures is smaller epsilon, the iteration stops before max_n is reached. - Returns: dict: with three possible keys: sym_mol: A symmetrized molecule instance. @@ -1513,7 +1545,11 @@ def iterative_symmetrize(mol, max_n=10, tolerance=0.3, epsilon=1e-2): return eq -def cluster_sites(mol: Molecule, tol: float, give_only_index: bool = False) -> tuple[Site | None, dict]: +def cluster_sites( + mol: Molecule, + tol: float, + give_only_index: bool = False, +) -> tuple[Site | None, dict]: """Cluster sites based on distance and species type. Args: @@ -1548,7 +1584,10 @@ def cluster_sites(mol: Molecule, tol: float, give_only_index: bool = False) -> t return origin_site, clustered_sites -def generate_full_symmops(symmops: Sequence[SymmOp], tol: float) -> Sequence[SymmOp]: +def generate_full_symmops( + symmops: Sequence[SymmOp], + tol: float, +) -> Sequence[SymmOp]: """Recursive algorithm to permute through all possible combinations of the initially supplied symmetry operations to arrive at a complete set of operations mapping a single atom to all other equivalent atoms in the point group. This assumes that the @@ -1593,7 +1632,12 @@ def generate_full_symmops(symmops: Sequence[SymmOp], tol: float) -> Sequence[Sym class SpacegroupOperations(list): """Represents a space group, which is a collection of symmetry operations.""" - def __init__(self, int_symbol, int_number, symmops): + def __init__( + self, + int_symbol: str, + int_number: int, + symmops: Sequence[SymmOp], + ) -> None: """ Args: int_symbol (str): International symbol of the spacegroup. @@ -1605,7 +1649,15 @@ def __init__(self, int_symbol, int_number, symmops): self.int_number = int_number super().__init__(symmops) - def are_symmetrically_equivalent(self, sites1, sites2, symm_prec=1e-3) -> bool: + def __str__(self) -> str: + return f"{self.int_symbol} ({self.int_number}) spacegroup" + + def are_symmetrically_equivalent( + self, + sites1: set[PeriodicSite], + sites2: set[PeriodicSite], + symm_prec: float = 1e-3, + ) -> bool: """Given two sets of PeriodicSites, test if they are actually symmetrically equivalent under this space group. Useful, for example, if you want to test if selecting atoms 1 and 2 out of a set of 4 atoms are symmetrically the same as @@ -1636,9 +1688,6 @@ def in_sites(site): return True return False - def __str__(self): - return f"{self.int_symbol} ({self.int_number}) spacegroup" - class PointGroupOperations(list): """Represents a point group, which is a sequence of symmetry operations. @@ -1647,7 +1696,12 @@ class PointGroupOperations(list): sch_symbol (str): Schoenflies symbol of the point group. """ - def __init__(self, sch_symbol, operations, tol: float = 0.1): + def __init__( + self, + sch_symbol: str, + operations: Sequence[SymmOp], + tol: float = 0.1, + ) -> None: """ Args: sch_symbol (str): Schoenflies symbol of the point group. @@ -1660,5 +1714,5 @@ def __init__(self, sch_symbol, operations, tol: float = 0.1): self.sch_symbol = sch_symbol super().__init__(generate_full_symmops(operations, tol)) - def __repr__(self): + def __repr__(self) -> str: return self.sch_symbol diff --git a/pymatgen/symmetry/bandstructure.py b/src/pymatgen/symmetry/bandstructure.py similarity index 99% rename from pymatgen/symmetry/bandstructure.py rename to src/pymatgen/symmetry/bandstructure.py index 05d416a0fbe..c37009792e1 100644 --- a/pymatgen/symmetry/bandstructure.py +++ b/src/pymatgen/symmetry/bandstructure.py @@ -9,7 +9,6 @@ import networkx as nx import numpy as np - from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine from pymatgen.electronic_structure.core import Spin from pymatgen.symmetry.analyzer import cite_conventional_cell_algo diff --git a/pymatgen/symmetry/groups.py b/src/pymatgen/symmetry/groups.py similarity index 84% rename from pymatgen/symmetry/groups.py rename to src/pymatgen/symmetry/groups.py index d9fbc66cfdb..fab21815d5e 100644 --- a/pymatgen/symmetry/groups.py +++ b/src/pymatgen/symmetry/groups.py @@ -17,19 +17,17 @@ import numpy as np from monty.design_patterns import cached_class from monty.serialization import loadfn - from pymatgen.util.string import Stringify if TYPE_CHECKING: from typing import ClassVar, Literal from numpy.typing import ArrayLike - from typing_extensions import Self - from pymatgen.core.lattice import Lattice # Don't import at runtime to avoid circular import from pymatgen.core.operations import SymmOp # noqa: TCH004 + from typing_extensions import Self CrystalSystem = Literal["cubic", "hexagonal", "monoclinic", "orthorhombic", "tetragonal", "triclinic", "trigonal"] @@ -114,6 +112,7 @@ class PointGroup(SymmetryGroup): def __init__(self, int_symbol: str) -> None: """Initialize a Point Group from its international symbol. + Please note that only the 32 crystal classes are supported right now. Args: int_symbol (str): International or Hermann-Mauguin Symbol. @@ -167,6 +166,54 @@ def get_orbit(self, p: ArrayLike, tol: float = 1e-5) -> list[np.ndarray]: orbit.append(pp) return orbit + @classmethod + def from_space_group(cls, sg_symbol: str) -> PointGroup: + """Instantiate one of the 32 crystal classes from a space group symbol in + Hermann Mauguin notation (int symbol or full symbol). + + Args: + sg_symbol: space group symbol in Hermann Mauguin notation. + + Raises: + AssertionError if a valid crystal class cannot be created + Returns: + crystal class in Hermann-Mauguin notation. + """ + abbrev_map = { + "2/m2/m2/m": "mmm", + "4/m2/m2/m": "4/mmm", + "-32/m": "-3m", + "6/m2/m2/m": "6/mmm", + "2/m-3": "m-3", + "4/m-32/m": "m-3m", + } + non_standard_map = { + "m2m": "mm2", + "2mm": "mm2", + "-4m2": "-42m", # technically not non-standard + "-62m": "-6m2", # technically not non-standard + } + symbol = re.sub(r" ", "", sg_symbol) + + symm_ops = loadfn(os.path.join(os.path.dirname(__file__), "symm_ops.json")) # get short symbol if possible + for spg in symm_ops: + if symbol in [spg["hermann_mauguin"], spg["universal_h_m"], spg["hermann_mauguin_u"]]: + symbol = spg["short_h_m"] + + assert symbol[0].isupper(), f"Invalid sg_symbol {sg_symbol}" + assert not symbol[1:].isupper(), f"Invalid sg_symbol {sg_symbol}" + + symbol = symbol[1:] # Remove centering + symbol = symbol.translate(str.maketrans("abcden", "mmmmmm")) # Remove translation from glide planes + symbol = re.sub(r"_.", "", symbol) # Remove translation from screw axes + symbol = abbrev_map.get(symbol, symbol) + symbol = non_standard_map.get(symbol, symbol) + + assert ( + symbol in SYMM_DATA["point_group_encoding"] + ), f"Could not create a valid crystal class ({symbol}) from sg_symbol {sg_symbol}" + return cls(symbol) + @cached_class class SpaceGroup(SymmetryGroup): @@ -196,7 +243,7 @@ class SpaceGroup(SymmetryGroup): v["full_symbol"]: k for k, v in SYMM_DATA["space_group_encoding"].items() } - def __init__(self, int_symbol: str) -> None: + def __init__(self, int_symbol: str, hexagonal: bool = True) -> None: """Initialize a Space Group from its full or abbreviated international symbol. Only standard settings are supported. @@ -211,9 +258,26 @@ def __init__(self, int_symbol: str) -> None: possible settings for a spacegroup, use the get_settings() classmethod. Alternative origin choices can be indicated by a translation vector, e.g. 'Fm-3m(a-1/4,b-1/4,c-1/4)'. + hexagonal (bool): For rhombohedral groups, whether to handle as in + hexagonal setting (default) or rhombohedral setting. + If the int_symbol of a rhombohedral spacegroup is given with the + setting ("(:)H"/"(:)R"), this parameter is overwritten accordingly + (please note that the setting is not contained in the symbol + attribute anymore). """ from pymatgen.core.operations import SymmOp + if int_symbol.endswith("H"): + self.hexagonal = True + if not int_symbol.endswith(":H"): + int_symbol = int_symbol[:-1] + ":H" + elif int_symbol.endswith("R"): + self.hexagonal = False + if not int_symbol.endswith(":R"): + int_symbol = int_symbol[:-1] + ":R" + else: + self.hexagonal = hexagonal + int_symbol = re.sub(r" ", "", int_symbol) if int_symbol in SpaceGroup.abbrev_sg_mapping: int_symbol = SpaceGroup.abbrev_sg_mapping[int_symbol] @@ -223,15 +287,22 @@ def __init__(self, int_symbol: str) -> None: self._symmetry_ops: set[SymmOp] | None for spg in SpaceGroup.SYMM_OPS: - if int_symbol in [spg["hermann_mauguin"], spg["universal_h_m"]]: + if int_symbol in [spg["hermann_mauguin"], spg["universal_h_m"], spg["hermann_mauguin_u"]]: ops = [SymmOp.from_xyz_str(s) for s in spg["symops"]] - self.symbol = re.sub(r":", "", re.sub(r" ", "", spg["universal_h_m"])) + self.symbol = spg["hermann_mauguin_u"] if int_symbol in SpaceGroup.sg_encoding: self.full_symbol = SpaceGroup.sg_encoding[int_symbol]["full_symbol"] self.point_group = SpaceGroup.sg_encoding[int_symbol]["point_group"] + elif self.symbol in SpaceGroup.sg_encoding: + self.full_symbol = SpaceGroup.sg_encoding[self.symbol]["full_symbol"] + self.point_group = SpaceGroup.sg_encoding[self.symbol]["point_group"] else: - self.full_symbol = re.sub(r" ", "", spg["universal_h_m"]) - self.point_group = spg["schoenflies"] + self.full_symbol = spg["hermann_mauguin_u"] + warnings.warn( + f"Full symbol not available, falling back to short Hermann Mauguin symbol " + f"{self.symbol} instead" + ) + self.point_group = spg["point_group"] self.int_number = spg["number"] self.order = len(ops) self._symmetry_ops = {*ops} @@ -268,15 +339,15 @@ def __init__(self, int_symbol: str) -> None: def _generate_full_symmetry_ops(self) -> np.ndarray: symm_ops = np.array(self.generators) for op in symm_ops: - op[0:3, 3] = np.mod(op[0:3, 3], 1) + op[:3, 3] = np.mod(op[:3, 3], 1) new_ops = symm_ops while len(new_ops) > 0 and len(symm_ops) < self.order: gen_ops = [] for g in new_ops: temp_ops = np.einsum("ijk,kl", symm_ops, g) for op in temp_ops: - op[0:3, 3] = np.mod(op[0:3, 3], 1) - ind = np.where(np.abs(1 - op[0:3, 3]) < 1e-5) + op[:3, 3] = np.mod(op[:3, 3], 1) + ind = np.where(np.abs(1 - op[:3, 3]) < 1e-5) op[ind, 3] = 0 if not in_array_list(symm_ops, op): gen_ops.append(op) @@ -401,7 +472,7 @@ def check(param, ref, tolerance): if crys_system == "hexagonal" or ( crys_system == "trigonal" and ( - self.symbol.endswith("H") + self.hexagonal or self.int_number in [143, 144, 145, 147, 149, 150, 151, 152, 153, 154, 156, 157, 158, 159, 162, 163, 164, 165] ) @@ -533,7 +604,8 @@ def sg_symbol_from_int_number(int_number: int, hexagonal: bool = True) -> str: hexagonal setting (default) or rhombohedral setting. Returns: - str: Spacegroup symbol + str: Spacegroup symbol / Space group symbol + "H" if group is + rhombohedral and hexagonal=True """ syms = [] for n, v in SYMM_DATA["space_group_encoding"].items(): diff --git a/pymatgen/symmetry/kpath.py b/src/pymatgen/symmetry/kpath.py similarity index 99% rename from pymatgen/symmetry/kpath.py rename to src/pymatgen/symmetry/kpath.py index 3d4ad5ea1f3..a1983f5047d 100644 --- a/pymatgen/symmetry/kpath.py +++ b/src/pymatgen/symmetry/kpath.py @@ -12,7 +12,6 @@ import numpy as np import spglib from monty.dev import requires - from pymatgen.core.lattice import Lattice from pymatgen.core.operations import MagSymmOp, SymmOp from pymatgen.symmetry.analyzer import SpacegroupAnalyzer, cite_conventional_cell_algo @@ -25,7 +24,7 @@ if TYPE_CHECKING: from typing import Any - from pymatgen.core import Structure + from pymatgen.core import Composition, Structure from pymatgen.util.typing import SpeciesLike __author__ = "Geoffroy Hautier, Katherine Latimer, Jason Munro" @@ -890,11 +889,11 @@ def __init__(self, structure: Structure, symprec: float = 0.01, angle_tolerance= sp = structure.site_properties species = [site.species for site in structure] - site_data = species + site_data: list[Composition] = species if not system_is_tri: warn("Non-zero 'magmom' data will be used to define unique atoms in the cell.") - site_data = zip(species, [tuple(vec) for vec in sp["magmom"]]) # type: ignore + site_data = zip(species, [tuple(vec) for vec in sp["magmom"]]) # type: ignore[assignment] unique_species: list[SpeciesLike] = [] numbers = [] @@ -1481,18 +1480,18 @@ def _get_key_lines(key_points, bz_as_key_point_inds): # not the face center point (don't need to check it since it's not # shared with other facets) face_center_ind = facet_as_key_point_inds[-1] - for j, ind in enumerate(facet_as_key_point_inds_bndy, start=-1): + for j, ind in enumerate(facet_as_key_point_inds_bndy): if ( - min(ind, facet_as_key_point_inds_bndy[j]), - max(ind, facet_as_key_point_inds_bndy[j]), + min(ind, facet_as_key_point_inds_bndy[j - 1]), + max(ind, facet_as_key_point_inds_bndy[j - 1]), ) not in key_lines: key_lines.append( ( - min(ind, facet_as_key_point_inds_bndy[j]), - max(ind, facet_as_key_point_inds_bndy[j]), + min(ind, facet_as_key_point_inds_bndy[j - 1]), + max(ind, facet_as_key_point_inds_bndy[j - 1]), ) ) - k = j + 2 if j != len(facet_as_key_point_inds_bndy) - 2 else 0 + k = j + 1 if j != len(facet_as_key_point_inds_bndy) - 1 else 0 if ( min(ind, facet_as_key_point_inds_bndy[k]), max(ind, facet_as_key_point_inds_bndy[k]), diff --git a/pymatgen/symmetry/maggroups.py b/src/pymatgen/symmetry/maggroups.py similarity index 99% rename from pymatgen/symmetry/maggroups.py rename to src/pymatgen/symmetry/maggroups.py index 33270ee8c82..1b7b72ee33a 100644 --- a/pymatgen/symmetry/maggroups.py +++ b/src/pymatgen/symmetry/maggroups.py @@ -11,7 +11,6 @@ import numpy as np from monty.design_patterns import cached_class - from pymatgen.core.operations import MagSymmOp from pymatgen.electronic_structure.core import Magmom from pymatgen.symmetry.groups import SymmetryGroup, in_array_list @@ -21,9 +20,8 @@ if TYPE_CHECKING: from collections.abc import Sequence - from typing_extensions import Self - from pymatgen.core.lattice import Lattice + from typing_extensions import Self __author__ = "Matthew Horton, Shyue Ping Ong" diff --git a/pymatgen/symmetry/settings.py b/src/pymatgen/symmetry/settings.py similarity index 99% rename from pymatgen/symmetry/settings.py rename to src/pymatgen/symmetry/settings.py index 3abd7f547f3..99597c1cbe3 100644 --- a/pymatgen/symmetry/settings.py +++ b/src/pymatgen/symmetry/settings.py @@ -7,12 +7,11 @@ from typing import TYPE_CHECKING import numpy as np -from sympy import Matrix -from sympy.parsing.sympy_parser import parse_expr - from pymatgen.core.lattice import Lattice from pymatgen.core.operations import MagSymmOp, SymmOp from pymatgen.util.string import transformation_to_string +from sympy import Matrix +from sympy.parsing.sympy_parser import parse_expr if TYPE_CHECKING: from typing_extensions import Self diff --git a/pymatgen/symmetry/site_symmetries.py b/src/pymatgen/symmetry/site_symmetries.py similarity index 99% rename from pymatgen/symmetry/site_symmetries.py rename to src/pymatgen/symmetry/site_symmetries.py index c73a321270a..ed889cb5f72 100644 --- a/pymatgen/symmetry/site_symmetries.py +++ b/src/pymatgen/symmetry/site_symmetries.py @@ -5,7 +5,6 @@ from typing import TYPE_CHECKING import numpy as np - from pymatgen.core.operations import SymmOp from pymatgen.symmetry.analyzer import SpacegroupAnalyzer diff --git a/pymatgen/symmetry/structure.py b/src/pymatgen/symmetry/structure.py similarity index 99% rename from pymatgen/symmetry/structure.py rename to src/pymatgen/symmetry/structure.py index 22d975c9b53..093b5f8af39 100644 --- a/pymatgen/symmetry/structure.py +++ b/src/pymatgen/symmetry/structure.py @@ -5,16 +5,14 @@ from typing import TYPE_CHECKING import numpy as np -from tabulate import tabulate - from pymatgen.core.structure import PeriodicSite, Structure +from tabulate import tabulate if TYPE_CHECKING: from collections.abc import Sequence - from typing_extensions import Self - from pymatgen.symmetry.analyzer import SpacegroupOperations + from typing_extensions import Self class SymmetrizedStructure(Structure): diff --git a/src/pymatgen/symmetry/symm_data.json b/src/pymatgen/symmetry/symm_data.json new file mode 100644 index 00000000000..c2fd78a702a --- /dev/null +++ b/src/pymatgen/symmetry/symm_data.json @@ -0,0 +1 @@ +{"abbreviated_spacegroup_symbols": {"C2": "C121", "C2/c": "C12/c1", "C2/m": "C12/m1", "Cc": "C1c1", "Cm": "C1m1", "P2": "P121", "P2/c": "P12/c1", "P2/m": "P12/m1", "P2_1": "P12_11", "P2_1/c": "P12_1/c1", "P2_1/m": "P12_1/m1", "Pc": "P1c1", "Pm": "P1m1"}, "generator_matrices": {"a": [[1, 0, 0], [0, 1, 0], [0, 0, 1]], "b": [[-1, 0, 0], [0, -1, 0], [0, 0, 1]], "c": [[-1, 0, 0], [0, 1, 0], [0, 0, -1]], "d": [[0, 0, 1], [1, 0, 0], [0, 1, 0]], "e": [[0, 1, 0], [1, 0, 0], [0, 0, -1]], "f": [[0, -1, 0], [-1, 0, 0], [0, 0, -1]], "g": [[0, -1, 0], [1, 0, 0], [0, 0, 1]], "h": [[-1, 0, 0], [0, -1, 0], [0, 0, -1]], "i": [[1, 0, 0], [0, 1, 0], [0, 0, -1]], "j": [[1, 0, 0], [0, -1, 0], [0, 0, 1]], "k": [[0, -1, 0], [-1, 0, 0], [0, 0, 1]], "l": [[0, 1, 0], [1, 0, 0], [0, 0, 1]], "m": [[0, 1, 0], [-1, 0, 0], [0, 0, -1]], "n": [[0, -1, 0], [1, -1, 0], [0, 0, 1]]}, "maximal_subgroups": {"1": [1], "2": [1, 2], "3": [1, 3, 4, 5], "4": [1, 4], "5": [1, 3, 4, 5], "6": [1, 6, 7, 8], "7": [1, 7, 9], "8": [1, 6, 7, 8, 9], "9": [1, 7, 9], "10": [2, 3, 6, 10, 11, 12, 13], "11": [2, 4, 6, 11, 14], "12": [2, 5, 8, 10, 11, 12, 13, 14, 15], "13": [2, 3, 7, 13, 14, 15], "14": [2, 4, 7, 14], "15": [2, 5, 9, 13, 14, 15], "16": [3, 16, 17, 21, 22], "17": [3, 4, 17, 18, 20], "18": [3, 4, 18, 19], "19": [4, 19], "20": [4, 5, 17, 18, 19, 20], "21": [3, 5, 16, 17, 18, 20, 21, 23, 24], "22": [5, 20, 21, 22], "23": [5, 16, 18, 23], "24": [5, 17, 19, 24], "25": [3, 6, 25, 26, 27, 28, 35, 38, 39, 42], "26": [4, 6, 7, 26, 29, 31, 36], "27": [3, 7, 27, 30, 37], "28": [3, 6, 7, 28, 29, 30, 31, 32, 40, 41], "29": [4, 7, 29, 33], "30": [3, 7, 30, 34], "31": [4, 6, 7, 31, 33], "32": [3, 7, 32, 33, 34], "33": [4, 7, 33], "34": [3, 7, 34, 43], "35": [3, 8, 25, 28, 32, 35, 36, 37, 44, 45, 46], "36": [4, 8, 9, 26, 29, 31, 33, 36], "37": [3, 9, 27, 30, 34, 37], "38": [5, 6, 8, 25, 26, 30, 31, 38, 40, 44, 46], "39": [5, 7, 8, 26, 27, 28, 29, 39, 41, 45, 46], "40": [5, 6, 9, 28, 31, 33, 34, 40], "41": [5, 7, 9, 29, 30, 32, 33, 41], "42": [5, 8, 35, 36, 37, 38, 39, 40, 41, 42], "43": [5, 9, 43], "44": [5, 8, 25, 31, 34, 44], "45": [5, 9, 27, 29, 32, 45], "46": [5, 8, 9, 26, 28, 30, 33, 46], "47": [10, 16, 25, 47, 49, 51, 65, 67, 69], "48": [13, 16, 34, 48, 70], "49": [10, 13, 16, 27, 28, 49, 50, 53, 54, 66, 68], "50": [13, 16, 30, 32, 48, 50, 52], "51": [10, 11, 13, 17, 25, 26, 28, 51, 53, 54, 55, 57, 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8, "patterson_symmetry": "P4/m", "point_group": "4/m"}, "P4_2/nbc": {"enc": "04bOOOgDDDcOODhDDD1YBY", "full_symbol": "P4_2/n2/b2/c", "int_number": 133, "order": 16, "patterson_symmetry": "P4/mmm", "point_group": "4/mmm"}, "P4_2/ncm": {"enc": "04bOOOgDDDcDDOhDDD1YBY", "full_symbol": "P4_2/n2_1/c2/m", "int_number": 138, "order": 16, "patterson_symmetry": "P4/mmm", "point_group": "4/mmm"}, "P4_2/nmc": {"enc": "04bOOOgDDDcDDDhDDD1YBY", "full_symbol": "P4_2/n2_1/m2/c", "int_number": 137, "order": 16, "patterson_symmetry": "P4/mmm", "point_group": "4/mmm"}, "P4_2/nnm": {"enc": "04bOOOgDDDcOOOhDDD1YBY", "full_symbol": "P4_2/n2/n2/m", "int_number": 134, "order": 16, "patterson_symmetry": "P4/mmm", "point_group": "4/mmm"}, "P4_222": {"enc": "03bOOOgOODcOOO0", "full_symbol": "P4_222", "int_number": 93, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "422"}, "P4_22_12": {"enc": "03bOOOgDDDcDDD0", "full_symbol": "P4_22_12", "int_number": 94, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "422"}, "P4_232": {"enc": "04bOOOcOOOdOOOeDDD0", "full_symbol": "P4_232", "int_number": 208, "order": 24, "patterson_symmetry": "Pm-3m", "point_group": "432"}, "P4_2bc": {"enc": "03bOOOgOODjDDO0", "full_symbol": "P4_2bc", "int_number": 106, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "4mm"}, "P4_2cm": {"enc": "03bOOOgOODjOOD0", "full_symbol": "P4_2cm", "int_number": 101, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "4mm"}, "P4_2mc": {"enc": "03bOOOgOODjOOO0", "full_symbol": "P4_2mc", "int_number": 105, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "4mm"}, "P4_2nm": {"enc": "03bOOOgDDDjDDD0", "full_symbol": "P4_2nm", "int_number": 102, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "4mm"}, "P4_3": {"enc": "02bOODgOOF0", "full_symbol": "P4_3", "int_number": 78, "order": 4, "patterson_symmetry": "P4/m", "point_group": "4"}, "P4_322": {"enc": "03bOODgOOFcOOO0", "full_symbol": "P4_322", "int_number": 95, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "422"}, "P4_32_12": {"enc": "03bOODgDDFcDDF0", "full_symbol": "P4_32_12", "int_number": 96, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "422"}, "P4_332": {"enc": "04bDODcODDdOOOeBFF0", "full_symbol": "P4_332", "int_number": 212, "order": 24, "patterson_symmetry": "Pm-3m", "point_group": "432"}, "P4bm": {"enc": "03bOOOgOOOjDDO0", "full_symbol": "P4bm", "int_number": 100, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "4mm"}, "P4cc": {"enc": "03bOOOgOOOjOOD0", "full_symbol": "P4cc", "int_number": 103, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "4mm"}, "P4mm": {"enc": "03bOOOgOOOjOOO0", "full_symbol": "P4mm", "int_number": 99, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "4mm"}, "P4nc": {"enc": "03bOOOgOOOjDDD0", "full_symbol": "P4nc", "int_number": 104, "order": 8, "patterson_symmetry": "P4/mmm", "point_group": "4mm"}, "P6": {"enc": "02nOOObOOO0", "full_symbol": "P6", "int_number": 168, "order": 6, "patterson_symmetry": "P6/m", "point_group": "6"}, "P6/m": {"enc": "12nOOObOOO0", "full_symbol": "P6/m", "int_number": 175, "order": 12, "patterson_symmetry": "P6/m", "point_group": "6/m"}, "P6/mcc": {"enc": "13nOOObOOOeOOD0", "full_symbol": "P6/m2/c2/c", "int_number": 192, "order": 24, "patterson_symmetry": "P6/mmm", "point_group": "6/mmm"}, "P6/mmm": {"enc": "13nOOObOOOeOOO0", "full_symbol": "P6/m2/m2/m", "int_number": 191, "order": 24, "patterson_symmetry": "P6/mmm", "point_group": "6/mmm"}, "P622": {"enc": "03nOOObOOOeOOO0", "full_symbol": "P622", "int_number": 177, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "622"}, "P6_1": {"enc": "02nOOCbOOD0", "full_symbol": "P6_1", "int_number": 169, "order": 6, "patterson_symmetry": "P6/m", "point_group": "6"}, "P6_122": {"enc": "03nOOCbOODeOOC0", "full_symbol": "P6_122", "int_number": 178, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "622"}, "P6_2": {"enc": "02nOOEbOOO0", "full_symbol": "P6_2", "int_number": 171, "order": 6, "patterson_symmetry": "P6/m", "point_group": "6"}, "P6_222": {"enc": "03nOOEbOOOeOOE0", "full_symbol": "P6_222", "int_number": 180, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "622"}, "P6_3": {"enc": "02nOOObOOD0", "full_symbol": "P6_3", "int_number": 173, "order": 6, "patterson_symmetry": "P6/m", "point_group": "6"}, "P6_3/m": {"enc": "12nOOObOOD0", "full_symbol": "P6_3/m", "int_number": 176, "order": 12, "patterson_symmetry": "P6/m", "point_group": "6/m"}, "P6_3/mcm": {"enc": "13nOOObOODeOOD0", "full_symbol": "P6_3/m2/c2/m", "int_number": 193, "order": 24, "patterson_symmetry": "P6/mmm", "point_group": "6/mmm"}, "P6_3/mmc": {"enc": "13nOOObOODeOOO0", "full_symbol": "P6_3/m2/m2/c", "int_number": 194, "order": 24, "patterson_symmetry": "P6/mmm", "point_group": "6/mmm"}, "P6_322": {"enc": "03nOOObOODeOOO0", "full_symbol": "P6_322", "int_number": 182, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "622"}, "P6_3cm": {"enc": "03nOOObOODkOOD0", "full_symbol": "P6_3cm", "int_number": 185, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "6mm"}, "P6_3mc": {"enc": "03nOOObOODkOOO0", "full_symbol": "P6_3mc", "int_number": 186, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "6mm"}, "P6_4": {"enc": "02nOOCbOOO0", "full_symbol": "P6_4", "int_number": 172, "order": 6, "patterson_symmetry": "P6/m", "point_group": "6"}, "P6_422": {"enc": "03nOOCbOOOeOOC0", "full_symbol": "P6_422", "int_number": 181, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "622"}, "P6_5": {"enc": "02nOOEbOOD0", "full_symbol": "P6_5", "int_number": 170, "order": 6, "patterson_symmetry": "P6/m", "point_group": "6"}, "P6_522": {"enc": "03nOOEbOODeOOE0", "full_symbol": "P6_522", "int_number": 179, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "622"}, "P6cc": {"enc": "03nOOObOOOkOOD0", "full_symbol": "P6cc", "int_number": 184, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "6mm"}, "P6mm": {"enc": "03nOOObOOOkOOO0", "full_symbol": "P6mm", "int_number": 183, "order": 12, "patterson_symmetry": "P6/mmm", "point_group": "6mm"}, "Pa-3": {"enc": "13bDODcODDdOOO0", "full_symbol": "P2_1/a-3", "int_number": 205, "order": 24, "patterson_symmetry": "Pm-3", "point_group": "m-3"}, "Pba2": {"enc": "02bOOOjDDO0", "full_symbol": "Pba2", "int_number": 32, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pbam": {"enc": "12bOOOcDDO0", "full_symbol": "P2_1/b2_1/a2/m", "int_number": 55, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pban": {"enc": "03bOOOcOOOhDDO1BBO", "full_symbol": "P2/b2/a2/n", "int_number": 50, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pbca": {"enc": "12bDODcODD0", "full_symbol": "P2_1/b2_1/c2_1/a", "int_number": 61, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pbcm": {"enc": "12bOODcODD0", "full_symbol": "P2/b2_1/c2_1/m", "int_number": 57, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pbcn": {"enc": "12bDDDcOOD0", "full_symbol": "P2_1/b2/c2_1/n", "int_number": 60, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pca2_1": {"enc": "02bOODjDOO0", "full_symbol": "Pca2_1", "int_number": 29, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pcc2": {"enc": "02bOOOjOOD0", "full_symbol": "Pcc2", "int_number": 27, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pcca": {"enc": "12bDOOcOOD0", "full_symbol": "P2_1/c2/c2/a", "int_number": 54, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pccm": {"enc": "12bOOOcOOD0", "full_symbol": "P2/c2/c2/m", "int_number": 49, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pccn": {"enc": "12bDDOcODD0", "full_symbol": "P2_1/c2_1/c2/n", "int_number": 56, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pm-3": {"enc": "13bOOOcOOOdOOO0", "full_symbol": "P2/m-3", "int_number": 200, "order": 24, "patterson_symmetry": "Pm-3", "point_group": "m-3"}, "Pm-3m": {"enc": "14bOOOcOOOdOOOeOOO0", "full_symbol": "P4/m-32/m", "int_number": 221, "order": 48, "patterson_symmetry": "Pm-3m", "point_group": "m-3m"}, "Pm-3n": {"enc": "14bOOOcOOOdOOOeDDD0", "full_symbol": "P4_2/m-32/n", "int_number": 223, "order": 48, "patterson_symmetry": "Pm-3m", "point_group": "m-3m"}, "Pma2": {"enc": "02bOOOjDOO0", "full_symbol": "Pma2", "int_number": 28, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pmc2_1": {"enc": "02bOODjOOD0", "full_symbol": "Pmc2_1", "int_number": 26, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pmm2": {"enc": "02bOOOjOOO0", "full_symbol": "Pmm2", "int_number": 25, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pmma": {"enc": "12bDOOcOOO0", "full_symbol": "P2_1/m2/m2/a", "int_number": 51, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pmmm": {"enc": "12bOOOcOOO0", "full_symbol": "P2/m2/m2/m", "int_number": 47, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pmmn": {"enc": "03bOOOcDDOhDDO1BBO", "full_symbol": "P2_1/m2_1/m2/n", "int_number": 59, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pmn2_1": {"enc": "02bDODjDOD0", "full_symbol": "Pmn2_1", "int_number": 31, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pmna": {"enc": "12bDODcDOD0", "full_symbol": "P2/m2/n2_1/a", "int_number": 53, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pn-3": {"enc": "04bOOOcOOOdOOOhDDD1YYY", "full_symbol": "P2/n-3", "int_number": 201, "order": 24, "patterson_symmetry": "Pm-3", "point_group": "m-3"}, "Pn-3m": {"enc": "05bOOOcOOOdOOOeDDDhDDD1YYY", "full_symbol": "P4_2/n-32/m", "int_number": 224, "order": 48, "patterson_symmetry": "Pm-3m", "point_group": "m-3m"}, "Pn-3n": {"enc": "05bOOOcOOOdOOOeOOOhDDD1YYY", "full_symbol": "P4/n-32/n", "int_number": 222, "order": 48, "patterson_symmetry": "Pm-3m", "point_group": "m-3m"}, "Pna2_1": {"enc": "02bOODjDDO0", "full_symbol": "Pna2_1", "int_number": 33, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pnc2": {"enc": "02bOOOjODD0", "full_symbol": "Pnc2", "int_number": 30, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pnma": {"enc": "12bDODcODO0", "full_symbol": "P2_1/n2_1/m2_1/a", "int_number": 62, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pnn2": {"enc": "02bOOOjDDD0", "full_symbol": "Pnn2", "int_number": 34, "order": 4, "patterson_symmetry": "Pmmm", "point_group": "mm2"}, "Pnna": {"enc": "12bDOOcDDD0", "full_symbol": "P2/n2_1/n2/a", "int_number": 52, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pnnm": {"enc": "12bOOOcDDD0", "full_symbol": "P2_1/n2_1/n2/m", "int_number": 58, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "Pnnn": {"enc": "03bOOOcOOOhDDD1BBB", "full_symbol": "P2/n2/n2/n", "int_number": 48, "order": 8, "patterson_symmetry": "Pmmm", "point_group": "mmm"}, "R-3": {"enc": "12aECCnOOO0", "full_symbol": "R-3", "int_number": 148, "order": 18, "patterson_symmetry": "R-3", "point_group": "-3"}, "R-3c": {"enc": "13aECCnOOOeOOD0", "full_symbol": "R-32/c", "int_number": 167, "order": 36, "patterson_symmetry": "R-3m", "point_group": "-3m"}, "R-3m": {"enc": "13aECCnOOOeOOO0", "full_symbol": "R-32/m", "int_number": 166, "order": 36, "patterson_symmetry": "R-3m", "point_group": "-3m"}, "R3": {"enc": "02aECCnOOO0", "full_symbol": "R3", "int_number": 146, "order": 9, "patterson_symmetry": "R-3", "point_group": "3"}, "R32": {"enc": "03aECCnOOOeOOO0", "full_symbol": "R32", "int_number": 155, "order": 18, "patterson_symmetry": "R-3m", "point_group": "32"}, "R3c": {"enc": "03aECCnOOOkOOD0", "full_symbol": "R3c", "int_number": 161, "order": 18, "patterson_symmetry": "R-3m", "point_group": "3m"}, "R3m": {"enc": "03aECCnOOOkOOO0", "full_symbol": "R3m", "int_number": 160, "order": 18, "patterson_symmetry": "R-3m", "point_group": "3m"}}, "translations": {"A": "1/6", "B": "1/4", "C": "1/3", "D": "1/2", "E": "2/3", "F": "3/4", "G": "5/6", "O": "0", "X": "-3/8", "Y": "-1/4", "Z": "-1/8"}} diff --git a/pymatgen/symmetry/symm_data.yaml b/src/pymatgen/symmetry/symm_data.yaml similarity index 100% rename from pymatgen/symmetry/symm_data.yaml rename to src/pymatgen/symmetry/symm_data.yaml diff --git a/pymatgen/symmetry/symm_data_magnetic.sqlite b/src/pymatgen/symmetry/symm_data_magnetic.sqlite similarity index 100% rename from pymatgen/symmetry/symm_data_magnetic.sqlite rename to src/pymatgen/symmetry/symm_data_magnetic.sqlite diff --git a/src/pymatgen/symmetry/symm_ops.json b/src/pymatgen/symmetry/symm_ops.json new file mode 100644 index 00000000000..0b845bdf5de --- /dev/null +++ b/src/pymatgen/symmetry/symm_ops.json @@ -0,0 +1 @@ +[{"symops": ["x,y,z"], "universal_h_m": "P 1", "number": 1, "schoenflies": "C1^1", "hall": " P 1", "hermann_mauguin": "P 1", "ncsym": ["x,y,z"], "short_h_m": "P1", "hermann_mauguin_u": "P1", "point_group": "1"}, {"symops": ["x,y,z", "-x,-y,-z"], "universal_h_m": "P -1", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1", "hermann_mauguin": "P -1", "ncsym": ["x,y,z", "-x,-y,-z"], "short_h_m": "P-1", "hermann_mauguin_u": "P-1", "point_group": "-1"}, {"symops": ["x,y,z", "-x,y,-z"], "universal_h_m": "P 1 2 1", "number": 3, "schoenflies": "C2^1", "hall": " P 2y", "hermann_mauguin": "P 1 2 1", "ncsym": ["x,y,z", "-x,y,-z"], "short_h_m": "P2", "hermann_mauguin_u": "P121", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y,z"], "universal_h_m": "P 1 1 2", "number": 3, "schoenflies": "C2^1", "hall": " P 2", "hermann_mauguin": "P 1 1 2", "ncsym": ["x,y,z", "-x,-y,z"], "short_h_m": "P2", "hermann_mauguin_u": "P112", "point_group": "2"}, {"symops": ["x,y,z", "x,-y,-z"], "universal_h_m": "P 2 1 1", "number": 3, "schoenflies": "C2^1", "hall": " P 2x", "hermann_mauguin": "P 2 1 1", "ncsym": ["x,y,z", "x,-y,-z"], "short_h_m": "P2", "hermann_mauguin_u": "P211", "point_group": "2"}, {"symops": ["x,y,z", "-x,y+1/2,-z"], "universal_h_m": "P 1 21 1", "number": 4, "schoenflies": "C2^2", "hall": " P 2yb", "hermann_mauguin": "P 1 21 1", "ncsym": ["x,y,z", "-x,y+1/2,-z"], "short_h_m": "P2_1", "hermann_mauguin_u": "P12_11", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y,z+1/2"], "universal_h_m": "P 1 1 21", "number": 4, "schoenflies": "C2^2", "hall": " P 2c", "hermann_mauguin": "P 1 1 21", "ncsym": ["x,y,z", "-x,-y,z+1/2"], "short_h_m": "P2_1", "hermann_mauguin_u": "P112_1", "point_group": "2"}, {"symops": ["x,y,z", "x+1/2,-y,-z"], "universal_h_m": "P 21 1 1", "number": 4, "schoenflies": "C2^2", "hall": " P 2xa", "hermann_mauguin": "P 21 1 1", "ncsym": ["x,y,z", "x+1/2,-y,-z"], "short_h_m": "P2_1", "hermann_mauguin_u": "P2_111", "point_group": "2"}, {"symops": ["x,y,z", "-x,y,-z", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "C 1 2 1", "number": 5, "schoenflies": "C2^3", "hall": " C 2y", "hermann_mauguin": "C 1 2 1", "ncsym": ["x,y,z", "-x,y,-z"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x,y,-z", "x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A 1 2 1", "number": 5, "schoenflies": "C2^3", "hall": " A 2y", "hermann_mauguin": "A 1 2 1", "ncsym": ["x,y,z", "-x,y,-z"], "short_h_m": "A2", "hermann_mauguin_u": "A121", "point_group": "2"}, {"symops": ["x,y,z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I 1 2 1", "number": 5, "schoenflies": "C2^3", "hall": " I 2y", "hermann_mauguin": "I 1 2 1", "ncsym": ["x,y,z", "-x,y,-z"], "short_h_m": "I2", "hermann_mauguin_u": "I121", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2"], "universal_h_m": "A 1 1 2", "number": 5, "schoenflies": "C2^3", "hall": " A 2", "hermann_mauguin": "A 1 1 2", "ncsym": ["x,y,z", "-x,-y,z"], "short_h_m": "A2", "hermann_mauguin_u": "A112", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2"], "universal_h_m": "B 1 1 2", "number": 5, "schoenflies": "C2^3", "hall": " B 2", "hermann_mauguin": "B 1 1 2", "ncsym": ["x,y,z", "-x,-y,z"], "short_h_m": "B2", "hermann_mauguin_u": "B112", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I 1 1 2", "number": 5, "schoenflies": "C2^3", "hall": " I 2", "hermann_mauguin": "I 1 1 2", "ncsym": ["x,y,z", "-x,-y,z"], "short_h_m": "I2", "hermann_mauguin_u": "I112", "point_group": "2"}, {"symops": ["x,y,z", "x,-y,-z", "x+1/2,y,z+1/2", "x+1/2,-y,-z+1/2"], "universal_h_m": "B 2 1 1", "number": 5, "schoenflies": "C2^3", "hall": " B 2x", "hermann_mauguin": "B 2 1 1", "ncsym": ["x,y,z", "x,-y,-z"], "short_h_m": "B2", "hermann_mauguin_u": "B211", "point_group": "2"}, {"symops": ["x,y,z", "x,-y,-z", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,-z"], "universal_h_m": "C 2 1 1", "number": 5, "schoenflies": "C2^3", "hall": " C 2x", "hermann_mauguin": "C 2 1 1", "ncsym": ["x,y,z", "x,-y,-z"], "short_h_m": "C2", "hermann_mauguin_u": "C211", "point_group": "2"}, {"symops": ["x,y,z", "x,-y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2"], "universal_h_m": "I 2 1 1", "number": 5, "schoenflies": "C2^3", "hall": " I 2x", "hermann_mauguin": "I 2 1 1", "ncsym": ["x,y,z", "x,-y,-z"], "short_h_m": "I2", "hermann_mauguin_u": "I211", "point_group": "2"}, {"symops": ["x,y,z", "x,-y,z"], "universal_h_m": "P 1 m 1", "number": 6, "schoenflies": "Cs^1", "hall": " P -2y", "hermann_mauguin": "P 1 m 1", "ncsym": ["x,y,z", "x,-y,z"], "short_h_m": "Pm", "hermann_mauguin_u": "P1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,y,-z"], "universal_h_m": "P 1 1 m", "number": 6, "schoenflies": "Cs^1", "hall": " P -2", "hermann_mauguin": "P 1 1 m", "ncsym": ["x,y,z", "x,y,-z"], "short_h_m": "Pm", "hermann_mauguin_u": "P11m", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,z"], "universal_h_m": "P m 1 1", "number": 6, "schoenflies": "Cs^1", "hall": " P -2x", "hermann_mauguin": "P m 1 1", "ncsym": ["x,y,z", "-x,y,z"], "short_h_m": "Pm", "hermann_mauguin_u": "Pm11", "point_group": "m"}, {"symops": ["x,y,z", "x,-y,z+1/2"], "universal_h_m": "P 1 c 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2yc", "hermann_mauguin": "P 1 c 1", "ncsym": ["x,y,z", "x,-y,z+1/2"], "short_h_m": "Pc", "hermann_mauguin_u": "P1c1", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,-y,z+1/2"], "universal_h_m": "P 1 n 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2yac", "hermann_mauguin": "P 1 n 1", "ncsym": ["x,y,z", "x+1/2,-y,z+1/2"], "short_h_m": "Pn", "hermann_mauguin_u": "P1n1", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,-y,z"], "universal_h_m": "P 1 a 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2ya", "hermann_mauguin": "P 1 a 1", "ncsym": ["x,y,z", "x+1/2,-y,z"], "short_h_m": "Pa", "hermann_mauguin_u": "P1a1", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,y,-z"], "universal_h_m": "P 1 1 a", "number": 7, "schoenflies": "Cs^2", "hall": " P -2a", "hermann_mauguin": "P 1 1 a", "ncsym": ["x,y,z", "x+1/2,y,-z"], "short_h_m": "Pa", "hermann_mauguin_u": "P11a", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z"], "universal_h_m": "P 1 1 n", "number": 7, "schoenflies": "Cs^2", "hall": " P -2ab", "hermann_mauguin": "P 1 1 n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z"], "short_h_m": "Pn", "hermann_mauguin_u": "P11n", "point_group": "m"}, {"symops": ["x,y,z", "x,y+1/2,-z"], "universal_h_m": "P 1 1 b", "number": 7, "schoenflies": "Cs^2", "hall": " P -2b", "hermann_mauguin": "P 1 1 b", "ncsym": ["x,y,z", "x,y+1/2,-z"], "short_h_m": "Pb", "hermann_mauguin_u": "P11b", "point_group": "m"}, {"symops": ["x,y,z", "-x,y+1/2,z"], "universal_h_m": "P b 1 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2xb", "hermann_mauguin": "P b 1 1", "ncsym": ["x,y,z", "-x,y+1/2,z"], "short_h_m": "Pb", "hermann_mauguin_u": "Pb11", "point_group": "m"}, {"symops": ["x,y,z", "-x,y+1/2,z+1/2"], "universal_h_m": "P n 1 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2xbc", "hermann_mauguin": "P n 1 1", "ncsym": ["x,y,z", "-x,y+1/2,z+1/2"], "short_h_m": "Pn", "hermann_mauguin_u": "Pn11", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,z+1/2"], "universal_h_m": "P c 1 1", "number": 7, "schoenflies": "Cs^2", "hall": " P -2xc", "hermann_mauguin": "P c 1 1", "ncsym": ["x,y,z", "-x,y,z+1/2"], "short_h_m": "Pc", "hermann_mauguin_u": "Pc11", "point_group": "m"}, {"symops": ["x,y,z", "x,-y,z", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "C 1 m 1", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y", "hermann_mauguin": "C 1 m 1", "ncsym": ["x,y,z", "x,-y,z"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,-y,z", "x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A 1 m 1", "number": 8, "schoenflies": "Cs^3", "hall": " A -2y", "hermann_mauguin": "A 1 m 1", "ncsym": ["x,y,z", "x,-y,z"], "short_h_m": "Am", "hermann_mauguin_u": "A1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I 1 m 1", "number": 8, "schoenflies": "Cs^3", "hall": " I -2y", "hermann_mauguin": "I 1 m 1", "ncsym": ["x,y,z", "x,-y,z"], "short_h_m": "Im", "hermann_mauguin_u": "I1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,y,-z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2"], "universal_h_m": "A 1 1 m", "number": 8, "schoenflies": "Cs^3", "hall": " A -2", "hermann_mauguin": "A 1 1 m", "ncsym": ["x,y,z", "x,y,-z"], "short_h_m": "Am", "hermann_mauguin_u": "A11m", "point_group": "m"}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2"], "universal_h_m": "B 1 1 m", "number": 8, "schoenflies": "Cs^3", "hall": " B -2", "hermann_mauguin": "B 1 1 m", "ncsym": ["x,y,z", "x,y,-z"], "short_h_m": "Bm", "hermann_mauguin_u": "B11m", "point_group": "m"}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I 1 1 m", "number": 8, "schoenflies": "Cs^3", "hall": " I -2", "hermann_mauguin": "I 1 1 m", "ncsym": ["x,y,z", "x,y,-z"], "short_h_m": "Im", "hermann_mauguin_u": "I11m", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,z", "x+1/2,y,z+1/2", "-x+1/2,y,z+1/2"], "universal_h_m": "B m 1 1", "number": 8, "schoenflies": "Cs^3", "hall": " B -2x", "hermann_mauguin": "B m 1 1", "ncsym": ["x,y,z", "-x,y,z"], "short_h_m": "Bm", "hermann_mauguin_u": "Bm11", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,z", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,z"], "universal_h_m": "C m 1 1", "number": 8, "schoenflies": "Cs^3", "hall": " C -2x", "hermann_mauguin": "C m 1 1", "ncsym": ["x,y,z", "-x,y,z"], "short_h_m": "Cm", "hermann_mauguin_u": "Cm11", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "I m 1 1", "number": 8, "schoenflies": "Cs^3", "hall": " I -2x", "hermann_mauguin": "I m 1 1", "ncsym": ["x,y,z", "-x,y,z"], "short_h_m": "Im", "hermann_mauguin_u": "Im11", "point_group": "m"}, {"symops": ["x,y,z", "x,-y,z+1/2", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C 1 c 1", "number": 9, "schoenflies": "Cs^4", "hall": " C -2yc", "hermann_mauguin": "C 1 c 1", "ncsym": ["x,y,z", "x,-y,z+1/2"], "short_h_m": "Cc", "hermann_mauguin_u": "C1c1", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "x+1/2,-y+1,z+1/2"], "universal_h_m": "A 1 n 1", "number": 9, "schoenflies": "Cs^4", "hall": " A -2yab", "hermann_mauguin": "A 1 n 1", "ncsym": ["x,y,z", "x+1/2,-y+1/2,z"], "short_h_m": "An", "hermann_mauguin_u": "A1n1", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,-y,z", "x+1/2,y+1/2,z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "I 1 a 1", "number": 9, "schoenflies": "Cs^4", "hall": " I -2ya", "hermann_mauguin": "I 1 a 1", "ncsym": ["x,y,z", "x+1/2,-y,z"], "short_h_m": "Ia", "hermann_mauguin_u": "I1a1", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A 1 a 1", "number": 9, "schoenflies": "Cs^4", "hall": " A -2ya", "hermann_mauguin": "A 1 a 1", "ncsym": ["x,y,z", "x+1/2,-y,z"], "short_h_m": "Aa", "hermann_mauguin_u": "A1a1", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "x+1,-y+1/2,z+1/2"], "universal_h_m": "C 1 n 1", "number": 9, "schoenflies": "Cs^4", "hall": " C -2yac", "hermann_mauguin": "C 1 n 1", "ncsym": ["x,y,z", "x+1/2,-y,z+1/2"], "short_h_m": "Cn", "hermann_mauguin_u": "C1n1", "point_group": "m"}, {"symops": ["x,y,z", "x,-y,z+1/2", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1"], "universal_h_m": "I 1 c 1", "number": 9, "schoenflies": "Cs^4", "hall": " I -2yc", "hermann_mauguin": "I 1 c 1", "ncsym": ["x,y,z", "x,-y,z+1/2"], "short_h_m": "Ic", "hermann_mauguin_u": "I1c1", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "A 1 1 a", "number": 9, "schoenflies": "Cs^4", "hall": " A -2a", "hermann_mauguin": "A 1 1 a", "ncsym": ["x,y,z", "x+1/2,y,-z"], "short_h_m": "Aa", "hermann_mauguin_u": "A11a", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x+1/2,y,z+1/2", "x+1,y+1/2,-z+1/2"], "universal_h_m": "B 1 1 n", "number": 9, "schoenflies": "Cs^4", "hall": " B -2ab", "hermann_mauguin": "B 1 1 n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z"], "short_h_m": "Bn", "hermann_mauguin_u": "B11n", "point_group": "m"}, {"symops": ["x,y,z", "x,y+1/2,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2"], "universal_h_m": "I 1 1 b", "number": 9, "schoenflies": "Cs^4", "hall": " I -2b", "hermann_mauguin": "I 1 1 b", "ncsym": ["x,y,z", "x,y+1/2,-z"], "short_h_m": "Ib", "hermann_mauguin_u": "I11b", "point_group": "m"}, {"symops": ["x,y,z", "x,y+1/2,-z", "x+1/2,y,z+1/2", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "B 1 1 b", "number": 9, "schoenflies": "Cs^4", "hall": " B -2b", "hermann_mauguin": "B 1 1 b", "ncsym": ["x,y,z", "x,y+1/2,-z"], "short_h_m": "Bb", "hermann_mauguin_u": "B11b", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2"], "universal_h_m": "A 1 1 n", "number": 9, "schoenflies": "Cs^4", "hall": " A -2ab", "hermann_mauguin": "A 1 1 n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z"], "short_h_m": "An", "hermann_mauguin_u": "A11n", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x+1/2,y+1/2,z+1/2", "x+1,y+1/2,-z+1/2"], "universal_h_m": "I 1 1 a", "number": 9, "schoenflies": "Cs^4", "hall": " I -2a", "hermann_mauguin": "I 1 1 a", "ncsym": ["x,y,z", "x+1/2,y,-z"], "short_h_m": "Ia", "hermann_mauguin_u": "I11a", "point_group": "m"}, {"symops": ["x,y,z", "-x,y+1/2,z", "x+1/2,y,z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "B b 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " B -2xb", "hermann_mauguin": "B b 1 1", "ncsym": ["x,y,z", "-x,y+1/2,z"], "short_h_m": "Bb", "hermann_mauguin_u": "Bb11", "point_group": "m"}, {"symops": ["x,y,z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x+1,y+1/2,z+1/2"], "universal_h_m": "C n 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " C -2xac", "hermann_mauguin": "C n 1 1", "ncsym": ["x,y,z", "-x+1/2,y,z+1/2"], "short_h_m": "Cn", "hermann_mauguin_u": "Cn11", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,z+1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,z+1"], "universal_h_m": "I c 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " I -2xc", "hermann_mauguin": "I c 1 1", "ncsym": ["x,y,z", "-x,y,z+1/2"], "short_h_m": "Ic", "hermann_mauguin_u": "Ic11", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "C c 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " C -2xc", "hermann_mauguin": "C c 1 1", "ncsym": ["x,y,z", "-x,y,z+1/2"], "short_h_m": "Cc", "hermann_mauguin_u": "Cc11", "point_group": "m"}, {"symops": ["x,y,z", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x+1,y+1/2,z+1/2"], "universal_h_m": "B n 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " B -2xab", "hermann_mauguin": "B n 1 1", "ncsym": ["x,y,z", "-x+1/2,y+1/2,z"], "short_h_m": "Bn", "hermann_mauguin_u": "Bn11", "point_group": "m"}, {"symops": ["x,y,z", "-x,y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1,z+1/2"], "universal_h_m": "I b 1 1", "number": 9, "schoenflies": "Cs^4", "hall": " I -2xb", "hermann_mauguin": "I b 1 1", "ncsym": ["x,y,z", "-x,y+1/2,z"], "short_h_m": "Ib", "hermann_mauguin_u": "Ib11", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"], "universal_h_m": "P 1 2/m 1", "number": 10, "schoenflies": "C2h^1", "hall": "-P 2y", "hermann_mauguin": "P 1 2/m 1", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"], "short_h_m": "P2/m", "hermann_mauguin_u": "P12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z"], "universal_h_m": "P 1 1 2/m", "number": 10, "schoenflies": "C2h^1", "hall": "-P 2", "hermann_mauguin": "P 1 1 2/m", "ncsym": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z"], "short_h_m": "P2/m", "hermann_mauguin_u": "P112/m", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z"], "universal_h_m": "P 2/m 1 1", "number": 10, "schoenflies": "C2h^1", "hall": "-P 2x", "hermann_mauguin": "P 2/m 1 1", "ncsym": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z"], "short_h_m": "P2/m", "hermann_mauguin_u": "P2/m11", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y-1/2,z"], "universal_h_m": "P 1 21/m 1", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2yb", "hermann_mauguin": "P 1 21/m 1", "ncsym": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y-1/2,z"], "short_h_m": "P2_1/m", "hermann_mauguin_u": "P12_1/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z-1/2"], "universal_h_m": "P 1 1 21/m", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2c", "hermann_mauguin": "P 1 1 21/m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z-1/2"], "short_h_m": "P2_1/m", "hermann_mauguin_u": "P112_1/m", "point_group": "2/m"}, {"symops": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x-1/2,y,z"], "universal_h_m": "P 21/m 1 1", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2xa", "hermann_mauguin": "P 21/m 1 1", "ncsym": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x-1/2,y,z"], "short_h_m": "P2_1/m", "hermann_mauguin_u": "P2_1/m11", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "C 1 2/m 1", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y", "hermann_mauguin": "C 1 2/m 1", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z", "x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A 1 2/m 1", "number": 12, "schoenflies": "C2h^3", "hall": "-A 2y", "hermann_mauguin": "A 1 2/m 1", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"], "short_h_m": "A2/m", "hermann_mauguin_u": "A12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I 1 2/m 1", "number": 12, "schoenflies": "C2h^3", "hall": "-I 2y", "hermann_mauguin": "I 1 2/m 1", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"], "short_h_m": "I2/m", "hermann_mauguin_u": "I12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2"], "universal_h_m": "A 1 1 2/m", "number": 12, "schoenflies": "C2h^3", "hall": "-A 2", "hermann_mauguin": "A 1 1 2/m", "ncsym": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z"], "short_h_m": "A2/m", "hermann_mauguin_u": "A112/m", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2"], "universal_h_m": "B 1 1 2/m", "number": 12, "schoenflies": "C2h^3", "hall": "-B 2", "hermann_mauguin": "B 1 1 2/m", "ncsym": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z"], "short_h_m": "B2/m", "hermann_mauguin_u": "B112/m", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I 1 1 2/m", "number": 12, "schoenflies": "C2h^3", "hall": "-I 2", "hermann_mauguin": "I 1 1 2/m", "ncsym": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z"], "short_h_m": "I2/m", "hermann_mauguin_u": "I112/m", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z", "x+1/2,y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,-y,-z+1/2", "-x+1/2,y,z+1/2"], "universal_h_m": "B 2/m 1 1", "number": 12, "schoenflies": "C2h^3", "hall": "-B 2x", "hermann_mauguin": "B 2/m 1 1", "ncsym": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z"], "short_h_m": "B2/m", "hermann_mauguin_u": "B2/m11", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,z"], "universal_h_m": "C 2/m 1 1", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2x", "hermann_mauguin": "C 2/m 1 1", "ncsym": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C2/m11", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "I 2/m 1 1", "number": 12, "schoenflies": "C2h^3", "hall": "-I 2x", "hermann_mauguin": "I 2/m 1 1", "ncsym": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z"], "short_h_m": "I2/m", "hermann_mauguin_u": "I2/m11", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z-1/2"], "universal_h_m": "P 1 2/c 1", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2yc", "hermann_mauguin": "P 1 2/c 1", "ncsym": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z-1/2"], "short_h_m": "P2/c", "hermann_mauguin_u": "P12/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,-y,z-1/2"], "universal_h_m": "P 1 2/n 1", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2yac", "hermann_mauguin": "P 1 2/n 1", "ncsym": ["x,y,z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,-y,z-1/2"], "short_h_m": "P2/n", "hermann_mauguin_u": "P12/n1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,-y,z"], "universal_h_m": "P 1 2/a 1", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2ya", "hermann_mauguin": "P 1 2/a 1", "ncsym": ["x,y,z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,-y,z"], "short_h_m": "P2/a", "hermann_mauguin_u": "P12/a1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z"], "universal_h_m": "P 1 1 2/a", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2a", "hermann_mauguin": "P 1 1 2/a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z"], "short_h_m": "P2/a", "hermann_mauguin_u": "P112/a", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z"], "universal_h_m": "P 1 1 2/n", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2ab", "hermann_mauguin": "P 1 1 2/n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z"], "short_h_m": "P2/n", "hermann_mauguin_u": "P112/n", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z"], "universal_h_m": "P 1 1 2/b", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2b", "hermann_mauguin": "P 1 1 2/b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z"], "short_h_m": "P2/b", "hermann_mauguin_u": "P112/b", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z"], "universal_h_m": "P 2/b 1 1", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2xb", "hermann_mauguin": "P 2/b 1 1", "ncsym": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z"], "short_h_m": "P2/b", "hermann_mauguin_u": "P2/b11", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y+1/2,-z+1/2", "-x,-y,-z", "-x,y-1/2,z-1/2"], "universal_h_m": "P 2/n 1 1", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2xbc", "hermann_mauguin": "P 2/n 1 1", "ncsym": ["x,y,z", "x,-y+1/2,-z+1/2", "-x,-y,-z", "-x,y-1/2,z-1/2"], "short_h_m": "P2/n", "hermann_mauguin_u": "P2/n11", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2"], "universal_h_m": "P 2/c 1 1", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2xc", "hermann_mauguin": "P 2/c 1 1", "ncsym": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2"], "short_h_m": "P2/c", "hermann_mauguin_u": "P2/c11", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,-y-1/2,z-1/2"], "universal_h_m": "P 1 21/c 1", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2ybc", "hermann_mauguin": "P 1 21/c 1", "ncsym": ["x,y,z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,-y-1/2,z-1/2"], "short_h_m": "P2_1/c", "hermann_mauguin_u": "P12_1/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,-y-1/2,z-1/2"], "universal_h_m": "P 1 21/n 1", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2yn", "hermann_mauguin": "P 1 21/n 1", "ncsym": ["x,y,z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,-y-1/2,z-1/2"], "short_h_m": "P2_1/n", "hermann_mauguin_u": "P12_1/n1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,-y-1/2,z"], "universal_h_m": "P 1 21/a 1", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2yab", "hermann_mauguin": "P 1 21/a 1", "ncsym": ["x,y,z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,-y-1/2,z"], "short_h_m": "P2_1/a", "hermann_mauguin_u": "P12_1/a1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2"], "universal_h_m": "P 1 1 21/a", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2ac", "hermann_mauguin": "P 1 1 21/a", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2"], "short_h_m": "P2_1/a", "hermann_mauguin_u": "P112_1/a", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2"], "universal_h_m": "P 1 1 21/n", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2n", "hermann_mauguin": "P 1 1 21/n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2"], "short_h_m": "P2_1/n", "hermann_mauguin_u": "P112_1/n", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2"], "universal_h_m": "P 1 1 21/b", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2bc", "hermann_mauguin": "P 1 1 21/b", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2"], "short_h_m": "P2_1/b", "hermann_mauguin_u": "P112_1/b", "point_group": "2/m"}, {"symops": ["x,y,z", "x+1/2,-y+1/2,-z", "-x,-y,-z", "-x-1/2,y-1/2,z"], "universal_h_m": "P 21/b 1 1", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2xab", "hermann_mauguin": "P 21/b 1 1", "ncsym": ["x,y,z", "x+1/2,-y+1/2,-z", "-x,-y,-z", "-x-1/2,y-1/2,z"], "short_h_m": "P2_1/b", "hermann_mauguin_u": "P2_1/b11", "point_group": "2/m"}, {"symops": ["x,y,z", "x+1/2,-y+1/2,-z+1/2", "-x,-y,-z", "-x-1/2,y-1/2,z-1/2"], "universal_h_m": "P 21/n 1 1", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2xn", "hermann_mauguin": "P 21/n 1 1", "ncsym": ["x,y,z", "x+1/2,-y+1/2,-z+1/2", "-x,-y,-z", "-x-1/2,y-1/2,z-1/2"], "short_h_m": "P2_1/n", "hermann_mauguin_u": "P2_1/n11", "point_group": "2/m"}, {"symops": ["x,y,z", "x+1/2,-y,-z+1/2", "-x,-y,-z", "-x-1/2,y,z-1/2"], "universal_h_m": "P 21/c 1 1", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2xac", "hermann_mauguin": "P 21/c 1 1", "ncsym": ["x,y,z", "x+1/2,-y,-z+1/2", "-x,-y,-z", "-x-1/2,y,z-1/2"], "short_h_m": "P2_1/c", "hermann_mauguin_u": "P2_1/c11", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z-1/2", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z-1/2"], "universal_h_m": "C 1 2/c 1", "number": 15, "schoenflies": "C2h^6", "hall": "-C 2yc", "hermann_mauguin": "C 1 2/c 1", "ncsym": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z-1/2"], "short_h_m": "C2/c", "hermann_mauguin_u": "C12/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,-y-1/2,z", "x,y+1/2,z+1/2", "-x+1/2,y+1,-z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,-y,z+1/2"], "universal_h_m": "A 