# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.ext.matproj import MPRester
from pymatgen.io.cif import CifParser
try:
from pymatgen.vis.structure_vtk import StructureVis
no_vis = False
except ImportError:
StructureVis = None # type: ignore
no_vis = True
from pymatgen.core.sites import PeriodicSite
import re
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import UNCLEAR_ENVIRONMENT_SYMBOL
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
from pymatgen.analysis.chemenv.utils.chemenv_errors import NeighborsNotComputedChemenvError
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import AbstractGeometry
from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import rotateCoords
from pymatgen.analysis.chemenv.utils.defs_utils import chemenv_citations
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy
from pymatgen.core.structure import Molecule
from collections import OrderedDict
import numpy as np
"""
This module contains some utils for the main script of the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__credits__ = "Geoffroy Hautier"
__version__ = "2.0"
__maintainer__ = "David Waroquiers"
__email__ = "david.waroquiers@gmail.com"
__date__ = "Feb 20, 2016"
strategies_class_lookup = OrderedDict() # type: dict
strategies_class_lookup['SimplestChemenvStrategy'] = SimplestChemenvStrategy
# strategies_class_lookup['SimpleAbundanceChemenvStrategy'] = SimpleAbundanceChemenvStrategy
# strategies_class_lookup['TargettedPenaltiedAbundanceChemenvStrategy'] = TargettedPenaltiedAbundanceChemenvStrategy
[docs]def draw_cg(vis, site, neighbors, cg=None, perm=None, perfect2local_map=None,
show_perfect=False, csm_info=None, symmetry_measure_type='csm_wcs_ctwcc', perfect_radius=0.1,
show_distorted=True, faces_color_override=None):
if show_perfect:
if csm_info is None:
raise ValueError('Not possible to show perfect environment without csm_info')
csm_suffix = symmetry_measure_type[4:]
perf_radius = (perfect_radius - 0.2) / 0.002
if perm is not None and perfect2local_map is not None:
raise ValueError('Only "perm" or "perfect2local_map" should be provided in draw_cg, not both')
if show_distorted:
vis.add_bonds(neighbors, site)
for n in neighbors:
vis.add_site(n)
if len(neighbors) < 3:
if show_distorted:
vis.add_bonds(neighbors, site, color=[0.0, 1.0, 0.0], opacity=0.4, radius=0.175)
if show_perfect:
if len(neighbors) == 2:
perfect_geometry = AbstractGeometry.from_cg(cg)
trans = csm_info['other_symmetry_measures']['translation_vector_{}'.format(csm_suffix)]
rot = csm_info['other_symmetry_measures']['rotation_matrix_{}'.format(csm_suffix)]
scale = csm_info['other_symmetry_measures']['scaling_factor_{}'.format(csm_suffix)]
points = perfect_geometry.points_wcs_ctwcc()
rotated_points = rotateCoords(points, rot)
points = [scale * pp + trans for pp in rotated_points]
if 'wcs' in csm_suffix:
ef_points = points[1:]
else:
ef_points = points
edges = cg.edges(ef_points, input='coords')
vis.add_edges(edges, color=[1.0, 0.0, 0.0])
for point in points:
vis.add_partial_sphere(coords=point, radius=perf_radius, color=[0.0, 0.0, 0.0],
start=0, end=360, opacity=1)
else:
if show_distorted:
if perm is not None:
faces = cg.faces(neighbors, permutation=perm)
edges = cg.edges(neighbors, permutation=perm)
elif perfect2local_map is not None:
faces = cg.faces(neighbors, perfect2local_map=perfect2local_map)
edges = cg.edges(neighbors, perfect2local_map=perfect2local_map)
else:
faces = cg.faces(neighbors)
edges = cg.edges(neighbors)
symbol = list(site.species.keys())[0].symbol
if faces_color_override:
mycolor = faces_color_override
else:
mycolor = [float(i) / 255 for i in vis.el_color_mapping[symbol]]
vis.add_faces(faces, mycolor, opacity=0.4)
vis.add_edges(edges)
if show_perfect:
perfect_geometry = AbstractGeometry.from_cg(cg)
trans = csm_info['other_symmetry_measures']['translation_vector_{}'.format(csm_suffix)]
rot = csm_info['other_symmetry_measures']['rotation_matrix_{}'.format(csm_suffix)]
scale = csm_info['other_symmetry_measures']['scaling_factor_{}'.format(csm_suffix)]
points = perfect_geometry.points_wcs_ctwcc()
rotated_points = rotateCoords(points, rot)
points = [scale * pp + trans for pp in rotated_points]
if 'wcs' in csm_suffix:
ef_points = points[1:]
else:
ef_points = points
edges = cg.edges(ef_points, input='coords')
vis.add_edges(edges, color=[1.0, 0.0, 0.0])
for point in points:
vis.add_partial_sphere(coords=point, radius=perf_radius, color=[0.0, 0.0, 0.0],
start=0, end=360, opacity=1)
# Visualizing a coordination geometry
[docs]def visualize(cg, zoom=None, vis=None, myfactor=1.0, view_index=True, faces_color_override=None):
if vis is None:
vis = StructureVis(show_polyhedron=False, show_unit_cell=False)
myspecies = ["O"] * (cg.coordination_number + 1)
myspecies[0] = "Cu"
coords = [np.zeros(3, np.float) + cg.central_site]
