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"""Development script to test the algorithms of all the model coordination environments."""
from __future__ import annotations
import itertools
from math import factorial
from random import shuffle
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
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"
if __name__ == "__main__":
all_coord_geoms = AllCoordinationGeometries()
test = input('Standard ("s", all permutations for cn <= 6, 500 random permutations for cn > 6) or on demand')
if test == "s":
perms_def = "standard"
elif test == "o":
perms_def = "on_demand"
else:
try:
n_perms = int(test)
perms_def = "n_defined"
except Exception:
perms_def = "on_demand"
for coordination in range(1, 13):
print(f"IN COORDINATION {coordination}")
symbol_name_mapping = all_coord_geoms.get_symbol_name_mapping(coordination=coordination)
if perms_def == "standard":
test = "500" if coordination > 6 else "all"
elif perms_def == "n_defined":
test = n_perms # type: ignore[assignment]
else:
test = input(
"Enter if you want to test all possible permutations ('all' or 'a') or "
"a given number of random permutations (i.e. '25')"
)
indices = range(coordination)
if test in ("all", "a"):
perms_type = "all"
perms_iterator = itertools.permutations(indices)
n_perms = factorial(coordination)
else:
perms_type = "explicit"
try:
n_perms = int(test)
except Exception:
raise ValueError(f"Could not turn {test} into integer ...")
perms_iterator = [] # type: ignore[assignment]
for _ in range(n_perms):
shuffle(indices) # type: ignore[arg-type]
perms_iterator.append(list(indices)) # type: ignore[attr-defined]
for cg_symbol, cg_name in symbol_name_mapping.items():
cg = all_coord_geoms[cg_symbol]
if cg.deactivate:
continue
print(f"Testing {cg_symbol} ({cg_name})")
cg = all_coord_geoms[cg_symbol]
if cg.points is None:
continue
lgf = LocalGeometryFinder()
lgf.setup_parameters(structure_refinement=lgf.STRUCTURE_REFINEMENT_NONE)
# Reinitialize the itertools permutations
if perms_type == "all":
perms_iterator = itertools.permutations(indices)
# Loop on the permutations
i_perm = 1
for indices_perm in perms_iterator:
lgf.setup_test_perfect_environment(
cg_symbol,
indices=indices_perm,
randomness=True,
max_random_dist=0.1,
random_translation=True,
random_rotation=True,
random_scale=True,
)
lgf.perfect_geometry = AbstractGeometry.from_cg(cg=cg)
points_perfect = lgf.perfect_geometry.points_wocs_ctwocc()
print(f"Perm # {i_perm}/{n_perms} : ", indices_perm)
algos_results = []
for algo in cg.algorithms:
if algo.algorithm_type == "EXPLICIT_PERMUTATIONS":
results = lgf.coordination_geometry_symmetry_measures(
coordination_geometry=cg, points_perfect=points_perfect
)
# raise ValueError('Do something for the explicit ones ... (these should anyway be by far ok!)')
else:
results = lgf.coordination_geometry_symmetry_measures_separation_plane(
coordination_geometry=cg,
separation_plane_algo=algo,
points_perfect=points_perfect,
)
algos_results.append(min(results[0]))
if not min(results[0]) < 1.5:
print("Following is not close to 0 ...")
input(results)
print(" => ", algos_results)
i_perm += 1
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