1 2/n 1", "number": 15, "schoenflies": "C2h^6", "hall": "-A 2yab", "hermann_mauguin": "A 1 2/n 1", "ncsym": ["x,y,z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,-y-1/2,z"], "short_h_m": "A2/n", "hermann_mauguin_u": "A12/n1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "I 1 2/a 1", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2ya", "hermann_mauguin": "I 1 2/a 1", "ncsym": ["x,y,z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,-y,z"], "short_h_m": "I2/a", "hermann_mauguin_u": "I12/a1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,-y,z", "x,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,-y+1/2,z+1/2"], "universal_h_m": "A 1 2/a 1", "number": 15, "schoenflies": "C2h^6", "hall": "-A 2ya", "hermann_mauguin": "A 1 2/a 1", "ncsym": ["x,y,z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,-y,z"], "short_h_m": "A2/a", "hermann_mauguin_u": "A12/a1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,-y,z-1/2", "x+1/2,y+1/2,z", "-x+1,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "x,-y+1/2,z-1/2"], "universal_h_m": "C 1 2/n 1", "number": 15, "schoenflies": "C2h^6", "hall": "-C 2yac", "hermann_mauguin": "C 1 2/n 1", "ncsym": ["x,y,z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,-y,z-1/2"], "short_h_m": "C2/n", "hermann_mauguin_u": "C12/n1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z-1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "I 1 2/c 1", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2yc", "hermann_mauguin": "I 1 2/c 1", "ncsym": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z-1/2"], "short_h_m": "I2/c", "hermann_mauguin_u": "I12/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z", "x,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,y+1/2,-z+1/2"], "universal_h_m": "A 1 1 2/a", "number": 15, "schoenflies": "C2h^6", "hall": "-A 2a", "hermann_mauguin": "A 1 1 2/a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z"], "short_h_m": "A2/a", "hermann_mauguin_u": "A112/a", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z", "x+1/2,y,z+1/2", "-x+1,-y+1/2,z+1/2", "-x+1/2,-y,-z+1/2", "x,y-1/2,-z+1/2"], "universal_h_m": "B 1 1 2/n", "number": 15, "schoenflies": "C2h^6", "hall": "-B 2ab", "hermann_mauguin": "B 1 1 2/n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z"], "short_h_m": "B2/n", "hermann_mauguin_u": "B112/n", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y,-z+1/2"], "universal_h_m": "I 1 1 2/b", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2b", "hermann_mauguin": "I 1 1 2/b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z"], "short_h_m": "I2/b", "hermann_mauguin_u": "I112/b", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z", "x+1/2,y,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y-1/2,-z+1/2"], "universal_h_m": "B 1 1 2/b", "number": 15, "schoenflies": "C2h^6", "hall": "-B 2b", "hermann_mauguin": "B 1 1 2/b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "-x,-y,-z", "x,y-1/2,-z"], "short_h_m": "B2/b", "hermann_mauguin_u": "B112/b", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z", "x,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,y,-z+1/2"], "universal_h_m": "A 1 1 2/n", "number": 15, "schoenflies": "C2h^6", "hall": "-A 2ab", "hermann_mauguin": "A 1 1 2/n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x-1/2,y-1/2,-z"], "short_h_m": "A2/n", "hermann_mauguin_u": "A112/n", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z", "x+1/2,y+1/2,z+1/2", "-x+1,-y+1/2,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2"], "universal_h_m": "I 1 1 2/a", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2a", "hermann_mauguin": "I 1 1 2/a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x-1/2,y,-z"], "short_h_m": "I2/a", "hermann_mauguin_u": "I112/a", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z", "x+1/2,y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "-x+1/2,y-1/2,z+1/2"], "universal_h_m": "B 2/b 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-B 2xb", "hermann_mauguin": "B 2/b 1 1", "ncsym": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z"], "short_h_m": "B2/b", "hermann_mauguin_u": "B2/b11", "point_group": "2/m"}, {"symops": ["x,y,z", "x+1/2,-y,-z+1/2", "-x,-y,-z", "-x-1/2,y,z-1/2", "x+1/2,y+1/2,z", "x+1,-y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "-x,y+1/2,z-1/2"], "universal_h_m": "C 2/n 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-C 2xac", "hermann_mauguin": "C 2/n 1 1", "ncsym": ["x,y,z", "x+1/2,-y,-z+1/2", "-x,-y,-z", "-x-1/2,y,z-1/2"], "short_h_m": "C2/n", "hermann_mauguin_u": "C2/n11", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1", "-x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,z"], "universal_h_m": "I 2/c 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2xc", "hermann_mauguin": "I 2/c 1 1", "ncsym": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2"], "short_h_m": "I2/c", "hermann_mauguin_u": "I2/c11", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,z-1/2"], "universal_h_m": "C 2/c 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-C 2xc", "hermann_mauguin": "C 2/c 1 1", "ncsym": ["x,y,z", "x,-y,-z+1/2", "-x,-y,-z", "-x,y,z-1/2"], "short_h_m": "C2/c", "hermann_mauguin_u": "C2/c11", "point_group": "2/m"}, {"symops": ["x,y,z", "x+1/2,-y+1/2,-z", "-x,-y,-z", "-x-1/2,y-1/2,z", "x+1/2,y,z+1/2", "x+1,-y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "-x,y-1/2,z+1/2"], "universal_h_m": "B 2/n 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-B 2xab", "hermann_mauguin": "B 2/n 1 1", "ncsym": ["x,y,z", "x+1/2,-y+1/2,-z", "-x,-y,-z", "-x-1/2,y-1/2,z"], "short_h_m": "B2/n", "hermann_mauguin_u": "B2/n11", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "-x+1/2,y,z+1/2"], "universal_h_m": "I 2/b 1 1", "number": 15, "schoenflies": "C2h^6", "hall": "-I 2xb", "hermann_mauguin": "I 2/b 1 1", "ncsym": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y-1/2,z"], "short_h_m": "I2/b", "hermann_mauguin_u": "I2/b11", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"], "universal_h_m": "P 2 2 2", "number": 16, "schoenflies": "D2^1", "hall": " P 2 2", "hermann_mauguin": "P 2 2 2", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"], "short_h_m": "P222", "hermann_mauguin_u": "P222", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2"], "universal_h_m": "P 2 2 21", "number": 17, "schoenflies": "D2^2", "hall": " P 2c 2", "hermann_mauguin": "P 2 2 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2"], "short_h_m": "P222_1", "hermann_mauguin_u": "P222_1", "point_group": "222"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z"], "universal_h_m": "P 21 2 2", "number": 17, "schoenflies": "D2^2", "hall": " P 2a 2a", "hermann_mauguin": "P 21 2 2", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z"], "short_h_m": "P2_122", "hermann_mauguin_u": "P2_122", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z"], "universal_h_m": "P 2 21 2", "number": 17, "schoenflies": "D2^2", "hall": " P 2 2b", "hermann_mauguin": "P 2 21 2", "ncsym": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z"], "short_h_m": "P22_12", "hermann_mauguin_u": "P22_12", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z"], "universal_h_m": "P 21 21 2", "number": 18, "schoenflies": "D2^3", "hall": " P 2 2ab", "hermann_mauguin": "P 21 21 2", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z"], "short_h_m": "P2_12_12", "hermann_mauguin_u": "P2_12_12", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z", "-x,y+1/2,-z+1/2"], "universal_h_m": "P 2 21 21", "number": 18, "schoenflies": "D2^3", "hall": " P 2bc 2", "hermann_mauguin": "P 2 21 21", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z", "-x,y+1/2,-z+1/2"], "short_h_m": "P22_12_1", "hermann_mauguin_u": "P22_12_1", "point_group": "222"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z"], "universal_h_m": "P 21 2 21", "number": 18, "schoenflies": "D2^3", "hall": " P 2ac 2ac", "hermann_mauguin": "P 21 2 21", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z"], "short_h_m": "P2_122_1", "hermann_mauguin_u": "P2_122_1", "point_group": "222"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z", "-x,y+1/2,-z+1/2"], "universal_h_m": "P 21 21 21", "number": 19, "schoenflies": "D2^4", "hall": " P 2ac 2ab", "hermann_mauguin": "P 21 21 21", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z", "-x,y+1/2,-z+1/2"], "short_h_m": "P2_12_12_1", "hermann_mauguin_u": "P2_12_12_1", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "C 2 2 21", "number": 20, "schoenflies": "D2^5", "hall": " C 2c 2", "hermann_mauguin": "C 2 2 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2"], "short_h_m": "C222_1", "hermann_mauguin_u": "C222_1", "point_group": "222"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "x,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A 21 2 2", "number": 20, "schoenflies": "D2^5", "hall": " A 2a 2a", "hermann_mauguin": "A 21 2 2", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z"], "short_h_m": "A2_122", "hermann_mauguin_u": "A2_122", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "B 2 21 2", "number": 20, "schoenflies": "D2^5", "hall": " B 2 2b", "hermann_mauguin": "B 2 21 2", "ncsym": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z"], "short_h_m": "B22_12", "hermann_mauguin_u": "B22_12", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z"], "universal_h_m": "C 2 2 2", "number": 21, "schoenflies": "D2^6", "hall": " C 2 2", "hermann_mauguin": "C 2 2 2", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"], "short_h_m": "C222", "hermann_mauguin_u": "C222", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A 2 2 2", "number": 21, "schoenflies": "D2^6", "hall": " A 2 2", "hermann_mauguin": "A 2 2 2", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"], "short_h_m": "A222", "hermann_mauguin_u": "A222", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2"], "universal_h_m": "B 2 2 2", "number": 21, "schoenflies": "D2^6", "hall": " B 2 2", "hermann_mauguin": "B 2 2 2", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"], "short_h_m": "B222", "hermann_mauguin_u": "B222", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z"], "universal_h_m": "F 2 2 2", "number": 22, "schoenflies": "D2^7", "hall": " F 2 2", "hermann_mauguin": "F 2 2 2", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"], "short_h_m": "F222", "hermann_mauguin_u": "F222", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I 2 2 2", "number": 23, "schoenflies": "D2^8", "hall": " I 2 2", "hermann_mauguin": "I 2 2 2", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z"], "short_h_m": "I222", "hermann_mauguin_u": "I222", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "x+1/2,-y+1/2,-z+1", "-x+1/2,y+1,-z+1"], "universal_h_m": "I 21 21 21", "number": 24, "schoenflies": "D2^9", "hall": " I 2b 2c", "hermann_mauguin": "I 21 21 21", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z+1/2", "-x,y+1/2,-z+1/2"], "short_h_m": "I2_12_12_1", "hermann_mauguin_u": "I2_12_12_1", "point_group": "222"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"], "universal_h_m": "P m m 2", "number": 25, "schoenflies": "C2v^1", "hall": " P 2 -2", "hermann_mauguin": "P m m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"], "short_h_m": "Pmm2", "hermann_mauguin_u": "Pmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"], "universal_h_m": "P 2 m m", "number": 25, "schoenflies": "C2v^1", "hall": " P -2 2", "hermann_mauguin": "P 2 m m", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"], "short_h_m": "P2mm", "hermann_mauguin_u": "P2mm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"], "universal_h_m": "P m 2 m", "number": 25, "schoenflies": "C2v^1", "hall": " P -2 -2", "hermann_mauguin": "P m 2 m", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"], "short_h_m": "Pm2m", "hermann_mauguin_u": "Pm2m", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"], "universal_h_m": "P m c 21", "number": 26, "schoenflies": "C2v^2", "hall": " P 2c -2", "hermann_mauguin": "P m c 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"], "short_h_m": "Pmc2_1", "hermann_mauguin_u": "Pmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"], "universal_h_m": "P c m 21", "number": 26, "schoenflies": "C2v^2", "hall": " P 2c -2c", "hermann_mauguin": "P c m 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"], "short_h_m": "Pcm2_1", "hermann_mauguin_u": "Pcm2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x,-y,z"], "universal_h_m": "P 21 m a", "number": 26, "schoenflies": "C2v^2", "hall": " P -2a 2a", "hermann_mauguin": "P 21 m a", "ncsym": ["x,y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x,-y,z"], "short_h_m": "P2_1ma", "hermann_mauguin_u": "P2_1ma", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,-y,-z", "x+1/2,-y,z"], "universal_h_m": "P 21 a m", "number": 26, "schoenflies": "C2v^2", "hall": " P -2 2a", "hermann_mauguin": "P 21 a m", "ncsym": ["x,y,z", "x,y,-z", "x+1/2,-y,-z", "x+1/2,-y,z"], "short_h_m": "P2_1am", "hermann_mauguin_u": "P2_1am", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"], "universal_h_m": "P b 21 m", "number": 26, "schoenflies": "C2v^2", "hall": " P -2 -2b", "hermann_mauguin": "P b 21 m", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"], "short_h_m": "Pb2_1m", "hermann_mauguin_u": "Pb2_1m", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"], "universal_h_m": "P m 21 b", "number": 26, "schoenflies": "C2v^2", "hall": " P -2b -2", "hermann_mauguin": "P m 21 b", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"], "short_h_m": "Pm2_1b", "hermann_mauguin_u": "Pm2_1b", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"], "universal_h_m": "P c c 2", "number": 27, "schoenflies": "C2v^3", "hall": " P 2 -2c", "hermann_mauguin": "P c c 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"], "short_h_m": "Pcc2", "hermann_mauguin_u": "Pcc2", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"], "universal_h_m": "P 2 a a", "number": 27, "schoenflies": "C2v^3", "hall": " P -2a 2", "hermann_mauguin": "P 2 a a", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"], "short_h_m": "P2aa", "hermann_mauguin_u": "P2aa", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"], "universal_h_m": "P b 2 b", "number": 27, "schoenflies": "C2v^3", "hall": " P -2b -2b", "hermann_mauguin": "P b 2 b", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"], "short_h_m": "Pb2b", "hermann_mauguin_u": "Pb2b", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"], "universal_h_m": "P m a 2", "number": 28, "schoenflies": "C2v^4", "hall": " P 2 -2a", "hermann_mauguin": "P m a 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"], "short_h_m": "Pma2", "hermann_mauguin_u": "Pma2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"], "universal_h_m": "P b m 2", "number": 28, "schoenflies": "C2v^4", "hall": " P 2 -2b", "hermann_mauguin": "P b m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"], "short_h_m": "Pbm2", "hermann_mauguin_u": "Pbm2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z"], "universal_h_m": "P 2 m b", "number": 28, "schoenflies": "C2v^4", "hall": " P -2b 2", "hermann_mauguin": "P 2 m b", "ncsym": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z"], "short_h_m": "P2mb", "hermann_mauguin_u": "P2mb", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2"], "universal_h_m": "P 2 c m", "number": 28, "schoenflies": "C2v^4", "hall": " P -2c 2", "hermann_mauguin": "P 2 c m", "ncsym": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2"], "short_h_m": "P2cm", "hermann_mauguin_u": "P2cm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"], "universal_h_m": "P c 2 m", "number": 28, "schoenflies": "C2v^4", "hall": " P -2c -2c", "hermann_mauguin": "P c 2 m", "ncsym": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"], "short_h_m": "Pc2m", "hermann_mauguin_u": "Pc2m", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"], "universal_h_m": "P m 2 a", "number": 28, "schoenflies": "C2v^4", "hall": " P -2a -2a", "hermann_mauguin": "P m 2 a", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"], "short_h_m": "Pm2a", "hermann_mauguin_u": "Pm2a", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"], "universal_h_m": "P c a 21", "number": 29, "schoenflies": "C2v^5", "hall": " P 2c -2ac", "hermann_mauguin": "P c a 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"], "short_h_m": "Pca2_1", "hermann_mauguin_u": "Pca2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x,-y+1/2,z+1/2"], "universal_h_m": "P b c 21", "number": 29, "schoenflies": "C2v^5", "hall": " P 2c -2b", "hermann_mauguin": "P b c 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x,-y+1/2,z+1/2"], "short_h_m": "Pbc2_1", "hermann_mauguin_u": "Pbc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "x+1/2,-y,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "P 21 a b", "number": 29, "schoenflies": "C2v^5", "hall": " P -2b 2a", "hermann_mauguin": "P 21 a b", "ncsym": ["x,y,z", "x,y+1/2,-z", "x+1/2,-y,-z", "x+1/2,-y+1/2,z"], "short_h_m": "P2_1ab", "hermann_mauguin_u": "P2_1ab", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "x+1/2,-y,-z", "x,-y,z+1/2"], "universal_h_m": "P 21 c a", "number": 29, "schoenflies": "C2v^5", "hall": " P -2ac 2a", "hermann_mauguin": "P 21 c a", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "x+1/2,-y,-z", "x,-y,z+1/2"], "short_h_m": "P2_1ca", "hermann_mauguin_u": "P2_1ca", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "P c 21 b", "number": 29, "schoenflies": "C2v^5", "hall": " P -2bc -2c", "hermann_mauguin": "P c 21 b", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"], "short_h_m": "Pc2_1b", "hermann_mauguin_u": "Pc2_1b", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y+1/2,z", "-x,y+1/2,-z"], "universal_h_m": "P b 21 a", "number": 29, "schoenflies": "C2v^5", "hall": " P -2a -2ab", "hermann_mauguin": "P b 21 a", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y+1/2,z", "-x,y+1/2,-z"], "short_h_m": "Pb2_1a", "hermann_mauguin_u": "Pb2_1a", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "P n c 2", "number": 30, "schoenflies": "C2v^6", "hall": " P 2 -2bc", "hermann_mauguin": "P n c 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "short_h_m": "Pnc2", "hermann_mauguin_u": "Pnc2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "P c n 2", "number": 30, "schoenflies": "C2v^6", "hall": " P 2 -2ac", "hermann_mauguin": "P c n 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "short_h_m": "Pcn2", "hermann_mauguin_u": "Pcn2", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "x,-y,-z", "x+1/2,-y,z+1/2"], "universal_h_m": "P 2 n a", "number": 30, "schoenflies": "C2v^6", "hall": " P -2ac 2", "hermann_mauguin": "P 2 n a", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "x,-y,-z", "x+1/2,-y,z+1/2"], "short_h_m": "P2na", "hermann_mauguin_u": "P2na", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x,-y,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "P 2 a n", "number": 30, "schoenflies": "C2v^6", "hall": " P -2ab 2", "hermann_mauguin": "P 2 a n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "x,-y,-z", "x+1/2,-y+1/2,z"], "short_h_m": "P2an", "hermann_mauguin_u": "P2an", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z"], "universal_h_m": "P b 2 n", "number": 30, "schoenflies": "C2v^6", "hall": " P -2ab -2ab", "hermann_mauguin": "P b 2 n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z"], "short_h_m": "Pb2n", "hermann_mauguin_u": "Pb2n", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "-x,y,-z"], "universal_h_m": "P n 2 b", "number": 30, "schoenflies": "C2v^6", "hall": " P -2bc -2bc", "hermann_mauguin": "P n 2 b", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "-x,y,-z"], "short_h_m": "Pn2b", "hermann_mauguin_u": "Pn2b", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"], "universal_h_m": "P m n 21", "number": 31, "schoenflies": "C2v^7", "hall": " P 2ac -2", "hermann_mauguin": "P m n 21", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"], "short_h_m": "Pmn2_1", "hermann_mauguin_u": "Pmn2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"], "universal_h_m": "P n m 21", "number": 31, "schoenflies": "C2v^7", "hall": " P 2bc -2bc", "hermann_mauguin": "P n m 21", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"], "short_h_m": "Pnm2_1", "hermann_mauguin_u": "Pnm2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x+1/2,-y+1/2,-z", "x,-y,z"], "universal_h_m": "P 21 m n", "number": 31, "schoenflies": "C2v^7", "hall": " P -2ab 2ab", "hermann_mauguin": "P 21 m n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "x+1/2,-y+1/2,-z", "x,-y,z"], "short_h_m": "P2_1mn", "hermann_mauguin_u": "P2_1mn", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "P 21 n m", "number": 31, "schoenflies": "C2v^7", "hall": " P -2 2ac", "hermann_mauguin": "P 21 n m", "ncsym": ["x,y,z", "x,y,-z", "x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2"], "short_h_m": "P2_1nm", "hermann_mauguin_u": "P2_1nm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "P n 21 m", "number": 31, "schoenflies": "C2v^7", "hall": " P -2 -2bc", "hermann_mauguin": "P n 21 m", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "short_h_m": "Pn2_1m", "hermann_mauguin_u": "Pn2_1m", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "P m 21 n", "number": 31, "schoenflies": "C2v^7", "hall": " P -2ab -2", "hermann_mauguin": "P m 21 n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"], "short_h_m": "Pm2_1n", "hermann_mauguin_u": "Pm2_1n", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "P b a 2", "number": 32, "schoenflies": "C2v^8", "hall": " P 2 -2ab", "hermann_mauguin": "P b a 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "short_h_m": "Pba2", "hermann_mauguin_u": "Pba2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z+1/2", "x,-y,-z", "x,-y+1/2,z+1/2"], "universal_h_m": "P 2 c b", "number": 32, "schoenflies": "C2v^8", "hall": " P -2bc 2", "hermann_mauguin": "P 2 c b", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "x,-y,-z", "x,-y+1/2,z+1/2"], "short_h_m": "P2cb", "hermann_mauguin_u": "P2cb", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x,y,-z"], "universal_h_m": "P c 2 a", "number": 32, "schoenflies": "C2v^8", "hall": " P -2ac -2ac", "hermann_mauguin": "P c 2 a", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x,y,-z"], "short_h_m": "Pc2a", "hermann_mauguin_u": "Pc2a", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "P n a 21", "number": 33, "schoenflies": "C2v^9", "hall": " P 2c -2n", "hermann_mauguin": "P n a 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z"], "short_h_m": "Pna2_1", "hermann_mauguin_u": "Pna2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P b n 21", "number": 33, "schoenflies": "C2v^9", "hall": " P 2c -2ab", "hermann_mauguin": "P b n 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"], "short_h_m": "Pbn2_1", "hermann_mauguin_u": "Pbn2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z+1/2", "x+1/2,-y,-z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P 21 n b", "number": 33, "schoenflies": "C2v^9", "hall": " P -2bc 2a", "hermann_mauguin": "P 21 n b", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "x+1/2,-y,-z", "x+1/2,-y+1/2,z+1/2"], "short_h_m": "P2_1nb", "hermann_mauguin_u": "P2_1nb", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y,-z", "x,-y+1/2,z+1/2"], "universal_h_m": "P 21 c n", "number": 33, "schoenflies": "C2v^9", "hall": " P -2n 2a", "hermann_mauguin": "P 21 c n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y,-z", "x,-y+1/2,z+1/2"], "short_h_m": "P2_1cn", "hermann_mauguin_u": "P2_1cn", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "P c 21 n", "number": 33, "schoenflies": "C2v^9", "hall": " P -2n -2ac", "hermann_mauguin": "P c 21 n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "-x,y+1/2,-z"], "short_h_m": "Pc2_1n", "hermann_mauguin_u": "Pc2_1n", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "P n 21 a", "number": 33, "schoenflies": "C2v^9", "hall": " P -2ac -2n", "hermann_mauguin": "P n 21 a", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z"], "short_h_m": "Pn2_1a", "hermann_mauguin_u": "Pn2_1a", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P n n 2", "number": 34, "schoenflies": "C2v^10", "hall": " P 2 -2n", "hermann_mauguin": "P n n 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "short_h_m": "Pnn2", "hermann_mauguin_u": "Pnn2", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "x,-y,-z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P 2 n n", "number": 34, "schoenflies": "C2v^10", "hall": " P -2n 2", "hermann_mauguin": "P 2 n n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "x,-y,-z", "x+1/2,-y+1/2,z+1/2"], "short_h_m": "P2nn", "hermann_mauguin_u": "P2nn", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y,-z"], "universal_h_m": "P n 2 n", "number": 34, "schoenflies": "C2v^10", "hall": " P -2n -2n", "hermann_mauguin": "P n 2 n", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y,-z"], "short_h_m": "Pn2n", "hermann_mauguin_u": "Pn2n", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "C m m 2", "number": 35, "schoenflies": "C2v^11", "hall": " C 2 -2", "hermann_mauguin": "C m m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"], "short_h_m": "Cmm2", "hermann_mauguin_u": "Cmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "x,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A 2 m m", "number": 35, "schoenflies": "C2v^11", "hall": " A -2 2", "hermann_mauguin": "A 2 m m", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"], "short_h_m": "A2mm", "hermann_mauguin_u": "A2mm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2"], "universal_h_m": "B m 2 m", "number": 35, "schoenflies": "C2v^11", "hall": " B -2 -2", "hermann_mauguin": "B m 2 m", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"], "short_h_m": "Bm2m", "hermann_mauguin_u": "Bm2m", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C m c 21", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2", "hermann_mauguin": "C m c 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"], "short_h_m": "Cmc2_1", "hermann_mauguin_u": "Cmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "C c m 21", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2c", "hermann_mauguin": "C c m 21", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"], "short_h_m": "Ccm2_1", "hermann_mauguin_u": "Ccm2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x,-y,z", "x,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A 21 m a", "number": 36, "schoenflies": "C2v^12", "hall": " A -2a 2a", "hermann_mauguin": "A 21 m a", "ncsym": ["x,y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x,-y,z"], "short_h_m": "A2_1ma", "hermann_mauguin_u": "A2_1ma", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "x+1/2,-y,-z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A 21 a m", "number": 36, "schoenflies": "C2v^12", "hall": " A -2 2a", "hermann_mauguin": "A 21 a m", "ncsym": ["x,y,z", "x,y,-z", "x+1/2,-y,-z", "x+1/2,-y,z"], "short_h_m": "A2_1am", "hermann_mauguin_u": "A2_1am", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "B b 21 m", "number": 36, "schoenflies": "C2v^12", "hall": " B -2 -2b", "hermann_mauguin": "B b 21 m", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"], "short_h_m": "Bb2_1m", "hermann_mauguin_u": "Bb2_1m", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z", "x+1/2,y,z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "B m 21 b", "number": 36, "schoenflies": "C2v^12", "hall": " B -2b -2", "hermann_mauguin": "B m 21 b", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"], "short_h_m": "Bm2_1b", "hermann_mauguin_u": "Bm2_1b", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C c c 2", "number": 37, "schoenflies": "C2v^13", "hall": " C 2 -2c", "hermann_mauguin": "C c c 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"], "short_h_m": "Ccc2", "hermann_mauguin_u": "Ccc2", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "x,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A 2 a a", "number": 37, "schoenflies": "C2v^13", "hall": " A -2a 2", "hermann_mauguin": "A 2 a a", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"], "short_h_m": "A2aa", "hermann_mauguin_u": "A2aa", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z", "x+1/2,y,z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x+1/2,y,-z+1/2"], "universal_h_m": "B b 2 b", "number": 37, "schoenflies": "C2v^13", "hall": " B -2b -2b", "hermann_mauguin": "B b 2 b", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"], "short_h_m": "Bb2b", "hermann_mauguin_u": "Bb2b", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A m m 2", "number": 38, "schoenflies": "C2v^14", "hall": " A 2 -2", "hermann_mauguin": "A m m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"], "short_h_m": "Amm2", "hermann_mauguin_u": "Amm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "B m m 2", "number": 38, "schoenflies": "C2v^14", "hall": " B 2 -2", "hermann_mauguin": "B m m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"], "short_h_m": "Bmm2", "hermann_mauguin_u": "Bmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "B 2 m m", "number": 38, "schoenflies": "C2v^14", "hall": " B -2 2", "hermann_mauguin": "B 2 m m", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"], "short_h_m": "B2mm", "hermann_mauguin_u": "B2mm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z", "x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "C 2 m m", "number": 38, "schoenflies": "C2v^14", "hall": " C -2 2", "hermann_mauguin": "C 2 m m", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"], "short_h_m": "C2mm", "hermann_mauguin_u": "C2mm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "C m 2 m", "number": 38, "schoenflies": "C2v^14", "hall": " C -2 -2", "hermann_mauguin": "C m 2 m", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"], "short_h_m": "Cm2m", "hermann_mauguin_u": "Cm2m", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A m 2 m", "number": 38, "schoenflies": "C2v^14", "hall": " A -2 -2", "hermann_mauguin": "A m 2 m", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"], "short_h_m": "Am2m", "hermann_mauguin_u": "Am2m", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,y+1,z+1/2", "x,-y+1,z+1/2"], "universal_h_m": "A e m 2", "number": 39, "schoenflies": "C2v^15", "hall": " A 2 -2b", "hermann_mauguin": "A e m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"], "short_h_m": "Aem2", "hermann_mauguin_u": "Aem2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1,y,z+1/2", "x+1,-y,z+1/2"], "universal_h_m": "B m e 2", "number": 39, "schoenflies": "C2v^15", "hall": " B 2 -2a", "hermann_mauguin": "B m e 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"], "short_h_m": "Bme2", "hermann_mauguin_u": "Bme2", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z", "x+1/2,y,z+1/2", "x+1,y,-z+1/2", "x+1/2,-y,-z+1/2", "x+1,-y,z+1/2"], "universal_h_m": "B 2 e m", "number": 39, "schoenflies": "C2v^15", "hall": " B -2a 2", "hermann_mauguin": "B 2 e m", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"], "short_h_m": "B2em", "hermann_mauguin_u": "B2em", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z", "x+1/2,y+1/2,z", "x+1,y+1/2,-z", "x+1/2,-y+1/2,-z", "x+1,-y+1/2,z"], "universal_h_m": "C 2 m e", "number": 39, "schoenflies": "C2v^15", "hall": " C -2a 2", "hermann_mauguin": "C 2 m e", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"], "short_h_m": "C2me", "hermann_mauguin_u": "C2me", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z", "x+1/2,y+1/2,z", "x+1,y+1/2,-z", "-x+1,y+1/2,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "C m 2 e", "number": 39, "schoenflies": "C2v^15", "hall": " C -2a -2a", "hermann_mauguin": "C m 2 e", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"], "short_h_m": "Cm2e", "hermann_mauguin_u": "Cm2e", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z", "x,y+1/2,z+1/2", "x,y+1,-z+1/2", "-x,y+1,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A e 2 m", "number": 39, "schoenflies": "C2v^15", "hall": " A -2b -2b", "hermann_mauguin": "A e 2 m", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"], "short_h_m": "Ae2m", "hermann_mauguin_u": "Ae2m", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A m a 2", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a", "hermann_mauguin": "A m a 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"], "short_h_m": "Ama2", "hermann_mauguin_u": "Ama2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "B b m 2", "number": 40, "schoenflies": "C2v^16", "hall": " B 2 -2b", "hermann_mauguin": "B b m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"], "short_h_m": "Bbm2", "hermann_mauguin_u": "Bbm2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z", "x+1/2,y,z+1/2", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "B 2 m b", "number": 40, "schoenflies": "C2v^16", "hall": " B -2b 2", "hermann_mauguin": "B 2 m b", "ncsym": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z"], "short_h_m": "B2mb", "hermann_mauguin_u": "B2mb", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C 2 c m", "number": 40, "schoenflies": "C2v^16", "hall": " C -2c 2", "hermann_mauguin": "C 2 c m", "ncsym": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2"], "short_h_m": "C2cm", "hermann_mauguin_u": "C2cm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z"], "universal_h_m": "C c 2 m", "number": 40, "schoenflies": "C2v^16", "hall": " C -2c -2c", "hermann_mauguin": "C c 2 m", "ncsym": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"], "short_h_m": "Cc2m", "hermann_mauguin_u": "Cc2m", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z", "x,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A m 2 a", "number": 40, "schoenflies": "C2v^16", "hall": " A -2a -2a", "hermann_mauguin": "A m 2 a", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"], "short_h_m": "Am2a", "hermann_mauguin_u": "Am2a", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x+1/2,y+1,z+1/2", "x+1/2,-y+1,z+1/2"], "universal_h_m": "A e a 2", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab", "hermann_mauguin": "A e a 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "short_h_m": "Aea2", "hermann_mauguin_u": "Aea2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1,y+1/2,z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "B b e 2", "number": 41, "schoenflies": "C2v^17", "hall": " B 2 -2ab", "hermann_mauguin": "B b e 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "short_h_m": "Bbe2", "hermann_mauguin_u": "Bbe2", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "x,-y,-z", "x+1/2,-y+1/2,z", "x+1/2,y,z+1/2", "x+1,y+1/2,-z+1/2", "x+1/2,-y,-z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "B 2 e b", "number": 41, "schoenflies": "C2v^17", "hall": " B -2ab 2", "hermann_mauguin": "B 2 e b", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "x,-y,-z", "x+1/2,-y+1/2,z"], "short_h_m": "B2eb", "hermann_mauguin_u": "B2eb", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "x,-y,-z", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "x+1,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z", "x+1,-y+1/2,z+1/2"], "universal_h_m": "C 2 e b", "number": 41, "schoenflies": "C2v^17", "hall": " C -2ac 2", "hermann_mauguin": "C 2 e b", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "x,-y,-z", "x+1/2,-y,z+1/2"], "short_h_m": "C2eb", "hermann_mauguin_u": "C2eb", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x,y,-z", "x+1/2,y+1/2,z", "x+1,y+1/2,-z+1/2", "-x+1,y+1/2,z+1/2", "-x+1/2,y+1/2,-z"], "universal_h_m": "C c 2 e", "number": 41, "schoenflies": "C2v^17", "hall": " C -2ac -2ac", "hermann_mauguin": "C c 2 e", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x,y,-z"], "short_h_m": "Cc2e", "hermann_mauguin_u": "Cc2e", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z", "x,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2", "-x+1/2,y+1,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "A e 2 a", "number": 41, "schoenflies": "C2v^17", "hall": " A -2ab -2ab", "hermann_mauguin": "A e 2 a", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z"], "short_h_m": "Ae2a", "hermann_mauguin_u": "Ae2a", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "F m m 2", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2", "hermann_mauguin": "F m m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"], "short_h_m": "Fmm2", "hermann_mauguin_u": "Fmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "x,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z", "x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z"], "universal_h_m": "F 2 m m", "number": 42, "schoenflies": "C2v^18", "hall": " F -2 2", "hermann_mauguin": "F 2 m m", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"], "short_h_m": "F2mm", "hermann_mauguin_u": "F2mm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x,y+1/2,z+1/2", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "F m 2 m", "number": 42, "schoenflies": "C2v^18", "hall": " F -2 -2", "hermann_mauguin": "F m 2 m", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"], "short_h_m": "Fm2m", "hermann_mauguin_u": "Fm2m", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/4,y+1/4,z+1/4", "x+3/4,-y+3/4,z+1/4", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x+1/4,y+3/4,z+3/4", "x+3/4,-y+5/4,z+3/4", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+3/4,y+1/4,z+3/4", "x+5/4,-y+3/4,z+3/4", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+3/4,y+3/4,z+1/4", "x+5/4,-y+5/4,z+1/4"], "universal_h_m": "F d d 2", "number": 43, "schoenflies": "C2v^19", "hall": " F 2 -2d", "hermann_mauguin": "F d d 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/4,y+1/4,z+1/4", "x+3/4,-y+3/4,z+1/4"], "short_h_m": "Fdd2", "hermann_mauguin_u": "Fdd2", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/4,y+1/4,-z+1/4", "x,-y,-z", "x+1/4,-y+1/4,z+1/4", "x,y+1/2,z+1/2", "x+1/4,y+3/4,-z+3/4", "x,-y+1/2,-z+1/2", "x+1/4,-y+3/4,z+3/4", "x+1/2,y,z+1/2", "x+3/4,y+1/4,-z+3/4", "x+1/2,-y,-z+1/2", "x+3/4,-y+1/4,z+3/4", "x+1/2,y+1/2,z", "x+3/4,y+3/4,-z+1/4", "x+1/2,-y+1/2,-z", "x+3/4,-y+3/4,z+1/4"], "universal_h_m": "F 2 d d", "number": 43, "schoenflies": "C2v^19", "hall": " F -2d 2", "hermann_mauguin": "F 2 d d", "ncsym": ["x,y,z", "x+1/4,y+1/4,-z+1/4", "x,-y,-z", "x+1/4,-y+1/4,z+1/4"], "short_h_m": "F2dd", "hermann_mauguin_u": "F2dd", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/4,y+1/4,-z+1/4", "-x+1/4,y+1/4,z+1/4", "-x+1/2,y+1/2,-z", "x,y+1/2,z+1/2", "x+1/4,y+3/4,-z+3/4", "-x+1/4,y+3/4,z+3/4", "-x+1/2,y+1,-z+1/2", "x+1/2,y,z+1/2", "x+3/4,y+1/4,-z+3/4", "-x+3/4,y+1/4,z+3/4", "-x+1,y+1/2,-z+1/2", "x+1/2,y+1/2,z", "x+3/4,y+3/4,-z+1/4", "-x+3/4,y+3/4,z+1/4", "-x+1,y+1,-z"], "universal_h_m": "F d 2 d", "number": 43, "schoenflies": "C2v^19", "hall": " F -2d -2d", "hermann_mauguin": "F d 2 d", "ncsym": ["x,y,z", "x+1/4,y+1/4,-z+1/4", "-x+1/4,y+1/4,z+1/4", "-x+1/2,y+1/2,-z"], "short_h_m": "Fd2d", "hermann_mauguin_u": "Fd2d", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I m m 2", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2", "hermann_mauguin": "I m m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z", "x,-y,z"], "short_h_m": "Imm2", "hermann_mauguin_u": "Imm2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I 2 m m", "number": 44, "schoenflies": "C2v^20", "hall": " I -2 2", "hermann_mauguin": "I 2 m m", "ncsym": ["x,y,z", "x,y,-z", "x,-y,-z", "x,-y,z"], "short_h_m": "I2mm", "hermann_mauguin_u": "I2mm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I m 2 m", "number": 44, "schoenflies": "C2v^20", "hall": " I -2 -2", "hermann_mauguin": "I m 2 m", "ncsym": ["x,y,z", "x,y,-z", "-x,y,z", "-x,y,-z"], "short_h_m": "Im2m", "hermann_mauguin_u": "Im2m", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1", "x+1/2,-y+1/2,z+1"], "universal_h_m": "I b a 2", "number": 45, "schoenflies": "C2v^21", "hall": " I 2 -2c", "hermann_mauguin": "I b a 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"], "short_h_m": "Iba2", "hermann_mauguin_u": "Iba2", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z", "x+1/2,y+1/2,z+1/2", "x+1,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "I 2 c b", "number": 45, "schoenflies": "C2v^21", "hall": " I -2a 2", "hermann_mauguin": "I 2 c b", "ncsym": ["x,y,z", "x+1/2,y,-z", "x,-y,-z", "x+1/2,-y,z"], "short_h_m": "I2cb", "hermann_mauguin_u": "I2cb", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2", "-x+1/2,y+1,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I c 2 a", "number": 45, "schoenflies": "C2v^21", "hall": " I -2b -2b", "hermann_mauguin": "I c 2 a", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"], "short_h_m": "Ic2a", "hermann_mauguin_u": "Ic2a", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1,y+1/2,z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "I m a 2", "number": 46, "schoenflies": "C2v^22", "hall": " I 2 -2a", "hermann_mauguin": "I m a 2", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"], "short_h_m": "Ima2", "hermann_mauguin_u": "Ima2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1,z+1/2", "x+1/2,-y+1,z+1/2"], "universal_h_m": "I b m 2", "number": 46, "schoenflies": "C2v^22", "hall": " I 2 -2b", "hermann_mauguin": "I b m 2", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z", "x,-y+1/2,z"], "short_h_m": "Ibm2", "hermann_mauguin_u": "Ibm2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1,z+1/2"], "universal_h_m": "I 2 m b", "number": 46, "schoenflies": "C2v^22", "hall": " I -2b 2", "hermann_mauguin": "I 2 m b", "ncsym": ["x,y,z", "x,y+1/2,-z", "x,-y,-z", "x,-y+1/2,z"], "short_h_m": "I2mb", "hermann_mauguin_u": "I2mb", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1", "x+1/2,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1"], "universal_h_m": "I 2 c m", "number": 46, "schoenflies": "C2v^22", "hall": " I -2c 2", "hermann_mauguin": "I 2 c m", "ncsym": ["x,y,z", "x,y,-z+1/2", "x,-y,-z", "x,-y,z+1/2"], "short_h_m": "I2cm", "hermann_mauguin_u": "I2cm", "point_group": "mm2"}, {"symops": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z+1", "-x+1/2,y+1/2,z+1", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I c 2 m", "number": 46, "schoenflies": "C2v^22", "hall": " I -2c -2c", "hermann_mauguin": "I c 2 m", "ncsym": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"], "short_h_m": "Ic2m", "hermann_mauguin_u": "Ic2m", "point_group": "mm2"}, {"symops": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z", "x+1/2,y+1/2,z+1/2", "x+1,y+1/2,-z+1/2", "-x+1,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "I m 2 a", "number": 46, "schoenflies": "C2v^22", "hall": " I -2a -2a", "hermann_mauguin": "I m 2 a", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y,z", "-x,y,-z"], "short_h_m": "Im2a", "hermann_mauguin_u": "Im2a", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z"], "universal_h_m": "P m m m", "number": 47, "schoenflies": "D2h^1", "hall": "-P 2 2", "hermann_mauguin": "P m m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z"], "short_h_m": "Pmmm", "hermann_mauguin_u": "Pmmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P n n n :1", "number": 48, "schoenflies": "D2h^2", "hall": " P 2 2 -1n", "hermann_mauguin": "P n n n", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "short_h_m": "Pnnn", "hermann_mauguin_u": "Pnnn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z-1/2", "x-1/2,-y,z-1/2"], "universal_h_m": "P n n n :2", "number": 48, "schoenflies": "D2h^2", "hall": "-P 2ab 2bc", "hermann_mauguin": "P n n n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z-1/2", "x-1/2,-y,z-1/2"], "short_h_m": "Pnnn", "hermann_mauguin_u": "Pnnn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y,z-1/2", "x,-y,z-1/2"], "universal_h_m": "P c c m", "number": 49, "schoenflies": "D2h^3", "hall": "-P 2 2c", "hermann_mauguin": "P c c m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y,z-1/2", "x,-y,z-1/2"], "short_h_m": "Pccm", "hermann_mauguin_u": "Pccm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z"], "universal_h_m": "P m a a", "number": 49, "schoenflies": "D2h^3", "hall": "-P 2a 2", "hermann_mauguin": "P m a a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z"], "short_h_m": "Pmaa", "hermann_mauguin_u": "Pmaa", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z", "x,-y,z"], "universal_h_m": "P b m b", "number": 49, "schoenflies": "D2h^3", "hall": "-P 2b 2b", "hermann_mauguin": "P b m b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z", "x,-y,z"], "short_h_m": "Pbmb", "hermann_mauguin_u": "Pbmb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "P b a n :1", "number": 50, "schoenflies": "D2h^4", "hall": " P 2 2 -1ab", "hermann_mauguin": "P b a n", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "short_h_m": "Pban", "hermann_mauguin_u": "Pban", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z", "x-1/2,-y,z"], "universal_h_m": "P b a n :2", "number": 50, "schoenflies": "D2h^4", "hall": "-P 2ab 2b", "hermann_mauguin": "P b a n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z", "x-1/2,-y,z"], "short_h_m": "Pban", "hermann_mauguin_u": "Pban", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "P n c b :1", "number": 50, "schoenflies": "D2h^4", "hall": " P 2 2 -1bc", "hermann_mauguin": "P n c b", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "short_h_m": "Pncb", "hermann_mauguin_u": "Pncb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z-1/2", "x,-y,z-1/2"], "universal_h_m": "P n c b :2", "number": 50, "schoenflies": "D2h^4", "hall": "-P 2b 2bc", "hermann_mauguin": "P n c b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z-1/2", "x,-y,z-1/2"], "short_h_m": "Pncb", "hermann_mauguin_u": "Pncb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "P c n a :1", "number": 50, "schoenflies": "D2h^4", "hall": " P 2 2 -1ac", "hermann_mauguin": "P c n a", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "short_h_m": "Pcna", "hermann_mauguin_u": "Pcna", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z-1/2", "x-1/2,-y,z-1/2"], "universal_h_m": "P c n a :2", "number": 50, "schoenflies": "D2h^4", "hall": "-P 2a 2c", "hermann_mauguin": "P c n a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z-1/2", "x-1/2,-y,z-1/2"], "short_h_m": "Pcna", "hermann_mauguin_u": "Pcna", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z", "x,-y,z"], "universal_h_m": "P m m a", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2a 2a", "hermann_mauguin": "P m m a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z", "x,-y,z"], "short_h_m": "Pmma", "hermann_mauguin_u": "Pmma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z", "x,-y-1/2,z"], "universal_h_m": "P m m b", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2b 2", "hermann_mauguin": "P m m b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z", "x,-y-1/2,z"], "short_h_m": "Pmmb", "hermann_mauguin_u": "Pmmb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z", "x,-y-1/2,z"], "universal_h_m": "P b m m", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2 2b", "hermann_mauguin": "P b m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z", "x,-y-1/2,z"], "short_h_m": "Pbmm", "hermann_mauguin_u": "Pbmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z-1/2", "x,-y,z"], "universal_h_m": "P c m m", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2c 2c", "hermann_mauguin": "P c m m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z-1/2", "x,-y,z"], "short_h_m": "Pcmm", "hermann_mauguin_u": "Pcmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z", "x,-y,z-1/2"], "universal_h_m": "P m c m", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2c 2", "hermann_mauguin": "P m c m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z", "x,-y,z-1/2"], "short_h_m": "Pmcm", "hermann_mauguin_u": "Pmcm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z", "x-1/2,-y,z"], "universal_h_m": "P m a m", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2 2a", "hermann_mauguin": "P m a m", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z", "x-1/2,-y,z"], "short_h_m": "Pmam", "hermann_mauguin_u": "Pmam", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x,y-1/2,z-1/2", "x-1/2,-y-1/2,z-1/2"], "universal_h_m": "P n n a", "number": 52, "schoenflies": "D2h^6", "hall": "-P 2a 2bc", "hermann_mauguin": "P n n a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x,y-1/2,z-1/2", "x-1/2,-y-1/2,z-1/2"], "short_h_m": "Pnna", "hermann_mauguin_u": "Pnna", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y-1/2,z-1/2", "x-1/2,-y,z-1/2"], "universal_h_m": "P n n b", "number": 52, "schoenflies": "D2h^6", "hall": "-P 2b 2n", "hermann_mauguin": "P n n b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y-1/2,z-1/2", "x-1/2,-y,z-1/2"], "short_h_m": "Pnnb", "hermann_mauguin_u": "Pnnb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y+1/2,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x,y-1/2,z", "x-1/2,-y,z-1/2"], "universal_h_m": "P b n n", "number": 52, "schoenflies": "D2h^6", "hall": "-P 2n 2b", "hermann_mauguin": "P b n n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y+1/2,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x,y-1/2,z", "x-1/2,-y,z-1/2"], "short_h_m": "Pbnn", "hermann_mauguin_u": "Pbnn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y,z-1/2", "x-1/2,-y-1/2,z-1/2"], "universal_h_m": "P c n n", "number": 52, "schoenflies": "D2h^6", "hall": "-P 2ab 2c", "hermann_mauguin": "P c n n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y,z-1/2", "x-1/2,-y-1/2,z-1/2"], "short_h_m": "Pcnn", "hermann_mauguin_u": "Pcnn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y-1/2,z-1/2", "x,-y,z-1/2"], "universal_h_m": "P n c n", "number": 52, "schoenflies": "D2h^6", "hall": "-P 2ab 2n", "hermann_mauguin": "P n c n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y-1/2,z-1/2", "x,-y,z-1/2"], "short_h_m": "Pncn", "hermann_mauguin_u": "Pncn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x,y-1/2,z-1/2", "x-1/2,-y,z"], "universal_h_m": "P n a n", "number": 52, "schoenflies": "D2h^6", "hall": "-P 2n 2bc", "hermann_mauguin": "P n a n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x,y-1/2,z-1/2", "x-1/2,-y,z"], "short_h_m": "Pnan", "hermann_mauguin_u": "Pnan", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y,z", "x-1/2,-y,z-1/2"], "universal_h_m": "P m n a", "number": 53, "schoenflies": "D2h^7", "hall": "-P 2ac 2", "hermann_mauguin": "P m n a", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y,z", "x-1/2,-y,z-1/2"], "short_h_m": "Pmna", "hermann_mauguin_u": "Pmna", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x,y-1/2,z-1/2", "x,-y,z"], "universal_h_m": "P n m b", "number": 53, "schoenflies": "D2h^7", "hall": "-P 2bc 2bc", "hermann_mauguin": "P n m b", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x,y-1/2,z-1/2", "x,-y,z"], "short_h_m": "Pnmb", "hermann_mauguin_u": "Pnmb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y-1/2,z", "x,-y,z"], "universal_h_m": "P b m n", "number": 53, "schoenflies": "D2h^7", "hall": "-P 2ab 2ab", "hermann_mauguin": "P b m n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y-1/2,z", "x,-y,z"], "short_h_m": "Pbmn", "hermann_mauguin_u": "Pbmn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z-1/2", "x-1/2,-y,z-1/2"], "universal_h_m": "P c n m", "number": 53, "schoenflies": "D2h^7", "hall": "-P 2 2ac", "hermann_mauguin": "P c n m", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z-1/2", "x-1/2,-y,z-1/2"], "short_h_m": "Pcnm", "hermann_mauguin_u": "Pcnm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z-1/2", "x,-y-1/2,z-1/2"], "universal_h_m": "P n c m", "number": 53, "schoenflies": "D2h^7", "hall": "-P 2 2bc", "hermann_mauguin": "P n c m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z-1/2", "x,-y-1/2,z-1/2"], "short_h_m": "Pncm", "hermann_mauguin_u": "Pncm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y,z", "x-1/2,-y-1/2,z"], "universal_h_m": "P m a n", "number": 53, "schoenflies": "D2h^7", "hall": "-P 2ab 2", "hermann_mauguin": "P m a n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y,z", "x-1/2,-y-1/2,z"], "short_h_m": "Pman", "hermann_mauguin_u": "Pman", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z-1/2", "x,-y,z-1/2"], "universal_h_m": "P c c a", "number": 54, "schoenflies": "D2h^8", "hall": "-P 2a 2ac", "hermann_mauguin": "P c c a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z-1/2", "x,-y,z-1/2"], "short_h_m": "Pcca", "hermann_mauguin_u": "Pcca", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z-1/2", "x,-y-1/2,z-1/2"], "universal_h_m": "P c c b", "number": 54, "schoenflies": "D2h^8", "hall": "-P 2b 2c", "hermann_mauguin": "P c c b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z-1/2", "x,-y-1/2,z-1/2"], "short_h_m": "Pccb", "hermann_mauguin_u": "Pccb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y-1/2,z", "x-1/2,-y-1/2,z"], "universal_h_m": "P b a a", "number": 54, "schoenflies": "D2h^8", "hall": "-P 2a 2b", "hermann_mauguin": "P b a a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y-1/2,z", "x-1/2,-y-1/2,z"], "short_h_m": "Pbaa", "hermann_mauguin_u": "Pbaa", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y,-z+1/2", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y,z-1/2", "x-1/2,-y,z"], "universal_h_m": "P c a a", "number": 54, "schoenflies": "D2h^8", "hall": "-P 2ac 2c", "hermann_mauguin": "P c a a", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y,-z+1/2", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y,z-1/2", "x-1/2,-y,z"], "short_h_m": "Pcaa", "hermann_mauguin_u": "Pcaa", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z", "-x,y,-z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x,y-1/2,z", "x,-y,z-1/2"], "universal_h_m": "P b c b", "number": 54, "schoenflies": "D2h^8", "hall": "-P 2bc 2b", "hermann_mauguin": "P b c b", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z", "-x,y,-z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x,y-1/2,z", "x,-y,z-1/2"], "short_h_m": "Pbcb", "hermann_mauguin_u": "Pbcb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y-1/2,z", "x-1/2,-y,z"], "universal_h_m": "P b a b", "number": 54, "schoenflies": "D2h^8", "hall": "-P 2b 2ab", "hermann_mauguin": "P b a b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y-1/2,z", "x-1/2,-y,z"], "short_h_m": "Pbab", "hermann_mauguin_u": "Pbab", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y-1/2,z", "x-1/2,-y-1/2,z"], "universal_h_m": "P b a m", "number": 55, "schoenflies": "D2h^9", "hall": "-P 2 2ab", "hermann_mauguin": "P b a m", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y-1/2,z", "x-1/2,-y-1/2,z"], "short_h_m": "Pbam", "hermann_mauguin_u": "Pbam", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x,y,z", "x,-y-1/2,z-1/2"], "universal_h_m": "P m c b", "number": 55, "schoenflies": "D2h^9", "hall": "-P 2bc 2", "hermann_mauguin": "P m c b", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x,y,z", "x,-y-1/2,z-1/2"], "short_h_m": "Pmcb", "hermann_mauguin_u": "Pmcb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y,z-1/2", "x,-y,z"], "universal_h_m": "P c m a", "number": 55, "schoenflies": "D2h^9", "hall": "-P 2ac 2ac", "hermann_mauguin": "P c m a", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y,z-1/2", "x,-y,z"], "short_h_m": "Pcma", "hermann_mauguin_u": "Pcma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y,z-1/2", "x,-y-1/2,z-1/2"], "universal_h_m": "P c c n", "number": 56, "schoenflies": "D2h^10", "hall": "-P 2ab 2ac", "hermann_mauguin": "P c c n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y,z-1/2", "x,-y-1/2,z-1/2"], "short_h_m": "Pccn", "hermann_mauguin_u": "Pccn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y-1/2,z-1/2", "x-1/2,-y-1/2,z"], "universal_h_m": "P n a a", "number": 56, "schoenflies": "D2h^10", "hall": "-P 2ac 2bc", "hermann_mauguin": "P n a a", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y-1/2,z-1/2", "x-1/2,-y-1/2,z"], "short_h_m": "Pnaa", "hermann_mauguin_u": "Pnaa", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x-1/2,y-1/2,z", "x-1/2,-y,z-1/2"], "universal_h_m": "P b n b", "number": 56, "schoenflies": "D2h^10", "hall": "-P 