Currently, this phase digram calculator only support calculations in solidus region. Support for liquidus region will be added later
First create a environment with python=3.8.x
conda create --name <name> python=3.8
conda activate <name>
Then, clone code with:
git clone https://github.com/rectify-mint/mint-PD.git
Then run:
cd mint-PD/PhaseDiagram-Clease
pip install .[all]
If you are using zsh, you need to run:
pip install '.[all]'
In the end, install tqdm
pip install tqdm
This should get you all set on python packages.
If you plan to rely solely on DFT, you can skip the all the following
To install LAMMPS, run: (make sure you are in the correct python environment)
git clone -b stable_29Sep2021_update2 --depth 1 https://github.com/lammps/lammps.git
cd lammps && mkdir build && cd build
cmake -C ../cmake/presets/basic.cmake -D PKG_MC=on -D PKG_MEAM=on -D PKG_MOLECULE=on -D BUILD_SHARED_LIBS=on -D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on -D PKG_MANYBODY=ON -D PKG_MISC=ON -D PKG_EXTRA-COMPUTE=ON -D PKG_EXTRA-DUMP=ON -D PKG_EXTRA-FIX=ON -D PKG_EXTRA-PAIR=ON -D BUILD_MPI=ON -D BUILD_OMP=yes -D PKG_MPIIO=ON ../cmake
cmake --build .
make install-python
To verify if LAMMPS can be successfully started from Python, start the Python interpreter, load the lammps Python module and create a LAMMPS instance. This should not generate an error message and produce output similar to the following:
$ python
Python 3.8.5 (default, Sep 5 2020, 10:50:12)
[GCC 10.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import lammps
>>> lmp = lammps.lammps()
LAMMPS (18 Sep 2020)
using 1 OpenMP thread(s) per MPI task
>>>
There are three main part in computationally plotting phase diagram:
- Get energy calculator ready (In this example, this will be fitting a Cluster Expansion (CE) model with CE training3.ipynb.)
- Setups for phase boundray tracing algorithm (running emc.py)
- Running the phase boundray tracing algorithm (phb.py)
If you go into PhaseDiagram-Clease directory, you'll find the example.yaml file. This is where a user specify all his/her input parameters. CLEASE, LAMMPS, DFT are sections for fitting CE models. EMC section is for emc.py, and PHB section is for phb.py.
To run LiNa example, open the example.yaml. If you decide to use LAMMPS, comment out the DFT section. Otherwise, comment-out the LAMMPS section and enter the name of the DFT energy file, a .db file that contains both structures of interests and their corresponding energy. Everything else in example.yaml should be good. You simply need to run CE training3.ipynb, emc.py, phb.py in sequence.