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"""
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
all_cg = AllCoordinationGeometries()
while True:
cg_symbol = input("Enter symbol of the geometry for which you want to get the explicit permutations : ")
try:
cg = all_cg[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 = list(itertools.permutations(range(cg.coordination)))
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()
csms, perms, algos, local2perfect_maps, perfect2local_maps = lgf.coordination_geometry_symmetry_measures_standard(
coordination_geometry=cg, algo=algo, points_perfect=points_perfect
)
csms_with_recorded_permutation: list[float] = []
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)]
new_geom_dir = "new_geometry_files"
os.makedirs(new_geom_dir, exist_ok=True)
with open(f"{new_geom_dir}/{cg_symbol}.json", mode="w", encoding="utf-8") as file:
json.dump(cg.as_dict(), file)
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