2bc 2ab", "hermann_mauguin": "P b n b", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x-1/2,y-1/2,z", "x-1/2,-y,z-1/2"], "short_h_m": "Pbnb", "hermann_mauguin_u": "Pbnb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y+1/2,-z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x,y-1/2,z", "x,-y-1/2,z-1/2"], "universal_h_m": "P b c m", "number": 57, "schoenflies": "D2h^11", "hall": "-P 2c 2b", "hermann_mauguin": "P b c m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y+1/2,-z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x,y-1/2,z", "x,-y-1/2,z-1/2"], "short_h_m": "Pbcm", "hermann_mauguin_u": "Pbcm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z-1/2", "-x-1/2,y,z-1/2", "x-1/2,-y,z"], "universal_h_m": "P c a m", "number": 57, "schoenflies": "D2h^11", "hall": "-P 2c 2ac", "hermann_mauguin": "P c a m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z-1/2", "-x-1/2,y,z-1/2", "x-1/2,-y,z"], "short_h_m": "Pcam", "hermann_mauguin_u": "Pcam", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y,z", "x,-y,z-1/2"], "universal_h_m": "P m c a", "number": 57, "schoenflies": "D2h^11", "hall": "-P 2ac 2a", "hermann_mauguin": "P m c a", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y,z", "x,-y,z-1/2"], "short_h_m": "Pmca", "hermann_mauguin_u": "Pmca", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y,z", "x-1/2,-y-1/2,z"], "universal_h_m": "P m a b", "number": 57, "schoenflies": "D2h^11", "hall": "-P 2b 2a", "hermann_mauguin": "P m a b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y,z", "x-1/2,-y-1/2,z"], "short_h_m": "Pmab", "hermann_mauguin_u": "Pmab", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y-1/2,z", "x,-y-1/2,z"], "universal_h_m": "P b m a", "number": 57, "schoenflies": "D2h^11", "hall": "-P 2a 2ab", "hermann_mauguin": "P b m a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y-1/2,z", "x,-y-1/2,z"], "short_h_m": "Pbma", "hermann_mauguin_u": "Pbma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x,y,z-1/2", "x,-y-1/2,z"], "universal_h_m": "P c m b", "number": 57, "schoenflies": "D2h^11", "hall": "-P 2bc 2c", "hermann_mauguin": "P c m b", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x,y,z-1/2", "x,-y-1/2,z"], "short_h_m": "Pcmb", "hermann_mauguin_u": "Pcmb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x,y,-z", "-x-1/2,y-1/2,z-1/2", "x-1/2,-y-1/2,z-1/2"], "universal_h_m": "P n n m", "number": 58, "schoenflies": "D2h^12", "hall": "-P 2 2n", "hermann_mauguin": "P n n m", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x,y,-z", "-x-1/2,y-1/2,z-1/2", "x-1/2,-y-1/2,z-1/2"], "short_h_m": "Pnnm", "hermann_mauguin_u": "Pnnm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y,-z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x,y,z", "x-1/2,-y-1/2,z-1/2"], "universal_h_m": "P m n n", "number": 58, "schoenflies": "D2h^12", "hall": "-P 2n 2", "hermann_mauguin": "P m n n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y,-z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x,y,z", "x-1/2,-y-1/2,z-1/2"], "short_h_m": "Pmnn", "hermann_mauguin_u": "Pmnn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x-1/2,y-1/2,z-1/2", "x,-y,z"], "universal_h_m": "P n m n", "number": 58, "schoenflies": "D2h^12", "hall": "-P 2n 2n", "hermann_mauguin": "P n m n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x-1/2,y-1/2,z-1/2", "x,-y,z"], "short_h_m": "Pnmn", "hermann_mauguin_u": "Pnmn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x,y,z", "x,-y,z"], "universal_h_m": "P m m n :1", "number": 59, "schoenflies": "D2h^13", "hall": " P 2 2ab -1ab", "hermann_mauguin": "P m m n", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x,y,z", "x,-y,z"], "short_h_m": "Pmmn", "hermann_mauguin_u": "Pmmn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y,-z", "-x,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y,z", "x,-y-1/2,z"], "universal_h_m": "P m m n :2", "number": 59, "schoenflies": "D2h^13", "hall": "-P 2ab 2a", "hermann_mauguin": "P m m n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y,-z", "-x,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y,z", "x,-y-1/2,z"], "short_h_m": "Pmmn", "hermann_mauguin_u": "Pmmn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,y,-z", "-x,y+1/2,z+1/2", "x,-y,z"], "universal_h_m": "P n m m :1", "number": 59, "schoenflies": "D2h^13", "hall": " P 2bc 2 -1bc", "hermann_mauguin": "P n m m", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x,-y,-z", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,y,-z", "-x,y+1/2,z+1/2", "x,-y,z"], "short_h_m": "Pnmm", "hermann_mauguin_u": "Pnmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y-1/2,z-1/2", "x,-y-1/2,z"], "universal_h_m": "P n m m :2", "number": 59, "schoenflies": "D2h^13", "hall": "-P 2c 2bc", "hermann_mauguin": "P n m m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y-1/2,z-1/2", "x,-y-1/2,z"], "short_h_m": "Pnmm", "hermann_mauguin_u": "Pnmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z", "-x+1/2,-y,-z+1/2", "x,y,-z", "-x,y,z", "x+1/2,-y,z+1/2"], "universal_h_m": "P m n m :1", "number": 59, "schoenflies": "D2h^13", "hall": " P 2ac 2ac -1ac", "hermann_mauguin": "P m n m", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z", "-x+1/2,-y,-z+1/2", "x,y,-z", "-x,y,z", "x+1/2,-y,z+1/2"], "short_h_m": "Pmnm", "hermann_mauguin_u": "Pmnm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x+1/2,-y,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x-1/2,y,z", "x-1/2,-y,z-1/2"], "universal_h_m": "P m n m :2", "number": 59, "schoenflies": "D2h^13", "hall": "-P 2c 2a", "hermann_mauguin": "P m n m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x+1/2,-y,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x-1/2,y,z", "x-1/2,-y,z-1/2"], "short_h_m": "Pmnm", "hermann_mauguin_u": "Pmnm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x-1/2,y-1/2,z", "x,-y,z-1/2"], "universal_h_m": "P b c n", "number": 60, "schoenflies": "D2h^14", "hall": "-P 2n 2ab", "hermann_mauguin": "P b c n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x-1/2,y-1/2,z", "x,-y,z-1/2"], "short_h_m": "Pbcn", "hermann_mauguin_u": "Pbcn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y,-z+1/2", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x,y,z-1/2", "x-1/2,-y-1/2,z"], "universal_h_m": "P c a n", "number": 60, "schoenflies": "D2h^14", "hall": "-P 2n 2c", "hermann_mauguin": "P c a n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y,-z+1/2", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x,y,z-1/2", "x-1/2,-y-1/2,z"], "short_h_m": "Pcan", "hermann_mauguin_u": "Pcan", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y-1/2,z-1/2", "x,-y-1/2,z-1/2"], "universal_h_m": "P n c a", "number": 60, "schoenflies": "D2h^14", "hall": "-P 2a 2n", "hermann_mauguin": "P n c a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y-1/2,z-1/2", "x,-y-1/2,z-1/2"], "short_h_m": "Pnca", "hermann_mauguin_u": "Pnca", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y,-z", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x-1/2,y-1/2,z-1/2", "x-1/2,-y,z"], "universal_h_m": "P n a b", "number": 60, "schoenflies": "D2h^14", "hall": "-P 2bc 2n", "hermann_mauguin": "P n a b", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y,-z", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x-1/2,y-1/2,z-1/2", "x-1/2,-y,z"], "short_h_m": "Pnab", "hermann_mauguin_u": "Pnab", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y+1/2,-z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y-1/2,z", "x-1/2,-y-1/2,z-1/2"], "universal_h_m": "P b n a", "number": 60, "schoenflies": "D2h^14", "hall": "-P 2ac 2b", "hermann_mauguin": "P b n a", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y+1/2,-z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y-1/2,z", "x-1/2,-y-1/2,z-1/2"], "short_h_m": "Pbna", "hermann_mauguin_u": "Pbna", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y,z-1/2", "x-1/2,-y-1/2,z-1/2"], "universal_h_m": "P c n b", "number": 60, "schoenflies": "D2h^14", "hall": "-P 2b 2ac", "hermann_mauguin": "P c n b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y,z-1/2", "x-1/2,-y-1/2,z-1/2"], "short_h_m": "Pcnb", "hermann_mauguin_u": "Pcnb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y-1/2,z", "x,-y-1/2,z-1/2"], "universal_h_m": "P b c a", "number": 61, "schoenflies": "D2h^15", "hall": "-P 2ac 2ab", "hermann_mauguin": "P b c a", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y-1/2,z", "x,-y-1/2,z-1/2"], "short_h_m": "Pbca", "hermann_mauguin_u": "Pbca", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x-1/2,y,z-1/2", "x-1/2,-y-1/2,z"], "universal_h_m": "P c a b", "number": 61, "schoenflies": "D2h^15", "hall": "-P 2bc 2ac", "hermann_mauguin": "P c a b", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x-1/2,y,z-1/2", "x-1/2,-y-1/2,z"], "short_h_m": "Pcab", "hermann_mauguin_u": "Pcab", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y-1/2,z-1/2", "x,-y-1/2,z"], "universal_h_m": "P n m a", "number": 62, "schoenflies": "D2h^16", "hall": "-P 2ac 2n", "hermann_mauguin": "P n m a", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y-1/2,z-1/2", "x,-y-1/2,z"], "short_h_m": "Pnma", "hermann_mauguin_u": "Pnma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "x+1/2,-y,-z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x-1/2,y,z", "x-1/2,-y-1/2,z-1/2"], "universal_h_m": "P m n b", "number": 62, "schoenflies": "D2h^16", "hall": "-P 2bc 2a", "hermann_mauguin": "P m n b", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "x+1/2,-y,-z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z-1/2", "-x-1/2,y,z", "x-1/2,-y-1/2,z-1/2"], "short_h_m": "Pmnb", "hermann_mauguin_u": "Pmnb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x-1/2,y-1/2,z", "x-1/2,-y-1/2,z-1/2"], "universal_h_m": "P b n m", "number": 62, "schoenflies": "D2h^16", "hall": "-P 2c 2ab", "hermann_mauguin": "P b n m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x-1/2,y-1/2,z", "x-1/2,-y-1/2,z-1/2"], "short_h_m": "Pbnm", "hermann_mauguin_u": "Pbnm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x-1/2,y,z-1/2", "x,-y-1/2,z"], "universal_h_m": "P c m n", "number": 62, "schoenflies": "D2h^16", "hall": "-P 2n 2ac", "hermann_mauguin": "P c m n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y,-z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x-1/2,y,z-1/2", "x,-y-1/2,z"], "short_h_m": "Pcmn", "hermann_mauguin_u": "Pcmn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y,-z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x-1/2,y,z", "x,-y-1/2,z-1/2"], "universal_h_m": "P m c n", "number": 62, "schoenflies": "D2h^16", "hall": "-P 2n 2a", "hermann_mauguin": "P m c n", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y,-z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x-1/2,y-1/2,-z-1/2", "-x-1/2,y,z", "x,-y-1/2,z-1/2"], "short_h_m": "Pmcn", "hermann_mauguin_u": "Pmcn", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y,-z-1/2", "-x-1/2,y-1/2,z-1/2", "x-1/2,-y-1/2,z"], "universal_h_m": "P n a m", "number": 62, "schoenflies": "D2h^16", "hall": "-P 2c 2n", "hermann_mauguin": "P n a m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y,-z-1/2", "-x-1/2,y-1/2,z-1/2", "x-1/2,-y-1/2,z"], "short_h_m": "Pnam", "hermann_mauguin_u": "Pnam", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z", "x,-y,z-1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z-1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z-1/2"], "universal_h_m": "C m c m", "number": 63, "schoenflies": "D2h^17", "hall": "-C 2c 2", "hermann_mauguin": "C m c m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z", "x,-y,z-1/2"], "short_h_m": "Cmcm", "hermann_mauguin_u": "Cmcm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z-1/2", "x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z-1/2", "-x+1/2,y+1/2,z-1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "C c m m", "number": 63, "schoenflies": "D2h^17", "hall": "-C 2c 2c", "hermann_mauguin": "C c m m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z-1/2", "x,-y,z"], "short_h_m": "Ccmm", "hermann_mauguin_u": "Ccmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z", "x,-y,z", "x,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,y+1/2,-z+1/2", "-x-1/2,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A m m a", "number": 63, "schoenflies": "D2h^17", "hall": "-A 2a 2a", "hermann_mauguin": "A m m a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z", "x,-y,z"], "short_h_m": "Amma", "hermann_mauguin_u": "Amma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z", "x-1/2,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x-1/2,y+1/2,z+1/2", "x-1/2,-y+1/2,z+1/2"], "universal_h_m": "A m a m", "number": 63, "schoenflies": "D2h^17", "hall": "-A 2 2a", "hermann_mauguin": "A m a m", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z", "x-1/2,-y,z"], "short_h_m": "Amam", "hermann_mauguin_u": "Amam", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z", "x,-y-1/2,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y-1/2,z+1/2", "x+1/2,-y-1/2,z+1/2"], "universal_h_m": "B b m m", "number": 63, "schoenflies": "D2h^17", "hall": "-B 2 2b", "hermann_mauguin": "B b m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z", "x,-y-1/2,z"], "short_h_m": "Bbmm", "hermann_mauguin_u": "Bbmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z", "x,-y-1/2,z", "x+1/2,y,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y-1/2,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y-1/2,z+1/2"], "universal_h_m": "B m m b", "number": 63, "schoenflies": "D2h^17", "hall": "-B 2b 2", "hermann_mauguin": "B m m b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z", "x,-y-1/2,z"], "short_h_m": "Bmmb", "hermann_mauguin_u": "Bmmb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y,z", "x-1/2,-y,z-1/2", "x+1/2,y+1/2,z", "-x+1,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z", "-x+1,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "x,y+1/2,-z-1/2", "-x+1/2,y+1/2,z", "x,-y+1/2,z-1/2"], "universal_h_m": "C m c e", "number": 64, "schoenflies": "D2h^18", "hall": "-C 2ac 2", "hermann_mauguin": "C m c e", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y,-z", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x,y,z", "x-1/2,-y,z-1/2"], "short_h_m": "Cmce", "hermann_mauguin_u": "Cmce", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y,z-1/2", "x,-y,z", "x+1/2,y+1/2,z", "-x+1,-y+1/2,z+1/2", "x+1,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x,y+1/2,-z-1/2", "-x,y+1/2,z-1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "C c m e", "number": 64, "schoenflies": "D2h^18", "hall": "-C 2ac 2ac", "hermann_mauguin": "C c m e", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z-1/2", "-x-1/2,y,z-1/2", "x,-y,z"], "short_h_m": "Ccme", "hermann_mauguin_u": "Ccme", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y-1/2,z", "x,-y,z", "x,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "x+1/2,-y+1,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,y,-z+1/2", "-x-1/2,y,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A e m a", "number": 64, "schoenflies": "D2h^18", "hall": "-A 2ab 2ab", "hermann_mauguin": "A e m a", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x-1/2,y-1/2,z", "x,-y,z"], "short_h_m": "Aema", "hermann_mauguin_u": "Aema", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y-1/2,z", "x-1/2,-y-1/2,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x+1/2,-y+1,-z+1/2", "-x+1/2,y+1,-z+1/2", "-x,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x-1/2,y,z+1/2", "x-1/2,-y,z+1/2"], "universal_h_m": "A e a m", "number": 64, "schoenflies": "D2h^18", "hall": "-A 2 2ab", "hermann_mauguin": "A e a m", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y-1/2,z", "x-1/2,-y-1/2,z"], "short_h_m": "Aeam", "hermann_mauguin_u": "Aeam", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y-1/2,z", "x-1/2,-y-1/2,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1,-y+1/2,-z+1/2", "-x+1,y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2", "-x,y-1/2,z+1/2", "x,-y-1/2,z+1/2"], "universal_h_m": "B b e m", "number": 64, "schoenflies": "D2h^18", "hall": "-B 2 2ab", "hermann_mauguin": "B b e m", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y-1/2,z", "x-1/2,-y-1/2,z"], "short_h_m": "Bbem", "hermann_mauguin_u": "Bbem", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y,z", "x-1/2,-y-1/2,z", "x+1/2,y,z+1/2", "-x+1,-y+1/2,z+1/2", "x+1/2,-y,-z+1/2", "-x+1,y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "x,y-1/2,-z+1/2", "-x+1/2,y,z+1/2", "x,-y-1/2,z+1/2"], "universal_h_m": "B m e b", "number": 64, "schoenflies": "D2h^18", "hall": "-B 2ab 2", "hermann_mauguin": "B m e b", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y,z", "x-1/2,-y-1/2,z"], "short_h_m": "Bmeb", "hermann_mauguin_u": "Bmeb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "C m m m", "number": 65, "schoenflies": "D2h^19", "hall": "-C 2 2", "hermann_mauguin": "C m m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z"], "short_h_m": "Cmmm", "hermann_mauguin_u": "Cmmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A m m m", "number": 65, "schoenflies": "D2h^19", "hall": "-A 2 2", "hermann_mauguin": "A m m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z"], "short_h_m": "Ammm", "hermann_mauguin_u": "Ammm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "B m m m", "number": 65, "schoenflies": "D2h^19", "hall": "-B 2 2", "hermann_mauguin": "B m m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z"], "short_h_m": "Bmmm", "hermann_mauguin_u": "Bmmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y,z-1/2", "x,-y,z-1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z-1/2", "x+1/2,-y+1/2,z-1/2"], "universal_h_m": "C c c m", "number": 66, "schoenflies": "D2h^20", "hall": "-C 2 2c", "hermann_mauguin": "C c c m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y,z-1/2", "x,-y,z-1/2"], "short_h_m": "Cccm", "hermann_mauguin_u": "Cccm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z", "x,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "x-1/2,-y+1/2,z+1/2"], "universal_h_m": "A m a a", "number": 66, "schoenflies": "D2h^20", "hall": "-A 2a 2", "hermann_mauguin": "A m a a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z"], "short_h_m": "Amaa", "hermann_mauguin_u": "Amaa", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z", "x,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y-1/2,-z+1/2", "-x+1/2,y-1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "B b m b", "number": 66, "schoenflies": "D2h^20", "hall": "-B 2b 2b", "hermann_mauguin": "B b m b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z", "x,-y,z"], "short_h_m": "Bbmb", "hermann_mauguin_u": "Bbmb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z", "x+1/2,y+1/2,z", "-x+1,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x,y+1/2,-z", "-x+1/2,y+1/2,z", "x,-y+1/2,z"], "universal_h_m": "C m m a", "number": 67, "schoenflies": "D2h^21", "hall": "-C 2a 2", "hermann_mauguin": "C m m a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z"], "short_h_m": "Cmma", "hermann_mauguin_u": "Cmma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z", "x,-y,z", "x+1/2,y+1/2,z", "-x+1,-y+1/2,z", "x+1,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x,y+1/2,-z", "-x,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "C m m b", "number": 67, "schoenflies": "D2h^21", "hall": "-C 2a 2a", "hermann_mauguin": "C m m b", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z", "x,-y,z"], "short_h_m": "Cmmb", "hermann_mauguin_u": "Cmmb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z", "x,-y,z", "x,y+1/2,z+1/2", "-x,-y+1,z+1/2", "x,-y+1,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,y,-z+1/2", "-x,y,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A b m m", "number": 67, "schoenflies": "D2h^21", "hall": "-A 2b 2b", "hermann_mauguin": "A b m m", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z", "x,-y,z"], "short_h_m": "Abmm", "hermann_mauguin_u": "Abmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z", "x,-y-1/2,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x,-y+1,-z+1/2", "-x,y+1,-z+1/2", "-x,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "x,-y,z+1/2"], "universal_h_m": "A c m m", "number": 67, "schoenflies": "D2h^21", "hall": "-A 2 2b", "hermann_mauguin": "A c m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z", "x,-y-1/2,z"], "short_h_m": "Acmm", "hermann_mauguin_u": "Acmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z", "x-1/2,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1,-y,-z+1/2", "-x+1,y,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2", "-x,y,z+1/2", "x,-y,z+1/2"], "universal_h_m": "B m c m", "number": 67, "schoenflies": "D2h^21", "hall": "-B 2 2a", "hermann_mauguin": "B m c m", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z", "x-1/2,-y,z"], "short_h_m": "Bmcm", "hermann_mauguin_u": "Bmcm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z", "x+1/2,y,z+1/2", "-x+1,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1,y,-z+1/2", "-x+1/2,-y,-z+1/2", "x,y,-z+1/2", "-x+1/2,y,z+1/2", "x,-y,z+1/2"], "universal_h_m": "B m a m", "number": 67, "schoenflies": "D2h^21", "hall": "-B 2a 2", "hermann_mauguin": "B m a m", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z"], "short_h_m": "Bmam", "hermann_mauguin_u": "Bmam", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x+1,-y+1/2,-z+1/2", "x+1,y+1/2,-z+1/2", "-x+1,y+1/2,z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "C c c e :1", "number": 68, "schoenflies": "D2h^22", "hall": " C 2 2 -1ac", "hermann_mauguin": "C c c e", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "short_h_m": "Ccce", "hermann_mauguin_u": "Ccce", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z-1/2", "x,-y,z-1/2", "x+1/2,y+1/2,z", "-x+1,-y+1/2,z", "x+1,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "x,y+1/2,-z", "-x,y+1/2,z-1/2", "x+1/2,-y+1/2,z-1/2"], "universal_h_m": "C c c a :2", "number": 68, "schoenflies": "D2h^22", "hall": "-C 2a 2ac", "hermann_mauguin": "C c c a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z-1/2", "x,-y,z-1/2"], "short_h_m": "Ccca", "hermann_mauguin_u": "Ccca", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z-1/2", "x-1/2,-y,z-1/2", "x+1/2,y+1/2,z", "-x+1,-y+1/2,z", "x+1/2,-y+1/2,-z+1/2", "-x+1,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z", "x,y+1/2,-z", "-x+1/2,y+1/2,z-1/2", "x,-y+1/2,z-1/2"], "universal_h_m": "C c c b :2", "number": 68, "schoenflies": "D2h^22", "hall": "-C 2a 2c", "hermann_mauguin": "C c c b", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z-1/2", "x-1/2,-y,z-1/2"], "short_h_m": "Cccb", "hermann_mauguin_u": "Cccb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x+1/2,-y+1,-z+1/2", "x+1/2,y+1,-z+1/2", "-x+1/2,y+1,z+1/2", "x+1/2,-y+1,z+1/2"], "universal_h_m": "A e a a :1", "number": 68, "schoenflies": "D2h^22", "hall": " A 2 2 -1ab", "hermann_mauguin": "A e a a", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "short_h_m": "Aeaa", "hermann_mauguin_u": "Aeaa", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y-1/2,z", "x-1/2,-y-1/2,z", "x,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x,-y+1,-z+1/2", "-x+1/2,y+1,-z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,y+1/2,-z+1/2", "-x,y,z+1/2", "x-1/2,-y,z+1/2"], "universal_h_m": "A b a a :2", "number": 68, "schoenflies": "D2h^22", "hall": "-A 2a 2b", "hermann_mauguin": "A b a a", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y-1/2,z", "x-1/2,-y-1/2,z"], "short_h_m": "Abaa", "hermann_mauguin_u": "Abaa", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z", "x-1/2,-y,z", "x,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "x,-y+1,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x-1/2,y,-z+1/2", "-x,y,z+1/2", "x-1/2,-y+1/2,z+1/2"], "universal_h_m": "A c a a :2", "number": 68, "schoenflies": "D2h^22", "hall": "-A 2ab 2b", "hermann_mauguin": "A c a a", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z", "x-1/2,-y,z"], "short_h_m": "Acaa", "hermann_mauguin_u": "Acaa", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x+1,-y+1/2,-z+1/2", "x+1,y+1/2,-z+1/2", "-x+1,y+1/2,z+1/2", "x+1,-y+1/2,z+1/2"], "universal_h_m": "B b e b :1", "number": 68, "schoenflies": "D2h^22", "hall": " B 2 2 -1ab", "hermann_mauguin": "B b e b", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "short_h_m": "Bbeb", "hermann_mauguin_u": "Bbeb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z", "x-1/2,-y,z", "x+1/2,y,z+1/2", "-x+1,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1,y,-z+1/2", "-x+1/2,-y,-z+1/2", "x,y-1/2,-z+1/2", "-x+1/2,y-1/2,z+1/2", "x,-y,z+1/2"], "universal_h_m": "B b c b :2", "number": 68, "schoenflies": "D2h^22", "hall": "-B 2ab 2b", "hermann_mauguin": "B b c b", "ncsym": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y-1/2,-z", "-x,y-1/2,z", "x-1/2,-y,z"], "short_h_m": "Bbcb", "hermann_mauguin_u": "Bbcb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y-1/2,z", "x-1/2,-y,z", "x+1/2,y,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1,-y+1/2,-z+1/2", "-x+1,y,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y-1/2,-z+1/2", "-x,y-1/2,z+1/2", "x,-y,z+1/2"], "universal_h_m": "B b a b :2", "number": 68, "schoenflies": "D2h^22", "hall": "-B 2b 2ab", "hermann_mauguin": "B b a b", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x-1/2,y-1/2,z", "x-1/2,-y,z"], "short_h_m": "Bbab", "hermann_mauguin_u": "Bbab", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "F m m m", "number": 69, "schoenflies": "D2h^23", "hall": "-F 2 2", "hermann_mauguin": "F m m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z"], "short_h_m": "Fmmm", "hermann_mauguin_u": "Fmmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/4,-y+1/4,-z+1/4", "x+1/4,y+1/4,-z+1/4", "-x+1/4,y+1/4,z+1/4", "x+1/4,-y+1/4,z+1/4", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x+1/4,-y+3/4,-z+3/4", "x+1/4,y+3/4,-z+3/4", "-x+1/4,y+3/4,z+3/4", "x+1/4,-y+3/4,z+3/4", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "x+1/2,-y,-z+1/2", "-x+1/2,y,-z+1/2", "-x+3/4,-y+1/4,-z+3/4", "x+3/4,y+1/4,-z+3/4", "-x+3/4,y+1/4,z+3/4", "x+3/4,-y+1/4,z+3/4", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x+3/4,-y+3/4,-z+1/4", "x+3/4,y+3/4,-z+1/4", "-x+3/4,y+3/4,z+1/4", "x+3/4,-y+3/4,z+1/4"], "universal_h_m": "F d d d :1", "number": 70, "schoenflies": "D2h^24", "hall": " F 2 2 -1d", "hermann_mauguin": "F d d d", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/4,-y+1/4,-z+1/4", "x+1/4,y+1/4,-z+1/4", "-x+1/4,y+1/4,z+1/4", "x+1/4,-y+1/4,z+1/4"], "short_h_m": "Fddd", "hermann_mauguin_u": "Fddd", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/4,-y+1/4,z", "x,-y+1/4,-z+1/4", "-x+1/4,y,-z+1/4", "-x,-y,-z", "x-1/4,y-1/4,-z", "-x,y-1/4,z-1/4", "x-1/4,-y,z-1/4", "x,y+1/2,z+1/2", "-x+1/4,-y+3/4,z+1/2", "x,-y+3/4,-z+3/4", "-x+1/4,y+1/2,-z+3/4", "-x,-y+1/2,-z+1/2", "x-1/4,y+1/4,-z+1/2", "-x,y+1/4,z+1/4", "x-1/4,-y+1/2,z+1/4", "x+1/2,y,z+1/2", "-x+3/4,-y+1/4,z+1/2", "x+1/2,-y+1/4,-z+3/4", "-x+3/4,y,-z+3/4", "-x+1/2,-y,-z+1/2", "x+1/4,y-1/4,-z+1/2", "-x+1/2,y-1/4,z+1/4", "x+1/4,-y,z+1/4", "x+1/2,y+1/2,z", "-x+3/4,-y+3/4,z", "x+1/2,-y+3/4,-z+1/4", "-x+3/4,y+1/2,-z+1/4", "-x+1/2,-y+1/2,-z", "x+1/4,y+1/4,-z", "-x+1/2,y+1/4,z-1/4", "x+1/4,-y+1/2,z-1/4"], "universal_h_m": "F d d d :2", "number": 70, "schoenflies": "D2h^24", "hall": "-F 2uv 2vw", "hermann_mauguin": "F d d d", "ncsym": ["x,y,z", "-x+1/4,-y+1/4,z", "x,-y+1/4,-z+1/4", "-x+1/4,y,-z+1/4", "-x,-y,-z", "x-1/4,y-1/4,-z", "-x,y-1/4,z-1/4", "x-1/4,-y,z-1/4"], "short_h_m": "Fddd", "hermann_mauguin_u": "Fddd", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I m m m", "number": 71, "schoenflies": "D2h^25", "hall": "-I 2 2", "hermann_mauguin": "I m m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x,-y,-z", "x,y,-z", "-x,y,z", "x,-y,z"], "short_h_m": "Immm", "hermann_mauguin_u": "Immm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y,z-1/2", "x,-y,z-1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1", "-x+1/2,y+1/2,-z+1", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "I b a m", "number": 72, "schoenflies": "D2h^26", "hall": "-I 2 2c", "hermann_mauguin": "I b a m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z", "-x,y,z-1/2", "x,-y,z-1/2"], "short_h_m": "Ibam", "hermann_mauguin_u": "Ibam", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1,-y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "I m c b", "number": 72, "schoenflies": "D2h^26", "hall": "-I 2a 2", "hermann_mauguin": "I m c b", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y,z", "x-1/2,-y,z"], "short_h_m": "Imcb", "hermann_mauguin_u": "Imcb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "x+1/2,-y+1,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I c m a", "number": 72, "schoenflies": "D2h^26", "hall": "-I 2b 2b", "hermann_mauguin": "I c m a", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y+1/2,-z", "-x,y,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y-1/2,z", "x,-y,z"], "short_h_m": "Icma", "hermann_mauguin_u": "Icma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z-1/2", "x,-y-1/2,z-1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "x+1/2,-y+1/2,-z+1", "-x+1/2,y+1,-z+1", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "I b c a", "number": 73, "schoenflies": "D2h^27", "hall": "-I 2b 2c", "hermann_mauguin": "I b c a", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z-1/2", "x,-y-1/2,z-1/2"], "short_h_m": "Ibca", "hermann_mauguin_u": "Ibca", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y-1/2,z", "x-1/2,-y-1/2,z", "x+1/2,y+1/2,z+1/2", "-x+1,-y+1/2,z+1/2", "x+1/2,-y+1,-z+1/2", "-x+1,y+1,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "x,-y,z+1/2"], "universal_h_m": "I c a b", "number": 73, "schoenflies": "D2h^27", "hall": "-I 2a 2b", "hermann_mauguin": "I c a b", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,-z", "-x+1/2,y+1/2,-z", "-x,-y,-z", "x-1/2,y,-z", "-x,y-1/2,z", "x-1/2,-y-1/2,z"], "short_h_m": "Icab", "hermann_mauguin_u": "Icab", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z", "x,-y-1/2,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "I m m a", "number": 74, "schoenflies": "D2h^28", "hall": "-I 2b 2", "hermann_mauguin": "I m m a", "ncsym": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y-1/2,-z", "-x,y,z", "x,-y-1/2,z"], "short_h_m": "Imma", "hermann_mauguin_u": "Imma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1,-y+1/2,z+1/2", "x+1,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I m m b", "number": 74, "schoenflies": "D2h^28", "hall": "-I 2a 2a", "hermann_mauguin": "I m m b", "ncsym": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,-z", "-x,y,-z", "-x,-y,-z", "x-1/2,y,-z", "-x-1/2,y,z", "x,-y,z"], "short_h_m": "Immb", "hermann_mauguin_u": "Immb", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z-1/2", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1", "x+1/2,-y+1/2,-z+1", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I b m m", "number": 74, "schoenflies": "D2h^28", "hall": "-I 2c 2c", "hermann_mauguin": "I b m m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z+1/2", "-x,y,-z", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z-1/2", "x,-y,z"], "short_h_m": "Ibmm", "hermann_mauguin_u": "Ibmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z", "x,-y-1/2,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1/2,-y+1,-z+1/2", "-x+1/2,y+1,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "I c m m", "number": 74, "schoenflies": "D2h^28", "hall": "-I 2 2b", "hermann_mauguin": "I c m m", "ncsym": ["x,y,z", "-x,-y,z", "x,-y+1/2,-z", "-x,y+1/2,-z", "-x,-y,-z", "x,y,-z", "-x,y-1/2,z", "x,-y-1/2,z"], "short_h_m": "Icmm", "hermann_mauguin_u": "Icmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z", "x-1/2,-y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "x+1,-y+1/2,-z+1/2", "-x+1,y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "I m c m", "number": 74, "schoenflies": "D2h^28", "hall": "-I 2 2a", "hermann_mauguin": "I m c m", "ncsym": ["x,y,z", "-x,-y,z", "x+1/2,-y,-z", "-x+1/2,y,-z", "-x,-y,-z", "x,y,-z", "-x-1/2,y,z", "x-1/2,-y,z"], "short_h_m": "Imcm", "hermann_mauguin_u": "Imcm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z", "x,-y,z-1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1", "x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "I m a m", "number": 74, "schoenflies": "D2h^28", "hall": "-I 2c 2", "hermann_mauguin": "I m a m", "ncsym": ["x,y,z", "-x,-y,z+1/2", "x,-y,-z", "-x,y,-z+1/2", "-x,-y,-z", "x,y,-z-1/2", "-x,y,z", "x,-y,z-1/2"], "short_h_m": "Imam", "hermann_mauguin_u": "Imam", "point_group": "mmm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z"], "universal_h_m": "P 4", "number": 75, "schoenflies": "C4^1", "hall": " P 4", "hermann_mauguin": "P 4", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z"], "short_h_m": "P4", "hermann_mauguin_u": "P4", "point_group": "4"}, {"symops": ["x,y,z", "-y,x,z+1/4", "-x,-y,z+1/2", "y,-x,z+3/4"], "universal_h_m": "P 41", "number": 76, "schoenflies": "C4^2", "hall": " P 4w", "hermann_mauguin": "P 41", "ncsym": ["x,y,z", "-y,x,z+1/4", "-x,-y,z+1/2", "y,-x,z+3/4"], "short_h_m": "P4_1", "hermann_mauguin_u": "P4_1", "point_group": "4"}, {"symops": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2"], "universal_h_m": "P 42", "number": 77, "schoenflies": "C4^3", "hall": " P 4c", "hermann_mauguin": "P 42", "ncsym": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2"], "short_h_m": "P4_2", "hermann_mauguin_u": "P4_2", "point_group": "4"}, {"symops": ["x,y,z", "-y,x,z+3/4", "-x,-y,z+1/2", "y,-x,z+1/4"], "universal_h_m": "P 43", "number": 78, "schoenflies": "C4^4", "hall": " P 4cw", "hermann_mauguin": "P 43", "ncsym": ["x,y,z", "-y,x,z+3/4", "-x,-y,z+1/2", "y,-x,z+1/4"], "short_h_m": "P4_3", "hermann_mauguin_u": "P4_3", "point_group": "4"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x+1/2,z+1/2"], "universal_h_m": "I 4", "number": 79, "schoenflies": "C4^5", "hall": " I 4", "hermann_mauguin": "I 4", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z"], "short_h_m": "I4", "hermann_mauguin_u": "I4", "point_group": "4"}, {"symops": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1,z+3/4", "-x+1,-y+1,z+1", "y+1,-x+1/2,z+5/4"], "universal_h_m": "I 41", "number": 80, "schoenflies": "C4^6", "hall": " I 4bw", "hermann_mauguin": "I 41", "ncsym": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4"], "short_h_m": "I4_1", "hermann_mauguin_u": "I4_1", "point_group": "4"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z"], "universal_h_m": "P -4", "number": 81, "schoenflies": "S4^1", "hall": " P -4", "hermann_mauguin": "P -4", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z"], "short_h_m": "P-4", "hermann_mauguin_u": "P-4", "point_group": "-4"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x+1/2,y+1/2,z+1/2", "y+1/2,-x+1/2,-z+1/2", "-x+1/2,-y+1/2,z+1/2", "-y+1/2,x+1/2,-z+1/2"], "universal_h_m": "I -4", "number": 82, "schoenflies": "S4^2", "hall": " I -4", "hermann_mauguin": "I -4", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z"], "short_h_m": "I-4", "hermann_mauguin_u": "I-4", "point_group": "-4"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z"], "universal_h_m": "P 4/m", "number": 83, "schoenflies": "C4h^1", "hall": "-P 4", "hermann_mauguin": "P 4/m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z"], "short_h_m": "P4/m", "hermann_mauguin_u": "P4/m", "point_group": "4/m"}, {"symops": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "-x,-y,-z", "y,-x,-z-1/2", "x,y,-z", "-y,x,-z-1/2"], "universal_h_m": "P 42/m", "number": 84, "schoenflies": "C4h^2", "hall": "-P 4c", "hermann_mauguin": "P 42/m", "ncsym": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "-x,-y,-z", "y,-x,-z-1/2", "x,y,-z", "-y,x,-z-1/2"], "short_h_m": "P4_2/m", "hermann_mauguin_u": "P4_2/m", "point_group": "4/m"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z", "-x,-y,z", "y+1/2,-x+1/2,z", "-x+1/2,-y+1/2,-z", "y,-x,-z", "x+1/2,y+1/2,-z", "-y,x,-z"], "universal_h_m": "P 4/n :1", "number": 85, "schoenflies": "C4h^3", "hall": " P 4ab -1ab", "hermann_mauguin": "P 4/n", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z", "-x,-y,z", "y+1/2,-x+1/2,z", "-x+1/2,-y+1/2,-z", "y,-x,-z", "x+1/2,y+1/2,-z", "-y,x,-z"], "short_h_m": "P4/n", "hermann_mauguin_u": "P4/n", "point_group": "4/m"}, {"symops": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z"], "universal_h_m": "P 4/n :2", "number": 85, "schoenflies": "C4h^3", "hall": "-P 4a", "hermann_mauguin": "P 4/n", "ncsym": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z"], "short_h_m": "P4/n", "hermann_mauguin_u": "P4/n", "point_group": "4/m"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "y,-x,-z", "x+1/2,y+1/2,-z+1/2", "-y,x,-z"], "universal_h_m": "P 42/n :1", "number": 86, "schoenflies": "C4h^4", "hall": " P 4n -1n", "hermann_mauguin": "P 42/n", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "y,-x,-z", "x+1/2,y+1/2,-z+1/2", "-y,x,-z"], "short_h_m": "P4_2/n", "hermann_mauguin_u": "P4_2/n", "point_group": "4/m"}, {"symops": ["x,y,z", "-y,x+1/2,z+1/2", "-x+1/2,-y+1/2,z", "y+1/2,-x,z+1/2", "-x,-y,-z", "y,-x-1/2,-z-1/2", "x-1/2,y-1/2,-z", "-y-1/2,x,-z-1/2"], "universal_h_m": "P 42/n :2", "number": 86, "schoenflies": "C4h^4", "hall": "-P 4bc", "hermann_mauguin": "P 42/n", "ncsym": ["x,y,z", "-y,x+1/2,z+1/2", "-x+1/2,-y+1/2,z", "y+1/2,-x,z+1/2", "-x,-y,-z", "y,-x-1/2,-z-1/2", "x-1/2,y-1/2,-z", "-y-1/2,x,-z-1/2"], "short_h_m": "P4_2/n", "hermann_mauguin_u": "P4_2/n", "point_group": "4/m"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x+1/2,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "y+1/2,-x+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-y+1/2,x+1/2,-z+1/2"], "universal_h_m": "I 4/m", "number": 87, "schoenflies": "C4h^5", "hall": "-I 4", "hermann_mauguin": "I 4/m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z"], "short_h_m": "I4/m", "hermann_mauguin_u": "I4/m", "point_group": "4/m"}, {"symops": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "-x,-y+1/2,-z+1/4", "y,-x,-z", "x-1/2,y,-z-1/4", "-y-1/2,x+1/2,-z-1/2", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1,z+3/4", "-x+1,-y+1,z+1", "y+1,-x+1/2,z+5/4", "-x+1/2,-y+1,-z+3/4", "y+1/2,-x+1/2,-z+1/2", "x,y+1/2,-z+1/4", "-y,x+1,-z"], "universal_h_m": "I 41/a :1", "number": 88, "schoenflies": "C4h^6", "hall": " I 4bw -1bw", "hermann_mauguin": "I 41/a", "ncsym": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "-x,-y+1/2,-z+1/4", "y,-x,-z", "x-1/2,y,-z-1/4", "-y-1/2,x+1/2,-z-1/2"], "short_h_m": "I4_1/a", "hermann_mauguin_u": "I4_1/a", "point_group": "4/m"}, {"symops": ["x,y,z", "-y+3/4,x+1/4,z+1/4", "-x+1/2,-y,z+1/2", "y+3/4,-x+3/4,z+3/4", "-x,-y,-z", "y-3/4,-x-1/4,-z-1/4", "x-1/2,y,-z-1/2", "-y-3/4,x-3/4,-z-3/4", "x+1/2,y+1/2,z+1/2", "-y+5/4,x+3/4,z+3/4", "-x+1,-y+1/2,z+1", "y+5/4,-x+5/4,z+5/4", "-x+1/2,-y+1/2,-z+1/2", "y-1/4,-x+1/4,-z+1/4", "x,y+1/2,-z", "-y-1/4,x-1/4,-z-1/4"], "universal_h_m": "I 41/a :2", "number": 88, "schoenflies": "C4h^6", "hall": "-I 4ad", "hermann_mauguin": "I 41/a", "ncsym": ["x,y,z", "-y+3/4,x+1/4,z+1/4", "-x+1/2,-y,z+1/2", "y+3/4,-x+3/4,z+3/4", "-x,-y,-z", "y-3/4,-x-1/4,-z-1/4", "x-1/2,y,-z-1/2", "-y-3/4,x-3/4,-z-3/4"], "short_h_m": "I4_1/a", "hermann_mauguin_u": "I4_1/a", "point_group": "4/m"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z"], "universal_h_m": "P 4 2 2", "number": 89, "schoenflies": "D4^1", "hall": " P 4 2", "hermann_mauguin": "P 4 2 2", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z"], "short_h_m": "P422", "hermann_mauguin_u": "P422", "point_group": "422"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z", "-x,-y,z", "y+1/2,-x+1/2,z", "x+1/2,-y+1/2,-z", "y,x,-z", "-x+1/2,y+1/2,-z", "-y,-x,-z"], "universal_h_m": "P 4 21 2", "number": 90, "schoenflies": "D4^2", "hall": " P 4ab 2ab", "hermann_mauguin": "P 4 21 2", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z", "-x,-y,z", "y+1/2,-x+1/2,z", "x+1/2,-y+1/2,-z", "y,x,-z", "-x+1/2,y+1/2,-z", "-y,-x,-z"], "short_h_m": "P42_12", "hermann_mauguin_u": "P42_12", "point_group": "422"}, {"symops": ["x,y,z", "-y,x,z+1/4", "-x,-y,z+1/2", "y,-x,z+3/4", "x,-y,-z+1/2", "y,x,-z+3/4", "-x,y,-z", "-y,-x,-z+1/4"], "universal_h_m": "P 41 2 2", "number": 91, "schoenflies": "D4^3", "hall": " P 4w 2c", "hermann_mauguin": "P 41 2 2", "ncsym": ["x,y,z", "-y,x,z+1/4", "-x,-y,z+1/2", "y,-x,z+3/4", "x,-y,-z+1/2", "y,x,-z+3/4", "-x,y,-z", "-y,-x,-z+1/4"], "short_h_m": "P4_122", "hermann_mauguin_u": "P4_122", "point_group": "422"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z+1/4", "-x,-y,z+1/2", "y+1/2,-x+1/2,z+3/4", "x+1/2,-y+1/2,-z+3/4", "y,x,-z", "-x+1/2,y+1/2,-z+1/4", "-y,-x,-z+1/2"], "universal_h_m": "P 41 21 2", "number": 92, "schoenflies": "D4^4", "hall": " P 4abw 2nw", "hermann_mauguin": "P 41 21 2", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z+1/4", "-x,-y,z+1/2", "y+1/2,-x+1/2,z+3/4", "x+1/2,-y+1/2,-z+3/4", "y,x,-z", "-x+1/2,y+1/2,-z+1/4", "-y,-x,-z+1/2"], "short_h_m": "P4_12_12", "hermann_mauguin_u": "P4_12_12", "point_group": "422"}, {"symops": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "x,-y,-z", "y,x,-z+1/2", "-x,y,-z", "-y,-x,-z+1/2"], "universal_h_m": "P 42 2 2", "number": 93, "schoenflies": "D4^5", "hall": " P 4c 2", "hermann_mauguin": "P 42 2 2", "ncsym": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "x,-y,-z", "y,x,-z+1/2", "-x,y,-z", "-y,-x,-z+1/2"], "short_h_m": "P4_222", "hermann_mauguin_u": "P4_222", "point_group": "422"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "y,x,-z", "-x+1/2,y+1/2,-z+1/2", "-y,-x,-z"], "universal_h_m": "P 42 21 2", "number": 94, "schoenflies": "D4^6", "hall": " P 4n 2n", "hermann_mauguin": "P 42 21 2", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "y,x,-z", "-x+1/2,y+1/2,-z+1/2", "-y,-x,-z"], "short_h_m": "P4_22_12", "hermann_mauguin_u": "P4_22_12", "point_group": "422"}, {"symops": ["x,y,z", "-y,x,z+3/4", "-x,-y,z+1/2", "y,-x,z+1/4", "x,-y,-z+1/2", "y,x,-z+1/4", "-x,y,-z", "-y,-x,-z+3/4"], "universal_h_m": "P 43 2 2", "number": 95, "schoenflies": "D4^7", "hall": " P 4cw 2c", "hermann_mauguin": "P 43 2 2", "ncsym": ["x,y,z", "-y,x,z+3/4", "-x,-y,z+1/2", "y,-x,z+1/4", "x,-y,-z+1/2", "y,x,-z+1/4", "-x,y,-z", "-y,-x,-z+3/4"], "short_h_m": "P4_322", "hermann_mauguin_u": "P4_322", "point_group": "422"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z+3/4", "-x,-y,z+1/2", "y+1/2,-x+1/2,z+1/4", "x+1/2,-y+1/2,-z+1/4", "y,x,-z", "-x+1/2,y+1/2,-z+3/4", "-y,-x,-z+1/2"], "universal_h_m": "P 43 21 2", "number": 96, "schoenflies": "D4^8", "hall": " P 4nw 2abw", "hermann_mauguin": "P 43 21 2", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z+3/4", "-x,-y,z+1/2", "y+1/2,-x+1/2,z+1/4", "x+1/2,-y+1/2,-z+1/4", "y,x,-z", "-x+1/2,y+1/2,-z+3/4", "-y,-x,-z+1/2"], "short_h_m": "P4_32_12", "hermann_mauguin_u": "P4_32_12", "point_group": "422"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "y+1/2,x+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-y+1/2,-x+1/2,-z+1/2"], "universal_h_m": "I 4 2 2", "number": 97, "schoenflies": "D4^9", "hall": " I 4 2", "hermann_mauguin": "I 4 2 2", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z"], "short_h_m": "I422", "hermann_mauguin_u": "I422", "point_group": "422"}, {"symops": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "x,-y+1/2,-z+1/4", "y+1/2,x+1/2,-z+1/2", "-x+1/2,y,-z+3/4", "-y,-x,-z", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1,z+3/4", "-x+1,-y+1,z+1", "y+1,-x+1/2,z+5/4", "x+1/2,-y+1,-z+3/4", "y+1,x+1,-z+1", "-x+1,y+1/2,-z+5/4", "-y+1/2,-x+1/2,-z+1/2"], "universal_h_m": "I 41 2 2", "number": 98, "schoenflies": "D4^10", "hall": " I 4bw 2bw", "hermann_mauguin": "I 41 2 2", "ncsym": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "x,-y+1/2,-z+1/4", "y+1/2,x+1/2,-z+1/2", "-x+1/2,y,-z+3/4", "-y,-x,-z"], "short_h_m": "I4_122", "hermann_mauguin_u": "I4_122", "point_group": "422"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,y,z", "-y,-x,z", "x,-y,z", "y,x,z"], "universal_h_m": "P 4 m m", "number": 99, "schoenflies": "C4v^1", "hall": " P 4 -2", "hermann_mauguin": "P 4 m m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,y,z", "-y,-x,z", "x,-y,z", "y,x,z"], "short_h_m": "P4mm", "hermann_mauguin_u": "P4mm", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z"], "universal_h_m": "P 4 b m", "number": 100, "schoenflies": "C4v^2", "hall": " P 4 -2ab", "hermann_mauguin": "P 4 b m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z"], "short_h_m": "P4bm", "hermann_mauguin_u": "P4bm", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "-x,y,z+1/2", "-y,-x,z", "x,-y,z+1/2", "y,x,z"], "universal_h_m": "P 42 c m", "number": 101, "schoenflies": "C4v^3", "hall": " P 4c -2c", "hermann_mauguin": "P 42 c m", "ncsym": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "-x,y,z+1/2", "-y,-x,z", "x,-y,z+1/2", "y,x,z"], "short_h_m": "P4_2cm", "hermann_mauguin_u": "P4_2cm", "point_group": "4mm"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "-y,-x,z", "x+1/2,-y+1/2,z+1/2", "y,x,z"], "universal_h_m": "P 42 n m", "number": 102, "schoenflies": "C4v^4", "hall": " P 4n -2n", "hermann_mauguin": "P 42 n m", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "-y,-x,z", "x+1/2,-y+1/2,z+1/2", "y,x,z"], "short_h_m": "P4_2nm", "hermann_mauguin_u": "P4_2nm", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,y,z+1/2", "-y,-x,z+1/2", "x,-y,z+1/2", "y,x,z+1/2"], "universal_h_m": "P 4 c c", "number": 103, "schoenflies": "C4v^5", "hall": " P 4 -2c", "hermann_mauguin": "P 4 c c", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,y,z+1/2", "-y,-x,z+1/2", "x,-y,z+1/2", "y,x,z+1/2"], "short_h_m": "P4cc", "hermann_mauguin_u": "P4cc", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "y+1/2,x+1/2,z+1/2"], "universal_h_m": "P 4 n c", "number": 104, "schoenflies": "C4v^6", "hall": " P 4 -2n", "hermann_mauguin": "P 4 n c", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "y+1/2,x+1/2,z+1/2"], "short_h_m": "P4nc", "hermann_mauguin_u": "P4nc", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "-x,y,z", "-y,-x,z+1/2", "x,-y,z", "y,x,z+1/2"], "universal_h_m": "P 42 m c", "number": 105, "schoenflies": "C4v^7", "hall": " P 4c -2", "hermann_mauguin": "P 42 m c", "ncsym": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "-x,y,z", "-y,-x,z+1/2", "x,-y,z", "y,x,z+1/2"], "short_h_m": "P4_2mc", "hermann_mauguin_u": "P4_2mc", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z+1/2"], "universal_h_m": "P 42 b c", "number": 106, "schoenflies": "C4v^8", "hall": " P 4c -2ab", "hermann_mauguin": "P 42 b c", "ncsym": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z+1/2"], "short_h_m": "P4_2bc", "hermann_mauguin_u": "P4_2bc", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,y,z", "-y,-x,z", "x,-y,z", "y,x,z", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "y+1/2,x+1/2,z+1/2"], "universal_h_m": "I 4 m m", "number": 107, "schoenflies": "C4v^9", "hall": " I 4 -2", "hermann_mauguin": "I 4 m m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,y,z", "-y,-x,z", "x,-y,z", "y,x,z"], "short_h_m": "I4mm", "hermann_mauguin_u": "I4mm", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,y,z+1/2", "-y,-x,z+1/2", "x,-y,z+1/2", "y,x,z+1/2", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x+1/2,z+1/2", "-x+1/2,y+1/2,z+1", "-y+1/2,-x+1/2,z+1", "x+1/2,-y+1/2,z+1", "y+1/2,x+1/2,z+1"], "universal_h_m": "I 4 c m", "number": 108, "schoenflies": "C4v^10", "hall": " I 4 -2c", "hermann_mauguin": "I 4 c m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x,y,z+1/2", "-y,-x,z+1/2", "x,-y,z+1/2", "y,x,z+1/2"], "short_h_m": "I4cm", "hermann_mauguin_u": "I4cm", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "-x,y,z", "-y,-x+1/2,z+1/4", "x+1/2,-y+1/2,z+1/2", "y+1/2,x,z+3/4", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1,z+3/4", "-x+1,-y+1,z+1", "y+1,-x+1/2,z+5/4", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1,z+3/4", "x+1,-y+1,z+1", "y+1,x+1/2,z+5/4"], "universal_h_m": "I 41 m d", "number": 109, "schoenflies": "C4v^11", "hall": " I 4bw -2", "hermann_mauguin": "I 41 m d", "ncsym": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "-x,y,z", "-y,-x+1/2,z+1/4", "x+1/2,-y+1/2,z+1/2", "y+1/2,x,z+3/4"], "short_h_m": "I4_1md", "hermann_mauguin_u": "I4_1md", "point_group": "4mm"}, {"symops": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "-x,y,z+1/2", "-y,-x+1/2,z+3/4", "x+1/2,-y+1/2,z", "y+1/2,x,z+1/4", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1,z+3/4", "-x+1,-y+1,z+1", "y+1,-x+1/2,z+5/4", "-x+1/2,y+1/2,z+1", "-y+1/2,-x+1,z+5/4", "x+1,-y+1,z+1/2", "y+1,x+1/2,z+3/4"], "universal_h_m": "I 41 c d", "number": 110, "schoenflies": "C4v^12", "hall": " I 4bw -2c", "hermann_mauguin": "I 41 c d", "ncsym": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "-x,y,z+1/2", "-y,-x+1/2,z+3/4", "x+1/2,-y+1/2,z", "y+1/2,x,z+1/4"], "short_h_m": "I4_1cd", "hermann_mauguin_u": "I4_1cd", "point_group": "4mm"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x,-y,-z", "-y,-x,z", "-x,y,-z", "y,x,z"], "universal_h_m": "P -4 2 m", "number": 111, "schoenflies": "D2d^1", "hall": " P -4 2", "hermann_mauguin": "P -4 2 m", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x,-y,-z", "-y,-x,z", "-x,y,-z", "y,x,z"], "short_h_m": "P-42m", "hermann_mauguin_u": "P-42m", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x,-y,-z+1/2", "-y,-x,z+1/2", "-x,y,-z+1/2", "y,x,z+1/2"], "universal_h_m": "P -4 2 c", "number": 112, "schoenflies": "D2d^2", "hall": " P -4 2c", "hermann_mauguin": "P -4 2 c", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x,-y,-z+1/2", "-y,-x,z+1/2", "-x,y,-z+1/2", "y,x,z+1/2"], "short_h_m": "P-42c", "hermann_mauguin_u": "P-42c", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x+1/2,-y+1/2,-z", "-y+1/2,-x+1/2,z", "-x+1/2,y+1/2,-z", "y+1/2,x+1/2,z"], "universal_h_m": "P -4 21 m", "number": 113, "schoenflies": "D2d^3", "hall": " P -4 2ab", "hermann_mauguin": "P -4 21 m", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x+1/2,-y+1/2,-z", "-y+1/2,-x+1/2,z", "-x+1/2,y+1/2,-z", "y+1/2,x+1/2,z"], "short_h_m": "P-42_1m", "hermann_mauguin_u": "P-42_1m", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x+1/2,-y+1/2,-z+1/2", "-y+1/2,-x+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2", "y+1/2,x+1/2,z+1/2"], "universal_h_m": "P -4 21 c", "number": 114, "schoenflies": "D2d^4", "hall": " P -4 2n", "hermann_mauguin": "P -4 21 c", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x+1/2,-y+1/2,-z+1/2", "-y+1/2,-x+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2", "y+1/2,x+1/2,z+1/2"], "short_h_m": "P-42_1c", "hermann_mauguin_u": "P-42_1c", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x,y,z", "y,x,-z", "x,-y,z", "-y,-x,-z"], "universal_h_m": "P -4 m 2", "number": 115, "schoenflies": "D2d^5", "hall": " P -4 -2", "hermann_mauguin": "P -4 m 2", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x,y,z", "y,x,-z", "x,-y,z", "-y,-x,-z"], "short_h_m": "P-4m2", "hermann_mauguin_u": "P-4m2", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x,y,z+1/2", "y,x,-z+1/2", "x,-y,z+1/2", "-y,-x,-z+1/2"], "universal_h_m": "P -4 c 2", "number": 116, "schoenflies": "D2d^6", "hall": " P -4 -2c", "hermann_mauguin": "P -4 c 2", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x,y,z+1/2", "y,x,-z+1/2", "x,-y,z+1/2", "-y,-x,-z+1/2"], "short_h_m": "P-4c2", "hermann_mauguin_u": "P-4c2", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x+1/2,y+1/2,z", "y+1/2,x+1/2,-z", "x+1/2,-y+1/2,z", "-y+1/2,-x+1/2,-z"], "universal_h_m": "P -4 b 2", "number": 117, "schoenflies": "D2d^7", "hall": " P -4 -2ab", "hermann_mauguin": "P -4 b 2", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x+1/2,y+1/2,z", "y+1/2,x+1/2,-z", "x+1/2,-y+1/2,z", "-y+1/2,-x+1/2,-z"], "short_h_m": "P-4b2", "hermann_mauguin_u": "P-4b2", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x+1/2,y+1/2,z+1/2", "y+1/2,x+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2", "-y+1/2,-x+1/2,-z+1/2"], "universal_h_m": "P -4 n 2", "number": 118, "schoenflies": "D2d^8", "hall": " P -4 -2n", "hermann_mauguin": "P -4 n 2", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x+1/2,y+1/2,z+1/2", "y+1/2,x+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2", "-y+1/2,-x+1/2,-z+1/2"], "short_h_m": "P-4n2", "hermann_mauguin_u": "P-4n2", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x,y,z", "y,x,-z", "x,-y,z", "-y,-x,-z", "x+1/2,y+1/2,z+1/2", "y+1/2,-x+1/2,-z+1/2", "-x+1/2,-y+1/2,z+1/2", "-y+1/2,x+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "y+1/2,x+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2", "-y+1/2,-x+1/2,-z+1/2"], "universal_h_m": "I -4 m 2", "number": 119, "schoenflies": "D2d^9", "hall": " I -4 -2", "hermann_mauguin": "I -4 m 2", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x,y,z", "y,x,-z", "x,-y,z", "-y,-x,-z"], "short_h_m": "I-4m2", "hermann_mauguin_u": "I-4m2", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x,y,z+1/2", "y,x,-z+1/2", "x,-y,z+1/2", "-y,-x,-z+1/2", "x+1/2,y+1/2,z+1/2", "y+1/2,-x+1/2,-z+1/2", "-x+1/2,-y+1/2,z+1/2", "-y+1/2,x+1/2,-z+1/2", "-x+1/2,y+1/2,z+1", "y+1/2,x+1/2,-z+1", "x+1/2,-y+1/2,z+1", "-y+1/2,-x+1/2,-z+1"], "universal_h_m": "I -4 c 2", "number": 120, "schoenflies": "D2d^10", "hall": " I -4 -2c", "hermann_mauguin": "I -4 c 2", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "-x,y,z+1/2", "y,x,-z+1/2", "x,-y,z+1/2", "-y,-x,-z+1/2"], "short_h_m": "I-4c2", "hermann_mauguin_u": "I-4c2", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x,-y,-z", "-y,-x,z", "-x,y,-z", "y,x,z", "x+1/2,y+1/2,z+1/2", "y+1/2,-x+1/2,-z+1/2", "-x+1/2,-y+1/2,z+1/2", "-y+1/2,x+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2", "-y+1/2,-x+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2", "y+1/2,x+1/2,z+1/2"], "universal_h_m": "I -4 2 m", "number": 121, "schoenflies": "D2d^11", "hall": " I -4 2", "hermann_mauguin": "I -4 2 m", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x,-y,-z", "-y,-x,z", "-x,y,-z", "y,x,z"], "short_h_m": "I-42m", "hermann_mauguin_u": "I-42m", "point_group": "-42m"}, {"symops": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x,-y+1/2,-z+1/4", "-y+1/2,-x,z+3/4", "-x,y+1/2,-z+1/4", "y+1/2,x,z+3/4", "x+1/2,y+1/2,z+1/2", "y+1/2,-x+1/2,-z+1/2", "-x+1/2,-y+1/2,z+1/2", "-y+1/2,x+1/2,-z+1/2", "x+1/2,-y+1,-z+3/4", "-y+1,-x+1/2,z+5/4", "-x+1/2,y+1,-z+3/4", "y+1,x+1/2,z+5/4"], "universal_h_m": "I -4 2 d", "number": 122, "schoenflies": "D2d^12", "hall": " I -4 2bw", "hermann_mauguin": "I -4 2 d", "ncsym": ["x,y,z", "y,-x,-z", "-x,-y,z", "-y,x,-z", "x,-y+1/2,-z+1/4", "-y+1/2,-x,z+3/4", "-x,y+1/2,-z+1/4", "y+1/2,x,z+3/4"], "short_h_m": "I-42d", "hermann_mauguin_u": "I-42d", "point_group": "-42m"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "-x,y,z", "-y,-x,z", "x,-y,z", "y,x,z"], "universal_h_m": "P 4/m m m", "number": 123, "schoenflies": "D4h^1", "hall": "-P 4 2", "hermann_mauguin": "P 4/m m m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "-x,y,z", "-y,-x,z", "x,-y,z", "y,x,z"], "short_h_m": "P4/mmm", "hermann_mauguin_u": "P4/mmm", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z+1/2", "y,x,-z+1/2", "-x,y,-z+1/2", "-y,-x,-z+1/2", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "-x,y,z-1/2", "-y,-x,z-1/2", "x,-y,z-1/2", "y,x,z-1/2"], "universal_h_m": "P 4/m c c", "number": 124, "schoenflies": "D4h^2", "hall": "-P 4 2c", "hermann_mauguin": "P 4/m c c", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z+1/2", "y,x,-z+1/2", "-x,y,-z+1/2", "-y,-x,-z+1/2", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "-x,y,z-1/2", "-y,-x,z-1/2", "x,-y,z-1/2", "y,x,z-1/2"], "short_h_m": "P4/mcc", "hermann_mauguin_u": "P4/mcc", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z", "-x+1/2,-y+1/2,-z", "y+1/2,-x+1/2,-z", "x+1/2,y+1/2,-z", "-y+1/2,x+1/2,-z", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z"], "universal_h_m": "P 4/n b m :1", "number": 125, "schoenflies": "D4h^3", "hall": " P 4 2 -1ab", "hermann_mauguin": "P 4/n b