Reintegrate nprocs_for_ntasks in relax_scanner

README.rst

@@ -106,7 +106,10 @@ in the `anaconda howto <http://abinit.github.io/abipy/installation#anaconda-howt
 Developmental version
 ---------------------
 
-Getting the developmental version of AbiPy is easy.
+To install the developmental version of AbiPy with pip, use::
+
+    pip install git+https://github.com/abinit/abipy.git@develop
+
 Clone the `github repository <https://github.com/abinit/abipy>`_ with::
 
     git clone https://github.com/abinit/abipy
@@ -143,22 +146,6 @@ or alternately::
 to install the package in developmental mode.
 This is the recommended approach, especially if you are planning to implement new features.
 
-Note, however, that the developmental version of AbiPy is kept in sync with the
-developmental version of pymatgen thus ```python setup.py develop``` may
-try to download new versions from the PyPi portal and then fail with e.g. the error message::
-
-    ...
-    processing dependencies for abipy==0.6.0.dev0
-    error: scipy 1.0.0 is installed but scipy>=1.0.1 is required by {'pymatgen'}
-
-due to inconsistent dependencies.
-To solve the problem, use conda to update scipy to a version >= 1.0.1 with::
-
-    conda install "scipy>=1.0.1"
-
-then issue again python setup.py develop. If this fails, supposing you were upgrading abipy inside 
-an already existing conda environment, try to restart by creating from scratch a fresh conda environment, see above.
-
 Also note that the BLAS/Lapack libraries provided by conda have multithreading support activated by default.
 Each process will try to use all of the cores on your machine, which quickly overloads things
 if there are multiple processes running.

abipy/ml/ml_phonopy.py

@@ -26,7 +26,6 @@
     Phonopy = None
 
 
-
 def cprint_traceback(color="red") -> None:
     """Print traceback."""
     import traceback
@@ -110,9 +109,6 @@ def __init__(self, ddb_filepath,
             prefix: Prefix for workdir
             supercell: with supercell dimensions. None to use the supercell from the DDB file.
         """
-        # Store args for reconstruction
-        #self.init_kwargs = {k: v for k, v in locals().items() if k not in ["self", "__class__", "kwargs"]}
-
         super().__init__(workdir, prefix)
 
         self.distance = float(distance)
@@ -284,7 +280,6 @@ def _run_nn_name(self, nn_name: str) -> None:
         for q_list, w_list, eig_list in zip(bands_dict['qpoints'], bands_dict['frequencies'], bands_dict['eigenvectors']):
             nqpt += len(q_list)
             py_phfreqs.extend(w_list)
-            #print(eig_list)
             py_displ_cart.extend(eig_list)
 
         py_phfreqs = np.reshape(py_phfreqs, (nqpt, 3*natom)) / abu.eV_to_THz
@@ -347,9 +342,6 @@ def __init__(self, structure, supercell,
             workdir: Working directory, None to generate temporary directory automatically.
             prefix: Prefix for workdir.
         """
-        # Store args for reconstruction
-        #self.init_kwargs = {k: v for k, v in locals().items() if k not in ["self", "__class__", "kwargs"]}
-
         super().__init__(workdir, prefix)
 
         self.initial_atoms = structure.to_ase_atoms()

abipy/ml/relax_scanner.py

@@ -28,7 +28,27 @@
 from abipy.tools.serialization import HasPickleIO
 from abipy.tools.printing import print_dataframe
 from abipy.ml.aseml import (relax_atoms, get_atoms, as_calculator, ase_optimizer_cls, RX_MODE, fix_atoms,
-                            MlNeb, MlGsList, CalcBuilder, make_ase_neb, nprocs_for_ntasks)
+                            MlNeb, MlGsList, CalcBuilder, make_ase_neb)
+
+
+
+def nprocs_for_ntasks(nprocs, ntasks, title=None) -> int:
+    """
+    Return the number of procs to be used in a multiprocessing Pool.
+    If negative or None, use all procs in the system.
+    """
+    import os
+    if nprocs is None or nprocs <= 0:
+        nprocs = max(1, os.cpu_count())
+    else:
+        nprocs = int(nprocs)
+
+    nprocs = min(nprocs, ntasks)
+    if title is not None:
+        print(title)
+        print(f"Using multiprocessing pool with {nprocs=} for {ntasks=} ...")
+    return nprocs
+
 
 
 @dataclasses.dataclass

abipy/scripts/abiml.py

@@ -692,15 +692,18 @@ def compare(ctx, filepath, nn_names,
 @click.pass_context
 @click.argument("filepath", type=str)
 @add_nn_name_opt
-@click.option('--config', default='abiml_magmoms.yml', type=click.Path(), callback=set_default, is_eager=True, expose_value=False)
-def magmoms(ctx, filepath, nn_name):
+@click.option('--config', default='abiml_gs.yml', type=click.Path(), callback=set_default, is_eager=True, expose_value=False)
+def gs(ctx, filepath, nn_name):
     """
-    Compute magnetic moments with ML potential.
+    Compute grounde-state properties and magnetic moments with ML potential.
     """
     atoms = _get_atoms_from_filepath(filepath)
-    atoms.calc = aseml.CalcBuilder(nn_name).get_calculator()
-    magmoms = atoms.get_magnetic_moments()
-    for ia, (atom, magmoms) in enumerate(zip(atoms, magmoms)):
+    calc = aseml.CalcBuilder(nn_name).get_calculator()
+    #magmoms = atoms.get_magnetic_moments()
+    from abipy.ml.aseml import AseResults
+    res = AseResults.from_atoms(atoms, calc=calc)
+
+    for ia, (atom, magmoms) in enumerate(zip(res.atoms, res.magmoms)):
         print(atom, magmoms)
 
     return 0

abipy/scripts/abiopen.py

@@ -239,6 +239,9 @@ def show_examples_and_exit(err_msg=None, error_code=1):
     if options.filepath.endswith(".json"):
         return handle_json(options)
 
+    if options.filepath.endswith(".traj"):
+        return handle_ase_traj(options)
+
     if os.path.basename(options.filepath) == "flows.db":
         from abipy.flowtk.launcher import print_flowsdb_file
         return print_flowsdb_file(options.filepath)
@@ -328,6 +331,15 @@ def show_examples_and_exit(err_msg=None, error_code=1):
     return 0
 
 
+def handle_ase_traj(options):
+    """Handle ASE trajectory file."""
+    from ase.io import read
+    traj = read(options.filepath, index=":")
+    print(f"ASE trajectory with {len(traj)} configurations")
+    from abipy.ml.aseml import AseResults
+    first, last = AseResults(traj[0]), AseResults(traj[-1])
+
+
 def handle_json(options):
     """Handle JSON file."""