explicit_permutations.py

# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

"""
Development script of the ChemEnv utility to get the explicit permutations for coordination environments identified
with the explicit permutations algorithms (typically with coordination numbers <= 6)
"""

from __future__ import annotations

import itertools
import json
import os

import numpy as np

from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
    AllCoordinationGeometries,
    ExplicitPermutationsAlgorithm,
)
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
    AbstractGeometry,
    LocalGeometryFinder,
)

__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "2.0"
__maintainer__ = "David Waroquiers"
__email__ = "david.waroquiers@gmail.com"
__date__ = "Feb 20, 2016"


class Algo:
    pass


if __name__ == "__main__":
    # Choose the geometry
    allcg = AllCoordinationGeometries()
    while True:
        cg_symbol = input("Enter symbol of the geometry for which you want to get the explicit permutations : ")
        try:
            cg = allcg[cg_symbol]
            break
        except LookupError:
            print("Wrong geometry, try again ...")
            continue

    # Check if the algorithm currently defined for this geometry corresponds to the explicit permutation algorithm
    for algo in cg.algorithms:
        if algo.algorithm_type != "EXPLICIT_PERMUTATIONS":
            raise ValueError("WRONG ALGORITHM !")

    algo = Algo()
    algo.permutations = []
    for perm in itertools.permutations(range(cg.coordination)):
        algo.permutations.append(perm)

    lgf = LocalGeometryFinder()
    lgf.setup_parameters(structure_refinement=lgf.STRUCTURE_REFINEMENT_NONE)
    lgf.setup_test_perfect_environment(cg_symbol, randomness=True, indices="ORDERED")

    lgf.perfect_geometry = AbstractGeometry.from_cg(cg=cg)

    points_perfect = lgf.perfect_geometry.points_wocs_ctwocc()
    res = lgf.coordination_geometry_symmetry_measures_standard(
        coordination_geometry=cg, algo=algo, points_perfect=points_perfect
    )
    (csms, perms, algos, local2perfect_maps, perfect2local_maps) = res

    csms_with_recorded_permutation = []
    explicit_permutations = []
    for icsm, csm in enumerate(csms):
        found = False
        for csm2 in csms_with_recorded_permutation:
            if np.isclose(csm, csm2):
                found = True
                break
        if not found:
            csms_with_recorded_permutation.append(csm)
            explicit_permutations.append(perms[icsm])

    print("Permutations found : ")
    print(explicit_permutations)

    print("Current algorithm(s) :")
    for algo in cg.algorithms:
        print(algo)
        if algo.algorithm_type == "EXPLICIT_PERMUTATIONS":
            print(algo.permutations)
        else:
            raise ValueError("WRONG ALGORITHM !")

    test = input('Save it ? ("y" to confirm)')
    if test == "y":
        if len(cg.algorithms) != 1:
            raise ValueError("Multiple algorithms !")
        cg._algorithms = [ExplicitPermutationsAlgorithm(permutations=explicit_permutations)]
        newgeom_dir = "new_geometry_files"
        if not os.path.exists(newgeom_dir):
            os.makedirs(newgeom_dir)
        with open(f"{newgeom_dir}/{cg_symbol}.json", "w") as f:
            json.dump(cg.as_dict(), f)