m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z", "-x+1/2,-y+1/2,-z", "y+1/2,-x+1/2,-z", "x+1/2,y+1/2,-z", "-y+1/2,x+1/2,-z", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z"], "short_h_m": "P4/nbm", "hermann_mauguin_u": "P4/nbm", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "x,-y+1/2,-z", "y,x,-z", "-x+1/2,y,-z", "-y+1/2,-x+1/2,-z", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z", "-x,y-1/2,z", "-y,-x,z", "x-1/2,-y,z", "y-1/2,x-1/2,z"], "universal_h_m": "P 4/n b m :2", "number": 125, "schoenflies": "D4h^3", "hall": "-P 4a 2b", "hermann_mauguin": "P 4/n b m", "ncsym": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "x,-y+1/2,-z", "y,x,-z", "-x+1/2,y,-z", "-y+1/2,-x+1/2,-z", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z", "-x,y-1/2,z", "-y,-x,z", "x-1/2,-y,z", "y-1/2,x-1/2,z"], "short_h_m": "P4/nbm", "hermann_mauguin_u": "P4/nbm", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z", "-x+1/2,-y+1/2,-z+1/2", "y+1/2,-x+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-y+1/2,x+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "y+1/2,x+1/2,z+1/2"], "universal_h_m": "P 4/n n c :1", "number": 126, "schoenflies": "D4h^4", "hall": " P 4 2 -1n", "hermann_mauguin": "P 4/n n c", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z", "y,x,-z", "-x,y,-z", "-y,-x,-z", "-x+1/2,-y+1/2,-z+1/2", "y+1/2,-x+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-y+1/2,x+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "y+1/2,x+1/2,z+1/2"], "short_h_m": "P4/nnc", "hermann_mauguin_u": "P4/nnc", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "x,-y+1/2,-z+1/2", "y,x,-z+1/2", "-x+1/2,y,-z+1/2", "-y+1/2,-x+1/2,-z+1/2", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z", "-x,y-1/2,z-1/2", "-y,-x,z-1/2", "x-1/2,-y,z-1/2", "y-1/2,x-1/2,z-1/2"], "universal_h_m": "P 4/n n c :2", "number": 126, "schoenflies": "D4h^4", "hall": "-P 4a 2bc", "hermann_mauguin": "P 4/n n c", "ncsym": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "x,-y+1/2,-z+1/2", "y,x,-z+1/2", "-x+1/2,y,-z+1/2", "-y+1/2,-x+1/2,-z+1/2", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z", "-x,y-1/2,z-1/2", "-y,-x,z-1/2", "x-1/2,-y,z-1/2", "y-1/2,x-1/2,z-1/2"], "short_h_m": "P4/nnc", "hermann_mauguin_u": "P4/nnc", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x+1/2,-y+1/2,-z", "y+1/2,x+1/2,-z", "-x+1/2,y+1/2,-z", "-y+1/2,-x+1/2,-z", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "-x-1/2,y-1/2,z", "-y-1/2,-x-1/2,z", "x-1/2,-y-1/2,z", "y-1/2,x-1/2,z"], "universal_h_m": "P 4/m b m", "number": 127, "schoenflies": "D4h^5", "hall": "-P 4 2ab", "hermann_mauguin": "P 4/m b m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x+1/2,-y+1/2,-z", "y+1/2,x+1/2,-z", "-x+1/2,y+1/2,-z", "-y+1/2,-x+1/2,-z", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "-x-1/2,y-1/2,z", "-y-1/2,-x-1/2,z", "x-1/2,-y-1/2,z", "y-1/2,x-1/2,z"], "short_h_m": "P4/mbm", "hermann_mauguin_u": "P4/mbm", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x+1/2,-y+1/2,-z+1/2", "y+1/2,x+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-y+1/2,-x+1/2,-z+1/2", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "-x-1/2,y-1/2,z-1/2", "-y-1/2,-x-1/2,z-1/2", "x-1/2,-y-1/2,z-1/2", "y-1/2,x-1/2,z-1/2"], "universal_h_m": "P 4/m n c", "number": 128, "schoenflies": "D4h^6", "hall": "-P 4 2n", "hermann_mauguin": "P 4/m n c", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x+1/2,-y+1/2,-z+1/2", "y+1/2,x+1/2,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-y+1/2,-x+1/2,-z+1/2", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "-x-1/2,y-1/2,z-1/2", "-y-1/2,-x-1/2,z-1/2", "x-1/2,-y-1/2,z-1/2", "y-1/2,x-1/2,z-1/2"], "short_h_m": "P4/mnc", "hermann_mauguin_u": "P4/mnc", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z", "-x,-y,z", "y+1/2,-x+1/2,z", "x+1/2,-y+1/2,-z", "y,x,-z", "-x+1/2,y+1/2,-z", "-y,-x,-z", "-x+1/2,-y+1/2,-z", "y,-x,-z", "x+1/2,y+1/2,-z", "-y,x,-z", "-x,y,z", "-y+1/2,-x+1/2,z", "x,-y,z", "y+1/2,x+1/2,z"], "universal_h_m": "P 4/n m m :1", "number": 129, "schoenflies": "D4h^7", "hall": " P 4ab 2ab -1ab", "hermann_mauguin": "P 4/n m m", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z", "-x,-y,z", "y+1/2,-x+1/2,z", "x+1/2,-y+1/2,-z", "y,x,-z", "-x+1/2,y+1/2,-z", "-y,-x,-z", "-x+1/2,-y+1/2,-z", "y,-x,-z", "x+1/2,y+1/2,-z", "-y,x,-z", "-x,y,z", "-y+1/2,-x+1/2,z", "x,-y,z", "y+1/2,x+1/2,z"], "short_h_m": "P4/nmm", "hermann_mauguin_u": "P4/nmm", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "x+1/2,-y,-z", "y+1/2,x+1/2,-z", "-x,y+1/2,-z", "-y,-x,-z", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z", "-x-1/2,y,z", "-y-1/2,-x-1/2,z", "x,-y-1/2,z", "y,x,z"], "universal_h_m": "P 4/n m m :2", "number": 129, "schoenflies": "D4h^7", "hall": "-P 4a 2a", "hermann_mauguin": "P 4/n m m", "ncsym": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "x+1/2,-y,-z", "y+1/2,x+1/2,-z", "-x,y+1/2,-z", "-y,-x,-z", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z", "-x-1/2,y,z", "-y-1/2,-x-1/2,z", "x,-y-1/2,z", "y,x,z"], "short_h_m": "P4/nmm", "hermann_mauguin_u": "P4/nmm", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z", "-x,-y,z", "y+1/2,-x+1/2,z", "x+1/2,-y+1/2,-z+1/2", "y,x,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-y,-x,-z+1/2", "-x+1/2,-y+1/2,-z", "y,-x,-z", "x+1/2,y+1/2,-z", "-y,x,-z", "-x,y,z-1/2", "-y+1/2,-x+1/2,z-1/2", "x,-y,z-1/2", "y+1/2,x+1/2,z-1/2"], "universal_h_m": "P 4/n c c :1", "number": 130, "schoenflies": "D4h^8", "hall": " P 4ab 2n -1ab", "hermann_mauguin": "P 4/n c c", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z", "-x,-y,z", "y+1/2,-x+1/2,z", "x+1/2,-y+1/2,-z+1/2", "y,x,-z+1/2", "-x+1/2,y+1/2,-z+1/2", "-y,-x,-z+1/2", "-x+1/2,-y+1/2,-z", "y,-x,-z", "x+1/2,y+1/2,-z", "-y,x,-z", "-x,y,z-1/2", "-y+1/2,-x+1/2,z-1/2", "x,-y,z-1/2", "y+1/2,x+1/2,z-1/2"], "short_h_m": "P4/ncc", "hermann_mauguin_u": "P4/ncc", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "x+1/2,-y,-z+1/2", "y+1/2,x+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-y,-x,-z+1/2", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z", "-x-1/2,y,z-1/2", "-y-1/2,-x-1/2,z-1/2", "x,-y-1/2,z-1/2", "y,x,z-1/2"], "universal_h_m": "P 4/n c c :2", "number": 130, "schoenflies": "D4h^8", "hall": "-P 4a 2ac", "hermann_mauguin": "P 4/n c c", "ncsym": ["x,y,z", "-y+1/2,x,z", "-x+1/2,-y+1/2,z", "y,-x+1/2,z", "x+1/2,-y,-z+1/2", "y+1/2,x+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-y,-x,-z+1/2", "-x,-y,-z", "y-1/2,-x,-z", "x-1/2,y-1/2,-z", "-y,x-1/2,-z", "-x-1/2,y,z-1/2", "-y-1/2,-x-1/2,z-1/2", "x,-y-1/2,z-1/2", "y,x,z-1/2"], "short_h_m": "P4/ncc", "hermann_mauguin_u": "P4/ncc", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "x,-y,-z", "y,x,-z+1/2", "-x,y,-z", "-y,-x,-z+1/2", "-x,-y,-z", "y,-x,-z-1/2", "x,y,-z", "-y,x,-z-1/2", "-x,y,z", "-y,-x,z-1/2", "x,-y,z", "y,x,z-1/2"], "universal_h_m": "P 42/m m c", "number": 131, "schoenflies": "D4h^9", "hall": "-P 4c 2", "hermann_mauguin": "P 42/m m c", "ncsym": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "x,-y,-z", "y,x,-z+1/2", "-x,y,-z", "-y,-x,-z+1/2", "-x,-y,-z", "y,-x,-z-1/2", "x,y,-z", "-y,x,-z-1/2", "-x,y,z", "-y,-x,z-1/2", "x,-y,z", "y,x,z-1/2"], "short_h_m": "P4_2/mmc", "hermann_mauguin_u": "P4_2/mmc", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "x,-y,-z+1/2", "y,x,-z", "-x,y,-z+1/2", "-y,-x,-z", "-x,-y,-z", "y,-x,-z-1/2", "x,y,-z", "-y,x,-z-1/2", "-x,y,z-1/2", "-y,-x,z", "x,-y,z-1/2", "y,x,z"], "universal_h_m": "P 42/m c m", "number": 132, "schoenflies": "D4h^10", "hall": "-P 4c 2c", "hermann_mauguin": "P 42/m c m", "ncsym": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "x,-y,-z+1/2", "y,x,-z", "-x,y,-z+1/2", "-y,-x,-z", "-x,-y,-z", "y,-x,-z-1/2", "x,y,-z", "-y,x,-z-1/2", "-x,y,z-1/2", "-y,-x,z", "x,-y,z-1/2", "y,x,z"], "short_h_m": "P4_2/mcm", "hermann_mauguin_u": "P4_2/mcm", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "x,-y,-z+1/2", "y+1/2,x+1/2,-z", "-x,y,-z+1/2", "-y+1/2,-x+1/2,-z", 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"x+1/2,-y+1/2,-z", "y+1/2,x+1/2,-z+1/2", "-x+1/2,y+1/2,-z", "-y+1/2,-x+1/2,-z+1/2", "-x,-y,-z", "y,-x,-z-1/2", "x,y,-z", "-y,x,-z-1/2", "-x-1/2,y-1/2,z", "-y-1/2,-x-1/2,z-1/2", "x-1/2,-y-1/2,z", "y-1/2,x-1/2,z-1/2"], "universal_h_m": "P 42/m b c", "number": 135, "schoenflies": "D4h^13", "hall": "-P 4c 2ab", "hermann_mauguin": "P 42/m b c", "ncsym": ["x,y,z", "-y,x,z+1/2", "-x,-y,z", "y,-x,z+1/2", "x+1/2,-y+1/2,-z", "y+1/2,x+1/2,-z+1/2", "-x+1/2,y+1/2,-z", "-y+1/2,-x+1/2,-z+1/2", "-x,-y,-z", "y,-x,-z-1/2", "x,y,-z", "-y,x,-z-1/2", "-x-1/2,y-1/2,z", "-y-1/2,-x-1/2,z-1/2", "x-1/2,-y-1/2,z", "y-1/2,x-1/2,z-1/2"], "short_h_m": "P4_2/mbc", "hermann_mauguin_u": "P4_2/mbc", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "y,x,-z", "-x+1/2,y+1/2,-z+1/2", "-y,-x,-z", "-x,-y,-z", "y-1/2,-x-1/2,-z-1/2", "x,y,-z", "-y-1/2,x-1/2,-z-1/2", "-x-1/2,y-1/2,z-1/2", "-y,-x,z", "x-1/2,-y-1/2,z-1/2", "y,x,z"], "universal_h_m": "P 42/m n m", "number": 136, "schoenflies": "D4h^14", "hall": "-P 4n 2n", "hermann_mauguin": "P 42/m n m", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "y,x,-z", "-x+1/2,y+1/2,-z+1/2", "-y,-x,-z", "-x,-y,-z", "y-1/2,-x-1/2,-z-1/2", "x,y,-z", "-y-1/2,x-1/2,-z-1/2", "-x-1/2,y-1/2,z-1/2", "-y,-x,z", "x-1/2,-y-1/2,z-1/2", "y,x,z"], "short_h_m": "P4_2/mnm", "hermann_mauguin_u": "P4_2/mnm", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "y,x,-z", "-x+1/2,y+1/2,-z+1/2", "-y,-x,-z", "-x+1/2,-y+1/2,-z+1/2", "y,-x,-z", "x+1/2,y+1/2,-z+1/2", "-y,x,-z", "-x,y,z", "-y+1/2,-x+1/2,z+1/2", "x,-y,z", "y+1/2,x+1/2,z+1/2"], "universal_h_m": "P 42/n m c :1", "number": 137, "schoenflies": "D4h^15", "hall": " P 4n 2n -1n", "hermann_mauguin": "P 42/n m c", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "y,x,-z", "-x+1/2,y+1/2,-z+1/2", 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"y+1/2,x+1/2,z"], "universal_h_m": "I 4/m c m", "number": 140, "schoenflies": "D4h^18", "hall": "-I 4 2c", "hermann_mauguin": "I 4/m c m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "x,-y,-z+1/2", "y,x,-z+1/2", "-x,y,-z+1/2", "-y,-x,-z+1/2", "-x,-y,-z", "y,-x,-z", "x,y,-z", "-y,x,-z", "-x,y,z-1/2", "-y,-x,z-1/2", "x,-y,z-1/2", "y,x,z-1/2"], "short_h_m": "I4/mcm", "hermann_mauguin_u": "I4/mcm", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "x,-y+1/2,-z+1/4", "y+1/2,x+1/2,-z+1/2", "-x+1/2,y,-z+3/4", "-y,-x,-z", "-x,-y+1/2,-z+1/4", "y,-x,-z", "x-1/2,y,-z-1/4", "-y-1/2,x+1/2,-z-1/2", "-x,y,z", "-y-1/2,-x,z-1/4", "x-1/2,-y+1/2,z-1/2", "y,x+1/2,z+1/4", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1,z+3/4", "-x+1,-y+1,z+1", "y+1,-x+1/2,z+5/4", "x+1/2,-y+1,-z+3/4", "y+1,x+1,-z+1", "-x+1,y+1/2,-z+5/4", "-y+1/2,-x+1/2,-z+1/2", "-x+1/2,-y+1,-z+3/4", "y+1/2,-x+1/2,-z+1/2", "x,y+1/2,-z+1/4", "-y,x+1,-z", "-x+1/2,y+1/2,z+1/2", "-y,-x+1/2,z+1/4", "x,-y+1,z", "y+1/2,x+1,z+3/4"], "universal_h_m": "I 41/a m d :1", "number": 141, "schoenflies": "D4h^19", "hall": " I 4bw 2bw -1bw", "hermann_mauguin": "I 41/a m d", "ncsym": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "x,-y+1/2,-z+1/4", "y+1/2,x+1/2,-z+1/2", "-x+1/2,y,-z+3/4", "-y,-x,-z", "-x,-y+1/2,-z+1/4", "y,-x,-z", "x-1/2,y,-z-1/4", "-y-1/2,x+1/2,-z-1/2", "-x,y,z", "-y-1/2,-x,z-1/4", "x-1/2,-y+1/2,z-1/2", "y,x+1/2,z+1/4"], "short_h_m": "I4_1/amd", "hermann_mauguin_u": "I4_1/amd", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/4,x+3/4,z+1/4", "-x+1/2,-y,z+1/2", "y+1/4,-x+1/4,z+3/4", "x,-y,-z", "y+1/4,x+3/4,-z+1/4", "-x+1/2,y,-z+1/2", "-y+1/4,-x+1/4,-z+3/4", "-x,-y,-z", "y-1/4,-x-3/4,-z-1/4", "x-1/2,y,-z-1/2", "-y-1/4,x-1/4,-z-3/4", "-x,y,z", "-y-1/4,-x-3/4,z-1/4", "x-1/2,-y,z-1/2", "y-1/4,x-1/4,z-3/4", "x+1/2,y+1/2,z+1/2", "-y+3/4,x+5/4,z+3/4", "-x+1,-y+1/2,z+1", "y+3/4,-x+3/4,z+5/4", "x+1/2,-y+1/2,-z+1/2", "y+3/4,x+5/4,-z+3/4", "-x+1,y+1/2,-z+1", "-y+3/4,-x+3/4,-z+5/4", "-x+1/2,-y+1/2,-z+1/2", "y+1/4,-x-1/4,-z+1/4", "x,y+1/2,-z", "-y+1/4,x+1/4,-z-1/4", "-x+1/2,y+1/2,z+1/2", "-y+1/4,-x-1/4,z+1/4", "x,-y+1/2,z", "y+1/4,x+1/4,z-1/4"], "universal_h_m": "I 41/a m d :2", "number": 141, "schoenflies": "D4h^19", "hall": "-I 4bd 2", "hermann_mauguin": "I 41/a m d", "ncsym": ["x,y,z", "-y+1/4,x+3/4,z+1/4", "-x+1/2,-y,z+1/2", "y+1/4,-x+1/4,z+3/4", "x,-y,-z", "y+1/4,x+3/4,-z+1/4", "-x+1/2,y,-z+1/2", "-y+1/4,-x+1/4,-z+3/4", "-x,-y,-z", "y-1/4,-x-3/4,-z-1/4", "x-1/2,y,-z-1/2", "-y-1/4,x-1/4,-z-3/4", "-x,y,z", "-y-1/4,-x-3/4,z-1/4", "x-1/2,-y,z-1/2", "y-1/4,x-1/4,z-3/4"], "short_h_m": "I4_1/amd", "hermann_mauguin_u": "I4_1/amd", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "x+1/2,-y,-z+1/4", "y,x,-z+1/2", "-x,y+1/2,-z+3/4", "-y+1/2,-x+1/2,-z", "-x,-y+1/2,-z+1/4", "y,-x,-z", "x-1/2,y,-z-1/4", "-y-1/2,x+1/2,-z-1/2", "-x-1/2,y+1/2,z", "-y,-x+1/2,z-1/4", "x,-y,z-1/2", "y-1/2,x,z+1/4", "x+1/2,y+1/2,z+1/2", "-y+1/2,x+1,z+3/4", "-x+1,-y+1,z+1", "y+1,-x+1/2,z+5/4", "x+1,-y+1/2,-z+3/4", "y+1/2,x+1/2,-z+1", "-x+1/2,y+1,-z+5/4", "-y+1,-x+1,-z+1/2", "-x+1/2,-y+1,-z+3/4", "y+1/2,-x+1/2,-z+1/2", "x,y+1/2,-z+1/4", "-y,x+1,-z", "-x,y+1,z+1/2", "-y+1/2,-x+1,z+1/4", "x+1/2,-y+1/2,z", "y,x+1/2,z+3/4"], "universal_h_m": "I 41/a c d :1", "number": 142, "schoenflies": "D4h^20", "hall": " I 4bw 2aw -1bw", "hermann_mauguin": "I 41/a c d", "ncsym": ["x,y,z", "-y,x+1/2,z+1/4", "-x+1/2,-y+1/2,z+1/2", "y+1/2,-x,z+3/4", "x+1/2,-y,-z+1/4", "y,x,-z+1/2", "-x,y+1/2,-z+3/4", "-y+1/2,-x+1/2,-z", "-x,-y+1/2,-z+1/4", "y,-x,-z", "x-1/2,y,-z-1/4", "-y-1/2,x+1/2,-z-1/2", "-x-1/2,y+1/2,z", "-y,-x+1/2,z-1/4", "x,-y,z-1/2", "y-1/2,x,z+1/4"], "short_h_m": "I4_1/acd", "hermann_mauguin_u": "I4_1/acd", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y+1/4,x+3/4,z+1/4", "-x+1/2,-y,z+1/2", "y+1/4,-x+1/4,z+3/4", "x,-y,-z+1/2", "y+1/4,x+3/4,-z+3/4", "-x+1/2,y,-z", "-y+1/4,-x+1/4,-z+1/4", "-x,-y,-z", "y-1/4,-x-3/4,-z-1/4", "x-1/2,y,-z-1/2", "-y-1/4,x-1/4,-z-3/4", "-x,y,z-1/2", "-y-1/4,-x-3/4,z-3/4", "x-1/2,-y,z", "y-1/4,x-1/4,z-1/4", "x+1/2,y+1/2,z+1/2", "-y+3/4,x+5/4,z+3/4", "-x+1,-y+1/2,z+1", "y+3/4,-x+3/4,z+5/4", "x+1/2,-y+1/2,-z+1", "y+3/4,x+5/4,-z+5/4", "-x+1,y+1/2,-z+1/2", "-y+3/4,-x+3/4,-z+3/4", "-x+1/2,-y+1/2,-z+1/2", "y+1/4,-x-1/4,-z+1/4", "x,y+1/2,-z", "-y+1/4,x+1/4,-z-1/4", "-x+1/2,y+1/2,z", "-y+1/4,-x-1/4,z-1/4", "x,-y+1/2,z+1/2", "y+1/4,x+1/4,z+1/4"], "universal_h_m": "I 41/a c d :2", "number": 142, "schoenflies": "D4h^20", "hall": "-I 4bd 2c", "hermann_mauguin": "I 41/a c d", "ncsym": ["x,y,z", "-y+1/4,x+3/4,z+1/4", "-x+1/2,-y,z+1/2", "y+1/4,-x+1/4,z+3/4", "x,-y,-z+1/2", "y+1/4,x+3/4,-z+3/4", "-x+1/2,y,-z", "-y+1/4,-x+1/4,-z+1/4", "-x,-y,-z", "y-1/4,-x-3/4,-z-1/4", "x-1/2,y,-z-1/2", "-y-1/4,x-1/4,-z-3/4", "-x,y,z-1/2", "-y-1/4,-x-3/4,z-3/4", "x-1/2,-y,z", "y-1/4,x-1/4,z-1/4"], "short_h_m": "I4_1/acd", "hermann_mauguin_u": "I4_1/acd", "point_group": "4/mmm"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z"], "universal_h_m": "P 3", "number": 143, "schoenflies": "C3^1", "hall": " P 3", "hermann_mauguin": "P 3", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z"], "short_h_m": "P3", "hermann_mauguin_u": "P3", "point_group": "3"}, {"symops": ["x,y,z", "-y,x-y,z+1/3", "-x+y,-x,z+2/3"], "universal_h_m": "P 31", "number": 144, "schoenflies": "C3^2", "hall": " P 31", "hermann_mauguin": "P 31", "ncsym": ["x,y,z", "-y,x-y,z+1/3", "-x+y,-x,z+2/3"], "short_h_m": "P3_1", "hermann_mauguin_u": "P3_1", "point_group": "3"}, {"symops": ["x,y,z", "-y,x-y,z+2/3", "-x+y,-x,z+1/3"], "universal_h_m": "P 32", "number": 145, "schoenflies": "C3^3", "hall": " P 32", "hermann_mauguin": "P 32", "ncsym": ["x,y,z", "-y,x-y,z+2/3", "-x+y,-x,z+1/3"], "short_h_m": "P3_2", "hermann_mauguin_u": "P3_2", "point_group": "3"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "x+2/3,y+1/3,z+1/3", "-y+2/3,x-y+1/3,z+1/3", "-x+y+2/3,-x+1/3,z+1/3", "x+1/3,y+2/3,z+2/3", "-y+1/3,x-y+2/3,z+2/3", "-x+y+1/3,-x+2/3,z+2/3"], "universal_h_m": "R 3 :H", "number": 146, "schoenflies": "C3^4", "hall": " R 3", "hermann_mauguin": "R 3", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z"], "short_h_m": "R3", "hermann_mauguin_u": "R3", "point_group": "3"}, {"symops": ["x,y,z", "z,x,y", "y,z,x"], "universal_h_m": "R 3 :R", "number": 146, "schoenflies": "C3^4", "hall": " P 3*", "hermann_mauguin": "R 3", "ncsym": ["x,y,z", "z,x,y", "y,z,x"], "short_h_m": "R3", "hermann_mauguin_u": "R3", "point_group": "3"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z"], "universal_h_m": "P -3", "number": 147, "schoenflies": "C3i^1", "hall": "-P 3", "hermann_mauguin": "P -3", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z"], "short_h_m": "P-3", "hermann_mauguin_u": "P-3", "point_group": "-3"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "x+2/3,y+1/3,z+1/3", "-y+2/3,x-y+1/3,z+1/3", "-x+y+2/3,-x+1/3,z+1/3", "-x+2/3,-y+1/3,-z+1/3", "y+2/3,-x+y+1/3,-z+1/3", "x-y+2/3,x+1/3,-z+1/3", "x+1/3,y+2/3,z+2/3", "-y+1/3,x-y+2/3,z+2/3", "-x+y+1/3,-x+2/3,z+2/3", "-x+1/3,-y+2/3,-z+2/3", "y+1/3,-x+y+2/3,-z+2/3", "x-y+1/3,x+2/3,-z+2/3"], "universal_h_m": "R -3 :H", "number": 148, "schoenflies": "C3i^2", "hall": "-R 3", "hermann_mauguin": "R -3", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z"], "short_h_m": "R-3", "hermann_mauguin_u": "R-3", "point_group": "-3"}, {"symops": ["x,y,z", "z,x,y", "y,z,x", "-x,-y,-z", "-z,-x,-y", "-y,-z,-x"], "universal_h_m": "R -3 :R", "number": 148, "schoenflies": "C3i^2", "hall": "-P 3*", "hermann_mauguin": "R -3", "ncsym": ["x,y,z", "z,x,y", "y,z,x", "-x,-y,-z", "-z,-x,-y", "-y,-z,-x"], "short_h_m": "R-3", "hermann_mauguin_u": "R-3", "point_group": "-3"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,-z", "x,x-y,-z", "-x+y,y,-z"], "universal_h_m": "P 3 1 2", "number": 149, "schoenflies": "D3^1", "hall": " P 3 2", "hermann_mauguin": "P 3 1 2", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,-z", "x,x-y,-z", "-x+y,y,-z"], "short_h_m": "P32", "hermann_mauguin_u": "P312", "point_group": "32"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z", "-x,-x+y,-z", "x-y,-y,-z"], "universal_h_m": "P 3 2 1", "number": 150, "schoenflies": "D3^2", "hall": " P 3 2\"", "hermann_mauguin": "P 3 2 1", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z", "-x,-x+y,-z", "x-y,-y,-z"], "short_h_m": "P32", "hermann_mauguin_u": "P321", "point_group": "32"}, {"symops": ["x,y,z", "-y,x-y,z+1/3", "-x+y,-x,z+2/3", "-y,-x,-z+2/3", "x,x-y,-z", "-x+y,y,-z+1/3"], "universal_h_m": "P 31 1 2", "number": 151, "schoenflies": "D3^3", "hall": " P 31 2 (0 0 4)", "hermann_mauguin": "P 31 1 2", "ncsym": ["x,y,z", "-y,x-y,z+1/3", "-x+y,-x,z+2/3", "-y,-x,-z+2/3", "x,x-y,-z", "-x+y,y,-z+1/3"], "short_h_m": "P3_12", "hermann_mauguin_u": "P3_112", "point_group": "32"}, {"symops": ["x,y,z", "-y,x-y,z+1/3", "-x+y,-x,z+2/3", "y,x,-z", "-x,-x+y,-z+1/3", "x-y,-y,-z+2/3"], "universal_h_m": "P 31 2 1", "number": 152, "schoenflies": "D3^4", "hall": " P 31 2\"", "hermann_mauguin": "P 31 2 1", "ncsym": ["x,y,z", "-y,x-y,z+1/3", "-x+y,-x,z+2/3", "y,x,-z", "-x,-x+y,-z+1/3", "x-y,-y,-z+2/3"], "short_h_m": "P3_12", "hermann_mauguin_u": "P3_121", "point_group": "32"}, {"symops": ["x,y,z", "-y,x-y,z+2/3", "-x+y,-x,z+1/3", "-y,-x,-z+1/3", "x,x-y,-z", "-x+y,y,-z+2/3"], "universal_h_m": "P 32 1 2", "number": 153, "schoenflies": "D3^5", "hall": " P 32 2 (0 0 2)", "hermann_mauguin": "P 32 1 2", "ncsym": ["x,y,z", "-y,x-y,z+2/3", "-x+y,-x,z+1/3", "-y,-x,-z+1/3", "x,x-y,-z", "-x+y,y,-z+2/3"], "short_h_m": "P3_22", "hermann_mauguin_u": "P3_212", "point_group": "32"}, {"symops": ["x,y,z", "-y,x-y,z+2/3", "-x+y,-x,z+1/3", "y,x,-z", "-x,-x+y,-z+2/3", "x-y,-y,-z+1/3"], "universal_h_m": "P 32 2 1", "number": 154, "schoenflies": "D3^6", "hall": " P 32 2\"", "hermann_mauguin": "P 32 2 1", "ncsym": ["x,y,z", "-y,x-y,z+2/3", "-x+y,-x,z+1/3", "y,x,-z", "-x,-x+y,-z+2/3", "x-y,-y,-z+1/3"], "short_h_m": "P3_22", "hermann_mauguin_u": "P3_221", "point_group": "32"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z", "-x,-x+y,-z", "x-y,-y,-z", "x+2/3,y+1/3,z+1/3", "-y+2/3,x-y+1/3,z+1/3", "-x+y+2/3,-x+1/3,z+1/3", "y+2/3,x+1/3,-z+1/3", "-x+2/3,-x+y+1/3,-z+1/3", "x-y+2/3,-y+1/3,-z+1/3", "x+1/3,y+2/3,z+2/3", "-y+1/3,x-y+2/3,z+2/3", "-x+y+1/3,-x+2/3,z+2/3", "y+1/3,x+2/3,-z+2/3", "-x+1/3,-x+y+2/3,-z+2/3", "x-y+1/3,-y+2/3,-z+2/3"], "universal_h_m": "R 3 2 :H", "number": 155, "schoenflies": "D3^7", "hall": " R 3 2\"", "hermann_mauguin": "R 3 2", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z", "-x,-x+y,-z", "x-y,-y,-z"], "short_h_m": "R32", "hermann_mauguin_u": "R32", "point_group": "32"}, {"symops": ["x,y,z", "z,x,y", "y,z,x", "-y,-x,-z", "-z,-y,-x", "-x,-z,-y"], "universal_h_m": "R 3 2 :R", "number": 155, "schoenflies": "D3^7", "hall": " P 3* 2", "hermann_mauguin": "R 3 2", "ncsym": ["x,y,z", "z,x,y", "y,z,x", "-y,-x,-z", "-z,-y,-x", "-x,-z,-y"], "short_h_m": "R32", "hermann_mauguin_u": "R32", "point_group": "32"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,z", "x,x-y,z", "-x+y,y,z"], "universal_h_m": "P 3 m 1", "number": 156, "schoenflies": "C3v^1", "hall": " P 3 -2\"", "hermann_mauguin": "P 3 m 1", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,z", "x,x-y,z", "-x+y,y,z"], "short_h_m": "P3m", "hermann_mauguin_u": "P3m1", "point_group": "3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,z", "-x,-x+y,z", "x-y,-y,z"], "universal_h_m": "P 3 1 m", "number": 157, "schoenflies": "C3v^2", "hall": " P 3 -2", "hermann_mauguin": "P 3 1 m", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,z", "-x,-x+y,z", "x-y,-y,z"], "short_h_m": "P3m", "hermann_mauguin_u": "P31m", "point_group": "3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,z+1/2", "x,x-y,z+1/2", "-x+y,y,z+1/2"], "universal_h_m": "P 3 c 1", "number": 158, "schoenflies": "C3v^3", "hall": " P 3 -2\"c", "hermann_mauguin": "P 3 c 1", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,z+1/2", "x,x-y,z+1/2", "-x+y,y,z+1/2"], "short_h_m": "P3c", "hermann_mauguin_u": "P3c1", "point_group": "3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,z+1/2", "-x,-x+y,z+1/2", "x-y,-y,z+1/2"], "universal_h_m": "P 3 1 c", "number": 159, "schoenflies": "C3v^4", "hall": " P 3 -2c", "hermann_mauguin": "P 3 1 c", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,z+1/2", "-x,-x+y,z+1/2", "x-y,-y,z+1/2"], "short_h_m": "P3c", "hermann_mauguin_u": "P31c", "point_group": "3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,z", "x,x-y,z", "-x+y,y,z", "x+2/3,y+1/3,z+1/3", "-y+2/3,x-y+1/3,z+1/3", "-x+y+2/3,-x+1/3,z+1/3", "-y+2/3,-x+1/3,z+1/3", "x+2/3,x-y+1/3,z+1/3", "-x+y+2/3,y+1/3,z+1/3", "x+1/3,y+2/3,z+2/3", "-y+1/3,x-y+2/3,z+2/3", "-x+y+1/3,-x+2/3,z+2/3", "-y+1/3,-x+2/3,z+2/3", "x+1/3,x-y+2/3,z+2/3", "-x+y+1/3,y+2/3,z+2/3"], "universal_h_m": "R 3 m :H", "number": 160, "schoenflies": "C3v^5", "hall": " R 3 -2\"", "hermann_mauguin": "R 3 m", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,z", "x,x-y,z", "-x+y,y,z"], "short_h_m": "R3m", "hermann_mauguin_u": "R3m", "point_group": "3m"}, {"symops": ["x,y,z", "z,x,y", "y,z,x", "y,x,z", "z,y,x", "x,z,y"], "universal_h_m": "R 3 m :R", "number": 160, "schoenflies": "C3v^5", "hall": " P 3* -2", "hermann_mauguin": "R 3 m", "ncsym": ["x,y,z", "z,x,y", "y,z,x", "y,x,z", "z,y,x", "x,z,y"], "short_h_m": "R3m", "hermann_mauguin_u": "R3m", "point_group": "3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,z+1/2", "x,x-y,z+1/2", "-x+y,y,z+1/2", "x+2/3,y+1/3,z+1/3", "-y+2/3,x-y+1/3,z+1/3", "-x+y+2/3,-x+1/3,z+1/3", "-y+2/3,-x+1/3,z+5/6", "x+2/3,x-y+1/3,z+5/6", "-x+y+2/3,y+1/3,z+5/6", "x+1/3,y+2/3,z+2/3", "-y+1/3,x-y+2/3,z+2/3", "-x+y+1/3,-x+2/3,z+2/3", "-y+1/3,-x+2/3,z+7/6", "x+1/3,x-y+2/3,z+7/6", "-x+y+1/3,y+2/3,z+7/6"], "universal_h_m": "R 3 c :H", "number": 161, "schoenflies": "C3v^6", "hall": " R 3 -2\"c", "hermann_mauguin": "R 3 c", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,z+1/2", "x,x-y,z+1/2", "-x+y,y,z+1/2"], "short_h_m": "R3c", "hermann_mauguin_u": "R3c", "point_group": "3m"}, {"symops": ["x,y,z", "z,x,y", "y,z,x", "y+1/2,x+1/2,z+1/2", "z+1/2,y+1/2,x+1/2", "x+1/2,z+1/2,y+1/2"], "universal_h_m": "R 3 c :R", "number": 161, "schoenflies": "C3v^6", "hall": " P 3* -2n", "hermann_mauguin": "R 3 c", "ncsym": ["x,y,z", "z,x,y", "y,z,x", "y+1/2,x+1/2,z+1/2", "z+1/2,y+1/2,x+1/2", "x+1/2,z+1/2,y+1/2"], "short_h_m": "R3c", "hermann_mauguin_u": "R3c", "point_group": "3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,-z", "x,x-y,-z", "-x+y,y,-z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "y,x,z", "-x,-x+y,z", "x-y,-y,z"], "universal_h_m": "P -3 1 m", "number": 162, "schoenflies": "D3d^1", "hall": "-P 3 2", "hermann_mauguin": "P -3 1 m", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,-z", "x,x-y,-z", "-x+y,y,-z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "y,x,z", "-x,-x+y,z", "x-y,-y,z"], "short_h_m": "P-3m", "hermann_mauguin_u": "P-31m", "point_group": "-3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,-z+1/2", "x,x-y,-z+1/2", "-x+y,y,-z+1/2", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "y,x,z-1/2", "-x,-x+y,z-1/2", "x-y,-y,z-1/2"], "universal_h_m": "P -3 1 c", "number": 163, "schoenflies": "D3d^2", "hall": "-P 3 2c", "hermann_mauguin": "P -3 1 c", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "-y,-x,-z+1/2", "x,x-y,-z+1/2", "-x+y,y,-z+1/2", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "y,x,z-1/2", "-x,-x+y,z-1/2", "x-y,-y,z-1/2"], "short_h_m": "P-3c", "hermann_mauguin_u": "P-31c", "point_group": "-3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z", "-x,-x+y,-z", "x-y,-y,-z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "-y,-x,z", "x,x-y,z", "-x+y,y,z"], "universal_h_m": "P -3 m 1", "number": 164, "schoenflies": "D3d^3", "hall": "-P 3 2\"", "hermann_mauguin": "P -3 m 1", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z", "-x,-x+y,-z", "x-y,-y,-z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "-y,-x,z", "x,x-y,z", "-x+y,y,z"], "short_h_m": "P-3m", "hermann_mauguin_u": "P-3m1", "point_group": "-3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z+1/2", "-x,-x+y,-z+1/2", "x-y,-y,-z+1/2", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "-y,-x,z-1/2", "x,x-y,z-1/2", "-x+y,y,z-1/2"], "universal_h_m": "P -3 c 1", "number": 165, "schoenflies": "D3d^4", "hall": "-P 3 2\"c", "hermann_mauguin": "P -3 c 1", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z+1/2", "-x,-x+y,-z+1/2", "x-y,-y,-z+1/2", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "-y,-x,z-1/2", "x,x-y,z-1/2", "-x+y,y,z-1/2"], "short_h_m": "P-3c", "hermann_mauguin_u": "P-3c1", "point_group": "-3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z", "-x,-x+y,-z", "x-y,-y,-z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "-y,-x,z", "x,x-y,z", "-x+y,y,z", "x+2/3,y+1/3,z+1/3", "-y+2/3,x-y+1/3,z+1/3", "-x+y+2/3,-x+1/3,z+1/3", "y+2/3,x+1/3,-z+1/3", "-x+2/3,-x+y+1/3,-z+1/3", "x-y+2/3,-y+1/3,-z+1/3", "-x+2/3,-y+1/3,-z+1/3", "y+2/3,-x+y+1/3,-z+1/3", "x-y+2/3,x+1/3,-z+1/3", "-y+2/3,-x+1/3,z+1/3", "x+2/3,x-y+1/3,z+1/3", "-x+y+2/3,y+1/3,z+1/3", "x+1/3,y+2/3,z+2/3", "-y+1/3,x-y+2/3,z+2/3", "-x+y+1/3,-x+2/3,z+2/3", "y+1/3,x+2/3,-z+2/3", "-x+1/3,-x+y+2/3,-z+2/3", "x-y+1/3,-y+2/3,-z+2/3", "-x+1/3,-y+2/3,-z+2/3", "y+1/3,-x+y+2/3,-z+2/3", "x-y+1/3,x+2/3,-z+2/3", "-y+1/3,-x+2/3,z+2/3", "x+1/3,x-y+2/3,z+2/3", "-x+y+1/3,y+2/3,z+2/3"], "universal_h_m": "R -3 m :H", "number": 166, "schoenflies": "D3d^5", "hall": "-R 3 2\"", "hermann_mauguin": "R -3 m", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z", "-x,-x+y,-z", "x-y,-y,-z", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "-y,-x,z", "x,x-y,z", "-x+y,y,z"], "short_h_m": "R-3m", "hermann_mauguin_u": "R-3m", "point_group": "-3m"}, {"symops": ["x,y,z", "z,x,y", "y,z,x", "-y,-x,-z", "-z,-y,-x", "-x,-z,-y", "-x,-y,-z", "-z,-x,-y", "-y,-z,-x", "y,x,z", "z,y,x", "x,z,y"], "universal_h_m": "R -3 m :R", "number": 166, "schoenflies": "D3d^5", "hall": "-P 3* 2", "hermann_mauguin": "R -3 m", "ncsym": ["x,y,z", "z,x,y", "y,z,x", "-y,-x,-z", "-z,-y,-x", "-x,-z,-y", "-x,-y,-z", "-z,-x,-y", "-y,-z,-x", "y,x,z", "z,y,x", "x,z,y"], "short_h_m": "R-3m", "hermann_mauguin_u": "R-3m", "point_group": "-3m"}, {"symops": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z+1/2", "-x,-x+y,-z+1/2", "x-y,-y,-z+1/2", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "-y,-x,z-1/2", "x,x-y,z-1/2", "-x+y,y,z-1/2", "x+2/3,y+1/3,z+1/3", "-y+2/3,x-y+1/3,z+1/3", "-x+y+2/3,-x+1/3,z+1/3", "y+2/3,x+1/3,-z+5/6", "-x+2/3,-x+y+1/3,-z+5/6", "x-y+2/3,-y+1/3,-z+5/6", "-x+2/3,-y+1/3,-z+1/3", "y+2/3,-x+y+1/3,-z+1/3", "x-y+2/3,x+1/3,-z+1/3", "-y+2/3,-x+1/3,z-1/6", "x+2/3,x-y+1/3,z-1/6", "-x+y+2/3,y+1/3,z-1/6", "x+1/3,y+2/3,z+2/3", "-y+1/3,x-y+2/3,z+2/3", "-x+y+1/3,-x+2/3,z+2/3", "y+1/3,x+2/3,-z+7/6", "-x+1/3,-x+y+2/3,-z+7/6", "x-y+1/3,-y+2/3,-z+7/6", "-x+1/3,-y+2/3,-z+2/3", "y+1/3,-x+y+2/3,-z+2/3", "x-y+1/3,x+2/3,-z+2/3", "-y+1/3,-x+2/3,z+1/6", "x+1/3,x-y+2/3,z+1/6", "-x+y+1/3,y+2/3,z+1/6"], "universal_h_m": "R -3 c :H", "number": 167, "schoenflies": "D3d^6", "hall": "-R 3 2\"c", "hermann_mauguin": "R -3 c", "ncsym": ["x,y,z", "-y,x-y,z", "-x+y,-x,z", "y,x,-z+1/2", "-x,-x+y,-z+1/2", "x-y,-y,-z+1/2", "-x,-y,-z", "y,-x+y,-z", "x-y,x,-z", "-y,-x,z-1/2", "x,x-y,z-1/2", "-x+y,y,z-1/2"], "short_h_m": "R-3c", "hermann_mauguin_u": "R-3c", "point_group": "-3m"}, {"symops": ["x,y,z", "z,x,y", "y,z,x", "-y+1/2,-x+1/2,-z+1/2", "-z+1/2,-y+1/2,-x+1/2", "-x+1/2,-z+1/2,-y+1/2", "-x,-y,-z", "-z,-x,-y", "-y,-z,-x", "y-1/2,x-1/2,z-1/2", "z-1/2,y-1/2,x-1/2", "x-1/2,z-1/2,y-1/2"], "universal_h_m": "R -3 c :R", "number": 167, "schoenflies": "D3d^6", "hall": "-P 3* 2n", "hermann_mauguin": "R -3 c", "ncsym": ["x,y,z", "z,x,y", "y,z,x", "-y+1/2,-x+1/2,-z+1/2", "-z+1/2,-y+1/2,-x+1/2", "-x+1/2,-z+1/2,-y+1/2", "-x,-y,-z", "-z,-x,-y", "-y,-z,-x", "y-1/2,x-1/2,z-1/2", "z-1/2,y-1/2,x-1/2", "x-1/2,z-1/2,y-1/2"], "short_h_m": "R-3c", "hermann_mauguin_u": "R-3c", "point_group": "-3m"}, {"symops": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z"], "universal_h_m": "P 6", "number": 168, "schoenflies": "C6^1", "hall": " P 6", "hermann_mauguin": "P 6", "ncsym": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z"], "short_h_m": "P6", "hermann_mauguin_u": "P6", "point_group": "6"}, {"symops": ["x,y,z", "x-y,x,z+1/6", "-y,x-y,z+1/3", "-x,-y,z+1/2", "-x+y,-x,z+2/3", "y,-x+y,z+5/6"], "universal_h_m": "P 61", "number": 169, "schoenflies": "C6^2", "hall": " P 61", "hermann_mauguin": "P 61", "ncsym": ["x,y,z", "x-y,x,z+1/6", "-y,x-y,z+1/3", "-x,-y,z+1/2", "-x+y,-x,z+2/3", "y,-x+y,z+5/6"], "short_h_m": "P6_1", "hermann_mauguin_u": "P6_1", "point_group": "6"}, {"symops": ["x,y,z", "x-y,x,z+5/6", "-y,x-y,z+2/3", "-x,-y,z+1/2", "-x+y,-x,z+1/3", "y,-x+y,z+1/6"], "universal_h_m": "P 65", "number": 170, "schoenflies": "C6^3", "hall": " P 65", "hermann_mauguin": "P 65", "ncsym": ["x,y,z", "x-y,x,z+5/6", "-y,x-y,z+2/3", "-x,-y,z+1/2", "-x+y,-x,z+1/3", "y,-x+y,z+1/6"], "short_h_m": "P6_5", "hermann_mauguin_u": "P6_5", "point_group": "6"}, {"symops": ["x,y,z", "x-y,x,z+1/3", "-y,x-y,z+2/3", "-x,-y,z", "-x+y,-x,z+1/3", "y,-x+y,z+2/3"], "universal_h_m": "P 62", "number": 171, "schoenflies": "C6^4", "hall": " P 62", "hermann_mauguin": "P 62", "ncsym": ["x,y,z", "x-y,x,z+1/3", "-y,x-y,z+2/3", "-x,-y,z", "-x+y,-x,z+1/3", "y,-x+y,z+2/3"], "short_h_m": "P6_2", "hermann_mauguin_u": "P6_2", "point_group": "6"}, {"symops": ["x,y,z", "x-y,x,z+2/3", "-y,x-y,z+1/3", "-x,-y,z", "-x+y,-x,z+2/3", "y,-x+y,z+1/3"], "universal_h_m": "P 64", "number": 172, "schoenflies": "C6^5", "hall": " P 64", "hermann_mauguin": "P 64", "ncsym": ["x,y,z", "x-y,x,z+2/3", "-y,x-y,z+1/3", "-x,-y,z", "-x+y,-x,z+2/3", "y,-x+y,z+1/3"], "short_h_m": "P6_4", "hermann_mauguin_u": "P6_4", "point_group": "6"}, {"symops": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2"], "universal_h_m": "P 63", "number": 173, "schoenflies": "C6^6", "hall": " P 6c", "hermann_mauguin": "P 63", "ncsym": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2"], "short_h_m": "P6_3", "hermann_mauguin_u": "P6_3", "point_group": "6"}, {"symops": ["x,y,z", "-x+y,-x,-z", "-y,x-y,z", "x,y,-z", "-x+y,-x,z", "-y,x-y,-z"], "universal_h_m": "P -6", "number": 174, "schoenflies": "C3h^1", "hall": " P -6", "hermann_mauguin": "P -6", "ncsym": ["x,y,z", "-x+y,-x,-z", "-y,x-y,z", "x,y,-z", "-x+y,-x,z", "-y,x-y,-z"], "short_h_m": "P-6", "hermann_mauguin_u": "P-6", "point_group": "-6"}, {"symops": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z", "-x,-y,-z", "-x+y,-x,-z", "y,-x+y,-z", "x,y,-z", "x-y,x,-z", "-y,x-y,-z"], "universal_h_m": "P 6/m", "number": 175, "schoenflies": "C6h^1", "hall": "-P 6", "hermann_mauguin": "P 6/m", "ncsym": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z", "-x,-y,-z", "-x+y,-x,-z", "y,-x+y,-z", "x,y,-z", "x-y,x,-z", "-y,x-y,-z"], "short_h_m": "P6/m", "hermann_mauguin_u": "P6/m", "point_group": "6/m"}, {"symops": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2", "-x,-y,-z", "-x+y,-x,-z-1/2", "y,-x+y,-z", "x,y,-z-1/2", "x-y,x,-z", "-y,x-y,-z-1/2"], "universal_h_m": "P 63/m", "number": 176, "schoenflies": "C6h^2", "hall": "-P 6c", "hermann_mauguin": "P 63/m", "ncsym": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2", "-x,-y,-z", "-x+y,-x,-z-1/2", "y,-x+y,-z", "x,y,-z-1/2", "x-y,x,-z", "-y,x-y,-z-1/2"], "short_h_m": "P6_3/m", "hermann_mauguin_u": "P6_3/m", "point_group": "6/m"}, {"symops": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z", "-y,-x,-z", "x-y,-y,-z", "x,x-y,-z", "y,x,-z", "-x+y,y,-z", "-x,-x+y,-z"], "universal_h_m": "P 6 2 2", "number": 177, "schoenflies": "D6^1", "hall": " P 6 2", "hermann_mauguin": "P 6 2 2", "ncsym": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z", "-y,-x,-z", "x-y,-y,-z", "x,x-y,-z", "y,x,-z", "-x+y,y,-z", "-x,-x+y,-z"], "short_h_m": "P622", "hermann_mauguin_u": "P622", "point_group": "622"}, {"symops": ["x,y,z", "x-y,x,z+1/6", "-y,x-y,z+1/3", "-x,-y,z+1/2", "-x+y,-x,z+2/3", "y,-x+y,z+5/6", "-y,-x,-z+5/6", "x-y,-y,-z", "x,x-y,-z+1/6", "y,x,-z+1/3", "-x+y,y,-z+1/2", "-x,-x+y,-z+2/3"], "universal_h_m": "P 61 2 2", "number": 178, "schoenflies": "D6^2", "hall": " P 61 2 (0 0 5)", "hermann_mauguin": "P 61 2 2", "ncsym": ["x,y,z", "x-y,x,z+1/6", "-y,x-y,z+1/3", "-x,-y,z+1/2", "-x+y,-x,z+2/3", "y,-x+y,z+5/6", "-y,-x,-z+5/6", "x-y,-y,-z", "x,x-y,-z+1/6", "y,x,-z+1/3", "-x+y,y,-z+1/2", "-x,-x+y,-z+2/3"], "short_h_m": "P6_122", "hermann_mauguin_u": "P6_122", "point_group": "622"}, {"symops": ["x,y,z", "x-y,x,z+5/6", "-y,x-y,z+2/3", "-x,-y,z+1/2", "-x+y,-x,z+1/3", "y,-x+y,z+1/6", "-y,-x,-z+1/6", "x-y,-y,-z", "x,x-y,-z+5/6", "y,x,-z+2/3", "-x+y,y,-z+1/2", "-x,-x+y,-z+1/3"], "universal_h_m": "P 65 2 2", "number": 179, "schoenflies": "D6^3", "hall": " P 65 2 (0 0 1)", "hermann_mauguin": "P 65 2 2", "ncsym": ["x,y,z", "x-y,x,z+5/6", "-y,x-y,z+2/3", "-x,-y,z+1/2", "-x+y,-x,z+1/3", "y,-x+y,z+1/6", "-y,-x,-z+1/6", "x-y,-y,-z", "x,x-y,-z+5/6", "y,x,-z+2/3", "-x+y,y,-z+1/2", "-x,-x+y,-z+1/3"], "short_h_m": "P6_522", "hermann_mauguin_u": "P6_522", "point_group": "622"}, {"symops": ["x,y,z", "x-y,x,z+1/3", "-y,x-y,z+2/3", "-x,-y,z", "-x+y,-x,z+1/3", "y,-x+y,z+2/3", "-y,-x,-z+2/3", "x-y,-y,-z", "x,x-y,-z+1/3", "y,x,-z+2/3", "-x+y,y,-z", "-x,-x+y,-z+1/3"], "universal_h_m": "P 62 2 2", "number": 180, "schoenflies": "D6^4", "hall": " P 62 2 (0 0 4)", "hermann_mauguin": "P 62 2 2", "ncsym": ["x,y,z", "x-y,x,z+1/3", "-y,x-y,z+2/3", "-x,-y,z", "-x+y,-x,z+1/3", "y,-x+y,z+2/3", "-y,-x,-z+2/3", "x-y,-y,-z", "x,x-y,-z+1/3", "y,x,-z+2/3", "-x+y,y,-z", "-x,-x+y,-z+1/3"], "short_h_m": "P6_222", "hermann_mauguin_u": "P6_222", "point_group": "622"}, {"symops": ["x,y,z", "x-y,x,z+2/3", "-y,x-y,z+1/3", "-x,-y,z", "-x+y,-x,z+2/3", "y,-x+y,z+1/3", "-y,-x,-z+1/3", "x-y,-y,-z", "x,x-y,-z+2/3", "y,x,-z+1/3", "-x+y,y,-z", "-x,-x+y,-z+2/3"], "universal_h_m": "P 64 2 2", "number": 181, "schoenflies": "D6^5", "hall": " P 64 2 (0 0 2)", "hermann_mauguin": "P 64 2 2", "ncsym": ["x,y,z", "x-y,x,z+2/3", "-y,x-y,z+1/3", "-x,-y,z", "-x+y,-x,z+2/3", "y,-x+y,z+1/3", "-y,-x,-z+1/3", "x-y,-y,-z", "x,x-y,-z+2/3", "y,x,-z+1/3", "-x+y,y,-z", "-x,-x+y,-z+2/3"], "short_h_m": "P6_422", "hermann_mauguin_u": "P6_422", "point_group": "622"}, {"symops": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2", "-y,-x,-z+1/2", "x-y,-y,-z", "x,x-y,-z+1/2", "y,x,-z", "-x+y,y,-z+1/2", "-x,-x+y,-z"], "universal_h_m": "P 63 2 2", "number": 182, "schoenflies": "D6^6", "hall": " P 6c 2c", "hermann_mauguin": "P 63 2 2", "ncsym": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2", "-y,-x,-z+1/2", "x-y,-y,-z", "x,x-y,-z+1/2", "y,x,-z", "-x+y,y,-z+1/2", "-x,-x+y,-z"], "short_h_m": "P6_322", "hermann_mauguin_u": "P6_322", "point_group": "622"}, {"symops": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z", "y,x,z", "-x+y,y,z", "-x,-x+y,z", "-y,-x,z", "x-y,-y,z", "x,x-y,z"], "universal_h_m": "P 6 m m", "number": 183, "schoenflies": "C6v^1", "hall": " P 6 -2", "hermann_mauguin": "P 6 m m", "ncsym": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z", "y,x,z", "-x+y,y,z", "-x,-x+y,z", "-y,-x,z", "x-y,-y,z", "x,x-y,z"], "short_h_m": "P6mm", "hermann_mauguin_u": "P6mm", "point_group": "6mm"}, {"symops": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z", "y,x,z+1/2", "-x+y,y,z+1/2", "-x,-x+y,z+1/2", "-y,-x,z+1/2", "x-y,-y,z+1/2", "x,x-y,z+1/2"], "universal_h_m": "P 6 c c", "number": 184, "schoenflies": "C6v^2", "hall": " P 6 -2c", "hermann_mauguin": "P 6 c c", "ncsym": ["x,y,z", "x-y,x,z", "-y,x-y,z", "-x,-y,z", "-x+y,-x,z", "y,-x+y,z", "y,x,z+1/2", "-x+y,y,z+1/2", "-x,-x+y,z+1/2", "-y,-x,z+1/2", "x-y,-y,z+1/2", "x,x-y,z+1/2"], "short_h_m": "P6cc", "hermann_mauguin_u": "P6cc", "point_group": "6mm"}, {"symops": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2", "y,x,z", "-x+y,y,z+1/2", "-x,-x+y,z", "-y,-x,z+1/2", "x-y,-y,z", "x,x-y,z+1/2"], "universal_h_m": "P 63 c m", "number": 185, "schoenflies": "C6v^3", "hall": " P 6c -2", "hermann_mauguin": "P 63 c m", "ncsym": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2", "y,x,z", "-x+y,y,z+1/2", "-x,-x+y,z", "-y,-x,z+1/2", "x-y,-y,z", "x,x-y,z+1/2"], "short_h_m": "P6_3cm", "hermann_mauguin_u": "P6_3cm", "point_group": "6mm"}, {"symops": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2", "y,x,z+1/2", "-x+y,y,z", "-x,-x+y,z+1/2", "-y,-x,z", "x-y,-y,z+1/2", "x,x-y,z"], "universal_h_m": "P 63 m c", "number": 186, "schoenflies": "C6v^4", "hall": " P 6c -2c", "hermann_mauguin": "P 63 m c", "ncsym": ["x,y,z", "x-y,x,z+1/2", "-y,x-y,z", "-x,-y,z+1/2", "-x+y,-x,z", "y,-x+y,z+1/2", "y,x,z+1/2", "-x+y,y,z", "-x,-x+y,z+1/2", "-y,-x,z", "x-y,-y,z+1/2", "x,x-y,z"], "short_h_m": "P6_3mc", "hermann_mauguin_u": "P6_3mc", "point_group": "6mm"}, {"symops": ["x,y,z", "-x+y,-x,-z", "-y,x-y,z", "x,y,-z", "-x+y,-x,z", "-y,x-y,-z", "-y,-x,-z", "-x+y,y,z", "x,x-y,-z", "-y,-x,z", "-x+y,y,-z", "x,x-y,z"], "universal_h_m": "P -6 m 2", "number": 187, "schoenflies": "D3h^1", "hall": " P -6 2", "hermann_mauguin": "P -6 m 2", "ncsym": ["x,y,z", "-x+y,-x,-z", "-y,x-y,z", "x,y,-z", "-x+y,-x,z", "-y,x-y,-z", "-y,-x,-z", "-x+y,y,z", "x,x-y,-z", "-y,-x,z", "-x+y,y,-z", "x,x-y,z"], "short_h_m": "P-6m2", "hermann_mauguin_u": "P-6m2", "point_group": "-6m2"}, {"symops": ["x,y,z", "-x+y,-x,-z+1/2", "-y,x-y,z", "x,y,-z+1/2", "-x+y,-x,z", "-y,x-y,-z+1/2", "-y,-x,-z", "-x+y,y,z+1/2", "x,x-y,-z", "-y,-x,z+1/2", "-x+y,y,-z", "x,x-y,z+1/2"], "universal_h_m": "P -6 c 2", "number": 188, "schoenflies": "D3h^2", "hall": " P -6c 2", "hermann_mauguin": "P -6 c 2", "ncsym": ["x,y,z", "-x+y,-x,-z+1/2", "-y,x-y,z", "x,y,-z+1/2", "-x+y,-x,z", "-y,x-y,-z+1/2", "-y,-x,-z", "-x+y,y,z+1/2", "x,x-y,-z", "-y,-x,z+1/2", "-x+y,y,-z", "x,x-y,z+1/2"], "short_h_m": "P-6c2", "hermann_mauguin_u": 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"-z+1/2,-x,y+1/2", "z+1/2,-x+1/2,-y", "-z,x+1/2,-y+1/2", "y,z,x", "y+1/2,-z+1/2,-x", "-y,z+1/2,-x+1/2", "-y+1/2,-z,x+1/2"], "universal_h_m": "P 21 3", "number": 198, "schoenflies": "T^4", "hall": " P 2ac 2ab 3", "hermann_mauguin": "P 21 3", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "x+1/2,-y+1/2,-z", "-x,y+1/2,-z+1/2", "z,x,y", "-z+1/2,-x,y+1/2", "z+1/2,-x+1/2,-y", "-z,x+1/2,-y+1/2", "y,z,x", "y+1/2,-z+1/2,-x", "-y,z+1/2,-x+1/2", "-y+1/2,-z,x+1/2"], "short_h_m": "P2_13", "hermann_mauguin_u": "P2_13", "point_group": "23"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,-y,-z+1/2", "-x,y+1/2,-z+1/2", "z,x,y", "-z,-x+1/2,y", "z,-x,-y+1/2", "-z,x+1/2,-y+1/2", "y,z,x", "y,-z,-x+1/2", "-y,z+1/2,-x+1/2", "-y+1/2,-z,x+1/2", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y+1,z+1/2", "x+1/2,-y+1/2,-z+1", "-x+1/2,y+1,-z+1", "z+1/2,x+1/2,y+1/2", "-z+1/2,-x+1,y+1/2", "z+1/2,-x+1/2,-y+1", "-z+1/2,x+1,-y+1", "y+1/2,z+1/2,x+1/2", "y+1/2,-z+1/2,-x+1", "-y+1/2,z+1,-x+1", "-y+1,-z+1/2,x+1"], "universal_h_m": "I 21 3", "number": 199, 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"x+1/4,z+1/4,y+1/4", "-y+1/2,-z+1/2,-x+1/2", "-y,z,x+1/2", "-z-1/4,-y+1/4,x+1/4", "y+1/2,-z,x", "z+1/4,y+1/4,x+1/4", "y,z+1/2,-x", "-z-1/4,y-1/4,-x+1/4", "z-1/4,-y+1/4,-x-1/4"], "universal_h_m": "I a -3 d", "number": 230, "schoenflies": "Oh^10", "hall": "-I 4bd 2c 3", "hermann_mauguin": "I a -3 d", "ncsym": ["x,y,z", "-y+1/4,x+3/4,z+1/4", "-x+1/2,-y,z+1/2", "y+1/4,-x+1/4,z+3/4", "x,-y,-z+1/2", "y+1/4,x+3/4,-z+3/4", "-x+1/2,y,-z", "-y+1/4,-x+1/4,-z+1/4", "z,x,y", "-x+1/4,z+3/4,y+1/4", "-z+1/2,-x,y+1/2", "x+1/4,-z+1/4,y+3/4", "z,-x,-y+1/2", "x+1/4,z+3/4,-y+3/4", "-z+1/2,x,-y", "-x+1/4,-z+1/4,-y+1/4", "y,z,x", "y+1/2,-z+1/2,-x", "z+3/4,y+1/4,-x+1/4", "-y,z+1/2,-x+1/2", "-z+1/4,-y+1/4,-x+1/4", "-y+1/2,-z,x+1/2", "z+3/4,-y+3/4,x+1/4", "-z+3/4,y+1/4,x+3/4", "-x,-y,-z", "y-1/4,-x-3/4,-z-1/4", "x-1/2,y,-z-1/2", "-y-1/4,x-1/4,-z-3/4", "-x,y,z-1/2", "-y-1/4,-x-3/4,z-3/4", "x-1/2,-y,z", "y-1/4,x-1/4,z-1/4", "-z,-x,-y", "x-1/4,-z-3/4,-y-1/4", "z-1/2,x,-y-1/2", "-x-1/4,z-1/4,-y-3/4", "-z,x,y-1/2", "-x-1/4,-z-3/4,y-3/4", "z-1/2,-x,y", "x-1/4,z-1/4,y-1/4", "-y,-z,-x", "-y-1/2,z-1/2,x", "-z-3/4,-y-1/4,x-1/4", "y,-z-1/2,x-1/2", "z-1/4,y-1/4,x-1/4", "y-1/2,z,-x-1/2", "-z-3/4,y-3/4,-x-1/4", "z-3/4,-y-1/4,-x-3/4"], "short_h_m": "Ia-3d", "hermann_mauguin_u": "Ia-3d", "point_group": "m-3m"}, {"symops": ["x,y,z", "1/2+x,1/2+y,z"], "universal_h_m": "C 1", "number": 1, "schoenflies": "C1^1", "hall": "P 1 (1/2*x+1/2*y,1/2*x-1/2*y,-z)", "hermann_mauguin": "C 1", "ncsym": ["x, y, z"], "short_h_m": "C1", "hermann_mauguin_u": "C1", "point_group": "1"}, {"symops": ["x,y,z", "-x,-y,-z", "x,1/2+y,1/2+z", "-x,1/2-y,1/2-z"], "universal_h_m": "A -1", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1 (-x,-1/2*y+1/2*z,1/2*y+1/2*z)", "hermann_mauguin": "A -1", "ncsym": ["x, y, z", "-x, -y, -z"], "short_h_m": "A-1", "hermann_mauguin_u": "A-1", "point_group": "-1"}, {"symops": ["x, y, z", "x+1/2, y, z+1/2", "-x, -y, -z", "-x+1/2, -y, -z+1/2"], "universal_h_m": "B -1", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1 (-1/2*x+1/2*z,-y,1/2*x+1/2*z)", "hermann_mauguin": "B -1", "ncsym": ["x, y, z", "-x, -y, -z"], "short_h_m": "B-1", "hermann_mauguin_u": "B-1", "point_group": "-1"}, {"symops": ["x,y,z", "1/2-x,1/2-y,1/2-z", "1/2+x,1/2+y,1/2+z", "-x,-y,-z"], "universal_h_m": "I -1", "number": 2, "schoenflies": "D2^4", "hall": "-P 1 (-1/2*x+1/2*y+1/2*z,1/2*x-1/2*y+1/2*z,1/2*x+1/2*y-1/2*z)", "hermann_mauguin": "I -1", "ncsym": ["x,y,z", "-x,-y,-z"], "short_h_m": "I-1", "hermann_mauguin_u": "I-1", "point_group": "-1"}, {"symops": ["x, y, z", "y, x, -z+1/2", "x+2/3, y+1/3, z+1/3", "y+2/3, x+1/3, -z+5/6", "x+1/3, y+2/3, z+2/3", "y+1/3, x+2/3, -z+7/6", "-x, -y, -z", "-y, -x, z-1/2", "-x+2/3, -y+1/3, -z+1/3", "-y+2/3, -x+1/3, z-1/6", "-x+1/3, -y+2/3, -z+2/3", "-y+1/3, -x+2/3, z+1/6"], "universal_h_m": "R 1 2/c 1", "number": 15, "schoenflies": "C2h^6", "hall": "-C 2yc (x+y-16/3*z,-x+y+16/3*z,1/3*z)", "hermann_mauguin": "R 1 2/c 1 ", "ncsym": ["x, y, z", "y, x, -z+1/2", "-x, -y, -z", "-y, -x, z-1/2"], "short_h_m": "R2/c", "hermann_mauguin_u": "R12/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x+1/2,-y,z+1/2"], "universal_h_m": "P 21 21 21 (origin shift x,y,z+1/4)", "number": 19, "schoenflies": "D2^4", "hall": " P 2ac 2ab (x,y,z+1/4)", "hermann_mauguin": "P 21 21 21 ", "ncsym": ["x,y,z", "x+1/2,-y+1/2,-z+1/2", "-x,y+1/2,-z", "-x+1/2,-y,z+1/2"], "short_h_m": "P2_12_12_1", "hermann_mauguin_u": "P2_12_12_1", "point_group": "222"}, {"symops": ["x, y, z", "-x, y+1/2, -z", "x+1/2, y, z+1/2", "-x+1/2, y+1/2, -z+1/2"], "universal_h_m": "B 1 21 1", "number": 4, "schoenflies": "C2^2", "hall": "P 2yb (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "B 1 21 1", "ncsym": ["x, y, z", "-x, y+1/2, -z"], "short_h_m": "B2_1", "hermann_mauguin_u": "B12_11", "point_group": "2"}, {"symops": ["x, y, z", "x+1/2, y+1/2, z", "-x, -y, -z", "-x+1/2, -y+1/2, -z"], "universal_h_m": "C -1", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1 (1/2*x+1/2*y,1/2*x-1/2*y,-z)", "hermann_mauguin": "C -1", "ncsym": ["x, y, z", "-x, -y, -z"], "short_h_m": "C-1", "hermann_mauguin_u": "C-1", "point_group": "-1"}, {"symops": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y-1/2,z", "x+1/2,y,z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,-y-1/2,z+1/2"], "universal_h_m": "B 1 21/m 1", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2yb (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "B 1 21/m 1", "ncsym": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y-1/2,z", "x+1/2,y,z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,-y-1/2,z+1/2"], "short_h_m": "B2_1/m", "hermann_mauguin_u": "B12_1/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "x,y+1/2,z+1/2"], "universal_h_m": "P 1 (-a,-b+c,b+c)", "number": 1, "schoenflies": "C1^1", "hall": " P 1 (-x,-1/2*y+1/2*z,1/2*y+1/2*z)", "hermann_mauguin": "P 1 ", "ncsym": ["x,y,z"], "short_h_m": "P1", "hermann_mauguin_u": "P1", "point_group": "1"}, {"symops": ["x,y,z", "x+1/2,y,z+1/2"], "universal_h_m": "P 1 (-a+c,-b,a+c)", "number": 1, "schoenflies": "C1^1", "hall": " P 1 (-1/2*x+1/2*z,-y,1/2*x+1/2*z)", "hermann_mauguin": "P 1 ", "ncsym": ["x,y,z"], "short_h_m": "P1", "hermann_mauguin_u": "P1", "point_group": "1"}, {"symops": ["x,y,z", "x+1/2,y+1/2,z+1/2"], "universal_h_m": "P 1 (b+c,a+c,a+b)", "number": 1, "schoenflies": "C1^1", "hall": " P 1 (-1/2*x+1/2*y+1/2*z,1/2*x-1/2*y+1/2*z,1/2*x+1/2*y-1/2*z)", "hermann_mauguin": "P 1 ", "ncsym": ["x,y,z"], "short_h_m": "P1", "hermann_mauguin_u": "P1", "point_group": "1"}, {"symops": ["x,y,z", "x,y+1/2,z+1/2", "x+1/2,y,z+1/2", "x+1/2,y+1/2,z"], "universal_h_m": "P 1 (-a+b+c,a-b+c,a+b-c)", "number": 1, "schoenflies": "C1^1", "hall": " P 1 (1/2*y+1/2*z,1/2*x+1/2*z,1/2*x+1/2*y)", "hermann_mauguin": "P 1 ", "ncsym": ["x,y,z"], "short_h_m": "P1", "hermann_mauguin_u": "P1", "point_group": "1"}, {"symops": ["x,y,z", "-x,-y,-z", "x,y+1/2,z+1/2", "-x,-y+1/2,-z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,-z"], "universal_h_m": "P -1 (-a+b+c,a-b+c,a+b-c)", "number": 2, "schoenflies": "Ci^1", "hall": "-P 1 (1/2*y+1/2*z,1/2*x+1/2*z,1/2*x+1/2*y)", "hermann_mauguin": "P -1 ", "ncsym": ["x,y,z", "-x,-y,-z"], "short_h_m": "P-1", "hermann_mauguin_u": "P-1", "point_group": "-1"}, {"symops": ["x,y,z", "-x,y,-z", "x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2"], "universal_h_m": "P 1 2 1 (2*a+c,b,c)", "number": 3, "schoenflies": "C2^1", "hall": " P 2y (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "P 1 2 1 ", "ncsym": ["x,y,z", "-x,y,-z"], "short_h_m": "P2", "hermann_mauguin_u": "P121", "point_group": "2"}, {"symops": ["x,y,z", "-x,y,-z", "x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z", "x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "universal_h_m": "C 1 2 1 (a,b,a+2*c)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (x-1/2*z,y,1/2*z)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,y,-z"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z"], "universal_h_m": "P 1 2 1 (c,2*a+c,b)", "number": 3, "schoenflies": "C2^1", "hall": " P 2y (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 2 1 ", "ncsym": ["x,y,z", "-x,-y,z"], "short_h_m": "P2", "hermann_mauguin_u": "P121", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y,z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2"], "universal_h_m": "C 1 2 1 (a+2*c,a,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (1/2*z,x-1/2*z,y)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,-y,z"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "x,y+1/2,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "C 1 2 1 (c-1/4,b-1/4,-a)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (z,y+1/4,-x-1/4)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,y+1/2,-z"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x+1/2,y+1/2,z", "-x,y+1/2,-z"], "universal_h_m": "C 1 2 1 (a-1/4,b-1/4,c)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (x+1/4,y+1/4,z)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,y+1/2,-z"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z"], "universal_h_m": "C 1 2 1 (a+c-1/4,b-1/4,c)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (x+1/4,y+1/4,-x+z-1/4)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,y+1/2,-z"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x+1/2,y,z+1/2", "-x,y,-z+1/2", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2"], "universal_h_m": "C 1 2 1 (a-1/4,b-1/4,a+2*c)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (x-1/2*z+1/4,y+1/4,1/2*z)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,y+1/2,-z"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2"], "universal_h_m": "C 1 2 1 (c-1/4,a-1/4,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (z,x+1/4,y+1/4)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,y,z+1/2", "-x,-y,z+1/2"], "universal_h_m": "C 1 2 1 (-a-1/4,c-1/4,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (-x-1/4,z,y+1/4)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2"], "universal_h_m": "P 1 21 1 (c,2*a+c,b)", "number": 4, "schoenflies": "C2^2", "hall": " P 2yb (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 21 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2"], "short_h_m": "P2_1", "hermann_mauguin_u": "P12_11", "point_group": "2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x,-y,z+1/2"], "universal_h_m": "C 1 2 1 (c-1/4,a+c-1/4,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (-x+z-1/4,x+1/4,y+1/4)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "x+1/2,y+1/2,z", "-x+1/2,-y,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y+1/2,z+1/2"], "universal_h_m": "C 1 2 1 (a+2*c-1/4,a-1/4,b)", "number": 5, "schoenflies": "C2^3", "hall": " C 2y (1/2*z,x-1/2*z+1/4,y+1/4)", "hermann_mauguin": "C 1 2 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2"], "short_h_m": "C2", "hermann_mauguin_u": "C121", "point_group": "2"}, {"symops": ["x,y,z", "x,-y,z", "x+1/2,y,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "P 1 m 1 (2*a+c,b,c)", "number": 6, "schoenflies": "Cs^1", "hall": " P -2y (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "P 1 m 1 ", "ncsym": ["x,y,z", "x,-y,z"], "short_h_m": "Pm", 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(z,y+1/4,-x-1/4)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "x,-y,z+1/2"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,-y,z+1/2", "x+1/2,y,z+1/2", "x+1/2,-y,z"], "universal_h_m": "P 1 c 1 (2*a+c,b,c)", "number": 7, "schoenflies": "Cs^2", "hall": " P -2yc (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "P 1 c 1 ", "ncsym": ["x,y,z", "x,-y,z+1/2"], "short_h_m": "Pc", "hermann_mauguin_u": "P1c1", "point_group": "m"}, {"symops": ["x,y,z", "x,-y+1/2,z", "x+1/2,y,z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "x,-y,z+1/2"], "universal_h_m": "C 1 m 1 (a-1/4,b-1/4,a+2*c)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (x-1/2*z+1/4,y+1/4,1/2*z)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "x,-y,z+1/2"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "C 1 m 1 (a+c-1/4,b-1/4,c)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (x+1/4,y+1/4,-x+z-1/4)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "x+1/2,-y,z+1/2"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,-y+1/2,z", "x+1/2,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "C 1 m 1 (a-1/4,b-1/4,c)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (x+1/4,y+1/4,z)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "x+1/2,-y,z"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,y,-z+1/2", "x+1/2,y,z+1/2", "x+1/2,y,-z"], "universal_h_m": "C 1 m 1 (-a-1/4,c-1/4,b)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (-x-1/4,z,y+1/4)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "x+1/2,y,-z"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "x+1/2,y,-z", "x+1/2,y+1/2,z", "x,y+1/2,-z"], "universal_h_m": "P 1 c 1 (c,2*a+c,b)", "number": 7, "schoenflies": "Cs^2", "hall": " P -2yc (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 c 1 ", "ncsym": ["x,y,z", "x+1/2,y,-z"], "short_h_m": "Pc", "hermann_mauguin_u": "P1c1", "point_group": "m"}, {"symops": ["x,y,z", "x,y,-z+1/2", "x+1/2,y+1/2,z", "x+1/2,y+1/2,-z+1/2", "x,y+1/2,z+1/2", "x,y+1/2,-z", "x+1/2,y,z+1/2", "x+1/2,y,-z"], "universal_h_m": "C 1 m 1 (a+2*c-1/4,a-1/4,b)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (1/2*z,x-1/2*z+1/4,y+1/4)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "x+1/2,y,-z"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,y,-z+1/2", "x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "C 1 m 1 (c-1/4,a+c-1/4,b)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (-x+z-1/4,x+1/4,y+1/4)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "x,y,-z+1/2", "x,y+1/2,z+1/2", "x,y+1/2,-z"], "universal_h_m": "C 1 m 1 (c-1/4,a-1/4,b)", 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(b-1/4,a+2*c-1/4,a)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (y+1/4,1/2*z,x-1/2*z+1/4)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "-x,y+1/2,z"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "-x+1/2,y,z", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "C 1 m 1 (b-1/4,c-1/4,a+c)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (y+1/4,-x+z-1/4,x+1/4)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "-x,y+1/2,z+1/2"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "-x+1/2,y,z", "x+1/2,y,z+1/2", "-x,y,z+1/2"], "universal_h_m": "C 1 m 1 (b-1/4,c-1/4,a)", "number": 8, "schoenflies": "Cs^3", "hall": " C -2y (y+1/4,z,x+1/4)", "hermann_mauguin": "C 1 m 1 ", "ncsym": ["x,y,z", "-x,y,z+1/2"], "short_h_m": "Cm", "hermann_mauguin_u": "C1m1", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z", "x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "P 1 2/m 1 (2*a+c,b,c)", "number": 10, "schoenflies": "C2h^1", "hall": "-P 2y (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "P 1 2/m 1 ", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"], "short_h_m": "P2/m", "hermann_mauguin_u": "P12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z", "x+1/2,y,z+1/2", "-x+1/2,y,-z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "C 1 2/m 1 (a,b,a+2*c)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (x-1/2*z,y,1/2*z)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,y,-z", "-x,-y,-z", "x,-y,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z"], "universal_h_m": "P 1 2/m 1 (c,2*a+c,b)", "number": 10, "schoenflies": "C2h^1", "hall": "-P 2y (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 2/m 1 ", "ncsym": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z"], "short_h_m": "P2/m", "hermann_mauguin_u": "P12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z", "x,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,-y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,-y,-z+1/2", "x+1/2,y,-z+1/2"], "universal_h_m": "C 1 2/m 1 (a+2*c,a,b)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (1/2*z,x-1/2*z,y)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,-y,z", "-x,-y,-z", "x,y,-z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z", "-x,-y,-z", "-x,y,z", "x,y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "P 1 2/m 1 (b,c,2*a+c)", "number": 10, 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2y (z,y-1/4,-x-1/4)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y+1/2,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "-x+1/2,-y+1/2,-z", "x,-y+1/2,z", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "-x,-y,-z", "x+1/2,-y,z"], "universal_h_m": "C 1 2/m 1 (a-1/4,b+1/4,c)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (x+1/4,y-1/4,z)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y+1/2,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "x,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z", "-x,-y,-z", "x+1/2,-y,z+1/2"], "universal_h_m": "C 1 2/m 1 (a+c-1/4,b+1/4,c)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (x+1/4,y-1/4,-x+z-1/4)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y+1/2,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "-x+1/2,-y+1/2,-z", "x,-y+1/2,z", "x+1/2,y,z+1/2", "-x,y,-z+1/2", "-x,-y+1/2,-z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "-x,-y,-z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,-y,-z+1/2", "x,-y,z+1/2"], "universal_h_m": "C 1 2/m 1 (a-1/4,b+1/4,a+2*c)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (x-1/2*z+1/4,y-1/4,1/2*z)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,y+1/2,-z", "-x,-y,-z", "x,-y+1/2,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,-y+1/2,-z+1/2", "x,y,-z+1/2", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "-x,-y,-z", "x,y+1/2,-z"], "universal_h_m": "C 1 2/m 1 (c-1/4,a+1/4,b)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (z,x+1/4,y-1/4)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z+1/2"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x+1/2,-y,-z+1/2", "x,y,-z+1/2", "x+1/2,y,z+1/2", "-x,-y,z+1/2", "-x,-y,-z", "x+1/2,y,-z"], "universal_h_m": "C 1 2/m 1 (-a-1/4,c+1/4,b)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (-x-1/4,z,y-1/4)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z+1/2"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,-y+1/2,-z", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "P 1 21/m 1 (c,2*a+c,b)", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2yb (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 21/m 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z+1/2"], "short_h_m": "P2_1/m", "hermann_mauguin_u": "P12_1/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x+1/2,-y+1/2,-z+1/2", "x,y,-z+1/2", "x+1/2,y+1/2,z+1/2", "-x,-y,z+1/2", "-x,-y,-z", "x+1/2,y+1/2,-z"], "universal_h_m": "C 1 2/m 1 (c-1/4,a+c+1/4,b)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (-x+z-1/4,x+1/4,y-1/4)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z+1/2"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,-y+1/2,-z+1/2", "x,y,-z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y,z", "-x+1/2,-y,-z+1/2", "x+1/2,y+1/2,-z+1/2", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "-x,-y,-z", "x,y+1/2,-z", "x+1/2,y,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,-y+1/2,-z", "x+1/2,y,-z"], "universal_h_m": "C 1 2/m 1 (a+2*c-1/4,a+1/4,b)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (1/2*z,x-1/2*z+1/4,y-1/4)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,-y,-z", "x,y,-z+1/2"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x+1/2,y,z", "x,y+1/2,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "P 1 21/m 1 (b,c,2*a+c)", "number": 11, "schoenflies": "C2h^2", "hall": "-P 2yb (y,-1/2*x+z,1/2*x)", "hermann_mauguin": "P 1 21/m 1 ", "ncsym": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x+1/2,y,z"], "short_h_m": "P2_1/m", "hermann_mauguin_u": "P12_1/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z+1/2", "-x+1/2,-y,-z+1/2", "-x+1/2,y,z", "x+1/2,y,z+1/2", "x+1/2,-y,-z", "-x,-y,-z", "-x,y,z+1/2"], "universal_h_m": "C 1 2/m 1 (b-1/4,c+1/4,a)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (y-1/4,z,x+1/4)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x+1/2,y,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y+1/2,-z", "-x+1/2,-y+1/2,-z", "-x+1/2,y,z", "x+1/2,y+1/2,z", "x+1/2,-y,-z", "-x,-y,-z", "-x,y+1/2,z"], "universal_h_m": "C 1 2/m 1 (b-1/4,-a+1/4,c)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (y-1/4,-x-1/4,z)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x+1/2,y,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y+1/2,-z+1/2", "-x+1/2,-y+1/2,-z+1/2", "-x+1/2,y,z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y,-z", "-x,-y,-z", "-x,y+1/2,z+1/2"], "universal_h_m": "C 1 2/m 1 (b-1/4,c+1/4,a+c)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (y-1/4,-x+z-1/4,x+1/4)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x+1/2,y,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y,-z+1/2", "-x+1/2,-y,-z+1/2", "-x+1/2,y,z", "x,y+1/2,z+1/2", "x,-y+1/2,-z", "-x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,z+1/2", "x+1/2,y,z+1/2", "x+1/2,-y,-z", "-x,-y,-z", "-x,y,z+1/2", "x+1/2,y+1/2,z", "x+1/2,-y+1/2,-z+1/2", "-x,-y+1/2,-z+1/2", "-x,y+1/2,z"], "universal_h_m": "C 1 2/m 1 (b-1/4,a+2*c+1/4,a)", "number": 12, "schoenflies": "C2h^3", "hall": "-C 2y (y-1/4,1/2*z,x-1/2*z+1/4)", "hermann_mauguin": "C 1 2/m 1 ", "ncsym": ["x,y,z", "x+1/2,-y,-z", "-x,-y,-z", "-x+1/2,y,z"], "short_h_m": "C2/m", "hermann_mauguin_u": "C12/m1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,y,-z", "-x+1/2,-y,-z+1/2", "x+1/2,-y,z"], "universal_h_m": "P 1 2/c 1 (2*a+c,b,c)", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2yc (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "P 1 2/c 1 ", "ncsym": ["x,y,z", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,z+1/2"], "short_h_m": "P2/c", "hermann_mauguin_u": "P12/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x+1/2,y,-z", "x+1/2,y+1/2,z", "-x,-y+1/2,z", "-x+1/2,-y+1/2,-z", "x,y+1/2,-z"], "universal_h_m": "P 1 2/c 1 (c,2*a+c,b)", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2yc (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 2/c 1 ", "ncsym": ["x,y,z", "-x+1/2,-y,z", "-x,-y,-z", "x+1/2,y,-z"], "short_h_m": "P2/c", "hermann_mauguin_u": "P12/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y+1/2,z", "x,y+1/2,z+1/2", "x,-y,-z+1/2", "-x,-y+1/2,-z+1/2", "-x,y,z+1/2"], "universal_h_m": "P 1 2/c 1 (b,c,2*a+c)", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2yc (y,-1/2*x+z,1/2*x)", "hermann_mauguin": "P 1 2/c 1 ", "ncsym": ["x,y,z", "x,-y+1/2,-z", "-x,-y,-z", "-x,y+1/2,z"], "short_h_m": "P2/c", "hermann_mauguin_u": "P12/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,-y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,y+1/2,-z", "-x+1/2,-y,-z+1/2", "x+1/2,-y+1/2,z"], "universal_h_m": "P 1 21/c 1 (2*a+c,b,c)", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2ybc (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "P 1 21/c 1 ", "ncsym": ["x,y,z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,-y+1/2,z+1/2"], "short_h_m": "P2_1/c", "hermann_mauguin_u": "P12_1/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,-y,-z", "x+1/2,y,-z+1/2", "x+1/2,y+1/2,z", "-x,-y+1/2,z+1/2", "-x+1/2,-y+1/2,-z", "x,y+1/2,-z+1/2"], "universal_h_m": "P 1 21/c 1 (c,2*a+c,b)", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2ybc (-1/2*x+z,1/2*x,y)", "hermann_mauguin": "P 1 21/c 1 ", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,-y,-z", "x+1/2,y,-z+1/2"], "short_h_m": "P2_1/c", "hermann_mauguin_u": "P12_1/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "x+1/2,-y+1/2,-z", "-x,-y,-z", "-x+1/2,y+1/2,z", "x,y+1/2,z+1/2", "x+1/2,-y,-z+1/2", "-x,-y+1/2,-z+1/2", "-x+1/2,y,z+1/2"], "universal_h_m": "P 1 21/c 1 (b,c,2*a+c)", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2ybc (y,-1/2*x+z,1/2*x)", "hermann_mauguin": "P 1 21/c 1 ", "ncsym": ["x,y,z", "x+1/2,-y+1/2,-z", "-x,-y,-z", "-x+1/2,y+1/2,z"], "short_h_m": "P2_1/c", "hermann_mauguin_u": "P12_1/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,y,z", "x,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z+1/2"], "universal_h_m": "A m m 2 (a,b+1/4,c-1/4)", "number": 38, "schoenflies": "C2v^14", "hall": " A 2 -2 (x,y-1/4,z+1/4)", "hermann_mauguin": "A m m 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"], "short_h_m": "Amm2", "hermann_mauguin_u": "Amm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y,z", "-x,y,z", "x+1/2,y,z+1/2", "-x,-y,z+1/2", "x,-y,z+1/2", "-x+1/2,y,z+1/2"], "universal_h_m": "A e m 2 (b,-a+1/4,c-1/4)", "number": 39, "schoenflies": "C2v^15", "hall": " A 2 -2b (y-1/4,-x,z+1/4)", "hermann_mauguin": "A e m 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"], "short_h_m": "Aem2", "hermann_mauguin_u": "Aem2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,y,z", "x+1/2,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x,-y,z+1/2"], "universal_h_m": "I m a 2 (a-1/4,b-1/4,c+1/4)", "number": 46, "schoenflies": "C2v^22", "hall": " I 2 -2a (x+1/4,y+1/4,z-1/4)", "hermann_mauguin": "I m a 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"], "short_h_m": "Ima2", "hermann_mauguin_u": "Ima2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,y,z", "x,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y,z", "-x+1/2,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "F m m 2 (a,b-1/4,c-1/4)", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2 (x,y+1/4,z+1/4)", "hermann_mauguin": "F m m 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z", "x,-y,z+1/2"], "short_h_m": "Fmm2", "hermann_mauguin_u": "Fmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,y+1/2,z", "x,-y,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y+1/2,z+1/2"], "universal_h_m": "A e m 2 (a,b+1/4,c-1/4)", "number": 39, "schoenflies": "C2v^15", "hall": " A 2 -2b (x,y-1/4,z+1/4)", "hermann_mauguin": "A e m 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"], "short_h_m": "Aem2", "hermann_mauguin_u": "Aem2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y,z", "-x+1/2,y,z", "x+1/2,y,z+1/2", "-x,-y,z+1/2", "x+1/2,-y,z+1/2", "-x,y,z+1/2"], "universal_h_m": "A m m 2 (b,-a+1/4,c-1/4)", "number": 38, "schoenflies": "C2v^14", "hall": " A 2 -2 (y-1/4,-x,z+1/4)", "hermann_mauguin": "A m m 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"], "short_h_m": "Amm2", "hermann_mauguin_u": "Amm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x,-y,z+1/2", "x+1/2,-y+1/2,z+1/2", "-x,y,z+1/2"], "universal_h_m": "I m a 2 (b-1/4,-a-1/4,c+1/4)", "number": 46, "schoenflies": "C2v^22", "hall": " I 2 -2a (y+1/4,-x-1/4,z-1/4)", "hermann_mauguin": "I m a 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"], "short_h_m": "Ima2", "hermann_mauguin_u": "Ima2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x+1/2,y,z", "x,-y,z", "x,y+1/2,z+1/2", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x,-y,z+1/2", "-x,y,z+1/2", "x+1/2,-y,z+1/2", "x+1/2,y+1/2,z", "-x,-y+1/2,z", "-x,y+1/2,z", "x+1/2,-y+1/2,z"], "universal_h_m": "F m m 2 (a+1/4,b,c+1/4)", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2 (x-1/4,y,z-1/4)", "hermann_mauguin": "F m m 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y,z+1/2", "x,-y,z"], "short_h_m": "Fmm2", "hermann_mauguin_u": "Fmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x,y,z+1/2", "x,y,-z", "x,y+1/2,z+1/2", "-x,y+1/2,-z", "-x,y+1/2,z", "x,y+1/2,-z+1/2"], "universal_h_m": "A e m 2 (-a,c+1/4,b-1/4)", "number": 39, "schoenflies": "C2v^15", "hall": " A 2 -2b (-x,z+1/4,y-1/4)", "hermann_mauguin": "A e m 2 ", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"], "short_h_m": "Aem2", "hermann_mauguin_u": "Aem2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x,y,-z", "-x+1/2,y,z", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x+1/2,y+1/2,-z", "-x,y+1/2,z"], "universal_h_m": "A m m 2 (b,c+1/4,a-1/4)", "number": 38, "schoenflies": "C2v^14", "hall": " A 2 -2 (y-1/4,z+1/4,x)", "hermann_mauguin": "A m m 2 ", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"], "short_h_m": "Amm2", "hermann_mauguin_u": "Amm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y,-z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z", "x+1/2,y+1/2,-z+1/2", "-x,y+1/2,z"], "universal_h_m": "I m a 2 (b-1/4,c-1/4,a+1/4)", "number": 46, "schoenflies": "C2v^22", "hall": " I 2 -2a (y+1/4,z-1/4,x+1/4)", "hermann_mauguin": "I m a 2 ", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"], "short_h_m": "Ima2", "hermann_mauguin_u": "Ima2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x,y,-z", "-x+1/2,y,z", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x+1/2,y+1/2,-z", "-x,y+1/2,z", "x,y+1/2,z+1/2", "-x+1/2,y+1/2,-z+1/2", "x,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x,y,-z+1/2", "x+1/2,y,-z+1/2", "-x,y,z+1/2"], "universal_h_m": "F m m 2 (b,c-1/4,a-1/4)", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2 (y+1/4,z+1/4,x)", "hermann_mauguin": "F m m 2 ", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z", "-x,y+1/2,-z"], "short_h_m": "Fmm2", "hermann_mauguin_u": "Fmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x,y,z", "x,y,-z+1/2", "x,y+1/2,z+1/2", "-x,y+1/2,-z", "-x,y+1/2,z+1/2", "x,y+1/2,-z"], "universal_h_m": "A m m 2 (-a,c+1/4,b-1/4)", "number": 38, "schoenflies": "C2v^14", "hall": " A 2 -2 (-x,z+1/4,y-1/4)", "hermann_mauguin": "A m m 2 ", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"], "short_h_m": "Amm2", "hermann_mauguin_u": "Amm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x+1/2,y,-z", "-x,y,z", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x,y+1/2,-z", "-x+1/2,y+1/2,z"], "universal_h_m": "A e m 2 (b,c+1/4,a-1/4)", "number": 39, "schoenflies": "C2v^15", "hall": " A 2 -2b (y-1/4,z+1/4,x)", "hermann_mauguin": "A e m 2 ", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"], "short_h_m": "Aem2", "hermann_mauguin_u": "Aem2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "-x,y,z", "x+1/2,y,-z+1/2", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z", "-x+1/2,y+1/2,z+1/2", "x,y+1/2,-z"], "universal_h_m": "I m a 2 (-a-1/4,c-1/4,b+1/4)", "number": 46, "schoenflies": "C2v^22", "hall": " I 2 -2a (-x-1/4,z-1/4,y+1/4)", "hermann_mauguin": "I m a 2 ", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"], "short_h_m": "Ima2", "hermann_mauguin_u": "Ima2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "x,y,-z+1/2", "-x,y,z", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z", "x,y+1/2,z+1/2", "-x,y+1/2,-z", "x,y+1/2,-z", "-x,y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x+1/2,y,-z", "x+1/2,y,-z", "-x+1/2,y,z+1/2"], "universal_h_m": "F m m 2 (b+1/4,c,a+1/4)", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2 (y,z-1/4,x-1/4)", "hermann_mauguin": "F m m 2 ", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y,z", "-x,y+1/2,-z"], "short_h_m": "Fmm2", "hermann_mauguin_u": "Fmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x+1/2,y,z", "x,-y+1/2,z", "x,y+1/2,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x,-y,z+1/2", "x+1/2,y,z+1/2", "-x,-y+1/2,z+1/2", "-x,y,z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x,-y,z", "-x,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "F m m 2 (a+1/4,b+1/4,c+1/2)", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2 (x-1/4,y-1/4,z+1/2)", "hermann_mauguin": "F m m 2 ", "ncsym": ["x,y,z", "-x,-y,z", "-x,y,z+1/2", "x,-y,z+1/2"], "short_h_m": "Fmm2", "hermann_mauguin_u": "Fmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y,-z+1/2", "-x+1/2,y,z", "x+1/2,y+1/2,z", "-x,y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x,y+1/2,z", "x,y+1/2,z+1/2", "-x+1/2,y+1/2,-z", "x,y+1/2,-z", "-x+1/2,y+1/2,z+1/2", "x+1/2,y,z+1/2", "-x,y,-z", "x+1/2,y,-z", "-x,y,z+1/2"], "universal_h_m": "F m m 2 (b+1/4,c+1/4,a+1/2)", "number": 42, "schoenflies": "C2v^18", "hall": " F 2 -2 (y-1/4,z+1/2,x-1/4)", "hermann_mauguin": "F m m 2 ", "ncsym": ["x,y,z", "x,y+1/2,-z", "-x,y+1/2,z", "-x,y,-z"], "short_h_m": "Fmm2", "hermann_mauguin_u": "Fmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x+1/2,y,z", "x,-y+1/2,z", "x+1/2,y+1/2,z", "-x,-y,z", "-x,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "C m m 2 (a-1/4,b-1/4,c)", "number": 35, "schoenflies": "C2v^11", "hall": " C 2 -2 (x+1/4,y+1/4,z)", "hermann_mauguin": "C m m 2 ", "ncsym": ["x,y,z", "-x,-y,z", "-x+1/2,y,z", "x+1/2,-y,z"], "short_h_m": "Cmm2", "hermann_mauguin_u": "Cmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y,-z+1/2", "-x+1/2,y,z", "x+1/2,y,z+1/2", "-x,y,-z", "x+1/2,y,-z", "-x,y,z+1/2"], "universal_h_m": "C m m 2 (b-1/4,c-1/4,a)", "number": 35, "schoenflies": "C2v^11", "hall": " C 2 -2 (y+1/4,z,x+1/4)", "hermann_mauguin": "C m m 2 ", "ncsym": ["x,y,z", "x,y,-z+1/2", "-x,y,z+1/2", "-x,y,-z"], "short_h_m": "Cmm2", "hermann_mauguin_u": "Cmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,-y,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "A e a 2 (a,b+1/4,c-1/4)", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab (x,y-1/4,z+1/4)", "hermann_mauguin": "A e a 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"], "short_h_m": "Aea2", "hermann_mauguin_u": "Aea2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "x,-y+1/2,z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x,-y,z+1/2", "x+1/2,-y,z", "-x,y+1/2,z+1/2"], "universal_h_m": "C m c 21 (b-1/4,-a-1/4,c)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (y+1/4,-x-1/4,z)", "hermann_mauguin": "C m c 21 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"], "short_h_m": "Cmc2_1", "hermann_mauguin_u": "Cmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x+1/2,y,z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y+1/2,z+1/2", "-x,-y,z+1/2", "-x,y+1/2,z", "x+1/2,-y,z"], "universal_h_m": "I b a 2 (a-1/4,b-1/4,c+1/4)", "number": 45, "schoenflies": "C2v^21", "hall": " I 2 -2c (x+1/4,y+1/4,z-1/4)", "hermann_mauguin": "I b a 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y,z+1/2", "x+1/2,-y,z"], "short_h_m": "Iba2", "hermann_mauguin_u": "Iba2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x+1/2,-y+1/2,z", "-x,y+1/2,z", "x+1/2,y,z+1/2", "-x,-y,z+1/2", "x,-y+1/2,z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "A e a 2 (b,-a+1/4,c-1/4)", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab (y-1/4,-x,z+1/4)", "hermann_mauguin": "A e a 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x,-y+1/2,z+1/2"], "short_h_m": "Aea2", "hermann_mauguin_u": "Aea2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z+1/2", "-x+1/2,y,z", "x,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x+1/2,-y,z+1/2"], "universal_h_m": "C m c 21 (a-1/4,b-1/4,c)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (x+1/4,y+1/4,z)", "hermann_mauguin": "C m c 21 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x,y+1/2,z", "x,-y+1/2,z+1/2"], "short_h_m": "Cmc2_1", "hermann_mauguin_u": "Cmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z", "x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "-x,y+1/2,-z", "-x,y,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "C m c 21 (-a-1/4,c-1/4,b)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (-x-1/4,z,y+1/4)", "hermann_mauguin": "C m c 21 ", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"], "short_h_m": "Cmc2_1", "hermann_mauguin_u": "Cmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x+1/2,y,-z+1/2", "-x,y,z+1/2", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "A e a 2 (b,c+1/4,a-1/4)", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab (y-1/4,z+1/4,x)", "hermann_mauguin": "A e a 2 ", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"], "short_h_m": "Aea2", "hermann_mauguin_u": "Aea2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y+1/2,-z+1/2", "-x+1/2,y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z", "x+1/2,y,-z", "-x,y,z+1/2"], "universal_h_m": "I b a 2 (b-1/4,c-1/4,a+1/4)", "number": 45, "schoenflies": "C2v^21", "hall": " I 2 -2c (y+1/4,z-1/4,x+1/4)", "hermann_mauguin": "I b a 2 ", "ncsym": ["x,y,z", "x,y+1/2,-z+1/2", "-x,y,z+1/2", "-x,y+1/2,-z"], "short_h_m": "Iba2", "hermann_mauguin_u": "Iba2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,y,-z", "x,y+1/2,z+1/2", "-x,y+1/2,-z", "-x+1/2,y+1/2,z", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "A e a 2 (-a,c+1/4,b-1/4)", "number": 41, "schoenflies": "C2v^17", "hall": " A 2 -2ab (-x,z+1/4,y-1/4)", "hermann_mauguin": "A e a 2 ", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y+1/2,z", "-x,y+1/2,-z"], "short_h_m": "Aea2", "hermann_mauguin_u": "Aea2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z+1/2", "x,y,-z+1/2", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,y+1/2,-z", "x+1/2,y,-z", "-x,y+1/2,z+1/2"], "universal_h_m": "C m c 21 (b-1/4,c-1/4,a)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (y+1/4,z,x+1/4)", "hermann_mauguin": "C m c 21 ", "ncsym": ["x,y,z", "x+1/2,y,-z", "-x+1/2,y+1/2,z", "-x,y+1/2,-z"], "short_h_m": "Cmc2_1", "hermann_mauguin_u": "Cmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x+1/2,y,z+1/2", "x,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x,-y,z", "-x,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "C c c 2 (a-1/4,b-1/4,c)", "number": 37, "schoenflies": "C2v^13", "hall": " C 2 -2c (x+1/4,y+1/4,z)", "hermann_mauguin": "C c c 2 ", "ncsym": ["x,y,z", "-x,-y,z", "-x,y+1/2,z+1/2", "x,-y+1/2,z+1/2"], "short_h_m": "Ccc2", "hermann_mauguin_u": "Ccc2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y+1/2,-z+1/2", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,y,-z", "x+1/2,y+1/2,-z", "-x,y+1/2,z+1/2"], "universal_h_m": "C c c 2 (b-1/4,c-1/4,a)", "number": 37, "schoenflies": "C2v^13", "hall": " C 2 -2c (y+1/4,z,x+1/4)", "hermann_mauguin": "C c c 2 ", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z", "-x,y,-z"], "short_h_m": "Ccc2", "hermann_mauguin_u": "Ccc2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "-x,y,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x+1/2,-y,z+1/2", "-x,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "A m a 2 (a+1/4,b+1/4,c-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (x-1/4,y-1/4,z+1/4)", "hermann_mauguin": "A m a 2 ", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"], "short_h_m": "Ama2", "hermann_mauguin_u": "Ama2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y,z", "x,-y+1/2,z+1/2", "x+1/2,y+1/2,z", "-x+1/2,-y,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y,z+1/2"], "universal_h_m": "C m c 21 (a,b+1/4,c)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (x,y-1/4,z)", "hermann_mauguin": "C m c 21 ", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"], "short_h_m": "Cmc2_1", "hermann_mauguin_u": "Cmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x,y,z", "x,-y+1/2,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "I m m 2 (a,b-1/4,c)", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2 (x,y+1/4,z)", "hermann_mauguin": "I m m 2 ", "ncsym": ["x,y,z", "-x+1/2,-y,z+1/2", "-x,y,z", "x+1/2,-y,z+1/2"], "short_h_m": "Imm2", "hermann_mauguin_u": "Imm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y+1/2,z", "x,-y,z", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,-y+1/2,z+1/2", "x+1/2,-y,z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "A m a 2 (b+1/4,-a+1/4,c-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (y-1/4,-x+1/4,z+1/4)", "hermann_mauguin": "A m a 2 ", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"], "short_h_m": "Ama2", "hermann_mauguin_u": "Ama2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y,z+1/2", "x,-y,z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x,-y+1/2,z+1/2", "x+1/2,-y+1/2,z", "-x,y+1/2,z+1/2"], "universal_h_m": "C m c 21 (b,-a+1/4,c)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (y-1/4,-x,z)", "hermann_mauguin": "C m c 21 ", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"], "short_h_m": "Cmc2_1", "hermann_mauguin_u": "Cmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "-x+1/2,y,z", "x,-y,z", "x+1/2,y+1/2,z+1/2", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "universal_h_m": "I m m 2 (a-1/4,b,c+1/4)", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2 (x+1/4,y,z-1/4)", "hermann_mauguin": "I m m 2 ", "ncsym": ["x,y,z", "-x,-y+1/2,z+1/2", "-x,y+1/2,z+1/2", "x,-y,z"], "short_h_m": "Imm2", "hermann_mauguin_u": "Imm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z", "x,y,-z", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y,-z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "C m c 21 (b,c+1/4,a)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (y-1/4,z,x)", "hermann_mauguin": "C m c 21 ", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "short_h_m": "Cmc2_1", "hermann_mauguin_u": "Cmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "x,y,-z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x,y+1/2,-z+1/2", "x+1/2,y+1/2,-z", "-x,y+1/2,z+1/2"], "universal_h_m": "A m a 2 (b+1/4,c+1/4,a-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (y-1/4,z+1/4,x-1/4)", "hermann_mauguin": "A m a 2 ", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "short_h_m": "Ama2", "hermann_mauguin_u": "Ama2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x,y,-z", "-x+1/2,y,z", "x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "I m m 2 (b,c-1/4,a)", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2 (y+1/4,z,x)", "hermann_mauguin": "I m m 2 ", "ncsym": ["x,y,z", "x,y,-z", "-x,y+1/2,z+1/2", "-x,y+1/2,-z+1/2"], "short_h_m": "Imm2", "hermann_mauguin_u": "Imm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z+1/2", "-x,y,z", "x+1/2,y,-z+1/2", "x,y+1/2,z+1/2", "-x+1/2,y+1/2,-z", "-x,y+1/2,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "A m a 2 (-a+1/4,c+1/4,b-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (-x+1/4,z+1/4,y-1/4)", "hermann_mauguin": "A m a 2 ", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"], "short_h_m": "Ama2", "hermann_mauguin_u": "Ama2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,y+1/2,-z+1/2", "-x,y,z", "x,y+1/2,-z+1/2", "x+1/2,y,z+1/2", "-x+1/2,y+1/2,-z", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "C m c 21 (-a,c+1/4,b)", "number": 36, "schoenflies": "C2v^12", "hall": " C 2c -2 (-x,z,y-1/4)", "hermann_mauguin": "C m c 21 ", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"], "short_h_m": "Cmc2_1", "hermann_mauguin_u": "Cmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "x,y,-z+1/2", "-x,y,z", "x+1/2,y+1/2,z+1/2", "-x+1/2,y+1/2,-z", "x+1/2,y+1/2,-z", "-x+1/2,y+1/2,z+1/2"], "universal_h_m": "I m m 2 (b-1/4,c,a+1/4)", "number": 44, "schoenflies": "C2v^20", "hall": " I 2 -2 (y,z-1/4,x+1/4)", "hermann_mauguin": "I m m 2 ", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z", "-x,y,z", "-x+1/2,y+1/2,-z"], "short_h_m": "Imm2", "hermann_mauguin_u": "Imm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,-y+1/2,z", "-x+1/2,y,z", "x+1/2,-y+1/2,z", "x,y+1/2,z+1/2", "-x,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y,z+1/2"], "universal_h_m": "A m a 2 (a,b+1/4,c-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (x,y-1/4,z+1/4)", "hermann_mauguin": "A m a 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z"], "short_h_m": "Ama2", "hermann_mauguin_u": "Ama2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,-y,z", "x,-y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,y,z+1/2", "-x,-y,z+1/2", "x+1/2,-y+1/2,z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "A m a 2 (b,-a+1/4,c-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (y-1/4,-x,z+1/4)", "hermann_mauguin": "A m a 2 ", "ncsym": ["x,y,z", "-x,-y,z+1/2", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z+1/2"], "short_h_m": "Ama2", "hermann_mauguin_u": "Ama2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/2,y,-z", "x,y,-z+1/2", "-x+1/2,y,z+1/2", "x+1/2,y+1/2,z", "-x,y+1/2,-z", "x+1/2,y+1/2,-z+1/2", "-x,y+1/2,z+1/2"], "universal_h_m": "A m a 2 (b,c+1/4,a-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (y-1/4,z+1/4,x)", "hermann_mauguin": "A m a 2 ", "ncsym": ["x,y,z", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y,z+1/2", "-x,y+1/2,-z"], "short_h_m": "Ama2", "hermann_mauguin_u": "Ama2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "-x+1/2,y,z", "x+1/2,y,-z+1/2", "x,y+1/2,z+1/2", "-x,y+1/2,-z", "-x+1/2,y+1/2,z+1/2", "x+1/2,y+1/2,-z"], "universal_h_m": "A m a 2 (-a,c+1/4,b-1/4)", "number": 40, "schoenflies": "C2v^16", "hall": " A 2 -2a (-x,z+1/4,y-1/4)", "hermann_mauguin": "A m a 2 ", "ncsym": ["x,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y+1/2,z+1/2", "-x,y+1/2,-z"], "short_h_m": "Ama2", "hermann_mauguin_u": "Ama2", "point_group": "mm2"}, {"symops": ["x,y,z", "x,-y,-z", "-x,y,-z", "-x,-y,z", "-x+1/2,-y,-z", "-x+1/2,y,z", "x+1/2,-y,z", "x+1/2,y,-z", "x,y+1/2,z+1/2", "x,-y+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-x,-y+1/2,z+1/2", "-x+1/2,-y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2"], "universal_h_m": "C c c m (c,a,b-1/4)", "number": 66, "schoenflies": "D2h^20", "hall": "-C 2 2c (z+1/4,x,y)", "hermann_mauguin": "C c c m ", "ncsym": ["x,y,z", "-x,-y,z", "x,-y,-z", "-x,y,-z", "-x+1/2,-y+1/2,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2"], "short_h_m": "Cccm", "hermann_mauguin_u": "Cccm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,y,-z", "-x,-y,z", "x,-y,-z", "-x,-y+1/2,-z", "x,-y+1/2,z", "x,y+1/2,-z", "-x,y+1/2,z", 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"z+1/2,-x+1/2,y+1/2", "x+1/2,z,y+1/2", "-y,-z+1/2,-x", "-y,z,x+1/2", "-z,-y+1/2,x+1/2", "y+1/2,-z+1/2,x+1/2", "z+1/2,y,x+1/2", "y+1/2,z,-x", "-z,y,-x", "z+1/2,-y+1/2,-x", "x+1/2,y+1/2,z", "-y,x+1/2,z", "-x,-y,z", "y+1/2,-x,z", "x+1/2,-y,-z+1/2", "y+1/2,x+1/2,-z+1/2", "-x,y+1/2,-z+1/2", "-y,-x,-z+1/2", "z+1/2,x+1/2,y", "-x,z+1/2,y", "-z,-x,y", "x+1/2,-z,y", "z+1/2,-x,-y+1/2", "x+1/2,z+1/2,-y+1/2", "-z,x+1/2,-y+1/2", "-x,-z,-y+1/2", "y+1/2,z+1/2,x", "y+1/2,-z,-x+1/2", "z+1/2,y+1/2,-x+1/2", "-y,z+1/2,-x+1/2", "-z,-y,-x+1/2", "-y,-z,x", "z+1/2,-y,x", "-z,y+1/2,x", "-x,-y,-z+1/2", "y+1/2,-x,-z+1/2", "x+1/2,y+1/2,-z+1/2", "-y,x+1/2,-z+1/2", "-x,y+1/2,z", "-y,-x,z", "x+1/2,-y,z", "y+1/2,x+1/2,z", "-z,-x,-y+1/2", "x+1/2,-z,-y+1/2", "z+1/2,x+1/2,-y+1/2", "-x,z+1/2,-y+1/2", "-z,x+1/2,y", "-x,-z,y", "z+1/2,-x,y", "x+1/2,z+1/2,y", "-y,-z,-x+1/2", "-y,z+1/2,x", "-z,-y,x", "y+1/2,-z,x", "z+1/2,y+1/2,x", "y+1/2,z+1/2,-x+1/2", "-z,y+1/2,-x+1/2", "z+1/2,-y,-x+1/2"], "universal_h_m": "F m -3 m (a-1/4,b-1/4,c-1/4)", "number": 225, "schoenflies": "Oh^5", "hall": "-F 4 2 3 (x+1/4,y+1/4,z+1/4)", "hermann_mauguin": "F m -3 m ", "ncsym": ["x,y,z", "-y+1/2,x+1/2,z+1/2", "-x,-y,z", "y+1/2,-x+1/2,z+1/2", "x,-y,-z", "y+1/2,x+1/2,-z+1/2", "-x,y,-z", "-y+1/2,-x+1/2,-z+1/2", "z,x,y", "-x+1/2,z+1/2,y+1/2", "-z,-x,y", "x+1/2,-z+1/2,y+1/2", "z,-x,-y", "x+1/2,z+1/2,-y+1/2", "-z,x,-y", "-x+1/2,-z+1/2,-y+1/2", "y,z,x", "y,-z,-x", "z+1/2,y+1/2,-x+1/2", "-y,z,-x", "-z+1/2,-y+1/2,-x+1/2", "-y,-z,x", "z+1/2,-y+1/2,x+1/2", "-z+1/2,y+1/2,x+1/2", "-x+1/2,-y+1/2,-z+1/2", "y,-x,-z", "x+1/2,y+1/2,-z+1/2", "-y,x,-z", "-x+1/2,y+1/2,z+1/2", "-y,-x,z", "x+1/2,-y+1/2,z+1/2", "y,x,z", "-z+1/2,-x+1/2,-y+1/2", "x,-z,-y", "z+1/2,x+1/2,-y+1/2", "-x,z,-y", "-z+1/2,x+1/2,y+1/2", "-x,-z,y", "z+1/2,-x+1/2,y+1/2", "x,z,y", "-y+1/2,-z+1/2,-x+1/2", "-y+1/2,z+1/2,x+1/2", "-z,-y,x", "y+1/2,-z+1/2,x+1/2", "z,y,x", "y+1/2,z+1/2,-x+1/2", "-z,y,-x", "z,-y,-x"], "short_h_m": "Fm-3m", "hermann_mauguin_u": "Fm-3m", "point_group": "m-3m"}, {"symops": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z", "x,y,z+1/2", "-y,x,z+1/2", "-x,-y,z+1/2", "y,-x,z+1/2", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "y+1/2,x+1/2,z+1/2"], "universal_h_m": "P 4 b m (a,b,2*c)", "number": 100, "schoenflies": "C4v^2", "hall": " P 4 -2ab (x,y,1/2*z)", "hermann_mauguin": "P 4 b m", "ncsym": ["x,y,z", "-y,x,z", "-x,-y,z", "y,-x,z", "-x+1/2,y+1/2,z", "-y+1/2,-x+1/2,z", "x+1/2,-y+1/2,z", "y+1/2,x+1/2,z", "x,y,z+1/2", "-y,x,z+1/2", "-x,-y,z+1/2", "y,-x,z+1/2", "-x+1/2,y+1/2,z+1/2", "-y+1/2,-x+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "y+1/2,x+1/2,z+1/2"], "short_h_m": "P4bm", "hermann_mauguin_u": "P4bm", "point_group": "4mm"}, {"symops": ["x,y,z", "x,-y,z+1/2", "x+1/2,y,z+1/2", "x+1/2,-y,z", "x+1/4,y+1/2,z+3/4", "x+1/4,-y+1/2,z+1/4", "x+3/4,y+1/2,z+1/4", "x+3/4,-y+1/2,z+3/4"], "universal_h_m": "C 1 c 1 (2*a+c,b,c)", "number": 9, "schoenflies": "Cs^4", "hall": " C -2yc (1/2*x,y,-1/2*x+z)", "hermann_mauguin": "C 1 c 1", "ncsym": ["x,y,z", "x,-y,z+1/2", "x+1/2,y,z+1/2", "x+1/2,-y,z"], "short_h_m": "Cc", "hermann_mauguin_u": "C1c1", "point_group": "m"}, {"symops": ["x,y,z", "-x,y,z", "x,-y,z+1/2", "-x,-y,z+1/2", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,-y,z+1/2", "-x+1/2,-y,z+1/2"], "universal_h_m": "P m c 21 (2*a,b,c)", "number": 26, "schoenflies": "C2v^2", "hall": " P 2c -2 (1/2*x,y,z)", "hermann_mauguin": "P m c 21", "ncsym": ["x,y,z", "-x,y,z", "x,-y,z+1/2", "-x,-y,z+1/2"], "short_h_m": "Pmc2_1", "hermann_mauguin_u": "Pmc2_1", "point_group": "mm2"}, {"symops": ["x,y,z", "x,-y,z", "x,y,-z", "x,-y,-z", "x,y+1/2,z+1/2", "x,-y+1/2,z+1/2", "x,y+1/2,-z+1/2", "x,-y+1/2,-z+1/2", "x+1/2,y,z", "x+1/2,-y,z", "x+1/2,y,-z", "x+1/2,-y,-z", "x+1/2,y+1/2,z+1/2", "x+1/2,-y+1/2,z+1/2", "x+1/2,y+1/2,-z+1/2", "x+1/2,-y+1/2,-z+1/2"], "universal_h_m": "C m m 2 (2*c,a,b)", "number": 35, "schoenflies": "C2v^11", "hall": " C 2 -2 (1/2*z,x,y)", "hermann_mauguin": "C m m 2", "ncsym": ["x,y,z", "x,-y,z", "x,y,-z", "x,-y,-z"], "short_h_m": "Cmm2", "hermann_mauguin_u": "Cmm2", "point_group": "mm2"}, {"symops": ["x,y,z", "-x+1/4,-y,z+1/2", "-x,-y,-z", "x-1/4,y,-z-1/2", "x+3/4,y+1/2,z", "-x+1,-y+1/2,z+1/2", "-x+3/4,-y+1/2,-z", "x+1/2,y+1/2,-z-1/2", "x+1/4,y+1/2,z", "-x+1/2,-y+1/2,z+1/2", "-x+1/4,-y+1/2,-z", "x,y+1/2,-z-1/2", "x+1/2,y,z", "-x+3/4,-y,z+1/2", "-x+1/2,-y,-z", "x+1/4,y,-z-1/2"], "universal_h_m": "P 1 21/c 1 (2*c,2*a+c,b)", "number": 14, "schoenflies": "C2h^5", "hall": "-P 2ybc (-1/4*x+1/2*z,1/2*x,y)", "hermann_mauguin": "P 1 21/c 1", "ncsym": ["x,y,z", "-x+1/4,-y,z+1/2", "-x,-y,-z", "x-1/4,y,-z-1/2"], "short_h_m": "P2_1/c", "hermann_mauguin_u": "P12_1/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,z", "x,y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,-z", "-x,-y,z-1/2", "x,-y,z-1/2", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,y,-z+1/2", "-x+1/2,y,-z+1/2", "-x+1/2,-y,-z", "x+1/2,-y,-z", "-x+1/2,-y,z-1/2", "x+1/2,-y,z-1/2"], "universal_h_m": "P m m a (2*b,c,a)", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2a 2a (1/2*y,z,x)", "hermann_mauguin": "P m m a", "ncsym": ["x,y,z", "-x,y,z", "x,y,-z+1/2", "-x,y,-z+1/2", "-x,-y,-z", "x,-y,-z", "-x,-y,z-1/2", "x,-y,z-1/2"], "short_h_m": "Pmma", "hermann_mauguin_u": "Pmma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,y,z", "x,y,-z", "-x,y,-z", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,y,-z", "-x+1/2,y,-z", "-x,-y+2/3,-z+1/2", "x,-y+2/3,-z+1/2", "-x,-y+2/3,z+1/2", "x,-y+2/3,z+1/2", "-x+1/2,-y+2/3,-z+1/2", "x+1/2,-y+2/3,-z+1/2", "-x+1/2,-y+2/3,z+1/2", "x+1/2,-y+2/3,z+1/2"], "universal_h_m": "P m m a (2*b+1/4,c,a-1/3)", "number": 51, "schoenflies": "D2h^5", "hall": "-P 2a 2a (1/2*y,z+1/3,x-1/4)", "hermann_mauguin": "P m m a", "ncsym": ["x,y,z", "-x,y,z", "x,y,-z", "-x,y,-z", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,y,-z", "-x+1/2,y,-z"], "short_h_m": "Pmma", "hermann_mauguin_u": "Pmma", "point_group": "mmm"}, {"symops": ["x,y,z", "-x,y,-z+1/2", "x,y+1/2,z", "-x,y+1/2,-z+1/2", "-x,-y,-z", "x,-y,z+1/2", "-x,-y+1/2,-z", "x,-y+1/2,z+1/2"], "universal_h_m": "P 1 2/c 1 (a,2*b,c)", "number": 13, "schoenflies": "C2h^4", "hall": "-P 2yc (x,1/2*y,z)", "hermann_mauguin": "P 1 2/c 1", "ncsym": ["x,y,z", "-x,y,-z+1/2", "x,y+1/2,z", "-x,y+1/2,-z+1/2"], "short_h_m": "P2/c", "hermann_mauguin_u": "P12/c1", "point_group": "2/m"}, {"symops": ["x,y,z", "-x,y,z", "x,-y,z", "-x,-y,z", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,-y,z", "-x+1/2,-y,z", "x,y+1/2,z", "-x,y+1/2,z", "x,-y+1/2,z", "-x,-y+1/2,z", "x+1/2,y+1/2,z", "-x+1/2,y+1/2,z", "x+1/2,-y+1/2,z", "-x+1/2,-y+1/2,z", "-x,-y,-z", "x,-y,-z", "-x,y,-z", "x,y,-z", "-x+1/2,-y,-z", "x+1/2,-y,-z", "-x+1/2,y,-z", "x+1/2,y,-z", "-x,-y+1/2,-z", "x,-y+1/2,-z", "-x,y+1/2,-z", "x,y+1/2,-z", "-x+1/2,-y+1/2,-z", "x+1/2,-y+1/2,-z", "-x+1/2,y+1/2,-z", "x+1/2,y+1/2,-z"], "universal_h_m": "P m m m (2*a,2*b,c)", "number": 47, "schoenflies": "D2h^1", "hall": "-P 2 2 (1/2*x,1/2*y,z)", "hermann_mauguin": "P m m m", "ncsym": ["x,y,z", "-x,y,z", "x,-y,z", "-x,-y,z", "x+1/2,y,z", "-x+1/2,y,z", "x+1/2,-y,z", "-x+1/2,-y,z"], "short_h_m": "Pmmm", "hermann_mauguin_u": "Pmmm", "point_group": "mmm"}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z"], "universal_h_m": "P 1 21 1 (a-1/4,b,c)", "number": 4, "schoenflies": "C2^2", "hall": " P 2yb (x+1/4,y,z)", "hermann_mauguin": "P 1 21 1", "ncsym": ["x,y,z", "-x+1/2,y+1/2,-z"], "short_h_m": "P2_1", "hermann_mauguin_u": "P12_11", "point_group": "2"}, {"symops": ["x,y,z", "-x+1/2,y+1/2,-z", "-x,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,-y,-z+1/2", "x+1/2,-y+1/2,z+1/2", "x,y,-z", "-x+1/2,y+1/2,z"], "universal_h_m": "P n m a (c,a-1/4,b)", "number": 62, "schoenflies": "D2h^16", "hall": "-P 2ac 2n (z,x,y+1/4)", "hermann_mauguin": "P n m a", "ncsym": ["x,y,z", "-x+1/2,y+1/2,-z", "-x,-y,z+1/2", "x+1/2,-y+1/2,-z+1/2", "-x,-y,-z+1/2", "x+1/2,-y+1/2,z+1/2", "x,y,-z", "-x+1/2,y+1/2,z"], "short_h_m": "Pnma", "hermann_mauguin_u": "Pnma", "point_group": "mmm"}] diff --git a/pymatgen/symmetry/symm_ops.yaml b/src/pymatgen/symmetry/symm_ops.yaml similarity index 100% rename from pymatgen/symmetry/symm_ops.yaml rename to src/pymatgen/symmetry/symm_ops.yaml diff --git a/pymatgen/transformations/__init__.py b/src/pymatgen/transformations/__init__.py similarity index 100% rename from pymatgen/transformations/__init__.py rename to src/pymatgen/transformations/__init__.py diff --git a/pymatgen/transformations/advanced_transformations.py b/src/pymatgen/transformations/advanced_transformations.py similarity index 98% rename from pymatgen/transformations/advanced_transformations.py rename to src/pymatgen/transformations/advanced_transformations.py index 3e44b713df6..57b89c43efe 100644 --- a/pymatgen/transformations/advanced_transformations.py +++ b/src/pymatgen/transformations/advanced_transformations.py @@ -16,7 +16,6 @@ from monty.dev import requires from monty.fractions import lcm from monty.json import MSONable - from pymatgen.analysis.adsorption import AdsorbateSiteFinder from pymatgen.analysis.bond_valence import BVAnalyzer from pymatgen.analysis.energy_models import SymmetryModel @@ -461,7 +460,7 @@ def sort_func(struct): self._all_structures = sorted(all_structures, key=sort_func) if return_ranked_list: - return self._all_structures[0:num_to_return] + return self._all_structures[:num_to_return] return self._all_structures[0]["structure"] def __repr__(self): @@ -638,7 +637,7 @@ def __init__(self, mag_species_spin, order_parameter=0.5, energy_model=None, **k if not any(ops): raise ValueError("Order parameter not correctly defined.") else: - raise ValueError("Order parameter not correctly defined.") + raise ValueError("Order parameter not correctly defined.") # noqa: TRY004 self.mag_species_spin = mag_species_spin # store order parameter constraints as dicts to save implementing @@ -860,9 +859,9 @@ def apply_transformation( alls = self._remove_dummy_species(alls) alls = self._add_spin_magnitudes(alls) # type: ignore[arg-type] else: - for idx in range(len(alls)): - alls[idx]["structure"] = self._remove_dummy_species(alls[idx]["structure"]) # type: ignore[index] - alls[idx]["structure"] = self._add_spin_magnitudes(alls[idx]["structure"]) # type: ignore[index, arg-type] + for idx, struct in enumerate(alls): + alls[idx]["structure"] = self._remove_dummy_species(struct["structure"]) # type: ignore[index] + alls[idx]["structure"] = self._add_spin_magnitudes(struct["structure"]) # type: ignore[index, arg-type] try: num_to_return = int(return_ranked_list) @@ -872,7 +871,7 @@ def apply_transformation( if num_to_return == 1 or not return_ranked_list: return alls[0]["structure"] if num_to_return else alls # type: ignore[return-value, index] - # remove duplicate structures and group according to energy model + # Remove duplicate structures and group according to energy model matcher = StructureMatcher(comparator=SpinComparator()) def key(struct: Structure) -> int: @@ -880,13 +879,13 @@ def key(struct: Structure) -> int: out = [] for _, group in groupby(sorted((dct["structure"] for dct in alls), key=key), key): # type: ignore[arg-type, index] - group = list(group) # type: ignore + group = list(group) # type: ignore[assignment] grouped = matcher.group_structures(group) out.extend([{"structure": g[0], "energy": self.energy_model.get_energy(g[0])} for g in grouped]) self._all_structures = sorted(out, key=lambda dct: dct["energy"]) - return self._all_structures[0:num_to_return] # type: ignore + return self._all_structures[:num_to_return] # type: ignore[return-value] @property def is_one_to_many(self) -> bool: @@ -1034,13 +1033,13 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | supercell = structure * scaling nsp = supercell.composition[sp] if sp.oxi_state == ox: - supercell.replace_species({sp: {sp: (nsp - 1) / nsp, self.dopant: 1 / nsp}}) # type: ignore + supercell.replace_species({sp: {sp: (nsp - 1) / nsp, self.dopant: 1 / nsp}}) logger.info(f"Doping {sp} for {self.dopant} at level {1 / nsp:.3f}") elif self.codopant: - codopant = find_codopant(sp, 2 * sp.oxi_state - ox) # type: ignore - supercell.replace_species({sp: {sp: (nsp - 2) / nsp, self.dopant: 1 / nsp, codopant: 1 / nsp}}) # type: ignore + codopant = find_codopant(sp, 2 * sp.oxi_state - ox) # type: ignore[arg-type, operator] + supercell.replace_species({sp: {sp: (nsp - 2) / nsp, self.dopant: 1 / nsp, codopant: 1 / nsp}}) logger.info(f"Doping {sp} for {self.dopant} + {codopant} at level {1 / nsp:.3f}") - elif abs(sp.oxi_state) < abs(ox): # type: ignore + elif abs(sp.oxi_state) < abs(ox): # type: ignore[arg-type] # Strategy: replace the target species with a # combination of dopant and vacancy. # We will choose the lowest oxidation state species as a @@ -1048,20 +1047,18 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | # energy sp_to_remove = min( (s for s in comp if s.oxi_state * ox > 0), - key=lambda ss: abs(ss.oxi_state), # type: ignore + key=lambda ss: abs(ss.oxi_state), # type: ignore[arg-type] ) if sp_to_remove == sp: - common_charge = lcm(int(abs(sp.oxi_state)), int(abs(ox))) # type: ignore + common_charge = lcm(int(abs(sp.oxi_state)), int(abs(ox))) # type: ignore[arg-type] n_dopant = common_charge / abs(ox) - nsp_to_remove = common_charge / abs(sp.oxi_state) # type: ignore + nsp_to_remove = common_charge / abs(sp.oxi_state) # type: ignore[arg-type] logger.info(f"Doping {nsp_to_remove} {sp} with {n_dopant} {self.dopant}.") - supercell.replace_species( - {sp: {sp: (nsp - nsp_to_remove) / nsp, self.dopant: n_dopant / nsp}} # type: ignore - ) + supercell.replace_species({sp: {sp: (nsp - nsp_to_remove) / nsp, self.dopant: n_dopant / nsp}}) else: ox_diff = int(abs(round(sp.oxi_state - ox))) - vac_ox = int(abs(sp_to_remove.oxi_state)) * ox_diff # type: ignore + vac_ox = int(abs(sp_to_remove.oxi_state)) * ox_diff # type: ignore[arg-type] common_charge = lcm(vac_ox, ox_diff) n_dopant = common_charge / ox_diff nx_to_remove = common_charge / vac_ox @@ -1071,11 +1068,11 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | ) supercell.replace_species( { - sp: {sp: (nsp - n_dopant) / nsp, self.dopant: n_dopant / nsp}, # type: ignore - sp_to_remove: {sp_to_remove: (nx - nx_to_remove) / nx}, # type: ignore + sp: {sp: (nsp - n_dopant) / nsp, self.dopant: n_dopant / nsp}, + sp_to_remove: {sp_to_remove: (nx - nx_to_remove) / nx}, } ) - elif abs(sp.oxi_state) > abs(ox): # type: ignore + elif abs(sp.oxi_state) > abs(ox): # type: ignore[arg-type] # Strategy: replace the target species with dopant and also # remove some opposite charged species for charge neutrality if ox > 0: @@ -1083,10 +1080,10 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | else: sp_to_remove = min(supercell.composition, key=lambda el: el.X) # Confirm species are of opposite oxidation states. - assert sp_to_remove.oxi_state * sp.oxi_state < 0 # type: ignore + assert sp_to_remove.oxi_state * sp.oxi_state < 0 # type: ignore[operator] ox_diff = int(abs(round(sp.oxi_state - ox))) - anion_ox = int(abs(sp_to_remove.oxi_state)) # type: ignore + anion_ox = int(abs(sp_to_remove.oxi_state)) # type: ignore[arg-type] nx = supercell.composition[sp_to_remove] common_charge = lcm(anion_ox, ox_diff) n_dopant = common_charge / ox_diff @@ -1094,8 +1091,8 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | logger.info(f"Doping {n_dopant} {sp} with {self.dopant} and removing {nx_to_remove} {sp_to_remove}.") supercell.replace_species( { - sp: {sp: (nsp - n_dopant) / nsp, self.dopant: n_dopant / nsp}, # type: ignore - sp_to_remove: {sp_to_remove: (nx - nx_to_remove) / nx}, # type: ignore + sp: {sp: (nsp - n_dopant) / nsp, self.dopant: n_dopant / nsp}, + sp_to_remove: {sp_to_remove: (nx - nx_to_remove) / nx}, } ) @@ -1233,7 +1230,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | if not return_ranked_list: return disordered_structures[0]["structure"] if len(disordered_structures) > return_ranked_list: - disordered_structures = disordered_structures[0:return_ranked_list] + disordered_structures = disordered_structures[:return_ranked_list] return disordered_structures @property @@ -1494,7 +1491,7 @@ def apply_transformation(self, structure: Structure) -> Structure: target_sc_size = self.min_length while sc_not_found: target_sc_lat_vecs = np.eye(3, 3) * target_sc_size - self.transformation_matrix = target_sc_lat_vecs @ np.linalg.inv(lat_vecs) # type: ignore + self.transformation_matrix = target_sc_lat_vecs @ np.linalg.inv(lat_vecs) # round the entries of T and force T to be non-singular self.transformation_matrix = _round_and_make_arr_singular( # type: ignore[assignment] diff --git a/pymatgen/transformations/site_transformations.py b/src/pymatgen/transformations/site_transformations.py similarity index 99% rename from pymatgen/transformations/site_transformations.py rename to src/pymatgen/transformations/site_transformations.py index 189adbbcda0..7ba3151fc90 100644 --- a/pymatgen/transformations/site_transformations.py +++ b/src/pymatgen/transformations/site_transformations.py @@ -14,7 +14,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.analysis.ewald import EwaldMinimizer, EwaldSummation from pymatgen.analysis.local_env import MinimumDistanceNN from pymatgen.symmetry.analyzer import SpacegroupAnalyzer @@ -442,7 +441,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | raise ValueError("Invalid algo.") opt_s = all_structures[0]["structure"] - return opt_s if not return_ranked_list else all_structures[0:num_to_return] + return opt_s if not return_ranked_list else all_structures[:num_to_return] def __repr__(self): return f"PartialRemoveSitesTransformation : Indices and fraction to remove = {self.indices}, ALGO = {self.algo}" diff --git a/pymatgen/transformations/standard_transformations.py b/src/pymatgen/transformations/standard_transformations.py similarity index 99% rename from pymatgen/transformations/standard_transformations.py rename to src/pymatgen/transformations/standard_transformations.py index ec5fa46e020..616c7de84a7 100644 --- a/pymatgen/transformations/standard_transformations.py +++ b/src/pymatgen/transformations/standard_transformations.py @@ -12,7 +12,6 @@ import numpy as np from numpy import around - from pymatgen.analysis.bond_valence import BVAnalyzer from pymatgen.analysis.elasticity.strain import Deformation from pymatgen.analysis.ewald import EwaldMinimizer, EwaldSummation @@ -25,10 +24,9 @@ from pymatgen.transformations.transformation_abc import AbstractTransformation if TYPE_CHECKING: - from typing_extensions import Self - from pymatgen.core.sites import PeriodicSite from pymatgen.util.typing import SpeciesLike + from typing_extensions import Self logger = logging.getLogger(__name__) @@ -218,7 +216,7 @@ def from_boundary_distance( # Try to find a scaling_matrix satisfying the required boundary distance with smaller cell. if allow_rotation and sum(min_expand != 0) > 1: - min1, min2, min3 = map(int, min_expand) # type: ignore # map(int) just for mypy's sake + min1, min2, min3 = map(int, min_expand) scaling_matrix = [ [min1 or 1, 1 if min1 and min2 else 0, 1 if min1 and min3 else 0], [-1 if min2 and min1 else 0, min2 or 1, 1 if min2 and min3 else 0], @@ -279,9 +277,9 @@ def __init__( """ self.species_map = species_map self._species_map = dict(species_map) - for k, v in self._species_map.items(): - if isinstance(v, (tuple, list)): - self._species_map[k] = dict(v) # type: ignore[assignment] + for key, val in self._species_map.items(): + if isinstance(val, (tuple, list)): + self._species_map[key] = dict(val) # type: ignore[assignment] def apply_transformation(self, structure: Structure) -> Structure: """Apply the transformation. diff --git a/pymatgen/transformations/transformation_abc.py b/src/pymatgen/transformations/transformation_abc.py similarity index 100% rename from pymatgen/transformations/transformation_abc.py rename to src/pymatgen/transformations/transformation_abc.py diff --git a/pymatgen/util/__init__.py b/src/pymatgen/util/__init__.py similarity index 100% rename from pymatgen/util/__init__.py rename to src/pymatgen/util/__init__.py diff --git a/pymatgen/util/coord.py b/src/pymatgen/util/coord.py similarity index 99% rename from pymatgen/util/coord.py rename to src/pymatgen/util/coord.py index eabbc2dadfa..e00dceb5655 100644 --- a/pymatgen/util/coord.py +++ b/src/pymatgen/util/coord.py @@ -11,7 +11,6 @@ import numpy as np from monty.json import MSONable - from pymatgen.util import coord_cython if TYPE_CHECKING: @@ -19,7 +18,6 @@ from typing import Literal from numpy.typing import ArrayLike - from pymatgen.util.typing import PbcLike diff --git a/pymatgen/util/coord_cython.pyx b/src/pymatgen/util/coord_cython.pyx similarity index 99% rename from pymatgen/util/coord_cython.pyx rename to src/pymatgen/util/coord_cython.pyx index 54c72e92508..3e553ebe80a 100644 --- a/pymatgen/util/coord_cython.pyx +++ b/src/pymatgen/util/coord_cython.pyx @@ -20,6 +20,8 @@ cimport numpy as np from libc.math cimport fabs, round from libc.stdlib cimport free, malloc +np.import_array() + #create images, 2d array of all length 3 combinations of [-1,0,1] rng = np.arange(-1, 2, dtype=np.float_) arange = rng[:, None] * np.array([1, 0, 0])[None, :] diff --git a/pymatgen/util/due.py b/src/pymatgen/util/due.py similarity index 94% rename from pymatgen/util/due.py rename to src/pymatgen/util/due.py index 62e27c63766..2f77758a45c 100644 --- a/pymatgen/util/due.py +++ b/src/pymatgen/util/due.py @@ -51,7 +51,7 @@ def _donothing_func(*args, **kwargs): raise RuntimeError("Imported due lacks .cite. DueCredit is now disabled") except Exception as exc: if not isinstance(exc, ImportError): - logging.getLogger("duecredit").error(f"Failed to import duecredit due to {exc}") + logging.getLogger("duecredit").exception("Failed to import duecredit") # Initiate due stub due = InactiveDueCreditCollector() BibTeX = Doi = Url = Text = _donothing_func diff --git a/pymatgen/util/graph_hashing.py b/src/pymatgen/util/graph_hashing.py similarity index 100% rename from pymatgen/util/graph_hashing.py rename to src/pymatgen/util/graph_hashing.py diff --git a/pymatgen/util/io_utils.py b/src/pymatgen/util/io_utils.py similarity index 100% rename from pymatgen/util/io_utils.py rename to src/pymatgen/util/io_utils.py diff --git a/pymatgen/util/num.py b/src/pymatgen/util/num.py similarity index 100% rename from pymatgen/util/num.py rename to src/pymatgen/util/num.py diff --git a/pymatgen/util/numba.py b/src/pymatgen/util/numba.py similarity index 100% rename from pymatgen/util/numba.py rename to src/pymatgen/util/numba.py diff --git a/pymatgen/util/plotly_chempot_layouts.json b/src/pymatgen/util/plotly_chempot_layouts.json similarity index 100% rename from pymatgen/util/plotly_chempot_layouts.json rename to src/pymatgen/util/plotly_chempot_layouts.json diff --git a/pymatgen/util/plotly_interface_rxn_layouts.json b/src/pymatgen/util/plotly_interface_rxn_layouts.json similarity index 100% rename from pymatgen/util/plotly_interface_rxn_layouts.json rename to src/pymatgen/util/plotly_interface_rxn_layouts.json diff --git a/pymatgen/util/plotly_pd_layouts.json b/src/pymatgen/util/plotly_pd_layouts.json similarity index 100% rename from pymatgen/util/plotly_pd_layouts.json rename to src/pymatgen/util/plotly_pd_layouts.json diff --git a/pymatgen/util/plotting.py b/src/pymatgen/util/plotting.py similarity index 99% rename from pymatgen/util/plotting.py rename to src/pymatgen/util/plotting.py index 13958cc9b22..b94cba844e0 100644 --- a/pymatgen/util/plotting.py +++ b/src/pymatgen/util/plotting.py @@ -12,7 +12,6 @@ import numpy as np import palettable.colorbrewer.diverging from matplotlib import cm, colors - from pymatgen.core import Element if TYPE_CHECKING: diff --git a/pymatgen/util/provenance.py b/src/pymatgen/util/provenance.py similarity index 99% rename from pymatgen/util/provenance.py rename to src/pymatgen/util/provenance.py index 4402653b9b5..0e72704b1cc 100644 --- a/pymatgen/util/provenance.py +++ b/src/pymatgen/util/provenance.py @@ -10,7 +10,6 @@ from typing import TYPE_CHECKING, NamedTuple from monty.json import MontyDecoder, MontyEncoder - from pymatgen.core.structure import Molecule, Structure try: @@ -214,7 +213,7 @@ def __init__( # check that references are valid BibTeX if not isinstance(references, str): - raise ValueError("Invalid format for SNL reference! Should be empty string or BibTeX string.") + raise TypeError("Invalid format for SNL reference! Should be empty string or BibTeX string.") if references and not is_valid_bibtex(references): raise ValueError("Invalid format for SNL reference! Should be BibTeX string.") if len(references) > MAX_BIBTEX_CHARS: diff --git a/pymatgen/util/string.py b/src/pymatgen/util/string.py similarity index 97% rename from pymatgen/util/string.py rename to src/pymatgen/util/string.py index c8d1703bb87..48a681c40cc 100644 --- a/pymatgen/util/string.py +++ b/src/pymatgen/util/string.py @@ -71,13 +71,13 @@ def to_unicode_string(self): with systems where the sub and superscripts are pure integers. """ str_ = self.to_latex_string() - for m in re.finditer(r"\$_\{(\d+)\}\$", str_): - s1 = m.group() - s2 = [SUBSCRIPT_UNICODE[s] for s in m.group(1)] + for match in re.finditer(r"\$_\{(\d+)\}\$", str_): + s1 = match.group() + s2 = [SUBSCRIPT_UNICODE[s] for s in match[1]] str_ = str_.replace(s1, "".join(s2)) - for m in re.finditer(r"\$\^\{([\d\+\-]+)\}\$", str_): - s1 = m.group() - s2 = [SUPERSCRIPT_UNICODE[s] for s in m.group(1)] + for match in re.finditer(r"\$\^\{([\d\+\-]+)\}\$", str_): + s1 = match.group() + s2 = [SUPERSCRIPT_UNICODE[s] for s in match[1]] str_ = str_.replace(s1, "".join(s2)) return str_ @@ -416,4 +416,4 @@ def disordered_formula(disordered_struct, symbols=("x", "y", "z"), fmt="plain"): disordered_formula.append(" ") disordered_formula += [f"{key}={formula_double_format(val)} " for key, val in variable_map.items()] - return "".join(map(str, disordered_formula))[0:-1] + return "".join(map(str, disordered_formula))[:-1] diff --git a/pymatgen/util/structures/BaNiO3.json b/src/pymatgen/util/structures/BaNiO3.json similarity index 100% rename from pymatgen/util/structures/BaNiO3.json rename to src/pymatgen/util/structures/BaNiO3.json diff --git a/pymatgen/util/structures/CsCl.json b/src/pymatgen/util/structures/CsCl.json similarity index 100% rename from pymatgen/util/structures/CsCl.json rename to src/pymatgen/util/structures/CsCl.json diff --git a/pymatgen/util/structures/Graphite.json b/src/pymatgen/util/structures/Graphite.json similarity index 100% rename from pymatgen/util/structures/Graphite.json rename to src/pymatgen/util/structures/Graphite.json diff --git a/pymatgen/util/structures/He_BCC.json b/src/pymatgen/util/structures/He_BCC.json similarity index 100% rename from pymatgen/util/structures/He_BCC.json rename to src/pymatgen/util/structures/He_BCC.json diff --git a/pymatgen/util/structures/K2O2.json b/src/pymatgen/util/structures/K2O2.json similarity index 100% rename from pymatgen/util/structures/K2O2.json rename to src/pymatgen/util/structures/K2O2.json diff --git a/pymatgen/util/structures/La2CoO4F.json b/src/pymatgen/util/structures/La2CoO4F.json similarity index 100% rename from pymatgen/util/structures/La2CoO4F.json rename to src/pymatgen/util/structures/La2CoO4F.json diff --git a/pymatgen/util/structures/Li10GeP2S12.json b/src/pymatgen/util/structures/Li10GeP2S12.json similarity index 100% rename from pymatgen/util/structures/Li10GeP2S12.json rename to src/pymatgen/util/structures/Li10GeP2S12.json diff --git a/pymatgen/util/structures/Li2O.json b/src/pymatgen/util/structures/Li2O.json similarity index 100% rename from pymatgen/util/structures/Li2O.json rename to src/pymatgen/util/structures/Li2O.json diff --git a/pymatgen/util/structures/Li2O2.json b/src/pymatgen/util/structures/Li2O2.json similarity index 100% rename from pymatgen/util/structures/Li2O2.json rename to src/pymatgen/util/structures/Li2O2.json diff --git a/pymatgen/util/structures/Li3V2(PO4)3.json b/src/pymatgen/util/structures/Li3V2(PO4)3.json similarity index 100% rename from pymatgen/util/structures/Li3V2(PO4)3.json rename to src/pymatgen/util/structures/Li3V2(PO4)3.json diff --git a/pymatgen/util/structures/LiFePO4.json b/src/pymatgen/util/structures/LiFePO4.json similarity index 100% rename from pymatgen/util/structures/LiFePO4.json rename to src/pymatgen/util/structures/LiFePO4.json diff --git a/pymatgen/util/structures/NaFePO4.json b/src/pymatgen/util/structures/NaFePO4.json similarity index 100% rename from pymatgen/util/structures/NaFePO4.json rename to src/pymatgen/util/structures/NaFePO4.json diff --git a/pymatgen/util/structures/Pb2TiZrO6.json b/src/pymatgen/util/structures/Pb2TiZrO6.json similarity index 100% rename from pymatgen/util/structures/Pb2TiZrO6.json rename to src/pymatgen/util/structures/Pb2TiZrO6.json diff --git a/pymatgen/util/structures/Si.json b/src/pymatgen/util/structures/Si.json similarity index 100% rename from pymatgen/util/structures/Si.json rename to src/pymatgen/util/structures/Si.json diff --git a/pymatgen/util/structures/SiO2.json b/src/pymatgen/util/structures/SiO2.json similarity index 100% rename from pymatgen/util/structures/SiO2.json rename to src/pymatgen/util/structures/SiO2.json diff --git a/pymatgen/util/structures/Si_SiO2_Interface.json b/src/pymatgen/util/structures/Si_SiO2_Interface.json similarity index 100% rename from pymatgen/util/structures/Si_SiO2_Interface.json rename to src/pymatgen/util/structures/Si_SiO2_Interface.json diff --git a/pymatgen/util/structures/Sn.json b/src/pymatgen/util/structures/Sn.json similarity index 100% rename from pymatgen/util/structures/Sn.json rename to src/pymatgen/util/structures/Sn.json diff --git a/pymatgen/util/structures/SrTiO3.json b/src/pymatgen/util/structures/SrTiO3.json similarity index 100% rename from pymatgen/util/structures/SrTiO3.json rename to src/pymatgen/util/structures/SrTiO3.json diff --git a/pymatgen/util/structures/TiO2.json b/src/pymatgen/util/structures/TiO2.json similarity index 100% rename from pymatgen/util/structures/TiO2.json rename to src/pymatgen/util/structures/TiO2.json diff --git a/pymatgen/util/structures/TlBiSe2.json b/src/pymatgen/util/structures/TlBiSe2.json similarity index 100% rename from pymatgen/util/structures/TlBiSe2.json rename to src/pymatgen/util/structures/TlBiSe2.json diff --git a/pymatgen/util/structures/VO2.json b/src/pymatgen/util/structures/VO2.json similarity index 100% rename from pymatgen/util/structures/VO2.json rename to src/pymatgen/util/structures/VO2.json diff --git a/pymatgen/util/testing/__init__.py b/src/pymatgen/util/testing/__init__.py similarity index 94% rename from pymatgen/util/testing/__init__.py rename to src/pymatgen/util/testing/__init__.py index c95fff8eada..211690effa9 100644 --- a/pymatgen/util/testing/__init__.py +++ b/src/pymatgen/util/testing/__init__.py @@ -1,8 +1,8 @@ -"""Common test support for pymatgen test scripts. +"""This module implements testing utilities for materials science codes. -This single module should provide all the common functionality for pymatgen -tests in a single location, so that test scripts can just import it and work -right away. +While the primary use is within pymatgen, the functionality is meant to be useful for external materials science +codes as well. For instance, obtaining example crystal structures to perform tests, specialized assert methods for +materials science, etc. """ from __future__ import annotations @@ -17,7 +17,6 @@ import pytest from monty.json import MontyDecoder, MontyEncoder, MSONable from monty.serialization import loadfn - from pymatgen.core import ROOT, SETTINGS, Structure if TYPE_CHECKING: @@ -26,7 +25,7 @@ MODULE_DIR = Path(__file__).absolute().parent STRUCTURES_DIR = MODULE_DIR / ".." / "structures" -TEST_FILES_DIR = Path(SETTINGS.get("PMG_TEST_FILES_DIR", f"{ROOT}/tests/files")) +TEST_FILES_DIR = Path(SETTINGS.get("PMG_TEST_FILES_DIR", f"{ROOT}/../tests/files")) VASP_IN_DIR = f"{TEST_FILES_DIR}/io/vasp/inputs" VASP_OUT_DIR = f"{TEST_FILES_DIR}/io/vasp/outputs" # fake POTCARs have original header information, meaning properties like number of electrons, diff --git a/pymatgen/util/testing/aims.py b/src/pymatgen/util/testing/aims.py similarity index 99% rename from pymatgen/util/testing/aims.py rename to src/pymatgen/util/testing/aims.py index 057df663083..ce5b85525a7 100644 --- a/pymatgen/util/testing/aims.py +++ b/src/pymatgen/util/testing/aims.py @@ -10,7 +10,6 @@ import numpy as np from monty.io import zopen - from pymatgen.core import Molecule, Structure diff --git a/pymatgen/util/typing.py b/src/pymatgen/util/typing.py similarity index 100% rename from pymatgen/util/typing.py rename to src/pymatgen/util/typing.py diff --git a/src/pymatgen/vis/ElementColorSchemes.yaml b/src/pymatgen/vis/ElementColorSchemes.yaml new file mode 100644 index 00000000000..c9896d6c732 --- /dev/null +++ b/src/pymatgen/vis/ElementColorSchemes.yaml @@ -0,0 +1,220 @@ +Jmol: + Ac: [ 112, 171, 250 ] + Ag: [ 192, 192, 192 ] + Al: [ 191, 166, 166 ] + Am: [ 84, 92, 242 ] + Ar: [ 128, 209, 227 ] + As: [ 189, 128, 227 ] + At: [ 117, 79, 69 ] + Au: [ 255, 209, 35 ] + B: [ 255, 181, 181 ] + Ba: [ 0, 201, 0 ] + Be: [ 194, 255, 0 ] + Bh: [ 224, 0, 56 ] + Bi: [ 158, 79, 181 ] + Bk: [ 138, 79, 227 ] + Br: [ 166, 41, 41 ] + C: [ 144, 144, 144 ] + Ca: [ 61, 255, 0 ] + Cd: [ 255, 217, 143 ] + Ce: [ 255, 255, 199 ] + Cf: [ 161, 54, 212 ] + Cl: [ 31, 240, 31 ] + Cm: [ 120, 92, 227 ] + Co: [ 240, 144, 160 ] + Cr: [ 138, 153, 199 ] + Cs: [ 87, 23, 143 ] + Cu: [ 200, 128, 51 ] + Db: [ 209, 0, 79 ] + Dy: [ 31, 255, 199 ] + Er: [ 0, 230, 117 ] + Es: [ 179, 31, 212 ] + Eu: [ 97, 255, 199 ] + F: [ 144, 224, 80 ] + Fe: [ 224, 102, 51 ] + Fm: [ 179, 31, 186 ] + Fr: [ 66, 0, 102 ] + Ga: [ 194, 143, 143 ] + Gd: [ 69, 255, 199 ] + Ge: [ 102, 143, 143 ] + H: [ 255, 255, 255 ] + He: [ 217, 255, 255 ] + Hf: [ 77, 194, 255 ] + Hg: [ 184, 184, 208 ] + Ho: [ 0, 255, 156 ] + Hs: [ 230, 0, 46 ] + I: [ 148, 0, 148 ] + In: [ 166, 117, 115 ] + Ir: [ 23, 84, 135 ] + K: [ 143, 64, 212 ] + Kr: [ 92, 184, 209 ] + La: [ 112, 212, 255 ] + Li: [ 204, 128, 255 ] + Lr: [ 199, 0, 102 ] + Lu: [ 0, 171, 36 ] + Md: [ 179, 13, 166 ] + Mg: [ 138, 255, 0 ] + Mn: [ 156, 122, 199 ] + Mo: [ 84, 181, 181 ] + Mt: [ 235, 0, 38 ] + N: [ 48, 80, 248 ] + Na: [ 171, 92, 242 ] + Nb: [ 115, 194, 201 ] + Nd: [ 199, 255, 199 ] + Ne: [ 179, 227, 245 ] + Ni: [ 80, 208, 80 ] + 'No': [ 189, 13, 135 ] + Np: [ 0, 128, 255 ] + O: [ 255, 13, 13 ] + Os: [ 38, 102, 150 ] + P: [ 255, 128, 0 ] + Pa: [ 0, 161, 255 ] + Pb: [ 87, 89, 97 ] + Pd: [ 0, 105, 133 ] + Pm: [ 163, 255, 199 ] + Po: [ 171, 92, 0 ] + Pr: [ 217, 255, 199 ] + Pt: [ 208, 208, 224 ] + Pu: [ 0, 107, 255 ] + Ra: [ 0, 125, 0 ] + Rb: [ 112, 46, 176 ] + Re: [ 38, 125, 171 ] + Rf: [ 204, 0, 89 ] + Rh: [ 10, 125, 140 ] + Rn: [ 66, 130, 150 ] + Ru: [ 36, 143, 143 ] + S: [ 255, 255, 48 ] + Sb: [ 158, 99, 181 ] + Sc: [ 230, 230, 230 ] + Se: [ 255, 161, 0 ] + Sg: [ 217, 0, 69 ] + Si: [ 240, 200, 160 ] + Sm: [ 143, 255, 199 ] + Sn: [ 102, 128, 128 ] + Sr: [ 0, 255, 0 ] + Ta: [ 77, 166, 255 ] + Tb: [ 48, 255, 199 ] + Tc: [ 59, 158, 158 ] + Te: [ 212, 122, 0 ] + Th: [ 0, 186, 255 ] + Ti: [ 191, 194, 199 ] + Tl: [ 166, 84, 77 ] + Tm: [ 0, 212, 82 ] + U: [ 0, 143, 255 ] + V: [ 166, 166, 171 ] + W: [ 33, 148, 214 ] + Xe: [ 66, 158, 176 ] + Y: [ 148, 255, 255 ] + Yb: [ 0, 191, 56 ] + Zn: [ 125, 128, 176 ] + Zr: [ 148, 224, 224 ] +VESTA: + Ac: [ 112, 171, 250 ] + Ag: [ 192, 192, 192 ] + Al: [ 129, 178, 214 ] + Am: [ 84, 92, 242 ] + Ar: [ 207, 254, 196 ] + As: [ 116, 208, 87 ] + At: [ 117, 79, 69 ] + Au: [ 255, 209, 35 ] + B: [ 31, 162, 15 ] + Ba: [ 0, 201, 0 ] + Be: [ 94, 215, 123 ] + Bh: [ 224, 0, 56 ] + Bi: [ 158, 79, 181 ] + Bk: [ 138, 79, 227 ] + Br: [ 126, 49, 2 ] + C: [ 76, 76, 76 ] + Ca: [ 90, 150, 189 ] + Cd: [ 255, 217, 143 ] + Ce: [ 255, 255, 199 ] + Cf: [ 161, 54, 212 ] + Cl: [ 49, 252, 2 ] + Cm: [ 120, 92, 227 ] + Co: [ 0, 0, 175 ] + Cr: [ 0, 0, 158 ] + Cs: [ 87, 23, 143 ] + Cu: [ 34, 71, 220 ] + Db: [ 209, 0, 79 ] + Dy: [ 31, 255, 199 ] + Er: [ 0, 230, 117 ] + Es: [ 179, 31, 212 ] + Eu: [ 97, 255, 199 ] + F: [ 176, 185, 230 ] + Fe: [ 181, 113, 0 ] + Fm: [ 179, 31, 186 ] + Fr: [ 66, 0, 102 ] + Ga: [ 158, 227, 115 ] + Gd: [ 69, 255, 199 ] + Ge: [ 126, 110, 166 ] + H: [ 255, 204, 204 ] + He: [ 252, 232, 206 ] + Hf: [ 77, 194, 255 ] + Hg: [ 184, 184, 208 ] + Ho: [ 0, 255, 156 ] + Hs: [ 230, 0, 46 ] + I: [ 148, 0, 148 ] + In: [ 166, 117, 115 ] + Ir: [ 23, 84, 135 ] + K: [ 161, 33, 246 ] + Kr: [ 250, 193, 243 ] + La: [ 90, 196, 73 ] + Li: [ 134, 223, 115 ] + Lr: [ 199, 0, 102 ] + Lu: [ 0, 171, 36 ] + Md: [ 179, 13, 166 ] + Mg: [ 251, 123, 21 ] + Mn: [ 167, 8, 157 ] + Mo: [ 84, 181, 181 ] + Mt: [ 235, 0, 38 ] + N: [ 176, 185, 230 ] + Na: [ 249, 220, 60 ] + Nb: [ 115, 194, 201 ] + Nd: [ 199, 255, 199 ] + Ne: [ 254, 55, 181 ] + Ni: [ 183, 187, 189 ] + 'No': [ 189, 13, 135 ] + Np: [ 0, 128, 255 ] + O: [ 254, 3, 0 ] + Os: [ 38, 102, 150 ] + P: [ 192, 156, 194 ] + Pa: [ 0, 161, 255 ] + Pb: [ 87, 89, 97 ] + Pd: [ 0, 105, 133 ] + Pm: [ 163, 255, 199 ] + Po: [ 171, 92, 0 ] + Pr: [ 217, 255, 199 ] + Pt: [ 208, 208, 224 ] + Pu: [ 0, 107, 255 ] + Ra: [ 0, 125, 0 ] + Rb: [ 112, 46, 176 ] + Re: [ 38, 125, 171 ] + Rf: [ 204, 0, 89 ] + Rh: [ 10, 125, 140 ] + Rn: [ 66, 130, 150 ] + Ru: [ 36, 143, 143 ] + S: [ 255, 250, 0 ] + Sb: [ 158, 99, 181 ] + Sc: [ 181, 99, 171 ] + Se: [ 154, 239, 15 ] + Sg: [ 217, 0, 69 ] + Si: [ 27, 59, 250 ] + Sm: [ 143, 255, 199 ] + Sn: [ 154, 142, 185 ] + Sr: [ 0, 255, 0 ] + Ta: [ 77, 166, 255 ] + Tb: [ 48, 255, 199 ] + Tc: [ 59, 158, 158 ] + Te: [ 212, 122, 0 ] + Th: [ 0, 186, 255 ] + Ti: [ 120, 202, 255 ] + Tl: [ 166, 84, 77 ] + Tm: [ 0, 212, 82 ] + U: [ 0, 143, 255 ] + V: [ 229, 25, 0 ] + W: [ 33, 148, 214 ] + Xe: [ 66, 158, 176 ] + Y: [ 148, 255, 255 ] + Yb: [ 0, 191, 56 ] + Zn: [ 143, 143, 129 ] + Zr: [ 0, 255, 0 ] diff --git a/pymatgen/vis/__init__.py b/src/pymatgen/vis/__init__.py similarity index 100% rename from pymatgen/vis/__init__.py rename to src/pymatgen/vis/__init__.py diff --git a/pymatgen/vis/plotters.py b/src/pymatgen/vis/plotters.py similarity index 95% rename from pymatgen/vis/plotters.py rename to src/pymatgen/vis/plotters.py index 1692c923562..e77d4c92ccb 100644 --- a/pymatgen/vis/plotters.py +++ b/src/pymatgen/vis/plotters.py @@ -5,14 +5,14 @@ import importlib import matplotlib.pyplot as plt - from pymatgen.util.plotting import pretty_plot class SpectrumPlotter: - """Plot Spectrum objects and subclasses. Note that the interface - is extremely flexible given that there are many different ways in which - people want to view spectra. The typical usage is: + """Plot Spectrum objects and subclasses. + + Note that the interface is extremely flexible given that there are many + different ways in which people want to view spectra. The typical usage is: # Initializes plotter with some optional args. Defaults are usually # fine, @@ -129,6 +129,7 @@ def save_plot(self, filename: str, **kwargs): Args: filename (str): Filename to write to. Must include extension to specify image format. + kwargs: passed to get_plot. """ self.get_plot(**kwargs) plt.savefig(filename) diff --git a/pymatgen/vis/structure_chemview.py b/src/pymatgen/vis/structure_chemview.py similarity index 99% rename from pymatgen/vis/structure_chemview.py rename to src/pymatgen/vis/structure_chemview.py index 9007bb9446f..73069535a91 100644 --- a/pymatgen/vis/structure_chemview.py +++ b/src/pymatgen/vis/structure_chemview.py @@ -3,7 +3,6 @@ from __future__ import annotations import numpy as np - from pymatgen.analysis.molecule_structure_comparator import CovalentRadius from pymatgen.symmetry.analyzer import SpacegroupAnalyzer diff --git a/pymatgen/vis/structure_vtk.py b/src/pymatgen/vis/structure_vtk.py similarity index 98% rename from pymatgen/vis/structure_vtk.py rename to src/pymatgen/vis/structure_vtk.py index b309372422c..cdb15313a80 100644 --- a/pymatgen/vis/structure_vtk.py +++ b/src/pymatgen/vis/structure_vtk.py @@ -12,7 +12,6 @@ import numpy as np from monty.dev import requires from monty.serialization import loadfn - from pymatgen.core import PeriodicSite, Species, Structure from pymatgen.util.coord import in_coord_list @@ -629,11 +628,11 @@ def add_faces(self, faces, color, opacity=0.35): else: raise ValueError("Number of points for a face should be >= 3") - def add_edges(self, edges, type="line", linewidth=2, color=(0.0, 0.0, 0.0)): + def add_edges(self, edges, type="line", linewidth=2, color=(0.0, 0.0, 0.0)): # noqa: A002 """ Args: edges (): List of edges - type (): + type (): placeholder linewidth (): Width of line color (nd.array/tuple): RGB color. """ @@ -702,7 +701,7 @@ def add_bonds(self, neighbors, center, color=None, opacity=None, radius=0.1): self.ren.AddActor(actor) def add_picker_fixed(self): - """Create a cell picker.Returns:""" + """Create a cell picker.""" picker = vtk.vtkCellPicker() # Create a Python function to create the text for the text mapper used @@ -772,6 +771,7 @@ class StructureInteractorStyle(TrackballCamera): """A custom interactor style for visualizing structures.""" def __init__(self, parent): + """Initialize StructureInteractorStyle.""" self.parent = parent self.AddObserver("LeftButtonPressEvent", self.leftButtonPressEvent) self.AddObserver("MouseMoveEvent", self.mouseMoveEvent) @@ -779,14 +779,17 @@ def __init__(self, parent): self.AddObserver("KeyPressEvent", self.keyPressEvent) def leftButtonPressEvent(self, obj, event): + """Left mouse button press event.""" self.mouse_motion = 0 self.OnLeftButtonDown() def mouseMoveEvent(self, obj, event): + """Mouse move event.""" self.mouse_motion = 1 self.OnMouseMove() def leftButtonReleaseEvent(self, obj, event): + """Left mouse button release event.""" ren = obj.GetCurrentRenderer() iren = ren.GetRenderWindow().GetInteractor() if self.mouse_motion == 0: @@ -795,6 +798,7 @@ def leftButtonReleaseEvent(self, obj, event): self.OnLeftButtonUp() def keyPressEvent(self, obj, _event): + """Key press event.""" parent = obj.GetCurrentRenderer().parent sym = parent.iren.GetKeySym() @@ -873,19 +877,19 @@ def make_movie(structures, output_filename="movie.mp4", zoom=1.0, fps=20, bitrat vis.write_image(filename.format(idx), 3) filename = f"image%0{sig_fig}d.png" args = ["ffmpeg", "-y", "-i", filename, "-q:v", str(quality), "-r", str(fps), "-b:v", str(bitrate), output_filename] - with subprocess.Popen(args) as p: - p.communicate() + with subprocess.Popen(args) as process: + process.communicate() class MultiStructuresVis(StructureVis): """Visualization for multiple structures.""" - DEFAULT_ANIMATED_MOVIE_OPTIONS: ClassVar[dict[str, str | float]] = dict( - time_between_frames=0.1, - looping_type="restart", - number_of_loops=1, - time_between_loops=1.0, - ) + DEFAULT_ANIMATED_MOVIE_OPTIONS: ClassVar[dict[str, str | float]] = { + "time_between_frames": 0.1, + "looping_type": "restart", + "number_of_loops": 1, + "time_between_loops": 1.0, + } def __init__( self, @@ -1049,7 +1053,7 @@ def apply_tags(self): def set_animated_movie_options(self, animated_movie_options=None): """ Args: - animated_movie_options (): + animated_movie_options (): animated movie options. """ if animated_movie_options is None: self.animated_movie_options = self.DEFAULT_ANIMATED_MOVIE_OPTIONS.copy() @@ -1138,9 +1142,11 @@ class MultiStructuresInteractorStyle(StructureInteractorStyle): """Interactor for MultiStructureVis.""" def __init__(self, parent) -> None: + """Initialize MultiStructuresInteractorStyle.""" StructureInteractorStyle.__init__(self, parent=parent) def keyPressEvent(self, obj, event): + """Key press event.""" parent = obj.GetCurrentRenderer().parent sym = parent.iren.GetKeySym() diff --git a/tasks.py b/tasks.py index 00d3cf0ef0d..d8b87a9f60d 100644 --- a/tasks.py +++ b/tasks.py @@ -1,9 +1,10 @@ """ Pyinvoke tasks.py file for automating releases and admin stuff. -To cut a new pymatgen release, use `invoke update-changelog` followed by `invoke release`. +To cut a new pymatgen release: -Author: Shyue Ping Ong + invoke update-changelog + invoke release """ from __future__ import annotations @@ -19,7 +20,6 @@ import requests from invoke import task from monty.os import cd - from pymatgen.core import __version__ if TYPE_CHECKING: @@ -38,7 +38,7 @@ def make_doc(ctx: Context) -> None: ctx.run("touch apidoc/index.rst", warn=True) ctx.run("rm pymatgen.*.rst", warn=True) # ctx.run("rm pymatgen.*.md", warn=True) - ctx.run("sphinx-apidoc --implicit-namespaces -M -d 7 -o apidoc -f ../pymatgen ../**/tests/*") + ctx.run("sphinx-apidoc --implicit-namespaces -M -d 7 -o apidoc -f ../src/pymatgen ../**/tests/*") # Note: we use HTML building for the API docs to preserve search functionality. ctx.run("sphinx-build -b html apidoc html") # HTML building. @@ -89,12 +89,21 @@ def publish(ctx: Context) -> None: @task def set_ver(ctx: Context, version: str): - with open("setup.py") as file: - contents = file.read() - contents = re.sub(r"version=([^,]+),", f"version={version!r},", contents) + """ + Set version in pyproject.toml file. + + Args: + ctx (Context): The context. + version (str): An input version. + """ + with open("pyproject.toml") as file: + lines = [re.sub(r"^version = \"([^,]+)\"", f'version = "{version}"', line.rstrip()) for line in file] + + with open("pyproject.toml", "w") as file: + file.write("\n".join(lines) + "\n") - with open("setup.py", mode="w") as file: - file.write(contents) + ctx.run("ruff check --fix src") + ctx.run("ruff format pyproject.toml") @task @@ -103,9 +112,10 @@ def release_github(ctx: Context, version: str) -> None: Release to Github using Github API. Args: + ctx (Context): The context. version (str): The version. """ - with open("docs/CHANGES.md") as file: + with open("docs/CHANGES.md", encoding="utf-8") as file: contents = file.read() tokens = re.split(r"\-+", contents) desc = tokens[1].strip() @@ -123,35 +133,7 @@ def release_github(ctx: Context, version: str) -> None: "https://api.github.com/repos/materialsproject/pymatgen/releases", data=json.dumps(payload), headers={"Authorization": f"token {os.environ['GITHUB_RELEASES_TOKEN']}"}, - ) - print(response.text) - - -def post_discourse(version: str) -> None: - """ - Post release announcement to http://discuss.matsci.org/c/pymatgen. - - Args: - version (str): The version. - """ - with open("CHANGES.rst") as file: - contents = file.read() - tokens = re.split(r"\-+", contents) - desc = tokens[1].strip() - tokens = desc.split("\n") - desc = "\n".join(tokens[:-1]).strip() - raw = f"v{version}\n\n{desc}" - payload = { - "topic_id": 36, - "raw": raw, - } - response = requests.post( - "https://discuss.matsci.org/c/pymatgen/posts.json", - data=payload, - params={ - "api_username": os.environ["DISCOURSE_API_USERNAME"], - "api_key": os.environ["DISCOURSE_API_KEY"], - }, + timeout=600, ) print(response.text) @@ -167,15 +149,15 @@ def update_changelog(ctx: Context, version: str | None = None, dry_run: bool = F dry_run (bool, optional): If True, the function will only print the changes without updating the actual change log file. Defaults to False. """ - version = version or f"{datetime.datetime.now():%Y.%-m.%-d}" + version = version or f"{datetime.datetime.now(tz=datetime.timezone.utc):%Y.%-m.%-d}" output = subprocess.check_output(["git", "log", "--pretty=format:%s", f"v{__version__}..HEAD"]) lines = [] ignored_commits = [] for line in output.decode("utf-8").strip().split("\n"): re_match = re.match(r"Merge pull request \#(\d+) from (.*)", line) if re_match and "materialsproject/dependabot/pip" not in line: - pr_number = re_match.group(1) - contributor, pr_name = re_match.group(2).split("/", 1) + pr_number = re_match[1] + contributor, pr_name = re_match[2].split("/", 1) response = requests.get( f"https://api.github.com/repos/materialsproject/pymatgen/pulls/{pr_number}", timeout=600 ) @@ -189,7 +171,7 @@ def update_changelog(ctx: Context, version: str | None = None, dry_run: bool = F break lines += [f" {ll}"] ignored_commits += [line] - with open("docs/CHANGES.md") as file: + with open("docs/CHANGES.md", encoding="utf-8") as file: contents = file.read() delim = "##" tokens = contents.split(delim) @@ -197,7 +179,7 @@ def update_changelog(ctx: Context, version: str | None = None, dry_run: bool = F if dry_run: print(tokens[0] + "##".join(tokens[1:])) else: - with open("docs/CHANGES.md", mode="w") as file: + with open("docs/CHANGES.md", mode="w", encoding="utf-8") as file: file.write(tokens[0] + "##".join(tokens[1:])) ctx.run("open docs/CHANGES.md") print("The following commit messages were not included...") @@ -214,7 +196,7 @@ def release(ctx: Context, version: str | None = None, nodoc: bool = False) -> No version (str, optional): The version to release. nodoc (bool, optional): Whether to skip documentation generation. """ - version = version or f"{datetime.datetime.now():%Y.%-m.%-d}" + version = version or f"{datetime.datetime.now(tz=datetime.timezone.utc):%Y.%-m.%-d}" ctx.run("rm -r dist build pymatgen.egg-info", warn=True) set_ver(ctx, version) if not nodoc: @@ -225,7 +207,7 @@ def release(ctx: Context, version: str | None = None, nodoc: bool = False) -> No release_github(ctx, version) ctx.run("rm -f dist/*.*", warn=True) - ctx.run("python setup.py sdist bdist_wheel", warn=True) + ctx.run("python -m build", warn=True) ctx.run("twine upload --skip-existing dist/*.whl", warn=True) ctx.run("twine upload --skip-existing dist/*.tar.gz", warn=True) # post_discourse(ctx, warn=True) @@ -235,6 +217,9 @@ def release(ctx: Context, version: str | None = None, nodoc: bool = False) -> No def open_doc(ctx: Context) -> None: """ Open local documentation in web browser. + + Args: + ctx (invoke.Context): The context object. """ pth = os.path.abspath("docs/_build/html/index.html") webbrowser.open(f"file://{pth}") diff --git a/tests/alchemy/test_filters.py b/tests/alchemy/test_filters.py index 16737ae67fa..418213e1dd3 100644 --- a/tests/alchemy/test_filters.py +++ b/tests/alchemy/test_filters.py @@ -4,7 +4,6 @@ from unittest import TestCase from monty.json import MontyDecoder - from pymatgen.alchemy.filters import ( ContainsSpecieFilter, RemoveDuplicatesFilter, diff --git a/tests/alchemy/test_materials.py b/tests/alchemy/test_materials.py index c667b27277e..0ec5c800f01 100644 --- a/tests/alchemy/test_materials.py +++ b/tests/alchemy/test_materials.py @@ -4,7 +4,6 @@ from copy import deepcopy import pytest - from pymatgen.alchemy.filters import ContainsSpecieFilter from pymatgen.alchemy.materials import TransformedStructure from pymatgen.core import SETTINGS diff --git a/tests/analysis/chemenv/connectivity/test_connected_components.py b/tests/analysis/chemenv/connectivity/test_connected_components.py index 2768fc5b815..dc9b01e62ea 100644 --- a/tests/analysis/chemenv/connectivity/test_connected_components.py +++ b/tests/analysis/chemenv/connectivity/test_connected_components.py @@ -7,7 +7,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose - from pymatgen.analysis.chemenv.connectivity.connected_components import ConnectedComponent from pymatgen.analysis.chemenv.connectivity.connectivity_finder import ConnectivityFinder from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode diff --git a/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py b/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py index 631aed31b01..ef2109769e5 100644 --- a/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py +++ b/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py @@ -1,8 +1,6 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import ( AdditionalConditionInt, AngleCutoffFloat, @@ -11,6 +9,7 @@ SimplestChemenvStrategy, ) from pymatgen.util.testing import PymatgenTest +from pytest import approx __author__ = "waroquiers" diff --git a/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py b/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py index 3cbda25a5fe..03a323c65e9 100644 --- a/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py +++ b/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py @@ -3,8 +3,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import ( AllCoordinationGeometries, CoordinationGeometry, @@ -12,6 +10,7 @@ SeparationPlane, ) from pymatgen.util.testing import PymatgenTest +from pytest import approx __author__ = "waroquiers" diff --git a/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py b/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py index fc26a3c33af..2428253b876 100644 --- a/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py +++ b/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py @@ -3,8 +3,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import ( AbstractGeometry, @@ -13,6 +11,7 @@ ) from pymatgen.core.structure import Lattice, Structure from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx __author__ = "waroquiers" diff --git a/tests/analysis/chemenv/coordination_environments/test_read_write.py b/tests/analysis/chemenv/coordination_environments/test_read_write.py index 42ee8b8cb91..0bb61b6163a 100644 --- a/tests/analysis/chemenv/coordination_environments/test_read_write.py +++ b/tests/analysis/chemenv/coordination_environments/test_read_write.py @@ -3,8 +3,6 @@ import json from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import ( AngleNbSetWeight, CNBiasNbSetWeight, @@ -23,6 +21,7 @@ from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer from pymatgen.core.structure import Structure from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx __author__ = "waroquiers" diff --git a/tests/analysis/chemenv/coordination_environments/test_structure_environments.py b/tests/analysis/chemenv/coordination_environments/test_structure_environments.py index b9a8ec160d7..8ce3f92ec4b 100644 --- a/tests/analysis/chemenv/coordination_environments/test_structure_environments.py +++ b/tests/analysis/chemenv/coordination_environments/test_structure_environments.py @@ -5,8 +5,6 @@ import numpy as np from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import ( MultiWeightsChemenvStrategy, SimplestChemenvStrategy, @@ -18,6 +16,7 @@ ) from pymatgen.core import Species, Structure from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx __author__ = "waroquiers" diff --git a/tests/analysis/chemenv/coordination_environments/test_voronoi.py b/tests/analysis/chemenv/coordination_environments/test_voronoi.py index cfe7b6af420..2adaa1f343c 100644 --- a/tests/analysis/chemenv/coordination_environments/test_voronoi.py +++ b/tests/analysis/chemenv/coordination_environments/test_voronoi.py @@ -3,7 +3,6 @@ import random import numpy as np - from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure diff --git a/tests/analysis/chemenv/coordination_environments/test_weights.py b/tests/analysis/chemenv/coordination_environments/test_weights.py index f4f117dbe38..5295d47c635 100644 --- a/tests/analysis/chemenv/coordination_environments/test_weights.py +++ b/tests/analysis/chemenv/coordination_environments/test_weights.py @@ -3,8 +3,6 @@ import json import pytest -from pytest import approx - from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import ( AngleNbSetWeight, CNBiasNbSetWeight, @@ -17,6 +15,7 @@ ) from pymatgen.analysis.chemenv.coordination_environments.structure_environments import StructureEnvironments from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx __author__ = "waroquiers" diff --git a/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py b/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py index 10e8ff8eb2e..7124904f7cd 100644 --- a/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py +++ b/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py @@ -5,10 +5,9 @@ import numpy as np from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane from pymatgen.util.testing import PymatgenTest +from pytest import approx __author__ = "David Waroquiers" diff --git a/tests/analysis/chemenv/utils/test_func_utils.py b/tests/analysis/chemenv/utils/test_func_utils.py index 265c26d39f4..e01c3d66cc8 100644 --- a/tests/analysis/chemenv/utils/test_func_utils.py +++ b/tests/analysis/chemenv/utils/test_func_utils.py @@ -2,13 +2,12 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.analysis.chemenv.utils.func_utils import ( CSMFiniteRatioFunction, CSMInfiniteRatioFunction, DeltaCSMRatioFunction, ) +from pytest import approx __author__ = "waroquiers" diff --git a/tests/analysis/chemenv/utils/test_graph_utils.py b/tests/analysis/chemenv/utils/test_graph_utils.py index 54ca8e9ef08..cf7ef01fa30 100644 --- a/tests/analysis/chemenv/utils/test_graph_utils.py +++ b/tests/analysis/chemenv/utils/test_graph_utils.py @@ -2,7 +2,6 @@ import pytest from numpy.testing import assert_allclose - from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode from pymatgen.analysis.chemenv.utils.graph_utils import MultiGraphCycle, SimpleGraphCycle, get_delta from pymatgen.util.testing import PymatgenTest diff --git a/tests/analysis/chemenv/utils/test_math_utils.py b/tests/analysis/chemenv/utils/test_math_utils.py index 87420c9c61e..3b0cab7d229 100644 --- a/tests/analysis/chemenv/utils/test_math_utils.py +++ b/tests/analysis/chemenv/utils/test_math_utils.py @@ -2,7 +2,6 @@ import numpy as np from numpy.testing import assert_allclose - from pymatgen.analysis.chemenv.utils.math_utils import ( _cartesian_product, cosinus_step, diff --git a/tests/analysis/diffraction/test_neutron.py b/tests/analysis/diffraction/test_neutron.py index f9f54d9d4fa..5256710bae1 100644 --- a/tests/analysis/diffraction/test_neutron.py +++ b/tests/analysis/diffraction/test_neutron.py @@ -1,12 +1,11 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.analysis.diffraction.neutron import NDCalculator from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.util.testing import PymatgenTest +from pytest import approx """ These calculated values were verified with VESTA and FullProf. diff --git a/tests/analysis/diffraction/test_tem.py b/tests/analysis/diffraction/test_tem.py index 7b5a79cea67..edbe77256ca 100644 --- a/tests/analysis/diffraction/test_tem.py +++ b/tests/analysis/diffraction/test_tem.py @@ -6,12 +6,11 @@ import pandas as pd import plotly.graph_objects as go from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.diffraction.tem import TEMCalculator from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.util.testing import PymatgenTest +from pytest import approx __author__ = "Frank Wan, Jason Liang" __copyright__ = "Copyright 2019, The Materials Project" diff --git a/tests/analysis/diffraction/test_xrd.py b/tests/analysis/diffraction/test_xrd.py index 9663d6fbf7d..ed4f9bcb2d2 100644 --- a/tests/analysis/diffraction/test_xrd.py +++ b/tests/analysis/diffraction/test_xrd.py @@ -1,12 +1,11 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.analysis.diffraction.xrd import XRDCalculator from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.util.testing import PymatgenTest +from pytest import approx """ TODO: Modify unittest doc. diff --git a/tests/analysis/elasticity/test_elastic.py b/tests/analysis/elasticity/test_elastic.py index 4fe8ecdc5da..85de3ac4728 100644 --- a/tests/analysis/elasticity/test_elastic.py +++ b/tests/analysis/elasticity/test_elastic.py @@ -8,9 +8,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose -from pytest import approx -from scipy.misc import central_diff_weights - from pymatgen.analysis.elasticity.elastic import ( ComplianceTensor, ElasticTensor, @@ -29,6 +26,8 @@ from pymatgen.core.tensors import Tensor from pymatgen.core.units import FloatWithUnit from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx +from scipy.misc import central_diff_weights TEST_DIR = f"{TEST_FILES_DIR}/analysis/elasticity" diff --git a/tests/analysis/elasticity/test_strain.py b/tests/analysis/elasticity/test_strain.py index e64de89f18d..2ffadf975e5 100644 --- a/tests/analysis/elasticity/test_strain.py +++ b/tests/analysis/elasticity/test_strain.py @@ -3,7 +3,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose - from pymatgen.analysis.elasticity.strain import Deformation, DeformedStructureSet, Strain, convert_strain_to_deformation from pymatgen.core.structure import Structure from pymatgen.core.tensors import Tensor diff --git a/tests/analysis/elasticity/test_stress.py b/tests/analysis/elasticity/test_stress.py index cc79322de83..66a656243ed 100644 --- a/tests/analysis/elasticity/test_stress.py +++ b/tests/analysis/elasticity/test_stress.py @@ -3,11 +3,10 @@ import numpy as np import pytest from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.elasticity.strain import Deformation from pymatgen.analysis.elasticity.stress import Stress from pymatgen.util.testing import PymatgenTest +from pytest import approx class TestStress(PymatgenTest): diff --git a/tests/analysis/ferroelectricity/test_polarization.py b/tests/analysis/ferroelectricity/test_polarization.py index 8c5de6645fc..67f90933990 100644 --- a/tests/analysis/ferroelectricity/test_polarization.py +++ b/tests/analysis/ferroelectricity/test_polarization.py @@ -2,8 +2,6 @@ import numpy as np from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.ferroelectricity.polarization import ( EnergyTrend, Polarization, @@ -14,6 +12,7 @@ from pymatgen.io.vasp.inputs import Potcar from pymatgen.io.vasp.outputs import Outcar from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/vasp/fixtures/BTO_221_99_polarization" bto_folders = ["nonpolar_polarization"] diff --git a/tests/analysis/interfaces/test_coherent_interface.py b/tests/analysis/interfaces/test_coherent_interface.py index 081cc3c4b62..1284bc8c731 100644 --- a/tests/analysis/interfaces/test_coherent_interface.py +++ b/tests/analysis/interfaces/test_coherent_interface.py @@ -1,7 +1,6 @@ from __future__ import annotations from numpy.testing import assert_allclose - from pymatgen.analysis.interfaces.coherent_interfaces import ( CoherentInterfaceBuilder, from_2d_to_3d, diff --git a/tests/analysis/interfaces/test_substrate_analyzer.py b/tests/analysis/interfaces/test_substrate_analyzer.py index a842cd4dad7..39e75ea53f5 100644 --- a/tests/analysis/interfaces/test_substrate_analyzer.py +++ b/tests/analysis/interfaces/test_substrate_analyzer.py @@ -1,7 +1,6 @@ from __future__ import annotations from numpy.testing import assert_allclose - from pymatgen.analysis.elasticity.elastic import ElasticTensor from pymatgen.analysis.interfaces.substrate_analyzer import SubstrateAnalyzer from pymatgen.symmetry.analyzer import SpacegroupAnalyzer diff --git a/tests/analysis/interfaces/test_zsl.py b/tests/analysis/interfaces/test_zsl.py index 3cc7732eb73..d4fc0bdef2a 100644 --- a/tests/analysis/interfaces/test_zsl.py +++ b/tests/analysis/interfaces/test_zsl.py @@ -2,8 +2,6 @@ import numpy as np from numpy.testing import assert_array_equal -from pytest import approx - from pymatgen.analysis.interfaces.zsl import ( ZSLGenerator, fast_norm, @@ -14,6 +12,7 @@ ) from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.testing import PymatgenTest +from pytest import approx __author__ = "Shyam Dwaraknath" __copyright__ = "Copyright 2016, The Materials Project" diff --git a/tests/analysis/magnetism/test_analyzer.py b/tests/analysis/magnetism/test_analyzer.py index bcdd02f1970..12e0f3029a6 100644 --- a/tests/analysis/magnetism/test_analyzer.py +++ b/tests/analysis/magnetism/test_analyzer.py @@ -6,8 +6,6 @@ import pytest from monty.serialization import loadfn from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.magnetism import ( CollinearMagneticStructureAnalyzer, MagneticStructureEnumerator, @@ -16,6 +14,7 @@ ) from pymatgen.core import Element, Lattice, Species, Structure from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/magnetic_orderings" diff --git a/tests/analysis/magnetism/test_heisenberg.py b/tests/analysis/magnetism/test_heisenberg.py index 3eea3bd6782..968e28524ce 100644 --- a/tests/analysis/magnetism/test_heisenberg.py +++ b/tests/analysis/magnetism/test_heisenberg.py @@ -3,7 +3,6 @@ from unittest import TestCase import pandas as pd - from pymatgen.analysis.magnetism.heisenberg import HeisenbergMapper from pymatgen.core.structure import Structure from pymatgen.util.testing import TEST_FILES_DIR diff --git a/tests/analysis/magnetism/test_jahnteller.py b/tests/analysis/magnetism/test_jahnteller.py index 6cc3356b4aa..3a5da6a5ef4 100644 --- a/tests/analysis/magnetism/test_jahnteller.py +++ b/tests/analysis/magnetism/test_jahnteller.py @@ -3,11 +3,10 @@ from unittest import TestCase import numpy as np -from pytest import approx - from pymatgen.analysis.magnetism.jahnteller import JahnTellerAnalyzer, Species from pymatgen.core import Structure from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx class TestJahnTeller(TestCase): diff --git a/tests/analysis/solar/test_slme.py b/tests/analysis/solar/test_slme.py index 4d2e12c1ef0..906dba63bc7 100644 --- a/tests/analysis/solar/test_slme.py +++ b/tests/analysis/solar/test_slme.py @@ -1,9 +1,8 @@ from __future__ import annotations -from pytest import approx - from pymatgen.analysis.solar.slme import optics, slme from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/solar" diff --git a/tests/analysis/structure_prediction/test_dopant_predictor.py b/tests/analysis/structure_prediction/test_dopant_predictor.py index f19d032624d..a763421b0bb 100644 --- a/tests/analysis/structure_prediction/test_dopant_predictor.py +++ b/tests/analysis/structure_prediction/test_dopant_predictor.py @@ -2,14 +2,13 @@ from unittest import TestCase -from pytest import approx - from pymatgen.analysis.local_env import CrystalNN from pymatgen.analysis.structure_prediction.dopant_predictor import ( get_dopants_from_shannon_radii, get_dopants_from_substitution_probabilities, ) from pymatgen.core import Species, Structure +from pytest import approx class TestDopantPrediction(TestCase): diff --git a/tests/analysis/structure_prediction/test_substitution_probability.py b/tests/analysis/structure_prediction/test_substitution_probability.py index e6c5f9786d0..eb9115995a3 100644 --- a/tests/analysis/structure_prediction/test_substitution_probability.py +++ b/tests/analysis/structure_prediction/test_substitution_probability.py @@ -3,14 +3,13 @@ import json from unittest import TestCase -from pytest import approx - from pymatgen.analysis.structure_prediction.substitution_probability import ( SubstitutionPredictor, SubstitutionProbability, ) from pymatgen.core import Composition, Species from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/struct_predictor" diff --git a/tests/analysis/structure_prediction/test_volume_predictor.py b/tests/analysis/structure_prediction/test_volume_predictor.py index 9f6a150aeb7..069a9dbc86f 100644 --- a/tests/analysis/structure_prediction/test_volume_predictor.py +++ b/tests/analysis/structure_prediction/test_volume_predictor.py @@ -1,11 +1,10 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.analysis.structure_prediction.volume_predictor import DLSVolumePredictor, RLSVolumePredictor from pymatgen.core import Structure from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/structure_prediction" diff --git a/tests/analysis/test_adsorption.py b/tests/analysis/test_adsorption.py index 9f611a2feaa..76fdc09a0cd 100644 --- a/tests/analysis/test_adsorption.py +++ b/tests/analysis/test_adsorption.py @@ -2,7 +2,6 @@ import numpy as np from numpy.testing import assert_allclose - from pymatgen.analysis.adsorption import AdsorbateSiteFinder, generate_all_slabs, get_rot, reorient_z from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Molecule, Structure diff --git a/tests/analysis/test_bond_dissociation.py b/tests/analysis/test_bond_dissociation.py index b29081413c9..6dd0d7f9af6 100644 --- a/tests/analysis/test_bond_dissociation.py +++ b/tests/analysis/test_bond_dissociation.py @@ -4,7 +4,6 @@ import pytest from monty.serialization import loadfn - from pymatgen.analysis.bond_dissociation import BondDissociationEnergies from pymatgen.util.testing import TEST_FILES_DIR diff --git a/tests/analysis/test_bond_valence.py b/tests/analysis/test_bond_valence.py index 8bfc158a574..5a0202e075b 100644 --- a/tests/analysis/test_bond_valence.py +++ b/tests/analysis/test_bond_valence.py @@ -1,11 +1,10 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.analysis.bond_valence import BVAnalyzer, calculate_bv_sum, calculate_bv_sum_unordered from pymatgen.core import Composition, Species, Structure from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/bond_valence" diff --git a/tests/analysis/test_chempot_diagram.py b/tests/analysis/test_chempot_diagram.py index 648d6a5a164..5465e1d050d 100644 --- a/tests/analysis/test_chempot_diagram.py +++ b/tests/analysis/test_chempot_diagram.py @@ -2,8 +2,6 @@ import numpy as np from plotly.graph_objects import Figure -from pytest import approx - from pymatgen.analysis.chempot_diagram import ( ChemicalPotentialDiagram, get_2d_orthonormal_vector, @@ -13,6 +11,7 @@ from pymatgen.core.composition import Element from pymatgen.entries.entry_tools import EntrySet from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis" diff --git a/tests/analysis/test_cost.py b/tests/analysis/test_cost.py index c20bed2fd54..4aa598bc5fa 100644 --- a/tests/analysis/test_cost.py +++ b/tests/analysis/test_cost.py @@ -2,10 +2,9 @@ from unittest import TestCase -from pytest import approx - from pymatgen.analysis.cost import CostAnalyzer, CostDBCSV, CostDBElements from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/cost" diff --git a/tests/analysis/test_dimensionality.py b/tests/analysis/test_dimensionality.py index 8b99c6fd5e2..b83c2cb5748 100644 --- a/tests/analysis/test_dimensionality.py +++ b/tests/analysis/test_dimensionality.py @@ -3,7 +3,6 @@ import networkx as nx import pytest from monty.serialization import loadfn - from pymatgen.analysis.dimensionality import ( calculate_dimensionality_of_site, get_dimensionality_cheon, diff --git a/tests/analysis/test_disorder.py b/tests/analysis/test_disorder.py index a4b930096ac..2384bc4e296 100644 --- a/tests/analysis/test_disorder.py +++ b/tests/analysis/test_disorder.py @@ -1,10 +1,9 @@ from __future__ import annotations -from pytest import approx - from pymatgen.analysis.disorder import get_warren_cowley_parameters from pymatgen.core import Element, Structure from pymatgen.util.testing import PymatgenTest +from pytest import approx class TestOrderParameter(PymatgenTest): diff --git a/tests/analysis/test_energy_models.py b/tests/analysis/test_energy_models.py index 36d3024ac75..a2c4aa40612 100644 --- a/tests/analysis/test_energy_models.py +++ b/tests/analysis/test_energy_models.py @@ -1,12 +1,11 @@ from __future__ import annotations -from pytest import approx - from pymatgen.analysis.energy_models import EwaldElectrostaticModel, IsingModel, SymmetryModel from pymatgen.core import Species from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx class TestEwaldElectrostaticModel: diff --git a/tests/analysis/test_eos.py b/tests/analysis/test_eos.py index 4c02d040fd4..f31c3723eb7 100644 --- a/tests/analysis/test_eos.py +++ b/tests/analysis/test_eos.py @@ -2,10 +2,9 @@ import numpy as np from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.eos import EOS, NumericalEOS from pymatgen.util.testing import PymatgenTest +from pytest import approx class TestEOS(PymatgenTest): diff --git a/tests/analysis/test_ewald.py b/tests/analysis/test_ewald.py index 285152bb8fd..7ada2e539dc 100644 --- a/tests/analysis/test_ewald.py +++ b/tests/analysis/test_ewald.py @@ -4,11 +4,10 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.analysis.ewald import EwaldMinimizer, EwaldSummation from pymatgen.core.structure import Structure from pymatgen.util.testing import VASP_IN_DIR +from pytest import approx class TestEwaldSummation(TestCase): diff --git a/tests/analysis/test_fragmenter.py b/tests/analysis/test_fragmenter.py index 611edcf58dd..26b2840b3ae 100644 --- a/tests/analysis/test_fragmenter.py +++ b/tests/analysis/test_fragmenter.py @@ -1,7 +1,6 @@ from __future__ import annotations import pytest - from pymatgen.analysis.fragmenter import Fragmenter from pymatgen.analysis.graphs import MoleculeGraph from pymatgen.analysis.local_env import OpenBabelNN diff --git a/tests/analysis/test_functional_groups.py b/tests/analysis/test_functional_groups.py index e53a62960a0..bc59a7da57d 100644 --- a/tests/analysis/test_functional_groups.py +++ b/tests/analysis/test_functional_groups.py @@ -3,7 +3,6 @@ from unittest import TestCase import pytest - from pymatgen.analysis.functional_groups import FunctionalGroupExtractor from pymatgen.analysis.graphs import MoleculeGraph from pymatgen.analysis.local_env import OpenBabelNN diff --git a/tests/analysis/test_graphs.py b/tests/analysis/test_graphs.py index dcb8809a818..f196cde29ad 100644 --- a/tests/analysis/test_graphs.py +++ b/tests/analysis/test_graphs.py @@ -10,8 +10,6 @@ import networkx.algorithms.isomorphism as iso import pytest from monty.serialization import loadfn -from pytest import approx - from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError, PeriodicSite, StructureGraph from pymatgen.analysis.local_env import ( CovalentBondNN, @@ -25,6 +23,7 @@ from pymatgen.core import Lattice, Molecule, Site, Structure from pymatgen.core.structure import FunctionalGroups from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx try: from openbabel import openbabel diff --git a/tests/analysis/test_hhi.py b/tests/analysis/test_hhi.py index 105072426fb..d1c95587124 100644 --- a/tests/analysis/test_hhi.py +++ b/tests/analysis/test_hhi.py @@ -1,8 +1,7 @@ from __future__ import annotations -from pytest import approx - from pymatgen.analysis.hhi import HHIModel +from pytest import approx class TestHHIModel: diff --git a/tests/analysis/test_interface_reactions.py b/tests/analysis/test_interface_reactions.py index 9b4483ba2c0..0b9665fef4f 100644 --- a/tests/analysis/test_interface_reactions.py +++ b/tests/analysis/test_interface_reactions.py @@ -8,13 +8,12 @@ from numpy.testing import assert_allclose from pandas import DataFrame from plotly.graph_objects import Figure -from scipy.spatial import ConvexHull - from pymatgen.analysis.interface_reactions import GrandPotentialInterfacialReactivity, InterfacialReactivity from pymatgen.analysis.phase_diagram import GrandPotentialPhaseDiagram, PhaseDiagram from pymatgen.analysis.reaction_calculator import Reaction from pymatgen.core.composition import Composition, Element from pymatgen.entries.computed_entries import ComputedEntry +from scipy.spatial import ConvexHull class TestInterfaceReaction(TestCase): @@ -143,12 +142,12 @@ def setUp(self): use_hull_energy=False, ) with pytest.raises( - ValueError, + TypeError, match="Please use the GrandPotentialInterfacialReactivity " "class for interfacial reactions with open elements!", ): _ = InterfacialReactivity(Composition("Li2O2"), Composition("Li"), pd=self.gpd, norm=True) - with pytest.raises(ValueError, match="Please provide non-grand phase diagram to compute no_mixing_energy!"): + with pytest.raises(TypeError, match="Please provide non-grand phase diagram to compute no_mixing_energy!"): _ = GrandPotentialInterfacialReactivity( Composition("O2"), Composition("Mn"), diff --git a/tests/analysis/test_local_env.py b/tests/analysis/test_local_env.py index ed8b72c677d..1fbed74da82 100644 --- a/tests/analysis/test_local_env.py +++ b/tests/analysis/test_local_env.py @@ -7,8 +7,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph from pymatgen.analysis.local_env import ( BrunnerNNReal, @@ -38,6 +36,7 @@ ) from pymatgen.core import Element, Lattice, Molecule, Structure from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/local_env/fragmenter_files" diff --git a/tests/analysis/test_molecule_matcher.py b/tests/analysis/test_molecule_matcher.py index 485e3c75f2f..cca70ae1c2c 100644 --- a/tests/analysis/test_molecule_matcher.py +++ b/tests/analysis/test_molecule_matcher.py @@ -4,8 +4,6 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.analysis.molecule_matcher import ( BruteForceOrderMatcher, GeneticOrderMatcher, @@ -19,6 +17,7 @@ from pymatgen.core.structure import Lattice, Molecule, Structure from pymatgen.io.xyz import XYZ from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx try: from openbabel import openbabel diff --git a/tests/analysis/test_nmr.py b/tests/analysis/test_nmr.py index 14490ec7a0c..86961996a71 100644 --- a/tests/analysis/test_nmr.py +++ b/tests/analysis/test_nmr.py @@ -2,10 +2,9 @@ import numpy as np from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.analysis.nmr import ChemicalShielding, ElectricFieldGradient from pymatgen.util.testing import PymatgenTest +from pytest import approx class TestChemicalShieldingNotation(PymatgenTest): diff --git a/tests/analysis/test_phase_diagram.py b/tests/analysis/test_phase_diagram.py index c42ca82ab6e..997a7cd0bac 100644 --- a/tests/analysis/test_phase_diagram.py +++ b/tests/analysis/test_phase_diagram.py @@ -3,6 +3,7 @@ import collections import unittest import unittest.mock +from itertools import combinations from numbers import Number from unittest import TestCase @@ -12,8 +13,6 @@ import pytest from monty.serialization import dumpfn, loadfn from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.phase_diagram import ( CompoundPhaseDiagram, GrandPotentialPhaseDiagram, @@ -32,6 +31,7 @@ from pymatgen.entries.computed_entries import ComputedEntry from pymatgen.entries.entry_tools import EntrySet from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis" @@ -710,6 +710,7 @@ def setUp(self): self.pd = PhaseDiagram(entries=self.entries) self.ppd = PatchedPhaseDiagram(entries=self.entries) + self.ppd_all = PatchedPhaseDiagram(entries=self.entries, keep_all_spaces=True) # novel entries not in any of the patches self.novel_comps = [Composition("H5C2OP"), Composition("V2PH4C")] @@ -757,7 +758,11 @@ def test_dimensionality(self): # test dims of sub PDs dim_counts = collections.Counter(pd.dim for pd in self.ppd.pds.values()) - assert dim_counts == {3: 7, 2: 6, 4: 2} + assert dim_counts == {4: 2, 3: 2} + + # test dims of sub PDs + dim_counts = collections.Counter(pd.dim for pd in self.ppd_all.pds.values()) + assert dim_counts == {2: 8, 3: 7, 4: 2} def test_get_hull_energy(self): for comp in self.novel_comps: @@ -773,7 +778,7 @@ def test_get_decomp_and_e_above_hull(self): assert np.isclose(e_above_hull_pd, e_above_hull_ppd) def test_repr(self): - assert repr(self.ppd) == str(self.ppd) == "PatchedPhaseDiagram covering 15 sub-spaces" + assert repr(self.ppd) == str(self.ppd) == "PatchedPhaseDiagram covering 4 sub-spaces" def test_as_from_dict(self): ppd_dict = self.ppd.as_dict() @@ -811,7 +816,8 @@ def test_getitem(self): pd = self.ppd[chem_space] assert isinstance(pd, PhaseDiagram) assert chem_space in pd._qhull_spaces - assert str(pd) == "V-C phase diagram\n4 stable phases: \nC, V, V6C5, V2C" + assert len(str(pd)) == 186 + assert str(pd).startswith("V-H-C-O phase diagram\n25 stable phases:") with pytest.raises(KeyError, match="frozenset"): self.ppd[frozenset(map(Element, "HBCNOFPS"))] @@ -831,6 +837,19 @@ def test_setitem_and_delitem(self): assert self.ppd[unlikely_chem_space] == self.pd del self.ppd[unlikely_chem_space] # test __delitem__() and restore original state + def test_remove_redundant_spaces(self): + spaces = tuple(frozenset(entry.elements) for entry in self.ppd.qhull_entries) + # NOTE this is 5 not 4 as "He" is a non redundant space that gets dropped for other reasons + assert len(self.ppd.remove_redundant_spaces(spaces)) == 5 + + test = ( + list(combinations(range(1, 7), 4)) + + list(combinations(range(1, 10), 2)) + + list(combinations([1, 4, 7, 9, 2], 5)) + ) + test = [frozenset(t) for t in test] + assert len(self.ppd.remove_redundant_spaces(test)) == 30 + class TestReactionDiagram(TestCase): def setUp(self): diff --git a/tests/analysis/test_piezo.py b/tests/analysis/test_piezo.py index 62569975053..0bd01459e6f 100644 --- a/tests/analysis/test_piezo.py +++ b/tests/analysis/test_piezo.py @@ -5,7 +5,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose, assert_array_equal - from pymatgen.analysis.piezo import PiezoTensor from pymatgen.util.testing import PymatgenTest @@ -19,7 +18,7 @@ class TestPiezo(PymatgenTest): def setUp(self): - self.piezo_struc = self.get_structure("BaNiO3") + self.piezo_struct = self.get_structure("BaNiO3") self.voigt_matrix = np.array( [ [0.0, 0.0, 0.0, 0.0, 0.03839, 0.0], diff --git a/tests/analysis/test_piezo_sensitivity.py b/tests/analysis/test_piezo_sensitivity.py index eafaaddc6b4..19f2444f028 100644 --- a/tests/analysis/test_piezo_sensitivity.py +++ b/tests/analysis/test_piezo_sensitivity.py @@ -5,10 +5,9 @@ import pickle import numpy as np +import pymatgen import pytest from numpy.testing import assert_allclose - -import pymatgen from pymatgen.analysis.piezo_sensitivity import ( BornEffectiveCharge, ForceConstantMatrix, diff --git a/tests/analysis/test_pourbaix_diagram.py b/tests/analysis/test_pourbaix_diagram.py index 3119877f33b..6ea90a801b3 100644 --- a/tests/analysis/test_pourbaix_diagram.py +++ b/tests/analysis/test_pourbaix_diagram.py @@ -7,13 +7,12 @@ import matplotlib.pyplot as plt import numpy as np from monty.serialization import dumpfn, loadfn -from pytest import approx - from pymatgen.analysis.pourbaix_diagram import IonEntry, MultiEntry, PourbaixDiagram, PourbaixEntry, PourbaixPlotter from pymatgen.core.composition import Composition from pymatgen.core.ion import Ion from pymatgen.entries.computed_entries import ComputedEntry from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/pourbaix_diagram" diff --git a/tests/analysis/test_quasi_harmonic_debye_approx.py b/tests/analysis/test_quasi_harmonic_debye_approx.py index 9a9aa86bce5..fce94e37d44 100644 --- a/tests/analysis/test_quasi_harmonic_debye_approx.py +++ b/tests/analysis/test_quasi_harmonic_debye_approx.py @@ -4,7 +4,6 @@ import numpy as np from numpy.testing import assert_allclose - from pymatgen.analysis.eos import EOS from pymatgen.analysis.quasiharmonic import QuasiHarmonicDebyeApprox from pymatgen.core.structure import Structure diff --git a/tests/analysis/test_quasirrho.py b/tests/analysis/test_quasirrho.py index 63cd0015ad4..37829e37a75 100644 --- a/tests/analysis/test_quasirrho.py +++ b/tests/analysis/test_quasirrho.py @@ -3,7 +3,6 @@ from unittest import TestCase import pytest - from pymatgen.analysis.quasirrho import QuasiRRHO, get_avg_mom_inertia from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.qchem.outputs import QCOutput diff --git a/tests/analysis/test_reaction_calculator.py b/tests/analysis/test_reaction_calculator.py index dcb06819574..f8584fd5549 100644 --- a/tests/analysis/test_reaction_calculator.py +++ b/tests/analysis/test_reaction_calculator.py @@ -6,11 +6,10 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.analysis.reaction_calculator import BalancedReaction, ComputedReaction, Reaction, ReactionError from pymatgen.core.composition import Composition from pymatgen.entries.computed_entries import ComputedEntry +from pytest import approx class TestReaction: diff --git a/tests/analysis/test_structure_analyzer.py b/tests/analysis/test_structure_analyzer.py index 12a0c02f991..1639729a56a 100644 --- a/tests/analysis/test_structure_analyzer.py +++ b/tests/analysis/test_structure_analyzer.py @@ -4,8 +4,6 @@ import numpy as np from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.structure_analyzer import ( RelaxationAnalyzer, VoronoiAnalyzer, @@ -19,6 +17,7 @@ from pymatgen.core import Element, Lattice, Structure from pymatgen.io.vasp.outputs import Xdatcar from pymatgen.util.testing import VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest +from pytest import approx class TestVoronoiAnalyzer(PymatgenTest): diff --git a/tests/analysis/test_structure_matcher.py b/tests/analysis/test_structure_matcher.py index c658585cf75..28707ef44de 100644 --- a/tests/analysis/test_structure_matcher.py +++ b/tests/analysis/test_structure_matcher.py @@ -6,8 +6,6 @@ import pytest from monty.json import MontyDecoder from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.analysis.structure_matcher import ( ElementComparator, FrameworkComparator, @@ -18,6 +16,7 @@ from pymatgen.core import Element, Lattice, Structure, SymmOp from pymatgen.util.coord import find_in_coord_list_pbc from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/structure_matcher" diff --git a/tests/analysis/test_surface_analysis.py b/tests/analysis/test_surface_analysis.py index 0e58a2099d5..07195437d80 100644 --- a/tests/analysis/test_surface_analysis.py +++ b/tests/analysis/test_surface_analysis.py @@ -3,12 +3,11 @@ import json from numpy.testing import assert_allclose -from pytest import approx -from sympy import Number, Symbol - from pymatgen.analysis.surface_analysis import NanoscaleStability, SlabEntry, SurfaceEnergyPlotter, WorkFunctionAnalyzer from pymatgen.entries.computed_entries import ComputedStructureEntry from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx +from sympy import Number, Symbol __author__ = "Richard Tran" __copyright__ = "Copyright 2012, The Materials Project" diff --git a/tests/analysis/test_transition_state.py b/tests/analysis/test_transition_state.py index 96841bc482a..0e404e02fc8 100644 --- a/tests/analysis/test_transition_state.py +++ b/tests/analysis/test_transition_state.py @@ -4,7 +4,6 @@ from matplotlib import pyplot as plt from numpy.testing import assert_allclose - from pymatgen.analysis.transition_state import NEBAnalysis, combine_neb_plots from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest diff --git a/tests/analysis/test_wulff.py b/tests/analysis/test_wulff.py index 11109c1e746..c4656a79097 100644 --- a/tests/analysis/test_wulff.py +++ b/tests/analysis/test_wulff.py @@ -2,14 +2,13 @@ import json -from pytest import approx - from pymatgen.analysis.wulff import WulffShape from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.coord import in_coord_list from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx __author__ = "Zihan Xu, Richard Tran, Balachandran Radhakrishnan" __copyright__ = "Copyright 2013, The Materials Virtual Lab" diff --git a/tests/analysis/topological/test_spillage.py b/tests/analysis/topological/test_spillage.py index 39224cdfc52..61652c97696 100644 --- a/tests/analysis/topological/test_spillage.py +++ b/tests/analysis/topological/test_spillage.py @@ -1,9 +1,8 @@ from __future__ import annotations -from pytest import approx - from pymatgen.analysis.topological.spillage import SOCSpillage from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/topological" diff --git a/tests/analysis/xas/test_spectrum.py b/tests/analysis/xas/test_spectrum.py index ccc1c3812a5..25772d15fb7 100644 --- a/tests/analysis/xas/test_spectrum.py +++ b/tests/analysis/xas/test_spectrum.py @@ -6,11 +6,10 @@ import pytest from monty.json import MontyDecoder from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.analysis.xas.spectrum import XAS, site_weighted_spectrum from pymatgen.core import Element from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/spectrum_test" diff --git a/tests/apps/battery/test_analyzer.py b/tests/apps/battery/test_analyzer.py index 61426c65510..a7a22ccf015 100644 --- a/tests/apps/battery/test_analyzer.py +++ b/tests/apps/battery/test_analyzer.py @@ -1,11 +1,10 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.apps.battery.analyzer import BatteryAnalyzer from pymatgen.core.structure import Structure from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx class TestBatteryAnalyzer(PymatgenTest): diff --git a/tests/apps/battery/test_conversion_battery.py b/tests/apps/battery/test_conversion_battery.py index ae17c969353..041702625a4 100644 --- a/tests/apps/battery/test_conversion_battery.py +++ b/tests/apps/battery/test_conversion_battery.py @@ -4,11 +4,10 @@ from unittest import TestCase from monty.json import MontyDecoder -from pytest import approx - from pymatgen.apps.battery.conversion_battery import ConversionElectrode, ConversionVoltagePair from pymatgen.core.composition import Composition from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/apps/battery" diff --git a/tests/apps/battery/test_insertion_battery.py b/tests/apps/battery/test_insertion_battery.py index 4c6b9caa951..06c6ef0802f 100644 --- a/tests/apps/battery/test_insertion_battery.py +++ b/tests/apps/battery/test_insertion_battery.py @@ -4,11 +4,10 @@ from unittest import TestCase from monty.json import MontyDecoder, MontyEncoder -from pytest import approx - from pymatgen.apps.battery.insertion_battery import InsertionElectrode, InsertionVoltagePair from pymatgen.entries.computed_entries import ComputedEntry from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/apps/battery" diff --git a/tests/apps/battery/test_plotter.py b/tests/apps/battery/test_plotter.py index 8b93b20f8bf..c9e14875e25 100644 --- a/tests/apps/battery/test_plotter.py +++ b/tests/apps/battery/test_plotter.py @@ -4,7 +4,6 @@ from unittest import TestCase from monty.json import MontyDecoder - from pymatgen.apps.battery.conversion_battery import ConversionElectrode from pymatgen.apps.battery.insertion_battery import InsertionElectrode from pymatgen.apps.battery.plotter import VoltageProfilePlotter diff --git a/tests/apps/borg/test_hive.py b/tests/apps/borg/test_hive.py index 766086d429b..64b64814c70 100644 --- a/tests/apps/borg/test_hive.py +++ b/tests/apps/borg/test_hive.py @@ -3,8 +3,6 @@ import os from unittest import TestCase -from pytest import approx - from pymatgen.apps.borg.hive import ( GaussianToComputedEntryDrone, SimpleVaspToComputedEntryDrone, @@ -12,6 +10,7 @@ ) from pymatgen.entries.computed_entries import ComputedStructureEntry from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/apps/borg" diff --git a/tests/apps/borg/test_queen.py b/tests/apps/borg/test_queen.py index b95e660f7f8..14cc20679a9 100644 --- a/tests/apps/borg/test_queen.py +++ b/tests/apps/borg/test_queen.py @@ -1,10 +1,9 @@ from __future__ import annotations -from pytest import approx - from pymatgen.apps.borg.hive import VaspToComputedEntryDrone from pymatgen.apps.borg.queen import BorgQueen from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx __author__ = "Shyue Ping Ong" __copyright__ = "Copyright 2012, The Materials Project" diff --git a/tests/command_line/test_bader_caller.py b/tests/command_line/test_bader_caller.py index c3d9b609946..5bff1599c62 100644 --- a/tests/command_line/test_bader_caller.py +++ b/tests/command_line/test_bader_caller.py @@ -8,10 +8,9 @@ import pytest from monty.shutil import copy_r from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.command_line.bader_caller import BaderAnalysis, bader_analysis_from_path from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/command_line/bader" diff --git a/tests/command_line/test_critic2_caller.py b/tests/command_line/test_critic2_caller.py index 46218f94e8c..4f1a7cf648f 100644 --- a/tests/command_line/test_critic2_caller.py +++ b/tests/command_line/test_critic2_caller.py @@ -4,11 +4,10 @@ from unittest import TestCase import pytest -from pytest import approx - from pymatgen.command_line.critic2_caller import Critic2Analysis, Critic2Caller from pymatgen.core.structure import Structure from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx __author__ = "Matthew Horton" __version__ = "0.1" diff --git a/tests/command_line/test_enumlib_caller.py b/tests/command_line/test_enumlib_caller.py index 010bb0bd1b8..d21b5b67986 100644 --- a/tests/command_line/test_enumlib_caller.py +++ b/tests/command_line/test_enumlib_caller.py @@ -5,14 +5,13 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.command_line.enumlib_caller import EnumError, EnumlibAdaptor from pymatgen.core import Element, Structure from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.transformations.site_transformations import RemoveSitesTransformation from pymatgen.transformations.standard_transformations import SubstitutionTransformation from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx enum_cmd = which("enum.x") or which("multienum.x") makestr_cmd = which("makestr.x") or which("makeStr.x") or which("makeStr.py") diff --git a/tests/command_line/test_gulp_caller.py b/tests/command_line/test_gulp_caller.py index 054d0e7c023..aa0faf1d16e 100644 --- a/tests/command_line/test_gulp_caller.py +++ b/tests/command_line/test_gulp_caller.py @@ -14,7 +14,6 @@ import numpy as np import pytest - from pymatgen.analysis.bond_valence import BVAnalyzer from pymatgen.command_line.gulp_caller import ( BuckinghamPotential, diff --git a/tests/command_line/test_mcsqs_caller.py b/tests/command_line/test_mcsqs_caller.py index 39714b1f4f1..9dd6303a1dc 100644 --- a/tests/command_line/test_mcsqs_caller.py +++ b/tests/command_line/test_mcsqs_caller.py @@ -4,7 +4,6 @@ import pytest from monty.serialization import loadfn - from pymatgen.command_line.mcsqs_caller import run_mcsqs from pymatgen.core.structure import Structure from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest diff --git a/tests/command_line/test_vampire_caller.py b/tests/command_line/test_vampire_caller.py index 19efe2eef1f..e8cc2330f02 100644 --- a/tests/command_line/test_vampire_caller.py +++ b/tests/command_line/test_vampire_caller.py @@ -4,11 +4,10 @@ import pandas as pd import pytest -from pytest import approx - from pymatgen.command_line.vampire_caller import VampireCaller from pymatgen.core.structure import Structure from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/analysis/magnetic_orderings" diff --git a/tests/core/test_bonds.py b/tests/core/test_bonds.py index 777d938619a..9154207aba6 100644 --- a/tests/core/test_bonds.py +++ b/tests/core/test_bonds.py @@ -1,10 +1,9 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.core import Element, Site from pymatgen.core.bonds import CovalentBond, get_bond_length, get_bond_order, obtain_all_bond_lengths +from pytest import approx __author__ = "Shyue Ping Ong" __copyright__ = "Copyright 2012, The Materials Project" diff --git a/tests/core/test_composition.py b/tests/core/test_composition.py index e55860df0d0..1cf2c688e31 100644 --- a/tests/core/test_composition.py +++ b/tests/core/test_composition.py @@ -10,11 +10,10 @@ import pytest from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core import Composition, DummySpecies, Element, Species from pymatgen.core.composition import ChemicalPotential from pymatgen.util.testing import PymatgenTest +from pytest import approx class TestComposition(PymatgenTest): @@ -633,7 +632,7 @@ def test_oxi_state_guesses(self): {"V": 5, "O": -2}, ) - expected_oxi_guesses = dict(Li=1, Fe=2, P=5, O=-2) + expected_oxi_guesses = {"Li": 1, "Fe": 2, "P": 5, "O": -2} # max_sites for very large composition - should timeout if incorrect assert Composition("Li10000Fe10000P10000O40000").oxi_state_guesses(max_sites=7)[0] == expected_oxi_guesses diff --git a/tests/core/test_interface.py b/tests/core/test_interface.py index 22cd178dd5b..1757265fd27 100644 --- a/tests/core/test_interface.py +++ b/tests/core/test_interface.py @@ -2,13 +2,12 @@ import numpy as np from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core.interface import GrainBoundary, GrainBoundaryGenerator, Interface from pymatgen.core.structure import Structure from pymatgen.core.surface import SlabGenerator from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/core/grain_boundary" diff --git a/tests/core/test_ion.py b/tests/core/test_ion.py index 16037ec35be..f501287ed6d 100644 --- a/tests/core/test_ion.py +++ b/tests/core/test_ion.py @@ -4,7 +4,6 @@ from unittest import TestCase import pytest - from pymatgen.core import Composition, Element from pymatgen.core.ion import Ion diff --git a/tests/core/test_lattice.py b/tests/core/test_lattice.py index ce5cff053aa..91a84688039 100644 --- a/tests/core/test_lattice.py +++ b/tests/core/test_lattice.py @@ -5,11 +5,10 @@ import numpy as np import pytest from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.core.lattice import Lattice, get_points_in_spheres from pymatgen.core.operations import SymmOp from pymatgen.util.testing import PymatgenTest +from pytest import approx class TestLattice(PymatgenTest): diff --git a/tests/core/test_molecular_orbitals.py b/tests/core/test_molecular_orbitals.py index 4476c856d17..a1699967585 100644 --- a/tests/core/test_molecular_orbitals.py +++ b/tests/core/test_molecular_orbitals.py @@ -1,7 +1,6 @@ from __future__ import annotations import pytest - from pymatgen.core.molecular_orbitals import MolecularOrbitals from pymatgen.util.testing import PymatgenTest diff --git a/tests/core/test_operations.py b/tests/core/test_operations.py index d2dcc26de42..abd9d4357a6 100644 --- a/tests/core/test_operations.py +++ b/tests/core/test_operations.py @@ -2,7 +2,6 @@ import numpy as np from numpy.testing import assert_allclose - from pymatgen.core.operations import MagSymmOp, SymmOp from pymatgen.electronic_structure.core import Magmom from pymatgen.util.testing import PymatgenTest diff --git a/tests/core/test_periodic_table.py b/tests/core/test_periodic_table.py index 90cfdc11eaf..f92335d5266 100644 --- a/tests/core/test_periodic_table.py +++ b/tests/core/test_periodic_table.py @@ -8,13 +8,12 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.core import DummySpecies, Element, Species, get_el_sp from pymatgen.core.periodic_table import ElementBase, ElementType from pymatgen.core.units import Ha_to_eV from pymatgen.io.core import ParseError from pymatgen.util.testing import PymatgenTest +from pytest import approx class TestElement(PymatgenTest): @@ -601,13 +600,55 @@ def test_sort(self): ) assert sp.spin == 5 - def test_not_implemented(self): - with pytest.raises(NotImplementedError): - _ = Species("Fe", 2).full_electronic_structure - with pytest.raises(NotImplementedError): - _ = Species("Fe", 2).electronic_structure - with pytest.raises(NotImplementedError): - _ = Species("Fe", 2).valence + def test_species_electronic_structure(self): + assert Species("Fe", 0).electronic_structure == "[Ar].3d6.4s2" + assert Species("Fe", 0).full_electronic_structure == [ + (1, "s", 2), + (2, "s", 2), + (2, "p", 6), + (3, "s", 2), + (3, "p", 6), + (3, "d", 6), + (4, "s", 2), + ] + assert Species("Fe", 0).valence == (2, 6) + + assert Species("Fe", 2).electronic_structure == "[Ar].3d6" + assert Species("Fe", 2).full_electronic_structure == [ + (1, "s", 2), + (2, "s", 2), + (2, "p", 6), + (3, "s", 2), + (3, "p", 6), + (3, "d", 6), + ] + assert Species("Fe", 2).valence == (2, 6) + + assert Species("Fe", 3).electronic_structure == "[Ar].3d5" + assert Species("Fe", 3).full_electronic_structure == [ + (1, "s", 2), + (2, "s", 2), + (2, "p", 6), + (3, "s", 2), + (3, "p", 6), + (3, "d", 5), + ] + assert Species("Fe", 3).valence == (2, 5) + + assert Species("Li", 1).electronic_structure == "1s2" + # alkali metals, all p + for el in ["Na", "K", "Rb", "Cs"]: + assert Species(el, 1).electronic_structure.split(".")[-1][1::] == "p6", f"Failure for {el} +1" + for el in ["Ca", "Mg", "Ba", "Sr"]: + assert Species(el, 2).electronic_structure.split(".")[-1][1::] == "p6", f"Failure for {el} +2" + + for el in Element: + for ox in el.common_oxidation_states: + if str(el) == "H" and ox == 1: + continue + n_electron_el = sum([orb[-1] for orb in el.full_electronic_structure]) + n_electron_sp = sum([orb[-1] for orb in Species(el, ox).full_electronic_structure]) + assert n_electron_el - n_electron_sp == ox, print(f"Failure for {el} {ox}") def test_get_el_sp(): diff --git a/tests/core/test_settings.py b/tests/core/test_settings.py index eb0ba992bbf..39107becc90 100644 --- a/tests/core/test_settings.py +++ b/tests/core/test_settings.py @@ -40,6 +40,11 @@ def test_load_settings(tmp_path: Path, monkeypatch: MonkeyPatch) -> None: ctx.setenv("PMG_MAPI_KEY", "BAZ") assert _load_pmg_settings() == {"PMG_MAPI_KEY": "BAZ"} + with monkeypatch.context() as ctx: + ctx.setenv("HOME", "/home/fakeuser") + ctx.setenv("PMG_VASP_PSP_DIR", "$HOME/psp") + assert _load_pmg_settings()["PMG_VASP_PSP_DIR"] == "/home/fakeuser/psp" + # should return empty dict if file is invalid settings_file.write_text("---") assert _load_pmg_settings() == {} diff --git a/tests/core/test_sites.py b/tests/core/test_sites.py index a80689d9dfd..ee3911c29eb 100644 --- a/tests/core/test_sites.py +++ b/tests/core/test_sites.py @@ -5,11 +5,10 @@ import numpy as np import pytest from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core import Composition, Element, Lattice, PeriodicSite, Site, Species from pymatgen.electronic_structure.core import Magmom from pymatgen.util.testing import PymatgenTest +from pytest import approx class TestSite(PymatgenTest): diff --git a/tests/core/test_spectrum.py b/tests/core/test_spectrum.py index 86fb7e7266b..9f6fe473eba 100644 --- a/tests/core/test_spectrum.py +++ b/tests/core/test_spectrum.py @@ -2,11 +2,10 @@ import numpy as np from numpy.testing import assert_allclose -from pytest import approx -from scipy import stats - from pymatgen.core.spectrum import Spectrum from pymatgen.util.testing import PymatgenTest +from pytest import approx +from scipy import stats class TestSpectrum(PymatgenTest): diff --git a/tests/core/test_structure.py b/tests/core/test_structure.py index 851b880adc4..d61616a9505 100644 --- a/tests/core/test_structure.py +++ b/tests/core/test_structure.py @@ -12,9 +12,7 @@ import pytest from monty.json import MontyDecoder, MontyEncoder from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - -from pymatgen.core import Composition, Element, Lattice, Species +from pymatgen.core import SETTINGS, Composition, Element, Lattice, Species from pymatgen.core.operations import SymmOp from pymatgen.core.structure import ( IMolecule, @@ -30,6 +28,7 @@ from pymatgen.io.cif import CifParser from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest +from pytest import approx try: from ase.atoms import Atoms @@ -924,6 +923,17 @@ def setUp(self): self.disordered = Structure.from_spacegroup("Im-3m", Lattice.cubic(3), [Composition("Fe0.5Mn0.5")], [[0, 0, 0]]) self.labeled_structure = Structure(lattice, ["Si", "Si"], coords, labels=["Si1", "Si2"]) + @pytest.mark.skipif( + SETTINGS.get("PMG_MAPI_KEY", "") == "", + reason="PMG_MAPI_KEY environment variable not set or MP API is down. This is also the case in a PR.", + ) + def test_from_id(self): + s = Structure.from_id("mp-1143") + assert isinstance(s, Structure) + assert s.reduced_formula == "Al2O3" + s = Structure.from_id("1101077", source="COD") + assert s.reduced_formula == "LiV2O4" + def test_mutable_sequence_methods(self): struct = self.struct struct[0] = "Fe" @@ -1758,7 +1768,6 @@ def test_relax_ase_opt_kwargs(self): assert traj[0] != traj[-1] assert os.path.isfile(traj_file) - @pytest.mark.skip("TODO remove skip once https://github.com/materialsvirtuallab/matgl/issues/238 is resolved") def test_calculate_m3gnet(self): pytest.importorskip("matgl") calculator = self.get_structure("Si").calculate() @@ -1770,7 +1779,6 @@ def test_calculate_m3gnet(self): assert np.linalg.norm(calculator.results["forces"]) == approx(7.8123485e-06, abs=0.2) assert np.linalg.norm(calculator.results["stress"]) == approx(1.7861567, abs=2) - @pytest.mark.skip("TODO remove skip once https://github.com/materialsvirtuallab/matgl/issues/238 is resolved") def test_relax_m3gnet(self): matgl = pytest.importorskip("matgl") struct = self.get_structure("Si") @@ -1781,7 +1789,6 @@ def test_relax_m3gnet(self): actual = relaxed.dynamics[key] assert actual == val, f"expected {key} to be {val}, {actual=}" - @pytest.mark.skip("TODO remove skip once https://github.com/materialsvirtuallab/matgl/issues/238 is resolved") def test_relax_m3gnet_fixed_lattice(self): matgl = pytest.importorskip("matgl") struct = self.get_structure("Si") @@ -1790,7 +1797,6 @@ def test_relax_m3gnet_fixed_lattice(self): assert isinstance(relaxed.calc, matgl.ext.ase.M3GNetCalculator) assert relaxed.dynamics["optimizer"] == "BFGS" - @pytest.mark.skip("TODO remove skip once https://github.com/materialsvirtuallab/matgl/issues/238 is resolved") def test_relax_m3gnet_with_traj(self): pytest.importorskip("matgl") struct = self.get_structure("Si") @@ -2396,8 +2402,6 @@ def test_relax_ase_mol_return_traj(self): assert traj[0] != traj[-1] assert os.path.isfile(traj_file) - # TODO remove skip once https://github.com/tblite/tblite/issues/110 is fixed - @pytest.mark.skip("Pytorch and TBLite clash. https://github.com/materialsproject/pymatgen/pull/3060") def test_calculate_gfnxtb(self): pytest.importorskip("tblite") mol_copy = self.mol.copy() diff --git a/tests/core/test_surface.py b/tests/core/test_surface.py index 8548e13d74e..f910efdfa03 100644 --- a/tests/core/test_surface.py +++ b/tests/core/test_surface.py @@ -6,10 +6,8 @@ import unittest import numpy as np -from numpy.testing import assert_allclose -from pytest import approx - import pymatgen +from numpy.testing import assert_allclose from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core import Lattice, Structure from pymatgen.core.surface import ( @@ -26,6 +24,7 @@ from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.symmetry.groups import SpaceGroup from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx class TestSlab(PymatgenTest): @@ -380,9 +379,9 @@ def test_get_slab(self): if sg.crystal_system == "hexagonal" or ( sg.crystal_system == "trigonal" and ( - sg.symbol.endswith("H") + sg.hexagonal or sg.int_number - in [143, 144, 145, 147, 149, 150, 151, 152, 153, 154, 156, 157, 158, 159, 162, 163, 164, 165] + in (143, 144, 145, 147, 149, 150, 151, 152, 153, 154, 156, 157, 158, 159, 162, 163, 164, 165) ) ): lattice = Lattice.hexagonal(5, 10) diff --git a/tests/core/test_tensors.py b/tests/core/test_tensors.py index ec794da99f5..0be6d488207 100644 --- a/tests/core/test_tensors.py +++ b/tests/core/test_tensors.py @@ -6,12 +6,11 @@ import pytest from monty.serialization import MontyDecoder, loadfn from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core.operations import SymmOp from pymatgen.core.tensors import SquareTensor, Tensor, TensorCollection, TensorMapping, itertools, symmetry_reduce from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx class TestTensor(PymatgenTest): @@ -159,7 +158,7 @@ def test_einsum_sequence(self): test = Tensor(np.arange(0, 3**4).reshape((3, 3, 3, 3))) assert_allclose([0, 27, 54], test.einsum_sequence([x] * 3)) assert test.einsum_sequence([np.eye(3)] * 2) == 360 - with pytest.raises(ValueError, match="other tensors must be list of tensors or tensor input"): + with pytest.raises(TypeError, match="other tensors must be list of tensors or tensor input"): test.einsum_sequence(Tensor(np.zeros(3))) def test_symmetrized(self): diff --git a/tests/core/test_trajectory.py b/tests/core/test_trajectory.py index 444b476c66b..f767412e7c8 100644 --- a/tests/core/test_trajectory.py +++ b/tests/core/test_trajectory.py @@ -6,7 +6,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Molecule, Structure from pymatgen.core.trajectory import Trajectory diff --git a/tests/core/test_units.py b/tests/core/test_units.py index ae785b20f7a..f2c2881b189 100644 --- a/tests/core/test_units.py +++ b/tests/core/test_units.py @@ -1,9 +1,9 @@ from __future__ import annotations +import warnings + import pytest from numpy.testing import assert_array_equal -from pytest import approx - from pymatgen.core.units import ( ArrayWithUnit, Energy, @@ -25,6 +25,7 @@ unitized, ) from pymatgen.util.testing import PymatgenTest +from pytest import approx def test_unit_conversions(): @@ -89,20 +90,34 @@ def test_length(self): assert x.to("cm") == approx(4.2e-08) assert x.to("pm") == 420 assert str(x / 2) == "2.1 ang" + y = x**3 assert y == approx(74.088) assert str(y.unit) == "ang^3" def test_memory(self): - mega = Memory(1, "Mb") - assert mega.to("byte") == 1024**2 - assert mega == Memory(1, "mb") + mega_0 = Memory(1, "MB") + assert mega_0.to("byte") == 1024**2 + + mega_1 = Memory.from_str("1 MB") + assert mega_1.unit_type == "memory" + + mega_2 = Memory.from_str("1MB") + assert mega_2.unit_type == "memory" + + mega_3 = Memory.from_str("+1.0 MB") + assert mega_0 == mega_1 == mega_2 == mega_3 - same_mega = Memory.from_str("1Mb") - assert same_mega.unit_type == "memory" + def test_deprecated_memory(self): + # TODO: remove after 2025-01-01 + for unit in ("Kb", "kb", "Mb", "mb", "Gb", "gb", "Tb", "tb"): + with pytest.warns(DeprecationWarning, match=f"Unit {unit} is deprecated"): + Memory(1, unit) - other_mega = Memory.from_str("+1.0 mb") - assert mega == other_mega + with warnings.catch_warnings(): + warnings.simplefilter("error") + for unit in ("KB", "MB", "GB", "TB"): + Memory(1, unit) def test_unitized(self): @unitized("eV") diff --git a/tests/core/test_xcfunc.py b/tests/core/test_xcfunc.py index be6b89c812d..8eba2c2dcc8 100644 --- a/tests/core/test_xcfunc.py +++ b/tests/core/test_xcfunc.py @@ -1,20 +1,24 @@ from __future__ import annotations +import pytest from pymatgen.core.xcfunc import XcFunc from pymatgen.util.testing import PymatgenTest class TestLibxcFunc(PymatgenTest): - def test_xcfunc_api(self): - """Testing XcFunc API.""" + def setUp(self) -> None: + self.ixc_11 = XcFunc.from_abinit_ixc(11) + + def test_aliases(self): # Aliases should be unique assert len(XcFunc.aliases()) == len(set(XcFunc.aliases())) + def test_lda(self): # LDA-Teter ixc_1 = XcFunc.from_abinit_ixc(1) assert ixc_1.type == "LDA" assert ixc_1.name == "LDA_XC_TETER93" - assert ixc_1 == ixc_1 + assert ixc_1 == ixc_1 # test __eq__ assert ixc_1 == "LDA_XC_TETER93" assert ixc_1 != "PBE" assert ixc_1.name not in XcFunc.aliases() @@ -28,7 +32,9 @@ def test_xcfunc_api(self): assert ixc_7.name == XcFunc.from_name(ixc_7.name) assert ixc_7 != ixc_1 + def test_gga_pbe(self): # GGA-PBE from ixc == 11 (in aliases) + ixc_1 = XcFunc.from_abinit_ixc(1) ixc_11 = XcFunc.from_abinit_ixc(11) assert ixc_11.type == "GGA" assert ixc_11.name == "PBE" @@ -42,25 +48,29 @@ def test_xcfunc_api(self): assert "PBE" in dct assert ixc_11 in dct - # Test if object can be serialized with Pickle. - self.serialize_with_pickle(ixc_11) + def test_pickle_serialize(self): + # Test if object can be serialized with Pickle + self.serialize_with_pickle(self.ixc_11) + @pytest.mark.skip() + def test_msonable(self): # Test if object supports MSONable # TODO - # ixc_11.x.as_dict() - # self.assertMSONable(ixc_11) + self.ixc_11.x.as_dict() + self.assertMSONable(self.ixc_11) + def test_from(self): # GGA-PBE from ixc given in abinit-libxc mode ixc_101130 = XcFunc.from_abinit_ixc(-101130) assert ixc_101130.type == "GGA" assert ixc_101130.name == "PBE" - assert ixc_101130 == ixc_11 + assert ixc_101130 == self.ixc_11 # GGA-PBE built from name gga_pbe = XcFunc.from_name("PBE") assert gga_pbe.type == "GGA" assert gga_pbe.name == "PBE" - assert ixc_11 == gga_pbe + assert self.ixc_11 == gga_pbe # Use X from GGA and C from LDA! unknown_xc = XcFunc.from_name("GGA_X_PBE+ LDA_C_PW") diff --git a/tests/electronic_structure/test_bandstructure.py b/tests/electronic_structure/test_bandstructure.py index a6d9d9dfc41..0daa57fcab2 100644 --- a/tests/electronic_structure/test_bandstructure.py +++ b/tests/electronic_structure/test_bandstructure.py @@ -8,8 +8,6 @@ import pytest from monty.serialization import loadfn from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core.lattice import Lattice from pymatgen.electronic_structure.bandstructure import ( BandStructureSymmLine, @@ -21,6 +19,7 @@ from pymatgen.electronic_structure.plotter import BSPlotterProjected from pymatgen.io.vasp import BSVasprun from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/bandstructure" diff --git a/tests/electronic_structure/test_boltztrap.py b/tests/electronic_structure/test_boltztrap.py index 4d1637dd56d..8bdb69a5e19 100644 --- a/tests/electronic_structure/test_boltztrap.py +++ b/tests/electronic_structure/test_boltztrap.py @@ -6,12 +6,11 @@ import pytest from monty.serialization import loadfn -from pytest import approx - from pymatgen.electronic_structure.bandstructure import BandStructure from pymatgen.electronic_structure.boltztrap import BoltztrapAnalyzer, BoltztrapRunner from pymatgen.electronic_structure.core import OrbitalType, Spin from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx try: from ase.io.cube import read_cube diff --git a/tests/electronic_structure/test_boltztrap2.py b/tests/electronic_structure/test_boltztrap2.py index 35926215e2e..b8660fbe61d 100644 --- a/tests/electronic_structure/test_boltztrap2.py +++ b/tests/electronic_structure/test_boltztrap2.py @@ -5,11 +5,10 @@ import numpy as np import pytest from monty.serialization import loadfn -from pytest import approx - from pymatgen.electronic_structure.core import OrbitalType, Spin from pymatgen.io.vasp import Vasprun from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx try: from pymatgen.electronic_structure.boltztrap2 import ( diff --git a/tests/electronic_structure/test_cohp.py b/tests/electronic_structure/test_cohp.py index 2f9f827ba8b..2b44b6eca1b 100644 --- a/tests/electronic_structure/test_cohp.py +++ b/tests/electronic_structure/test_cohp.py @@ -5,8 +5,6 @@ import pytest from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.electronic_structure.cohp import ( Cohp, CompleteCohp, @@ -16,6 +14,7 @@ ) from pymatgen.electronic_structure.core import Orbital, Spin from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/cohp" diff --git a/tests/electronic_structure/test_core.py b/tests/electronic_structure/test_core.py index 2abad986cc4..243d1bef73b 100644 --- a/tests/electronic_structure/test_core.py +++ b/tests/electronic_structure/test_core.py @@ -3,7 +3,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose - from pymatgen.core import Lattice from pymatgen.electronic_structure.core import Magmom, Orbital, Spin diff --git a/tests/electronic_structure/test_dos.py b/tests/electronic_structure/test_dos.py index c69cbcc54ba..e515f0411c4 100644 --- a/tests/electronic_structure/test_dos.py +++ b/tests/electronic_structure/test_dos.py @@ -8,12 +8,11 @@ from monty.io import zopen from monty.serialization import loadfn from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core import Element, Structure from pymatgen.electronic_structure.core import Orbital, OrbitalType, Spin from pymatgen.electronic_structure.dos import DOS, CompleteDos, FermiDos, LobsterCompleteDos from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/dos" diff --git a/tests/electronic_structure/test_plotter.py b/tests/electronic_structure/test_plotter.py index 9728bc8d5d4..304c7216083 100644 --- a/tests/electronic_structure/test_plotter.py +++ b/tests/electronic_structure/test_plotter.py @@ -10,8 +10,6 @@ import pytest from matplotlib import rc from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core.structure import Structure from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine from pymatgen.electronic_structure.boltztrap import BoltztrapAnalyzer @@ -31,6 +29,7 @@ ) from pymatgen.io.vasp import Vasprun from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest +from pytest import approx BAND_TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/bandstructure" diff --git a/tests/entries/test_compatibility.py b/tests/entries/test_compatibility.py index 850a4234d69..7eeea95e918 100644 --- a/tests/entries/test_compatibility.py +++ b/tests/entries/test_compatibility.py @@ -9,11 +9,9 @@ from typing import TYPE_CHECKING from unittest import TestCase +import pymatgen import pytest from monty.json import MontyDecoder -from pytest import approx - -import pymatgen from pymatgen.core import Element, Species from pymatgen.core.composition import Composition from pymatgen.core.lattice import Lattice @@ -34,6 +32,7 @@ ) from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry, ConstantEnergyAdjustment from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx if TYPE_CHECKING: from pymatgen.util.typing import CompositionLike diff --git a/tests/entries/test_computed_entries.py b/tests/entries/test_computed_entries.py index e7495f0e489..a7a00c7f88c 100644 --- a/tests/entries/test_computed_entries.py +++ b/tests/entries/test_computed_entries.py @@ -7,8 +7,6 @@ import pytest from monty.json import MontyDecoder -from pytest import approx - from pymatgen.analysis.phase_diagram import PhaseDiagram from pymatgen.entries.compatibility import MaterialsProject2020Compatibility from pymatgen.entries.computed_entries import ( @@ -23,6 +21,7 @@ ) from pymatgen.io.vasp.outputs import Vasprun from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/entries" @@ -238,6 +237,19 @@ def test_copy(self): assert entry == copy assert str(entry) == str(copy) + def test_from_dict_null_fields(self): + ce_dict = self.entry.as_dict() + for k in ( + "energy_adjustments", + "parameters", + "data", + ): + ce = ce_dict.copy() + ce[k] = None + new_ce = ComputedEntry.from_dict(ce) + assert new_ce == self.entry + assert getattr(new_ce, k, None) is not None + class TestComputedStructureEntry(TestCase): def setUp(self): diff --git a/tests/entries/test_correction_calculator.py b/tests/entries/test_correction_calculator.py index 02d0fb517a8..c5b8f90a657 100644 --- a/tests/entries/test_correction_calculator.py +++ b/tests/entries/test_correction_calculator.py @@ -3,7 +3,6 @@ from unittest import TestCase import pytest - from pymatgen.entries.correction_calculator import CorrectionCalculator from pymatgen.util.testing import TEST_FILES_DIR diff --git a/tests/entries/test_entry_tools.py b/tests/entries/test_entry_tools.py index 01f4255d8ff..a939dd4106e 100644 --- a/tests/entries/test_entry_tools.py +++ b/tests/entries/test_entry_tools.py @@ -4,7 +4,6 @@ import pytest from monty.serialization import dumpfn, loadfn - from pymatgen.core import Element from pymatgen.entries.computed_entries import ComputedEntry from pymatgen.entries.entry_tools import EntrySet, group_entries_by_composition, group_entries_by_structure diff --git a/tests/entries/test_exp_entries.py b/tests/entries/test_exp_entries.py index b73be4ad8a4..4ebb14d9d70 100644 --- a/tests/entries/test_exp_entries.py +++ b/tests/entries/test_exp_entries.py @@ -4,10 +4,9 @@ from unittest import TestCase from monty.json import MontyDecoder -from pytest import approx - from pymatgen.entries.exp_entries import ExpEntry from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx class TestExpEntry(TestCase): diff --git a/tests/entries/test_mixing_scheme.py b/tests/entries/test_mixing_scheme.py index 860ab42a0e7..33d71c5a5b8 100644 --- a/tests/entries/test_mixing_scheme.py +++ b/tests/entries/test_mixing_scheme.py @@ -108,7 +108,6 @@ import pytest from monty.json import MontyDecoder from numpy.testing import assert_allclose - from pymatgen.analysis.phase_diagram import PhaseDiagram from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core.lattice import Lattice diff --git a/tests/ext/test_cod.py b/tests/ext/test_cod.py index 9a3164d03d0..e2bc6ba9143 100644 --- a/tests/ext/test_cod.py +++ b/tests/ext/test_cod.py @@ -6,7 +6,6 @@ import pytest import requests - from pymatgen.ext.cod import COD if "CI" in os.environ: # test is slow and flaky, skip in CI. see diff --git a/tests/ext/test_matproj.py b/tests/ext/test_matproj.py index ec5ee928620..8489cf438c3 100644 --- a/tests/ext/test_matproj.py +++ b/tests/ext/test_matproj.py @@ -7,9 +7,6 @@ import pytest import requests from numpy.testing import assert_allclose -from pytest import approx -from ruamel.yaml import YAML - from pymatgen.analysis.phase_diagram import PhaseDiagram from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixEntry from pymatgen.analysis.reaction_calculator import Reaction @@ -24,6 +21,8 @@ from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine from pymatgen.phonon.dos import CompletePhononDos from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx +from ruamel.yaml import YAML try: skip_mprester_tests = requests.get("https://materialsproject.org", timeout=600).status_code != 200 diff --git a/tests/ext/test_optimade.py b/tests/ext/test_optimade.py index ea351acb8c7..2af457c38af 100644 --- a/tests/ext/test_optimade.py +++ b/tests/ext/test_optimade.py @@ -2,7 +2,6 @@ import pytest import requests - from pymatgen.ext.optimade import OptimadeRester from pymatgen.util.testing import PymatgenTest diff --git a/tests/files/.pytest-split-durations b/tests/files/.pytest-split-durations index 1f99ed37c72..35cd7f162b0 100644 --- a/tests/files/.pytest-split-durations +++ b/tests/files/.pytest-split-durations @@ -2017,7 +2017,7 @@ "tests/io/lobster/test_inputsenv.py::TestLobsterNeighbors::test_get_nn_info": 0.23225333401933312, "tests/io/lobster/test_inputsenv.py::TestLobsterNeighbors::test_get_plot_label": 0.2305897069745697, "tests/io/lobster/test_inputsenv.py::TestLobsterNeighbors::test_get_structure_environments": 0.2838197909295559, - "tests/io/lobster/test_inputsenv.py::TestLobsterNeighbors::test_get_strucuture_environments_further_tests": 0.2533352089812979, + "tests/io/lobster/test_inputsenv.py::TestLobsterNeighbors::test_get_structure_environments_further_tests": 0.2533352089812979, "tests/io/lobster/test_inputsenv.py::TestLobsterNeighbors::test_get_sum_icohps_between_neighbors_of_atom": 0.24758987501263618, "tests/io/lobster/test_inputsenv.py::TestLobsterNeighbors::test_molecules_allowed": 0.23277270805556327, "tests/io/lobster/test_inputsenv.py::TestLobsterNeighbors::test_order_parameter": 0.2319688760326244, diff --git a/tests/files/io/abinit/28ni.paw b/tests/files/io/abinit/28ni.paw new file mode 100644 index 00000000000..5f24f121ac4 --- /dev/null +++ b/tests/files/io/abinit/28ni.paw @@ -0,0 +1,3146 @@ +Paw atomic data for element Ni - Generated by AtomPAW (N. 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PHI 2 ===== #phi(r), for phi(r)/r*Ylm) + 1 : radial mesh index + 0.0000000000000000E+00 3.6123854535272722E-05 3.7411727855766806E-05 + 3.8745558134900286E-05 4.0126988356988640E-05 4.1557720461695676E-05 + 4.3039517475037788E-05 4.4574205718504979E-05 4.6163677099240728E-05 + 4.7809891484329556E-05 4.9514879162372027E-05 5.1280743395643793E-05 + 5.3109663066271793E-05 5.5003895419992671E-05 5.6965778911204132E-05 + 5.8997736153166519E-05 6.1102276977365372E-05 6.3282001606208623E-05 + 6.5539603943401471E-05 6.7877874986510466E-05 7.0299706366422818E-05 + 7.2808094018584311E-05 7.5406141991111932E-05 7.8097066395073163E-05 + 8.0884199502450103E-05 8.3770993997527956E-05 8.6761027387685834E-05 + 8.9858006579814133E-05 9.3065772628842623E-05 9.6388305665128733E-05 + 9.9829730007741210E-05 1.0339431947096735E-04 1.0708650287167277E-04 + 1.1091086974547579E-04 1.1487217628001971E-04 1.1897535147398593E-04 + 1.2322550353085113E-04 1.2762792649677782E-04 1.3218810715241941E-04 + 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6.1458925372588546E-01 6.4018862359056727E-01 + 6.6543400354658444E-01 6.9014300832090170E-01 7.1412635307989658E-01 + 7.3719019586417589E-01 7.5913861451642517E-01 7.7977617414274381E-01 + 7.9891054395238770E-01 8.1635512614356209E-01 8.3193166313837585E-01 + 8.4547279190595404E-01 8.5682451458982867E-01 8.6584855312255826E-01 + 8.7242455251834994E-01 8.7645209418211178E-01 8.7785247814272693E-01 + 8.7657023275055490E-01 8.7257431277457820E-01 +===== PHI 3 ===== #phi(r), for phi(r)/r*Ylm) + 1 : radial mesh index + 0.0000000000000000E+00 -1.3280945903791293E-05 -1.3751242759728414E-05 + -1.4238091463581038E-05 -1.4742067154014561E-05 -1.5263764416904873E-05 + -1.5803797903529114E-05 -1.6362802965467781E-05 -1.6941436306429305E-05 + -1.7540376651212652E-05 -1.8160325431976803E-05 -1.8802007491983237E-05 + -1.9466171806938332E-05 -2.0153592224043065E-05 -2.0865068218817291E-05 + -2.1601425669732720E-05 -2.2363517650652224E-05 -2.3152225241024587E-05 + -2.3968458353732002E-05 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1.9845960975029214E-01 + 2.0576641298244019E-01 2.1290515817127700E-01 2.1991176130685261E-01 + 2.2682763026941438E-01 2.3369894984218653E-01 2.4057584529313872E-01 + 2.4751144227603844E-01 2.5456084314523314E-01 2.6178004148403050E-01 + 2.6922479760045270E-01 2.7694949808534192E-01 2.8500602217084708E-01 + 2.9344263690132710E-01 3.0230294179215017E-01 3.1162488203337763E-01 + 3.2143984722611757E-01 3.3177187032673544E-01 3.4263693878368395E-01 + 3.5404242699613031E-01 3.6598665613600129E-01 3.7845858427437656E-01 + 3.9143762674764770E-01 4.0489360402218055E-01 4.1878681218763508E-01 + 4.3306820984924238E-01 4.4767971472724832E-01 4.6255460372134438E-01 + 4.7761801137171522E-01 4.9278752319085212E-01 5.0797386172563130E-01 + 5.2308166391493371E-01 5.3801034788310553E-01 5.5265506558574473E-01 + 5.6690773482757784E-01 5.8065814054636933E-01 5.9379509151497434E-01 + 6.0620761540788204E-01 6.1778617303164796E-01 +===== PHI 5 ===== #phi(r), for phi(r)/r*Ylm) + 1 : radial mesh index + 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3.3608913540986834E-01 3.8004693496760961E-01 4.2421865067976200E-01 + 4.6818734933145612E-01 5.1151822865725027E-01 5.5377074268661119E-01 + 5.9451243840464407E-01 6.3333386456116569E-01 6.6986366899462790E-01 + 7.0378277583156834E-01 7.3483635983100415E-01 7.6284224831946612E-01 + 7.8769442224725239E-01 8.0936050245320079E-01 8.2787254596486959E-01 + 8.4331119639487362E-01 8.5578428544564145E-01 8.6540239017943277E-01 + 8.7225552520682181E-01 8.7639673407395047E-01 8.7783892843352174E-01 + 8.7656898816319029E-01 8.7257431277457820E-01 +===== TPHI 3 ===== #tphi(r), for tphi(r)/r*Ylm) + 1 : radial mesh index + 0.0000000000000000E+00 1.1679131619091125E-07 1.2092632526982877E-07 + 1.2520681035177783E-07 1.2963782248696726E-07 1.3422458322858221E-07 + 1.3897249003092148E-07 1.4388712179171395E-07 1.4897424454026883E-07 + 1.5423981727314444E-07 1.5968999793858841E-07 1.6533114957096754E-07 + 1.7116984657603893E-07 1.7721288116772682E-07 1.8346726995669537E-07 + 1.8994026069069556E-07 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b/tests/files/io/abinit/Fe_magmoms_collinear_GSR.nc new file mode 100644 index 00000000000..c549c641496 Binary files /dev/null and b/tests/files/io/abinit/Fe_magmoms_collinear_GSR.nc differ diff --git a/tests/files/io/abinit/Fe_magmoms_noncollinear_GSR.nc b/tests/files/io/abinit/Fe_magmoms_noncollinear_GSR.nc new file mode 100644 index 00000000000..9608d72cb35 Binary files /dev/null and b/tests/files/io/abinit/Fe_magmoms_noncollinear_GSR.nc differ diff --git a/tests/io/abinit/test_abiobjects.py b/tests/io/abinit/test_abiobjects.py index 8bbfa3a7441..5dcbff0b26d 100644 --- a/tests/io/abinit/test_abiobjects.py +++ b/tests/io/abinit/test_abiobjects.py @@ -3,8 +3,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.core.structure import Structure from pymatgen.core.units import Ha_to_eV, bohr_to_ang from pymatgen.io.abinit.abiobjects import ( @@ -20,6 +18,7 @@ structure_to_abivars, ) from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx class TestLatticeFromAbivars(PymatgenTest): diff --git a/tests/io/abinit/test_inputs.py b/tests/io/abinit/test_inputs.py index 5d95dc95fb9..287bfa68401 100644 --- a/tests/io/abinit/test_inputs.py +++ b/tests/io/abinit/test_inputs.py @@ -6,7 +6,6 @@ import numpy as np import pytest from numpy.testing import assert_array_equal - from pymatgen.core.structure import Structure from pymatgen.io.abinit.inputs import ( BasicAbinitInput, @@ -185,8 +184,8 @@ def test_api(self): assert len(multi) == 1 assert multi.ndtset == 1 assert multi.isnc - for i, inp in enumerate(multi): - assert list(inp) == list(multi[i]) + for inp in multi: + assert list(inp) == list(inp) multi.addnew_from(0) assert multi.ndtset == 2 diff --git a/tests/io/abinit/test_netcdf.py b/tests/io/abinit/test_netcdf.py index cd01b0e4b90..410323bef26 100644 --- a/tests/io/abinit/test_netcdf.py +++ b/tests/io/abinit/test_netcdf.py @@ -3,7 +3,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose, assert_array_equal - from pymatgen.core.structure import Structure from pymatgen.io.abinit import EtsfReader from pymatgen.io.abinit.netcdf import AbinitHeader @@ -19,7 +18,7 @@ class TestEtsfReader(PymatgenTest): def setUp(self): - formulas = ["Si2"] + formulas = ["Si2", "Fe_magmoms_collinear", "Fe_magmoms_noncollinear"] self.GSR_paths = dct = {} for formula in formulas: dct[formula] = f"{TEST_DIR}/{formula}_GSR.nc" @@ -73,12 +72,29 @@ def test_read_si2(self): # Initialize pymatgen structure from GSR. structure = data.read_structure() assert isinstance(structure, Structure) + assert "magmom" not in structure.site_properties # Read ixc. # TODO: Upgrade GSR file. # xc = data.read_abinit_xcfunc() # assert xc == "LDA" + @pytest.mark.skipif(netCDF4 is None, reason="Requires Netcdf4") + def test_read_fe(self): + path = self.GSR_paths["Fe_magmoms_collinear"] + ref_magmom_collinear = [-0.5069359730980665] + + with EtsfReader(path) as data: + structure = data.read_structure() + assert structure.site_properties["magmom"] == ref_magmom_collinear + + path = self.GSR_paths["Fe_magmoms_noncollinear"] + ref_magmom_noncollinear = [[0.357939487, 0.357939487, 0]] + + with EtsfReader(path) as data: + structure = data.read_structure() + assert structure.site_properties["magmom"] == ref_magmom_noncollinear + class TestAbinitHeader(PymatgenTest): def test_api(self): diff --git a/tests/io/abinit/test_pseudos.py b/tests/io/abinit/test_pseudos.py index 6ce09c08042..c8fac2e187e 100644 --- a/tests/io/abinit/test_pseudos.py +++ b/tests/io/abinit/test_pseudos.py @@ -4,10 +4,9 @@ from collections import defaultdict import pytest -from pytest import approx - from pymatgen.io.abinit.pseudos import Pseudo, PseudoTable from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/abinit" @@ -17,7 +16,11 @@ def setUp(self): nc_pseudo_fnames = defaultdict(list) nc_pseudo_fnames["Si"] = [f"{TEST_DIR}/{file}" for file in ("14si.pspnc", "14si.4.hgh", "14-Si.LDA.fhi")] + paw_pseudo_fnames = defaultdict(list) + paw_pseudo_fnames["Ni"] = [f"{TEST_DIR}/28ni.paw"] + self.nc_pseudos = defaultdict(list) + self.paw_pseudos = defaultdict(list) for symbol, file_names in nc_pseudo_fnames.items(): for file_name in file_names: @@ -33,6 +36,20 @@ def setUp(self): setattr(self, attribute, pseudo) + for symbol, file_names in paw_pseudo_fnames.items(): + for file_name in file_names: + _root, ext = os.path.splitext(file_name) + pseudo = Pseudo.from_file(file_name) + self.paw_pseudos[symbol].append(pseudo) + + # Save the pseudo as instance attribute whose name + # is constructed with the rule: symbol_ppformat + attribute = f"{symbol}_{ext[1:]}" + if hasattr(self, attribute): + raise RuntimeError(f"self has already {attribute=}") + + setattr(self, attribute, pseudo) + def test_nc_pseudos(self): """Test norm-conserving pseudopotentials.""" for symbol, pseudos in self.nc_pseudos.items(): @@ -91,6 +108,31 @@ def test_nc_pseudos(self): # Test pickle self.serialize_with_pickle(table, test_eq=False) + def test_paw_pseudos(self): + """Test 28ni.paw.""" + for symbol, pseudos in self.paw_pseudos.items(): + for pseudo in pseudos: + assert repr(pseudo) + assert str(pseudo) + assert not pseudo.isnc + assert pseudo.ispaw + assert pseudo.Z == 28 + assert pseudo.symbol == symbol + assert pseudo.Z_val == 18 + assert pseudo.paw_radius >= 0.0 + + # Test pickle + self.serialize_with_pickle(pseudo) + + # Test MSONable + self.assert_msonable(pseudo) + + pseudo = self.Ni_paw + assert pseudo.l_max == 2 + assert pseudo.l_local == 0 + assert pseudo.supports_soc + assert pseudo.md5 is not None + def test_pawxml_pseudos(self): """Test O.GGA_PBE-JTH-paw.xml.""" oxygen = Pseudo.from_file(f"{TEST_DIR}/O.GGA_PBE-JTH-paw.xml") diff --git a/tests/io/aims/aims_input_generator_ref/md-si/control.in.gz b/tests/io/aims/aims_input_generator_ref/md-si/control.in.gz new file mode 100644 index 00000000000..d50a761f109 Binary files /dev/null and b/tests/io/aims/aims_input_generator_ref/md-si/control.in.gz differ diff --git a/tests/io/aims/aims_input_generator_ref/md-si/geometry.in.gz b/tests/io/aims/aims_input_generator_ref/md-si/geometry.in.gz new file mode 100644 index 00000000000..c110b4b3ddf Binary files /dev/null and b/tests/io/aims/aims_input_generator_ref/md-si/geometry.in.gz differ diff --git a/tests/io/aims/aims_input_generator_ref/md-si/parameters.json b/tests/io/aims/aims_input_generator_ref/md-si/parameters.json new file mode 100644 index 00000000000..fde9e691edb --- /dev/null +++ b/tests/io/aims/aims_input_generator_ref/md-si/parameters.json @@ -0,0 +1 @@ +{"xc": "pbe", "relativistic": "atomic_zora scalar", "MD_run": "10.0 NVT_parrinello 300 0.4", "MD_time_step": 0.002, "MD_MB_init": 300, "species_dir": "/home/andrey/workspace/pymatgen/tests/io/aims/species_directory/light", "k_grid": [2, 2, 2]} diff --git a/tests/io/aims/conftest.py b/tests/io/aims/conftest.py index 9d13f62dc56..177aeb38001 100644 --- a/tests/io/aims/conftest.py +++ b/tests/io/aims/conftest.py @@ -3,10 +3,16 @@ import os import pytest +from pymatgen.core import SETTINGS module_dir = os.path.dirname(__file__) @pytest.fixture(autouse=True) def _set_aims_species_dir_env_var(monkeypatch: pytest.MonkeyPatch) -> None: - monkeypatch.setenv("AIMS_SPECIES_DIR", f"{module_dir}/species_directory/light") + monkeypatch.setenv("AIMS_SPECIES_DIR", f"{module_dir}/species_directory") + + +@pytest.fixture(autouse=True) +def _set_aims_species_dir_settings(monkeypatch: pytest.MonkeyPatch): + monkeypatch.setitem(SETTINGS, "AIMS_SPECIES_DIR", f"{module_dir}/species_directory") diff --git a/tests/io/aims/input_files/geometry.in.si.gz b/tests/io/aims/input_files/geometry.in.si.gz index 6b8791fac6f..9a1b5513afa 100644 Binary files a/tests/io/aims/input_files/geometry.in.si.gz and b/tests/io/aims/input_files/geometry.in.si.gz differ diff --git a/tests/io/aims/input_files/geometry.in.si.ref.gz b/tests/io/aims/input_files/geometry.in.si.ref.gz index c5b46dfae44..304a3b328a9 100644 Binary files a/tests/io/aims/input_files/geometry.in.si.ref.gz and b/tests/io/aims/input_files/geometry.in.si.ref.gz differ diff --git a/tests/io/aims/input_files/si_ref.json.gz b/tests/io/aims/input_files/si_ref.json.gz index 29148f3f399..1fda517d267 100644 Binary files a/tests/io/aims/input_files/si_ref.json.gz and b/tests/io/aims/input_files/si_ref.json.gz differ diff --git a/tests/io/aims/test_aims_inputs.py b/tests/io/aims/test_aims_inputs.py index d0b0d5a30c4..5ded1722eaf 100644 --- a/tests/io/aims/test_aims_inputs.py +++ b/tests/io/aims/test_aims_inputs.py @@ -8,13 +8,15 @@ import pytest from monty.json import MontyDecoder, MontyEncoder from numpy.testing import assert_allclose - +from pymatgen.core import SETTINGS from pymatgen.io.aims.inputs import ( ALLOWED_AIMS_CUBE_TYPES, ALLOWED_AIMS_CUBE_TYPES_STATE, AimsControlIn, AimsCube, AimsGeometryIn, + AimsSpeciesFile, + SpeciesDefaults, ) from pymatgen.util.testing.aims import compare_single_files as compare_files @@ -74,23 +76,23 @@ def test_read_h2o_in(tmp_path: Path): assert h2o.structure == h2o_from_dct.structure -def check_wrong_type_aims_cube(type, exp_err): +def check_wrong_type_aims_cube(cube_type, exp_err): with pytest.raises(ValueError, match=exp_err): - AimsCube(type=type) + AimsCube(type=cube_type) def test_aims_cube(): - check_wrong_type_aims_cube(type="INCORRECT_TYPE", exp_err="Cube type undefined") + check_wrong_type_aims_cube(cube_type="INCORRECT_TYPE", exp_err="Cube type undefined") for cube_type in ALLOWED_AIMS_CUBE_TYPES_STATE: check_wrong_type_aims_cube( - type=cube_type, + cube_type=cube_type, exp_err=f"{cube_type=} must have a state associated with it", ) for cube_type in ALLOWED_AIMS_CUBE_TYPES: check_wrong_type_aims_cube( - type=f"{cube_type} 1", + cube_type=f"{cube_type} 1", exp_err=f"{cube_type=} can not have a state associated with it", ) @@ -164,7 +166,7 @@ def test_aims_control_in(tmp_path: Path): "compute_forces": True, "relax_geometry": ["trm", "1e-3"], "batch_size_limit": 200, - "species_dir": str(TEST_DIR.parent / "species_directory/light"), + "species_dir": "light", } aims_control = AimsControlIn(parameters.copy()) @@ -204,30 +206,27 @@ def test_aims_control_in(tmp_path: Path): compare_files(TEST_DIR / "control.in.si", f"{tmp_path}/control.in") -def test_aims_control_in_default_species_dir(tmp_path: Path, monkeypatch: pytest.MonkeyPatch): - monkeypatch.setenv("AIMS_SPECIES_DIR", str(TEST_DIR.parent / "species_directory/light")) - - parameters = { - "cubes": [ - AimsCube(type="eigenstate 1", points=[10, 10, 10]), - AimsCube(type="total_density", points=[10, 10, 10]), - ], - "xc": "LDA", - "smearing": ["fermi-dirac", 0.01], - "vdw_correction_hirshfeld": True, - "compute_forces": True, - "relax_geometry": ["trm", "1e-3"], - "batch_size_limit": 200, - "output": ["band 0 0 0 0.5 0 0.5 10 G X", "band 0 0 0 0.5 0.5 0.5 10 G L"], - "k_grid": [1, 1, 1], - } - - aims_control = AimsControlIn(parameters.copy()) +def test_species_file(monkeypatch: pytest.MonkeyPatch): + """Tests an AimsSpeciesFile class""" + monkeypatch.setitem(SETTINGS, "AIMS_SPECIES_DIR", str(TEST_DIR.parent / "species_directory")) + species_file = AimsSpeciesFile.from_element_and_basis_name("Si", "light", label="Si_surface") + assert species_file.label == "Si_surface" + assert species_file.element == "Si" - for key, val in parameters.items(): - assert aims_control[key] == val +def test_species_defaults(monkeypatch: pytest.MonkeyPatch): + """Tests an AimsSpeciesDefaults class""" + monkeypatch.setitem(SETTINGS, "AIMS_SPECIES_DIR", str(TEST_DIR.parent / "species_directory")) si = AimsGeometryIn.from_file(TEST_DIR / "geometry.in.si.gz").structure - - aims_control.write_file(si, directory=tmp_path, verbose_header=True, overwrite=True) - compare_files(TEST_DIR / "control.in.si.no_sd", f"{tmp_path}/control.in") + species_defaults = SpeciesDefaults.from_structure(si, "light") + assert species_defaults.labels == [ + "Si", + ] + assert species_defaults.elements == {"Si": "Si"} + + si.relabel_sites() + species_defaults = SpeciesDefaults.from_structure(si, "light") + assert species_defaults.labels == ["Si_1", "Si_2"] + assert species_defaults.elements == {"Si_1": "Si", "Si_2": "Si"} + assert "Si_1" in str(species_defaults) + assert "Si_2" in str(species_defaults) diff --git a/tests/io/aims/test_aims_outputs.py b/tests/io/aims/test_aims_outputs.py index deb0554f658..1d675dad2a3 100644 --- a/tests/io/aims/test_aims_outputs.py +++ b/tests/io/aims/test_aims_outputs.py @@ -6,7 +6,6 @@ from monty.json import MontyDecoder, MontyEncoder from numpy.testing import assert_allclose - from pymatgen.core import Structure from pymatgen.io.aims.outputs import AimsOutput diff --git a/tests/io/aims/test_aims_parsers.py b/tests/io/aims/test_aims_parsers.py index 1d30799122d..e6cb7d6eb7a 100644 --- a/tests/io/aims/test_aims_parsers.py +++ b/tests/io/aims/test_aims_parsers.py @@ -6,7 +6,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose - from pymatgen.core.tensors import Tensor from pymatgen.io.aims.parsers import ( EV_PER_A3_TO_KBAR, diff --git a/tests/io/aims/test_sets/test_input_set.py b/tests/io/aims/test_sets/test_input_set.py index fb7acf5011d..f5d87fe3881 100644 --- a/tests/io/aims/test_sets/test_input_set.py +++ b/tests/io/aims/test_sets/test_input_set.py @@ -5,7 +5,6 @@ from pathlib import Path import pytest - from pymatgen.core import Structure from pymatgen.io.aims.sets import AimsInputSet diff --git a/tests/io/aims/test_sets/test_md_generator.py b/tests/io/aims/test_sets/test_md_generator.py new file mode 100644 index 00000000000..13c6f8f6859 --- /dev/null +++ b/tests/io/aims/test_sets/test_md_generator.py @@ -0,0 +1,48 @@ +"""Tests the MD input set generator""" + +from __future__ import annotations + +from pathlib import Path + +import pytest +from pymatgen.io.aims.sets.core import MDSetGenerator +from pymatgen.util.testing.aims import Si, compare_files + +module_dir = Path(__file__).resolve().parents[1] +species_dir = module_dir / "species_directory" +ref_path = (module_dir / "aims_input_generator_ref").resolve() + + +def test_si_md(tmp_path): + # default behaviour + parameters = { + "species_dir": str(species_dir / "light"), + "k_grid": [2, 2, 2], + } + test_name = "md-si" + # First do the exceptions + with pytest.raises(ValueError, match="Ensemble something not valid"): + MDSetGenerator(ensemble="something").get_input_set(Si) + with pytest.raises(ValueError, match="Type parrinello is not valid for nve ensemble"): + MDSetGenerator(ensemble="nve", ensemble_specs={"type": "parrinello"}).get_input_set(Si) + with pytest.raises(ValueError, match="Velocities must be initialized"): + MDSetGenerator(ensemble="nve", init_velocities=False).get_input_set(Si) + with pytest.raises(ValueError, match="Temperature must be set"): + MDSetGenerator(ensemble="nve").get_input_set(Si) + with pytest.raises(ValueError, match="Temperature must be set"): + MDSetGenerator(ensemble="nvt").get_input_set(Si) + with pytest.raises(ValueError, match="parameter is not defined"): + MDSetGenerator(ensemble="nve", ensemble_specs={"type": "damped"}, temp=300).get_input_set(Si) + # then do the actual input set + generator = MDSetGenerator( + ensemble="nvt", + ensemble_specs={"type": "parrinello", "parameter": 0.4}, + temp=300, + time=10.0, + time_step=0.002, + user_params=parameters, + ) + input_set = generator.get_input_set(Si) + input_set.write_input(tmp_path / test_name) + + return compare_files(test_name, tmp_path, ref_path) diff --git a/tests/io/aims/test_sets/test_relax_generator.py b/tests/io/aims/test_sets/test_relax_generator.py index 93fdfca329b..1f2798c1514 100644 --- a/tests/io/aims/test_sets/test_relax_generator.py +++ b/tests/io/aims/test_sets/test_relax_generator.py @@ -12,29 +12,17 @@ def test_relax_si(tmp_path): params = { - "species_dir": str(species_dir / "light"), + "species_dir": "light", "k_grid": [2, 2, 2], } comp_system(Si, params, "relax-si/", tmp_path, ref_path, RelaxSetGenerator) def test_relax_si_no_kgrid(tmp_path): - params = {"species_dir": str(species_dir / "light")} + params = {"species_dir": "light"} comp_system(Si, params, "relax-no-kgrid-si", tmp_path, ref_path, RelaxSetGenerator) -def test_relax_default_species_dir(tmp_path): - params = {"k_grid": [2, 2, 2]} - - comp_system(Si, params, "relax-si", tmp_path, ref_path, RelaxSetGenerator) - - def test_relax_o2(tmp_path): params = {"species_dir": str(species_dir / "light")} comp_system(O2, params, "relax-o2", tmp_path, ref_path, RelaxSetGenerator) - - -def test_relax_default_species_dir_o2(tmp_path): - params = {"k_grid": [2, 2, 2]} - - comp_system(O2, params, "relax-o2", tmp_path, ref_path, RelaxSetGenerator) diff --git a/tests/io/aims/test_sets/test_static_generator.py b/tests/io/aims/test_sets/test_static_generator.py index 4dd5c5879fa..39415758b1e 100644 --- a/tests/io/aims/test_sets/test_static_generator.py +++ b/tests/io/aims/test_sets/test_static_generator.py @@ -6,35 +6,22 @@ from pymatgen.util.testing.aims import O2, Si, comp_system module_dir = Path(__file__).resolve().parents[1] -species_dir = module_dir / "species_directory" ref_path = (module_dir / "aims_input_generator_ref").resolve() def test_static_si(tmp_path): parameters = { - "species_dir": str(species_dir / "light"), + "species_dir": "light", "k_grid": [2, 2, 2], } comp_system(Si, parameters, "static-si", tmp_path, ref_path, StaticSetGenerator) def test_static_si_no_kgrid(tmp_path): - parameters = {"species_dir": str(species_dir / "light")} + parameters = {"species_dir": "light"} comp_system(Si, parameters, "static-no-kgrid-si", tmp_path, ref_path, StaticSetGenerator) -def test_static_default_species_dir(tmp_path): - parameters = {"k_grid": [2, 2, 2]} - - comp_system(Si, parameters, "static-si", tmp_path, ref_path, StaticSetGenerator) - - def test_static_o2(tmp_path): - parameters = {"species_dir": str(species_dir / "light")} - comp_system(O2, parameters, "static-o2", tmp_path, ref_path, StaticSetGenerator) - - -def test_static_default_species_dir_o2(tmp_path): - parameters = {"k_grid": [2, 2, 2]} - + parameters = {"species_dir": "light"} comp_system(O2, parameters, "static-o2", tmp_path, ref_path, StaticSetGenerator) diff --git a/tests/io/cp2k/test_inputs.py b/tests/io/cp2k/test_inputs.py index a4b344cda19..9120a789f6d 100644 --- a/tests/io/cp2k/test_inputs.py +++ b/tests/io/cp2k/test_inputs.py @@ -3,8 +3,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.core.structure import Molecule, Structure from pymatgen.io.cp2k.inputs import ( BasisFile, @@ -23,6 +21,7 @@ SectionList, ) from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/cp2k" diff --git a/tests/io/cp2k/test_outputs.py b/tests/io/cp2k/test_outputs.py index cd3214af175..fafe2b8be91 100644 --- a/tests/io/cp2k/test_outputs.py +++ b/tests/io/cp2k/test_outputs.py @@ -4,10 +4,9 @@ import numpy as np from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.io.cp2k.outputs import Cp2kOutput from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/cp2k" diff --git a/tests/io/cp2k/test_sets.py b/tests/io/cp2k/test_sets.py index ecb644a82a3..c986f02db6a 100644 --- a/tests/io/cp2k/test_sets.py +++ b/tests/io/cp2k/test_sets.py @@ -1,11 +1,10 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.core.structure import Molecule, Structure from pymatgen.io.cp2k.sets import SETTINGS, Cp2kValidationError, DftSet, GaussianTypeOrbitalBasisSet, GthPotential from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/cp2k" diff --git a/tests/io/exciting/test_inputs.py b/tests/io/exciting/test_inputs.py index a5a221221b3..02528023893 100644 --- a/tests/io/exciting/test_inputs.py +++ b/tests/io/exciting/test_inputs.py @@ -3,7 +3,6 @@ from xml.etree import ElementTree from numpy.testing import assert_allclose - from pymatgen.core import Lattice, Structure from pymatgen.io.exciting import ExcitingInput from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest diff --git a/tests/io/feff/test_inputs.py b/tests/io/feff/test_inputs.py index b95bcc536e1..cf06dd92bf9 100644 --- a/tests/io/feff/test_inputs.py +++ b/tests/io/feff/test_inputs.py @@ -4,11 +4,10 @@ from unittest import TestCase from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core import Molecule, Structure from pymatgen.io.feff.inputs import Atoms, Header, Paths, Potential, Tags from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx FEFF_TEST_DIR = f"{TEST_FILES_DIR}/io/feff" diff --git a/tests/io/feff/test_sets.py b/tests/io/feff/test_sets.py index e57e560996c..059d2422550 100644 --- a/tests/io/feff/test_sets.py +++ b/tests/io/feff/test_sets.py @@ -5,7 +5,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose - from pymatgen.core.structure import Lattice, Molecule, Structure from pymatgen.io.feff.inputs import Atoms, Header, Potential, Tags from pymatgen.io.feff.sets import FEFFDictSet, MPELNESSet, MPEXAFSSet, MPXANESSet diff --git a/tests/io/lammps/test_data.py b/tests/io/lammps/test_data.py index d2fb6541926..e88732fb033 100644 --- a/tests/io/lammps/test_data.py +++ b/tests/io/lammps/test_data.py @@ -10,12 +10,11 @@ import pytest from monty.json import MontyDecoder, MontyEncoder from numpy.testing import assert_allclose -from pytest import approx -from ruamel.yaml import YAML - from pymatgen.core import Element, Lattice, Molecule, Structure from pymatgen.io.lammps.data import CombinedData, ForceField, LammpsBox, LammpsData, Topology, lattice_2_lmpbox from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx +from ruamel.yaml import YAML TEST_DIR = f"{TEST_FILES_DIR}/io/lammps" diff --git a/tests/io/lammps/test_inputs.py b/tests/io/lammps/test_inputs.py index d56765fdad3..a3abdcceb16 100644 --- a/tests/io/lammps/test_inputs.py +++ b/tests/io/lammps/test_inputs.py @@ -6,7 +6,6 @@ import pandas as pd import pytest - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.io.lammps.data import LammpsData diff --git a/tests/io/lammps/test_outputs.py b/tests/io/lammps/test_outputs.py index 6d5e83c3089..e982cf21f18 100644 --- a/tests/io/lammps/test_outputs.py +++ b/tests/io/lammps/test_outputs.py @@ -7,7 +7,6 @@ import numpy as np import pandas as pd from numpy.testing import assert_allclose - from pymatgen.io.lammps.outputs import LammpsDump, parse_lammps_dumps, parse_lammps_log from pymatgen.util.testing import TEST_FILES_DIR diff --git a/tests/io/lobster/test_inputs.py b/tests/io/lobster/test_inputs.py index 574676952d6..62f413a1947 100644 --- a/tests/io/lobster/test_inputs.py +++ b/tests/io/lobster/test_inputs.py @@ -7,8 +7,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.core.structure import Structure from pymatgen.electronic_structure.cohp import IcohpCollection from pymatgen.electronic_structure.core import Orbital, Spin @@ -32,6 +30,7 @@ from pymatgen.io.vasp import Vasprun from pymatgen.io.vasp.inputs import Incar, Kpoints, Potcar from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/cohp" @@ -1839,10 +1838,10 @@ def test_dict_functionality(self): assert len_after == len_before - 1 # Test case sensitivity of |= operator - self.Lobsterin["skipCOHP"] = True # Camel case + self.Lobsterin |= {"skipCOHP": True} # Camel case assert self.Lobsterin["skipcohp"] is True - self.Lobsterin["skipcohp"] = False # lower case + self.Lobsterin |= {"skipcohp": False} # lower case assert self.Lobsterin["skipcohp"] is False def test_read_write_lobsterin(self): diff --git a/tests/io/lobster/test_lobsterenv.py b/tests/io/lobster/test_lobsterenv.py index 713c4b17eff..9a4230e232e 100644 --- a/tests/io/lobster/test_lobsterenv.py +++ b/tests/io/lobster/test_lobsterenv.py @@ -5,8 +5,6 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.analysis.graphs import StructureGraph from pymatgen.core import Element from pymatgen.core.structure import Structure @@ -15,6 +13,7 @@ from pymatgen.io.lobster import Charge, Icohplist from pymatgen.io.lobster.lobsterenv import LobsterNeighbors from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx __author__ = "Janine George" __copyright__ = "Copyright 2021, The Materials Project" @@ -688,7 +687,7 @@ def test_get_structure_environments(self): lse2 = self.chem_env_lobster1.get_light_structure_environment() assert lse2.coordination_environments[0][0]["ce_symbol"] == "O:6" - def test_get_strucuture_environments_further_tests(self): + def test_get_structure_environments_further_tests(self): lse = self.chem_env_lobster1_second.get_light_structure_environment() lse.as_dict() lse.get_statistics() diff --git a/tests/io/pwmat/test_inputs.py b/tests/io/pwmat/test_inputs.py index 1343ef6832a..8ee41de8552 100644 --- a/tests/io/pwmat/test_inputs.py +++ b/tests/io/pwmat/test_inputs.py @@ -3,7 +3,6 @@ import pytest from monty.io import zopen from numpy.testing import assert_allclose - from pymatgen.core import Composition, Structure from pymatgen.io.pwmat.inputs import ( ACExtractor, diff --git a/tests/io/qchem/test_inputs.py b/tests/io/qchem/test_inputs.py index 6a49daba428..c5c0515fa57 100644 --- a/tests/io/qchem/test_inputs.py +++ b/tests/io/qchem/test_inputs.py @@ -5,7 +5,6 @@ import pytest from monty.serialization import loadfn - from pymatgen.core.structure import Molecule from pymatgen.io.qchem.inputs import QCInput from pymatgen.io.qchem.sets import OptSet diff --git a/tests/io/qchem/test_outputs.py b/tests/io/qchem/test_outputs.py index bd900253583..31e54f67b3f 100644 --- a/tests/io/qchem/test_outputs.py +++ b/tests/io/qchem/test_outputs.py @@ -7,8 +7,6 @@ import pytest from monty.serialization import dumpfn, loadfn from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core.structure import Molecule from pymatgen.io.qchem.outputs import ( QCOutput, @@ -18,6 +16,7 @@ orbital_coeffs_parser, ) from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx try: from openbabel import openbabel diff --git a/tests/io/qchem/test_sets.py b/tests/io/qchem/test_sets.py index 041003d4428..aa2037dac17 100644 --- a/tests/io/qchem/test_sets.py +++ b/tests/io/qchem/test_sets.py @@ -3,7 +3,6 @@ import os import pytest - from pymatgen.io.qchem.sets import ( ForceSet, FreqSet, diff --git a/tests/io/qchem/test_utils.py b/tests/io/qchem/test_utils.py index 394ab8c142b..260dd803462 100644 --- a/tests/io/qchem/test_utils.py +++ b/tests/io/qchem/test_utils.py @@ -5,7 +5,6 @@ import pytest from monty.io import zopen - from pymatgen.io.qchem.utils import lower_and_check_unique, process_parsed_hess from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest diff --git a/tests/io/test_adf.py b/tests/io/test_adf.py index d3b6785320f..702fbc87d72 100644 --- a/tests/io/test_adf.py +++ b/tests/io/test_adf.py @@ -1,10 +1,9 @@ from __future__ import annotations -from pytest import approx - from pymatgen.core.structure import Molecule from pymatgen.io.adf import AdfInput, AdfKey, AdfOutput, AdfTask from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx __author__ = "Xin Chen, chenxin13@mails.tsinghua.edu.cn" diff --git a/tests/io/test_ase.py b/tests/io/test_ase.py index daf7b0c77bd..5ed59b6afff 100644 --- a/tests/io/test_ase.py +++ b/tests/io/test_ase.py @@ -3,7 +3,6 @@ import numpy as np import pytest from monty.json import MontyDecoder, jsanitize - from pymatgen.core import Composition, Lattice, Molecule, Structure from pymatgen.core.structure import StructureError from pymatgen.io.ase import AseAtomsAdaptor, MSONAtoms diff --git a/tests/io/test_atat.py b/tests/io/test_atat.py index a9562f92511..6cf13574495 100644 --- a/tests/io/test_atat.py +++ b/tests/io/test_atat.py @@ -1,11 +1,10 @@ from __future__ import annotations from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core.structure import Structure from pymatgen.io.atat import Mcsqs from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/atat/mcsqs" diff --git a/tests/io/test_babel.py b/tests/io/test_babel.py index e1724176ec4..589330d94c5 100644 --- a/tests/io/test_babel.py +++ b/tests/io/test_babel.py @@ -4,14 +4,13 @@ from unittest import TestCase import pytest -from pytest import approx - from pymatgen.analysis.graphs import MoleculeGraph from pymatgen.analysis.molecule_matcher import MoleculeMatcher from pymatgen.core.structure import Molecule from pymatgen.io.babel import BabelMolAdaptor from pymatgen.io.xyz import XYZ from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx pybel = pytest.importorskip("openbabel.pybel") diff --git a/tests/io/test_cif.py b/tests/io/test_cif.py index b9d8644bc6a..8abc5127813 100644 --- a/tests/io/test_cif.py +++ b/tests/io/test_cif.py @@ -2,14 +2,13 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core import Composition, DummySpecies, Element, Lattice, Species, Structure from pymatgen.electronic_structure.core import Magmom from pymatgen.io.cif import CifBlock, CifParser, CifWriter from pymatgen.symmetry.structure import SymmetrizedStructure from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest +from pytest import approx try: import pybtex @@ -163,7 +162,7 @@ class TestCifIO(PymatgenTest): def test_cif_parser(self): parser = CifParser(f"{TEST_FILES_DIR}/cif/LiFePO4.cif") for struct in parser.parse_structures(): - assert struct.formula == "Li4 Fe4 P4 O16", "Incorrectly parsed cif." + assert struct.formula == "Li4 Fe4 P4 O16", "Incorrectly parsed CIF" parser = CifParser(f"{TEST_FILES_DIR}/cif/V2O3.cif") for struct in parser.parse_structures(): diff --git a/tests/io/test_core.py b/tests/io/test_core.py index f3f08b46185..7c457339249 100644 --- a/tests/io/test_core.py +++ b/tests/io/test_core.py @@ -6,7 +6,6 @@ import pytest from monty.serialization import MontyDecoder - from pymatgen.core.structure import Structure from pymatgen.io.cif import CifParser, CifWriter from pymatgen.io.core import InputFile, InputSet diff --git a/tests/io/test_gaussian.py b/tests/io/test_gaussian.py index 7dc76b78b1b..fc694fa7f97 100644 --- a/tests/io/test_gaussian.py +++ b/tests/io/test_gaussian.py @@ -3,12 +3,11 @@ from unittest import TestCase import pytest -from pytest import approx - from pymatgen.core.structure import Molecule from pymatgen.electronic_structure.core import Spin from pymatgen.io.gaussian import GaussianInput, GaussianOutput from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/gaussian" diff --git a/tests/io/test_jarvis.py b/tests/io/test_jarvis.py index 75c3c78eb82..00a6b4f88f0 100644 --- a/tests/io/test_jarvis.py +++ b/tests/io/test_jarvis.py @@ -1,7 +1,6 @@ from __future__ import annotations import pytest - from pymatgen.core import Structure from pymatgen.io.jarvis import Atoms, JarvisAtomsAdaptor from pymatgen.util.testing import VASP_IN_DIR diff --git a/tests/io/test_lmto.py b/tests/io/test_lmto.py index 393a0b06bae..d398bd431b3 100644 --- a/tests/io/test_lmto.py +++ b/tests/io/test_lmto.py @@ -4,7 +4,6 @@ import numpy as np from numpy.testing import assert_array_equal - from pymatgen.core.structure import Structure from pymatgen.core.units import Ry_to_eV from pymatgen.electronic_structure.core import Spin diff --git a/tests/io/test_nwchem.py b/tests/io/test_nwchem.py index a81dc751ec0..5f4a13c8b5a 100644 --- a/tests/io/test_nwchem.py +++ b/tests/io/test_nwchem.py @@ -4,11 +4,10 @@ from unittest import TestCase import pytest -from pytest import approx - from pymatgen.core.structure import Molecule from pymatgen.io.nwchem import NwInput, NwInputError, NwOutput, NwTask from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/nwchem" diff --git a/tests/io/test_openff.py b/tests/io/test_openff.py index 2152b3e955e..41057daeb0b 100644 --- a/tests/io/test_openff.py +++ b/tests/io/test_openff.py @@ -5,7 +5,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose - from pymatgen.analysis.graphs import MoleculeGraph from pymatgen.analysis.local_env import OpenBabelNN from pymatgen.core import Molecule diff --git a/tests/io/test_packmol.py b/tests/io/test_packmol.py index 15d3c86b547..e82f627e310 100644 --- a/tests/io/test_packmol.py +++ b/tests/io/test_packmol.py @@ -6,7 +6,6 @@ from subprocess import TimeoutExpired import pytest - from pymatgen.analysis.molecule_matcher import MoleculeMatcher from pymatgen.core import Molecule from pymatgen.io.packmol import PackmolBoxGen diff --git a/tests/io/test_phonopy.py b/tests/io/test_phonopy.py index f12cce1f0a0..c3bc2e18187 100644 --- a/tests/io/test_phonopy.py +++ b/tests/io/test_phonopy.py @@ -7,8 +7,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.core import Element from pymatgen.io.phonopy import ( CompletePhononDos, @@ -29,6 +27,7 @@ get_thermal_displacement_matrices, ) from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx try: from phonopy import Phonopy diff --git a/tests/io/test_pwscf.py b/tests/io/test_pwscf.py index 6666b3c7938..124e4784a42 100644 --- a/tests/io/test_pwscf.py +++ b/tests/io/test_pwscf.py @@ -3,10 +3,9 @@ import numpy as np import pytest from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.io.pwscf import PWInput, PWInputError, PWOutput from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/pwscf" @@ -377,7 +376,7 @@ def test_read_str(self): assert pw_in.sections["system"]["smearing"] == "cold" -class TestPWOuput(PymatgenTest): +class TestPWOutput(PymatgenTest): def setUp(self): self.pw_out = PWOutput(f"{TEST_DIR}/Si.pwscf.out") diff --git a/tests/io/test_res.py b/tests/io/test_res.py index 5617ad86492..2e05ee5769a 100644 --- a/tests/io/test_res.py +++ b/tests/io/test_res.py @@ -1,11 +1,10 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.core import Structure from pymatgen.io.res import AirssProvider, ResParseError, ResWriter from pymatgen.util.testing import TEST_FILES_DIR +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/res" diff --git a/tests/io/test_shengbte.py b/tests/io/test_shengbte.py index 67779c458a1..60bc58b2a4a 100644 --- a/tests/io/test_shengbte.py +++ b/tests/io/test_shengbte.py @@ -4,7 +4,6 @@ import pytest from numpy.testing import assert_array_equal - from pymatgen.io.shengbte import Control from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest diff --git a/tests/io/test_template_input.py b/tests/io/test_template_input.py index 3be8ae45374..313fa8fc540 100644 --- a/tests/io/test_template_input.py +++ b/tests/io/test_template_input.py @@ -3,7 +3,6 @@ import os import pytest - from pymatgen.io.template import TemplateInputGen from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest diff --git a/tests/io/test_wannier90.py b/tests/io/test_wannier90.py index ca4704dfe72..32757970eeb 100644 --- a/tests/io/test_wannier90.py +++ b/tests/io/test_wannier90.py @@ -5,10 +5,9 @@ import numpy as np import pytest from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.io.wannier90 import Unk from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/io/wannier90" diff --git a/tests/io/test_xcrysden.py b/tests/io/test_xcrysden.py index 3a13a2cf7b5..88db940bcf8 100644 --- a/tests/io/test_xcrysden.py +++ b/tests/io/test_xcrysden.py @@ -1,7 +1,6 @@ from __future__ import annotations import numpy as np - from pymatgen.core.structure import Structure from pymatgen.io.xcrysden import XSF from pymatgen.util.testing import PymatgenTest diff --git a/tests/io/test_xyz.py b/tests/io/test_xyz.py index 2314eefdc8e..77e3c582efa 100644 --- a/tests/io/test_xyz.py +++ b/tests/io/test_xyz.py @@ -4,12 +4,11 @@ import pandas as pd import pytest -from pytest import approx - from pymatgen.core import Structure from pymatgen.core.structure import Molecule from pymatgen.io.xyz import XYZ from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR +from pytest import approx class TestXYZ(TestCase): diff --git a/tests/io/test_zeopp.py b/tests/io/test_zeopp.py index 2f38d24086c..3656530cb4e 100644 --- a/tests/io/test_zeopp.py +++ b/tests/io/test_zeopp.py @@ -4,8 +4,6 @@ from unittest import TestCase import pytest -from pytest import approx - from pymatgen.analysis.bond_valence import BVAnalyzer from pymatgen.core import Molecule, Species, Structure from pymatgen.io.zeopp import ( @@ -16,6 +14,7 @@ get_voronoi_nodes, ) from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR +from pytest import approx try: import zeo diff --git a/tests/io/vasp/test_inputs.py b/tests/io/vasp/test_inputs.py index cfd2769ff5e..aba859bea1f 100644 --- a/tests/io/vasp/test_inputs.py +++ b/tests/io/vasp/test_inputs.py @@ -15,8 +15,6 @@ from monty.io import zopen from monty.serialization import loadfn from numpy.testing import assert_allclose -from pytest import MonkeyPatch, approx - from pymatgen.core import SETTINGS from pymatgen.core.composition import Composition from pymatgen.core.structure import Structure @@ -36,6 +34,7 @@ _gen_potcar_summary_stats, ) from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest +from pytest import MonkeyPatch, approx # make sure _gen_potcar_summary_stats runs and works with all tests in this file _summ_stats = _gen_potcar_summary_stats(append=False, vasp_psp_dir=str(FAKE_POTCAR_DIR), summary_stats_filename=None) diff --git a/tests/io/vasp/test_optics.py b/tests/io/vasp/test_optics.py index 3a2caf7a94a..3e660a58797 100644 --- a/tests/io/vasp/test_optics.py +++ b/tests/io/vasp/test_optics.py @@ -4,7 +4,6 @@ import pytest import scipy.special from numpy.testing import assert_allclose - from pymatgen.io.vasp.optics import DielectricFunctionCalculator, delta_func, delta_methfessel_paxton, step_func from pymatgen.io.vasp.outputs import Vasprun from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest diff --git a/tests/io/vasp/test_outputs.py b/tests/io/vasp/test_outputs.py index a5faadac3ca..fb2a9697842 100644 --- a/tests/io/vasp/test_outputs.py +++ b/tests/io/vasp/test_outputs.py @@ -13,8 +13,6 @@ import pytest from monty.io import zopen from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core import Element from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure @@ -42,6 +40,7 @@ ) from pymatgen.io.wannier90 import Unk from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest +from pytest import approx try: import h5py diff --git a/tests/io/vasp/test_sets.py b/tests/io/vasp/test_sets.py index d0a8312ba87..354acd70b46 100644 --- a/tests/io/vasp/test_sets.py +++ b/tests/io/vasp/test_sets.py @@ -10,8 +10,6 @@ from monty.json import MontyDecoder from monty.serialization import loadfn from numpy.testing import assert_allclose -from pytest import MonkeyPatch, approx, mark - from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core import SETTINGS, Lattice, Species, Structure from pymatgen.core.composition import Composition @@ -55,6 +53,7 @@ ) from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest +from pytest import MonkeyPatch, approx, mark TEST_DIR = f"{TEST_FILES_DIR}/io/vasp" @@ -170,7 +169,6 @@ class TestMITMPRelaxSet(PymatgenTest): def setUpClass(cls): cls.set = MITRelaxSet cls.mp_set = MPRelaxSet - cls.monkeypatch = MonkeyPatch() filepath = f"{VASP_IN_DIR}/POSCAR" cls.structure = Structure.from_file(filepath) @@ -256,8 +254,8 @@ def test_potcar_validation(self): structure = Structure(self.lattice, ["P", "Fe"], self.coords) # Use pytest's monkeypatch to temporarily point pymatgen to a directory # containing the wrong POTCARs (LDA potcars in a PBE directory) - with self.monkeypatch.context() as m: - m.setitem(SETTINGS, "PMG_VASP_PSP_DIR", str(f"{VASP_IN_DIR}/wrong_potcars")) + with MonkeyPatch().context() as monkeypatch: + monkeypatch.setitem(SETTINGS, "PMG_VASP_PSP_DIR", str(f"{VASP_IN_DIR}/wrong_potcars")) with pytest.warns(BadInputSetWarning, match="not known by pymatgen"): _ = self.set(structure).potcar @@ -730,12 +728,12 @@ def test_init(self): vis = self.set(vis.structure, user_incar_settings={"LUSE_VDW": True, "LASPH": False}) vis.incar.items() with pytest.warns(BadInputSetWarning, match=r"LASPH"): - dummy_struc = Structure( + dummy_struct = Structure( lattice=[[0, 2, 2], [2, 0, 2], [2, 2, 0]], species=["Fe", "O"], coords=[[0, 0, 0], [0.5, 0.5, 0.5]], ) - vis = self.set(dummy_struc, user_incar_settings={"LDAU": True, "LASPH": False}) + vis = self.set(dummy_struct, user_incar_settings={"LDAU": True, "LASPH": False}) vis.incar.items() def test_user_incar_kspacing(self): diff --git a/tests/io/xtb/test_outputs.py b/tests/io/xtb/test_outputs.py index c4d3fe69777..dd1afc090af 100644 --- a/tests/io/xtb/test_outputs.py +++ b/tests/io/xtb/test_outputs.py @@ -2,12 +2,11 @@ import os -from pytest import approx - from pymatgen.core.structure import Molecule from pymatgen.io.qchem.outputs import check_for_structure_changes from pymatgen.io.xtb.outputs import CRESTOutput from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx try: from openbabel import openbabel diff --git a/tests/optimization/test_linear_assignment.py b/tests/optimization/test_linear_assignment.py index 961a5032b6d..163a1ac3132 100644 --- a/tests/optimization/test_linear_assignment.py +++ b/tests/optimization/test_linear_assignment.py @@ -4,9 +4,8 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.optimization.linear_assignment import LinearAssignment +from pytest import approx class TestLinearAssignment(TestCase): diff --git a/tests/optimization/test_neighbors.py b/tests/optimization/test_neighbors.py index a6374c1f929..8d66dcd9b91 100644 --- a/tests/optimization/test_neighbors.py +++ b/tests/optimization/test_neighbors.py @@ -1,7 +1,6 @@ from __future__ import annotations import numpy as np - from pymatgen.core.lattice import Lattice from pymatgen.optimization.neighbors import find_points_in_spheres from pymatgen.util.testing import PymatgenTest diff --git a/tests/phonon/test_bandstructure.py b/tests/phonon/test_bandstructure.py index 7f449792544..6f46c3dca38 100644 --- a/tests/phonon/test_bandstructure.py +++ b/tests/phonon/test_bandstructure.py @@ -4,11 +4,10 @@ import json from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.electronic_structure.bandstructure import Kpoint from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/bandstructure" diff --git a/tests/phonon/test_dos.py b/tests/phonon/test_dos.py index 0fecb44d6fd..013cfa7e8b3 100644 --- a/tests/phonon/test_dos.py +++ b/tests/phonon/test_dos.py @@ -5,11 +5,10 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.core import Element from pymatgen.phonon.dos import CompletePhononDos, PhononDos from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/phonon/dos" diff --git a/tests/phonon/test_gruneisen.py b/tests/phonon/test_gruneisen.py index 5b84acbc33f..3040db72cf3 100644 --- a/tests/phonon/test_gruneisen.py +++ b/tests/phonon/test_gruneisen.py @@ -1,13 +1,14 @@ from __future__ import annotations import matplotlib.pyplot as plt +import numpy as np import pytest -from pytest import approx - +from matplotlib import colors from pymatgen.io.phonopy import get_gruneisen_ph_bs_symm_line, get_gruneisenparameter from pymatgen.phonon.gruneisen import GruneisenParameter from pymatgen.phonon.plotter import GruneisenPhononBandStructureSymmLine, GruneisenPhononBSPlotter, GruneisenPlotter from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx try: import phonopy @@ -32,6 +33,39 @@ def test_plot(self): ax = plotter.get_plot_gs() assert isinstance(ax, plt.Axes) + def test_ph_plot_w_gruneisen(self): + plotter = GruneisenPhononBSPlotter(bs=self.bs_symm_line) + ax = plotter.get_plot_gs(plot_ph_bs_with_gruneisen=True, units="THz", cmap=["red", "royalblue"]) + assert ax.get_ylabel() == "Frequencies (THz)" + assert ax.get_xlabel() == "$\\mathrm{Wave\\ Vector}$" + assert ax.get_figure()._localaxes[-1].get_ylabel() == "$\\gamma \\ \\mathrm{(logarithmized)}$" + assert len(ax._children) == plotter.n_bands + 1 # check for number of bands + # check for x and y data is really the band-structure data + for inx, band in enumerate(plotter._bs.bands): + xy_data = { + "x": [point[0] for point in ax._children[inx].get_offsets().data], + "y": [point[1] for point in ax._children[inx].get_offsets().data], + } + assert band == pytest.approx(xy_data["y"]) + assert plotter._bs.distance == pytest.approx(xy_data["x"]) + + # check if color bar max value matches maximum gruneisen parameter value + data = plotter.bs_plot_data() + + # get reference min and max Grüneisen parameter values + max_gruneisen = np.array(data["gruneisen"]).max() + min_gruneisen = np.array(data["gruneisen"]).min() + + norm = colors.SymLogNorm( + vmin=min_gruneisen, + vmax=max_gruneisen, + linthresh=1e-2, + linscale=1, + ) + + assert max(norm.inverse(ax.get_figure()._localaxes[-1].get_yticks())) == pytest.approx(max_gruneisen) + assert isinstance(ax, plt.Axes) + def test_as_dict_from_dict(self): new_dict = self.bs_symm_line.as_dict() self.new_bs_symm_line = GruneisenPhononBandStructureSymmLine.from_dict(new_dict) diff --git a/tests/phonon/test_ir_spectra.py b/tests/phonon/test_ir_spectra.py index 7a7eb40f4ce..11bae39d9f7 100644 --- a/tests/phonon/test_ir_spectra.py +++ b/tests/phonon/test_ir_spectra.py @@ -1,7 +1,6 @@ from __future__ import annotations from monty.serialization import loadfn - from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest diff --git a/tests/phonon/test_plotter.py b/tests/phonon/test_plotter.py index 01e657e7eaf..2e0c762804b 100644 --- a/tests/phonon/test_plotter.py +++ b/tests/phonon/test_plotter.py @@ -6,7 +6,6 @@ import matplotlib.pyplot as plt import pytest from numpy.testing import assert_allclose - from pymatgen.phonon import CompletePhononDos, PhononBandStructureSymmLine from pymatgen.phonon.plotter import PhononBSPlotter, PhononDosPlotter, ThermoPlotter from pymatgen.util.testing import TEST_FILES_DIR diff --git a/tests/phonon/test_thermal_displacements.py b/tests/phonon/test_thermal_displacements.py index 725c197263f..315680e28d8 100644 --- a/tests/phonon/test_thermal_displacements.py +++ b/tests/phonon/test_thermal_displacements.py @@ -2,11 +2,10 @@ import numpy as np from numpy.testing import assert_allclose -from pytest import approx - from pymatgen.core.structure import Structure from pymatgen.phonon.thermal_displacements import ThermalDisplacementMatrices from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/phonon/thermal_displacement_matrices" diff --git a/tests/symmetry/test_analyzer.py b/tests/symmetry/test_analyzer.py index b4d602d75e9..41c7b72e6c1 100644 --- a/tests/symmetry/test_analyzer.py +++ b/tests/symmetry/test_analyzer.py @@ -1,12 +1,11 @@ from __future__ import annotations +from dataclasses import asdict from unittest import TestCase import numpy as np import pytest from numpy.testing import assert_allclose -from pytest import approx, raises - from pymatgen.core import Lattice, Molecule, PeriodicSite, Site, Species, Structure from pymatgen.io.vasp.outputs import Vasprun from pymatgen.symmetry.analyzer import ( @@ -18,6 +17,8 @@ ) from pymatgen.symmetry.structure import SymmetrizedStructure from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest +from pytest import approx, raises +from spglib import SpglibDataset TEST_DIR = f"{TEST_FILES_DIR}/symmetry/analyzer" @@ -124,7 +125,7 @@ def test_get_point_group_operations_uniq(self): def test_get_symmetry_dataset(self): ds = self.sg.get_symmetry_dataset() - assert ds["international"] == "Pnma" + assert ds.international == "Pnma" def test_init_cell(self): # see https://github.com/materialsproject/pymatgen/pull/3179 @@ -171,13 +172,13 @@ def test_get_crystal_system(self): assert crystal_system == "orthorhombic" assert self.disordered_sg.get_crystal_system() == "tetragonal" - orig_spg = self.sg._space_group_data["number"] - self.sg._space_group_data["number"] = 0 + def test_invalid_space_group_number(self): + invalid_sg = asdict(self.sg.get_symmetry_dataset()) + invalid_sg["number"] = 0 + self.sg._space_group_data = SpglibDataset(**invalid_sg) with pytest.raises(ValueError, match="Received invalid space group 0"): self.sg.get_crystal_system() - self.sg._space_group_data["number"] = orig_spg - def test_get_refined_structure(self): for pg_analyzer in self.sg.get_refined_structure().lattice.angles: assert pg_analyzer == 90 @@ -263,76 +264,75 @@ def test_get_ir_reciprocal_mesh_map(self): def test_get_conventional_standard_structure(self): structure = Structure.from_file(f"{TEST_FILES_DIR}/cif/bcc_1927.cif") - assert structure == structure spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure() - assert conv.lattice.angles == (90, 90, 90) - assert conv.lattice.lengths == approx([9.1980270633769461] * 3) + conventional = spga.get_conventional_standard_structure() + assert conventional.lattice.angles == (90, 90, 90) + assert conventional.lattice.lengths == approx([9.1980270633769461] * 3) structure = Structure.from_file(f"{TEST_FILES_DIR}/cif/btet_1915.cif") spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure() - assert conv.lattice.angles == (90, 90, 90) - assert conv.lattice.a == approx(5.0615106678044235) - assert conv.lattice.b == approx(5.0615106678044235) - assert conv.lattice.c == approx(4.2327080177761687) + conventional = spga.get_conventional_standard_structure() + assert conventional.lattice.angles == (90, 90, 90) + assert conventional.lattice.a == approx(5.0615106678044235) + assert conventional.lattice.b == approx(5.0615106678044235) + assert conventional.lattice.c == approx(4.2327080177761687) structure = Structure.from_file(f"{TEST_FILES_DIR}/cif/orci_1010.cif") spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure() - assert conv.lattice.angles == (90, 90, 90) - assert conv.lattice.a == approx(2.9542233922299999) - assert conv.lattice.b == approx(4.6330325651443296) - assert conv.lattice.c == approx(5.373703587040775) + conventional = spga.get_conventional_standard_structure() + assert conventional.lattice.angles == (90, 90, 90) + assert conventional.lattice.a == approx(2.9542233922299999) + assert conventional.lattice.b == approx(4.6330325651443296) + assert conventional.lattice.c == approx(5.373703587040775) structure = Structure.from_file(f"{TEST_FILES_DIR}/cif/orcc_1003.cif") spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure() - assert conv.lattice.angles == (90, 90, 90) - assert conv.lattice.a == approx(4.1430033493799998) - assert conv.lattice.b == approx(31.437979757624728) - assert conv.lattice.c == approx(3.99648651) + conventional = spga.get_conventional_standard_structure() + assert conventional.lattice.angles == (90, 90, 90) + assert conventional.lattice.a == approx(4.1430033493799998) + assert conventional.lattice.b == approx(31.437979757624728) + assert conventional.lattice.c == approx(3.99648651) structure = Structure.from_file(f"{TEST_FILES_DIR}/cif/orac_632475.cif") spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure() - assert conv.lattice.angles == (90, 90, 90) - assert conv.lattice.lengths == approx([3.1790663399999999, 9.9032878699999998, 3.5372412099999999]) + conventional = spga.get_conventional_standard_structure() + assert conventional.lattice.angles == (90, 90, 90) + assert conventional.lattice.lengths == approx([3.1790663399999999, 9.9032878699999998, 3.5372412099999999]) structure = Structure.from_file(f"{TEST_FILES_DIR}/cif/monoc_1028.cif") spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure() - assert conv.lattice.angles == approx([90, 117.53832420192903, 90]) - assert conv.lattice.lengths == approx([14.033435583000625, 3.96052850731, 6.8743926325200002]) + conventional = spga.get_conventional_standard_structure() + assert conventional.lattice.angles == approx([90, 117.53832420192903, 90]) + assert conventional.lattice.lengths == approx([14.033435583000625, 3.96052850731, 6.8743926325200002]) structure = Structure.from_file(f"{TEST_FILES_DIR}/cif/hex_1170.cif") spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure() - assert conv.lattice.angles == approx([90, 90, 120]) - assert conv.lattice.lengths == approx([3.699919902005897, 3.699919902005897, 6.9779585500000003]) + conventional = spga.get_conventional_standard_structure() + assert conventional.lattice.angles == approx([90, 90, 120]) + assert conventional.lattice.lengths == approx([3.699919902005897, 3.699919902005897, 6.9779585500000003]) STRUCTURE = f"{TEST_FILES_DIR}/symmetry/analyzer/tric_684654.json" structure = Structure.from_file(STRUCTURE) spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure() - assert conv.lattice.alpha == approx(74.09581916308757) - assert conv.lattice.beta == approx(75.72817279281173) - assert conv.lattice.gamma == approx(63.63234318667333) - assert conv.lattice.a == approx(3.741372924048738) - assert conv.lattice.b == approx(3.9883228679270686) - assert conv.lattice.c == approx(7.288495840048958) + conventional = spga.get_conventional_standard_structure() + assert conventional.lattice.alpha == approx(74.09581916308757) + assert conventional.lattice.beta == approx(75.72817279281173) + assert conventional.lattice.gamma == approx(63.63234318667333) + assert conventional.lattice.a == approx(3.741372924048738) + assert conventional.lattice.b == approx(3.9883228679270686) + assert conventional.lattice.c == approx(7.288495840048958) structure = Structure.from_file(STRUCTURE) structure.add_site_property("magmom", [1.0] * len(structure)) spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure(keep_site_properties=True) - assert conv.site_properties["magmom"] == [1.0] * len(conv) + conventional = spga.get_conventional_standard_structure(keep_site_properties=True) + assert conventional.site_properties["magmom"] == [1.0] * len(conventional) structure = Structure.from_file(STRUCTURE) structure.add_site_property("magmom", [1.0] * len(structure)) spga = SpacegroupAnalyzer(structure, symprec=1e-2) - conv = spga.get_conventional_standard_structure(keep_site_properties=False) - assert conv.site_properties.get("magmom") is None + conventional = spga.get_conventional_standard_structure(keep_site_properties=False) + assert conventional.site_properties.get("magmom") is None def test_get_primitive_standard_structure(self): for file_name, expected_angles, expected_abc in [ diff --git a/tests/symmetry/test_groups.py b/tests/symmetry/test_groups.py index 273a6a6d6c3..ae9b3a0a9f7 100644 --- a/tests/symmetry/test_groups.py +++ b/tests/symmetry/test_groups.py @@ -2,11 +2,10 @@ import numpy as np import pytest -from pytest import approx - from pymatgen.core.lattice import Lattice from pymatgen.core.operations import SymmOp from pymatgen.symmetry.groups import SYMM_DATA, PointGroup, SpaceGroup +from pytest import approx __author__ = "Shyue Ping Ong" __copyright__ = "Copyright 2012, The Materials Virtual Lab" @@ -17,18 +16,18 @@ ORDERED_SYMBOLS = ( "P1 P-1 P121 P12_11 C121 P1m1 P1c1 C1m1 C1c1 P12/m1 P12_1/m1 C12/m1 P12/c1 P12_1/c1 C12/c1 P222 P222_1" - " P2_12_12 P2_12_121 C222_1 C222 F222 I222 I2_12_121 Pmm2 Pmc2_1 Pcc2 Pma2 Pca2_1 Pnc2 Pmn2_1 Pba2 Pna2_1 Pnn2 " - "Cmm2 Cmc2_1 Ccc2 Amm2 Aem2 Ama2 Aea2 Fmm2 Fdd2 Imm2 Iba2 Ima2 Pmmm Pnnn1 Pccm Pban1 Pmma Pnna Pmna Pcca Pbam " - "Pccn Pbcm Pnnm Pmmn1 Pbcn Pbca Pnma Cmcm Cmce Cmmm Cccm Cmme Ccce1 Fmmm Fddd1 Immm Ibam Ibca Imma P4 P4_1 P4_2 " - "P4_3 I4 I4_1 P-4 I-4 P4/m P4_2/m P4/n1 P4_2/n I4/m I4_1/a P422 P42_12 P4_122 P4_12_12 P4_222 P4_22_12 P4_322 " + " P2_12_12 P2_12_12_1 C222_1 C222 F222 I222 I2_12_12_1 Pmm2 Pmc2_1 Pcc2 Pma2 Pca2_1 Pnc2 Pmn2_1 Pba2 Pna2_1 Pnn2 " + "Cmm2 Cmc2_1 Ccc2 Amm2 Aem2 Ama2 Aea2 Fmm2 Fdd2 Imm2 Iba2 Ima2 Pmmm Pnnn Pccm Pban Pmma Pnna Pmna Pcca Pbam " + "Pccn Pbcm Pnnm Pmmn Pbcn Pbca Pnma Cmcm Cmce Cmmm Cccm Cmme Ccce Fmmm Fddd Immm Ibam Ibca Imma P4 P4_1 P4_2 " + "P4_3 I4 I4_1 P-4 I-4 P4/m P4_2/m P4/n P4_2/n I4/m I4_1/a P422 P42_12 P4_122 P4_12_12 P4_222 P4_22_12 P4_322 " "P4_32_12 I422 I4_122 P4mm P4bm P4_2cm P4_2nm P4cc P4nc P4_2mc P4_2bc I4mm I4cm I4_1md I4_1cd P-42m P-42c P-42_1m " - "P-42_1c P-4m2 P-4c2 P-4b2 P-4n2 I-4m2 I-4c2 I-42m I-42d P4/mmm P4/mcc P4/nbm1 P4/nnc1 P4/mbm P4/mnc P4/nmm1 " - "P4/ncc1 P4_2/mmc P4_2/mcm P4_2/nbc P4_2/nnm P4_2/mbc P4_2/mnm P4_2/nmc P4_2/ncm I4/mmm I4/mcm I4_1/amd I4_1/acd " - "P3 P3_1 P3_2 R3H P-3 R-3H P312 P321 P3_112 P3_121 P3_212 P3_221 R32H P3m1 P31m P3c1 P31c R3mH R3cH P-31m P-31c " - "P-3m1 P-3c1 R-3mH R-3cH P6 P6_1 P6_5 P6_2 P6_4 P6_3 P-6 P6/m P6_3/m P622 P6_122 P6_522 P6_222 P6_422 P6_322 " + "P-42_1c P-4m2 P-4c2 P-4b2 P-4n2 I-4m2 I-4c2 I-42m I-42d P4/mmm P4/mcc P4/nbm P4/nnc P4/mbm P4/mnc P4/nmm " + "P4/ncc P4_2/mmc P4_2/mcm P4_2/nbc P4_2/nnm P4_2/mbc P4_2/mnm P4_2/nmc P4_2/ncm I4/mmm I4/mcm I4_1/amd I4_1/acd " + "P3 P3_1 P3_2 R3 P-3 R-3 P312 P321 P3_112 P3_121 P3_212 P3_221 R32 P3m1 P31m P3c1 P31c R3m R3c P-31m P-31c " + "P-3m1 P-3c1 R-3m R-3c P6 P6_1 P6_5 P6_2 P6_4 P6_3 P-6 P6/m P6_3/m P622 P6_122 P6_522 P6_222 P6_422 P6_322 " "P6mm P6cc P6_3cm P6_3mc P-6m2 P-6c2 P-62m P-62c P6/mmm P6/mcc P6_3/mcm P6_3/mmc P23 F23 I23 P2_13 I2_13 Pm-3 " - "Pn-31 Fm-3 Fd-31 Im-3 Pa-3 Ia-3 P432 P4_232 F432 F4_132 I432 P4_332 P4_132 I4_132 P-43m F-43m I-43m P-43n F-43c " - "I-43d Pm-3m Pn-3n1 Pm-3n Pn-3m1 Fm-3m Fm-3c Fd-3m1 Fd-3c1 Im-3m Ia-3d" + "Pn-3 Fm-3 Fd-3 Im-3 Pa-3 Ia-3 P432 P4_232 F432 F4_132 I432 P4_332 P4_132 I4_132 P-43m F-43m I-43m P-43n F-43c " + "I-43d Pm-3m Pn-3n Pm-3n Pn-3m Fm-3m Fm-3c Fd-3m Fd-3c Im-3m Ia-3d" ).split() @@ -61,6 +60,14 @@ def test_is_sub_super_group(self): assert pg_3m.is_subgroup(pg_6mmm) assert not pg_m3m.is_supergroup(pg_6mmm) + def test_from_space_group(self): + assert PointGroup.from_space_group("P 2_1/n2_1/m2_1/a").symbol == "mmm" + assert PointGroup.from_space_group("F d d d").symbol == "mmm" + assert PointGroup.from_space_group("I -4").symbol == "-4" + assert PointGroup.from_space_group("P4_32_12_1").symbol == "422" + assert PointGroup.from_space_group("F4_1/d-32/m").symbol == "m-3m" + assert PointGroup.from_space_group("P121").symbol == "2" + class TestSpaceGroup: def test_renamed_e_symbols(self): @@ -100,17 +107,9 @@ def test_order_symm_ops(self): def test_get_settings(self): assert SpaceGroup.get_settings("Fm-3m") == {"Fm-3m(a-1/4,b-1/4,c-1/4)", "Fm-3m"} - assert SpaceGroup.get_settings("Pmmn") == { - "Pmmn", - "Pmnm:1", - "Pnmm:2", - "Pmnm:2", - "Pnmm", - "Pnmm:1", - "Pmmn:1", - "Pmnm", - "Pmmn:2", - } + + pmmn_settings = {"Pmmn", "Pmnm:1", "Pnmm:2", "Pmnm:2", "Pnmm", "Pnmm:1", "Pmmn:1", "Pmnm", "Pmmn:2"} + assert SpaceGroup.get_settings("Pmmn") == pmmn_settings assert SpaceGroup.get_settings("Pmna") == {"Pnmb", "Pman", "Pncm", "Pmna", "Pcnm", "Pbmn"} def test_crystal_system(self): @@ -150,6 +149,13 @@ def test_is_compatible(self): assert sg.is_compatible(cubic) assert sg.is_compatible(rhom) assert not sg.is_compatible(hexagonal) + sg = SpaceGroup("R-3m", hexagonal=True) + assert not sg.is_compatible(cubic) + assert sg.is_compatible(hexagonal) + sg = SpaceGroup("R-3m", hexagonal=False) + assert sg.is_compatible(cubic) + assert sg.is_compatible(rhom) + assert not sg.is_compatible(hexagonal) sg = SpaceGroup("Pnma") assert sg.is_compatible(cubic) assert sg.is_compatible(tet) @@ -201,15 +207,34 @@ def test_subgroup_supergroup(self): def test_hexagonal(self): for num in (146, 148, 155, 160, 161, 166, 167): sg = SpaceGroup.from_int_number(num, hexagonal=False) - assert not sg.symbol.endswith("H") + assert sg.hexagonal is False + sg = SpaceGroup.from_int_number(num, hexagonal=True) + assert sg.hexagonal is True + + def test_full_symbol_warning(self): + warning_msg = "Full symbol not available, falling back to short Hermann Mauguin symbol P2_1ma instead" + # TODO need to find a way to reset the warnings registry. + # by default, warnings are raised only once and the same warning being tested here is raised below by + # assert sg.to_unicode_string() == "P2₁ma" + # so don't move this test below test_string + + with pytest.warns(UserWarning, match=warning_msg) as warns: + _ = SpaceGroup("P2_1ma") + assert len(warns) == 1 def test_string(self): sg = SpaceGroup("R-3c") - assert sg.to_latex_string() == r"R$\overline{3}$cH" + assert sg.to_latex_string() == r"R$\overline{3}$c" sg = SpaceGroup("P6/mmm") assert sg.to_latex_string() == "P6/mmm" sg = SpaceGroup("P4_1") assert sg.to_unicode_string() == "P4₁" + sg = SpaceGroup("P41") # Added after issue #3862 + assert sg.to_unicode_string() == "P4₁" + sg = SpaceGroup("P21ma") # Added after issue #3862 + assert sg.to_unicode_string() == "P2₁ma" + sg = SpaceGroup("P2_1ma") # Added after issue #3862 + assert sg.to_unicode_string() == "P2₁ma" def test_repr(self): for num in range(1, 231): @@ -217,6 +242,11 @@ def test_repr(self): symbol = ORDERED_SYMBOLS[num - 1] assert repr(sg) in f"SpaceGroup({symbol=})" + def test_valid_symbol(self): # Added after issue #3845 + for num in range(1, 231): + symbol = SpaceGroup.from_int_number(num).symbol + assert SpaceGroup(symbol).int_number == num + def test_raises_on_bad_int_number(self): for num in (-5, 0, 231, 1000): with pytest.raises(ValueError, match=f"International number must be between 1 and 230, got {num}"): diff --git a/tests/symmetry/test_kpath_hin.py b/tests/symmetry/test_kpath_hin.py index 61d71fd9dd3..63dab783ac2 100644 --- a/tests/symmetry/test_kpath_hin.py +++ b/tests/symmetry/test_kpath_hin.py @@ -1,12 +1,11 @@ from __future__ import annotations import pytest -from pytest import approx - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.symmetry.kpath import KPathSeek from pymatgen.util.testing import PymatgenTest +from pytest import approx try: from seekpath import get_path diff --git a/tests/symmetry/test_kpath_lm.py b/tests/symmetry/test_kpath_lm.py index dbc8187e6a9..e72ff7ef9d7 100644 --- a/tests/symmetry/test_kpath_lm.py +++ b/tests/symmetry/test_kpath_lm.py @@ -1,14 +1,13 @@ from __future__ import annotations import numpy as np -from pytest import approx - from pymatgen.analysis.magnetism.analyzer import CollinearMagneticStructureAnalyzer from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pymatgen.symmetry.kpath import KPathLatimerMunro from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx class TestKPathLatimerMunro(PymatgenTest): diff --git a/tests/symmetry/test_kpath_sc.py b/tests/symmetry/test_kpath_sc.py index d88c97f79dd..2dd37d0d77e 100644 --- a/tests/symmetry/test_kpath_sc.py +++ b/tests/symmetry/test_kpath_sc.py @@ -1,12 +1,11 @@ from __future__ import annotations import numpy as np -from pytest import approx - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.symmetry.kpath import KPathSetyawanCurtarolo from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest +from pytest import approx TEST_DIR = f"{TEST_FILES_DIR}/symmetry/space_group_structs" diff --git a/tests/symmetry/test_kpaths.py b/tests/symmetry/test_kpaths.py index 2c907e87135..f13ae4b7a9b 100644 --- a/tests/symmetry/test_kpaths.py +++ b/tests/symmetry/test_kpaths.py @@ -4,7 +4,6 @@ import pytest from monty.serialization import loadfn - from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure from pymatgen.symmetry.bandstructure import HighSymmKpath diff --git a/tests/symmetry/test_maggroups.py b/tests/symmetry/test_maggroups.py index 72f184d553f..cc4d529b87c 100644 --- a/tests/symmetry/test_maggroups.py +++ b/tests/symmetry/test_maggroups.py @@ -2,7 +2,6 @@ import numpy as np from numpy.testing import assert_allclose - from pymatgen.core.lattice import Lattice from pymatgen.symmetry.groups import SpaceGroup from pymatgen.symmetry.maggroups import MagneticSpaceGroup diff --git a/tests/symmetry/test_settings.py b/tests/symmetry/test_settings.py index 24db5b2b6dc..a6a8ff3e80a 100644 --- a/tests/symmetry/test_settings.py +++ b/tests/symmetry/test_settings.py @@ -4,7 +4,6 @@ import numpy as np from numpy.testing import assert_allclose - from pymatgen.symmetry.settings import JonesFaithfulTransformation, Lattice, SymmOp __author__ = "Matthew Horton" diff --git a/tests/symmetry/test_site_symmetries.py b/tests/symmetry/test_site_symmetries.py index 21972990e8b..c5696b31f46 100644 --- a/tests/symmetry/test_site_symmetries.py +++ b/tests/symmetry/test_site_symmetries.py @@ -4,7 +4,6 @@ import json from monty.json import MontyDecoder - from pymatgen.symmetry import site_symmetries as ss from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest diff --git a/tests/test_cli.py b/tests/test_cli.py index 225664313dc..1893d0a5738 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -4,7 +4,6 @@ from typing import TYPE_CHECKING import pytest - from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR if TYPE_CHECKING: diff --git a/tests/transformations/test_advanced_transformations.py b/tests/transformations/test_advanced_transformations.py index 5dcc3fae6d4..ea0feed09b8 100644 --- a/tests/transformations/test_advanced_transformations.py +++ b/tests/transformations/test_advanced_transformations.py @@ -7,8 +7,6 @@ import pytest from monty.serialization import loadfn from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.analysis.energy_models import IsingModel, SymmetryModel from pymatgen.analysis.gb.grain import GrainBoundaryGenerator from pymatgen.core import Lattice, Molecule, Species, Structure @@ -41,6 +39,7 @@ SubstitutionTransformation, ) from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest +from pytest import approx try: import hiphive diff --git a/tests/transformations/test_site_transformations.py b/tests/transformations/test_site_transformations.py index 3b30670fad3..cddc9bfb53f 100644 --- a/tests/transformations/test_site_transformations.py +++ b/tests/transformations/test_site_transformations.py @@ -6,7 +6,6 @@ import numpy as np import pytest from numpy.testing import assert_allclose - from pymatgen.core.structure import Molecule, Structure from pymatgen.transformations.site_transformations import ( AddSitePropertyTransformation, diff --git a/tests/transformations/test_standard_transformations.py b/tests/transformations/test_standard_transformations.py index 331ed94b9c9..029fad0f8e7 100644 --- a/tests/transformations/test_standard_transformations.py +++ b/tests/transformations/test_standard_transformations.py @@ -9,8 +9,6 @@ import numpy as np import pytest from monty.json import MontyDecoder -from pytest import approx - from pymatgen.core import Element, PeriodicSite from pymatgen.core.lattice import Lattice from pymatgen.symmetry.structure import SymmetrizedStructure @@ -36,6 +34,7 @@ SupercellTransformation, ) from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR +from pytest import approx enumlib_present = which("enum.x") and which("makestr.x") diff --git a/tests/util/test_coord.py b/tests/util/test_coord.py index 15cfab9d7dc..433831f3c5d 100644 --- a/tests/util/test_coord.py +++ b/tests/util/test_coord.py @@ -6,10 +6,9 @@ import numpy as np import pytest from numpy.testing import assert_allclose, assert_array_equal -from pytest import approx - from pymatgen.core.lattice import Lattice from pymatgen.util import coord +from pytest import approx class TestCoordUtils: diff --git a/tests/util/test_num.py b/tests/util/test_num.py index e391ba92412..8891e37ca0f 100644 --- a/tests/util/test_num.py +++ b/tests/util/test_num.py @@ -1,7 +1,6 @@ from __future__ import annotations import pytest - from pymatgen.util.num import round_to_sigfigs diff --git a/tests/util/test_plotting.py b/tests/util/test_plotting.py index ae0b6eca76b..85d91b457e8 100644 --- a/tests/util/test_plotting.py +++ b/tests/util/test_plotting.py @@ -1,7 +1,6 @@ from __future__ import annotations import matplotlib.pyplot as plt - from pymatgen.util.plotting import periodic_table_heatmap, van_arkel_triangle from pymatgen.util.testing import PymatgenTest diff --git a/tests/util/test_provenance.py b/tests/util/test_provenance.py index 08bc1c0cedc..9019ee50ebd 100644 --- a/tests/util/test_provenance.py +++ b/tests/util/test_provenance.py @@ -1,18 +1,15 @@ +"""Unit tests for StructureNL (SNL) format.""" + from __future__ import annotations -import datetime +from datetime import datetime, timedelta, timezone from unittest import TestCase import numpy as np import pytest - from pymatgen.core.structure import Molecule, Structure from pymatgen.util.provenance import Author, HistoryNode, StructureNL -""" -Unit tests for StructureNL (SNL) format -""" - __author__ = "Anubhav Jain" __credits__ = "Shyue Ping Ong" __copyright__ = "Copyright 2012, The Materials Project" @@ -98,7 +95,7 @@ def test_references(self): # An empty list should not work with pytest.raises( - ValueError, + TypeError, match="Invalid format for SNL reference! Should be empty string or BibTeX string.", ): StructureNL(self.struct, self.hulk, references=[]) @@ -155,7 +152,7 @@ def test_remarks(self): def test_eq(self): # test basic Equal() - created_at = datetime.datetime.now() + created_at = datetime.now(tz=timezone.utc) struct_nl = StructureNL( self.struct, self.hulk, @@ -179,7 +176,7 @@ def test_eq(self): assert struct_nl == struct_nl2 # change the created at date, now they are no longer equal - created_at = datetime.datetime.now() + datetime.timedelta(days=-1) + created_at = datetime.now(tz=timezone.utc) + timedelta(days=-1) snl_new_date = StructureNL( self.struct, self.hulk, diff --git a/tests/util/test_string.py b/tests/util/test_string.py index 5c04a1d51ea..1bb0785cef3 100644 --- a/tests/util/test_string.py +++ b/tests/util/test_string.py @@ -2,7 +2,6 @@ import numpy as np import pytest - from pymatgen.core import Structure from pymatgen.util.string import ( Stringify, diff --git a/tests/util/test_typing.py b/tests/util/test_typing.py index ec04deffbb7..9b56e8d4705 100644 --- a/tests/util/test_typing.py +++ b/tests/util/test_typing.py @@ -10,7 +10,6 @@ from typing import TYPE_CHECKING, get_args import pytest - from pymatgen.core import Composition, DummySpecies, Element, Species from pymatgen.entries import Entry from pymatgen.util.typing import CompositionLike, EntryLike, PathLike, PbcLike, SpeciesLike @@ -69,7 +68,7 @@ def test_composition_like(): def test_pbc_like(): - assert type(PbcLike) == GenericAlias + assert isinstance(PbcLike, GenericAlias) assert get_args(PbcLike) == (bool, bool, bool) diff --git a/tests/vis/test_plotters.py b/tests/vis/test_plotters.py index ca0594b4c2d..ab9c95ad547 100644 --- a/tests/vis/test_plotters.py +++ b/tests/vis/test_plotters.py @@ -6,7 +6,6 @@ import matplotlib.pyplot as plt import numpy as np from monty.json import MontyDecoder - from pymatgen.analysis.xas.spectrum import XAS from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest from pymatgen.vis.plotters import SpectrumPlotter