for pp in cg.points:
coords.append(np.array(pp) + cg.central_site)
coords = [cc * myfactor for cc in coords]
structure = Molecule(species=myspecies, coords=coords)
vis.set_structure(structure=structure, reset_camera=True)
# neighbors_list = coords[1:]
draw_cg(vis, site=structure[0], neighbors=structure[1:], cg=cg, faces_color_override=faces_color_override)
if view_index:
for ineighbor, neighbor in enumerate(structure[1:]):
vis.add_text(neighbor.coords, '{}'.format(ineighbor), color=(0, 0, 0))
if zoom is not None:
vis.zoom(zoom)
return vis
[docs]def welcome(chemenv_config):
print('Chemical Environment package (ChemEnv)')
print(chemenv_citations())
print(chemenv_config.package_options_description())
[docs]def thankyou():
print('Thank you for using the ChemEnv package')
print(chemenv_citations())
[docs]def compute_environments(chemenv_configuration):
string_sources = {'cif': {'string': 'a Cif file', 'regexp': r'.*\.cif$'},
'mp': {'string': 'the Materials Project database',
'regexp': r'mp-[0-9]+$'}}
questions = {'c': 'cif'}
questions['m'] = 'mp'
lgf = LocalGeometryFinder()
lgf.setup_parameters()
allcg = AllCoordinationGeometries()
strategy_class = strategies_class_lookup[chemenv_configuration.package_options['default_strategy']['strategy']]
# TODO: Add the possibility to change the parameters and save them in the chemenv_configuration
default_strategy = strategy_class()
default_strategy.setup_options(chemenv_configuration.package_options['default_strategy']['strategy_options'])
max_dist_factor = chemenv_configuration.package_options['default_max_distance_factor']
firsttime = True
while True:
if len(questions) > 1:
found = False
print('Enter the source from which the structure is coming or <q> to quit :')
for key_character, qq in questions.items():
print(' - <{}> for a structure from {}'.format(key_character, string_sources[qq]['string']))
test = input(' ... ')
if test == 'q':
break
if test not in list(questions.keys()):
for key_character, qq in questions.items():
if re.match(string_sources[qq]['regexp'], str(test)) is not None:
found = True
source_type = qq
if not found:
print('Wrong key, try again ...')
continue
else:
source_type = questions[test]
else:
found = False
source_type = list(questions.values())[0]
if found and len(questions) > 1:
input_source = test
if source_type == 'cif':
if not found:
input_source = input('Enter path to cif file : ')
cp = CifParser(input_source)
structure = cp.get_structures()[0]
elif source_type == 'mp':
if not found:
input_source = input('Enter materials project id (e.g. "mp-1902") : ')
a = MPRester()
structure = a.get_structure_by_material_id(input_source)
lgf.setup_structure(structure)
print('Computing environments for {} ... '.format(structure.composition.reduced_formula))
se = lgf.compute_structure_environments(maximum_distance_factor=max_dist_factor)
print('Computing environments finished')
while True:
test = input('See list of environments determined for each (unequivalent) site ? '
'("y" or "n", "d" with details, "g" to see the grid) : ')
strategy = default_strategy
if test in ['y', 'd', 'g']:
strategy.set_structure_environments(se)
for eqslist in se.equivalent_sites:
site = eqslist[0]
isite = se.structure.index(site)
try:
if strategy.uniquely_determines_coordination_environments:
ces = strategy.get_site_coordination_environments(site)
else:
ces = strategy.get_site_coordination_environments_fractions(site)
except NeighborsNotComputedChemenvError:
continue
if ces is None:
continue
if len(ces) == 0:
continue
comp = site.species
# ce = strategy.get_site_coordination_environment(site)
if strategy.uniquely_determines_coordination_environments:
ce = ces[0]
if ce is None:
continue
thecg = allcg.get_geometry_from_mp_symbol(ce[0])
mystring = 'Environment for site #{} {} ({}) : {} ({})\n'.format(
str(isite), comp.get_reduced_formula_and_factor()[0],
str(comp), thecg.name, ce[0])
else:
mystring = 'Environments for site #{} {} ({}) : \n'.format(
str(isite), comp.get_reduced_formula_and_factor()[0], str(comp))
for ce in ces:
cg = allcg.get_geometry_from_mp_symbol(ce[0])
csm = ce[1]['other_symmetry_measures']['csm_wcs_ctwcc']
mystring += ' - {} ({}): {:.2f} % (csm : {:2f})\n'.format(cg.name, cg.mp_symbol,
100.0 * ce[2],
csm)
if test in ['d', 'g'] and strategy.uniquely_determines_coordination_environments:
if thecg.mp_symbol != UNCLEAR_ENVIRONMENT_SYMBOL:
mystring += ' <Continuous symmetry measures> '
mingeoms = se.ce_list[isite][thecg.coordination_number][0].minimum_geometries()
for mingeom in mingeoms:
csm = mingeom[1]['other_symmetry_measures']['csm_wcs_ctwcc']
mystring += '{} : {:.2f} '.format(mingeom[0], csm)
print(mystring)
if test == 'g':
while True:
test = input(
'Enter index of site(s) (e.g. 0 1 2, separated by spaces) for which you want to see the grid '
'of parameters : ')
try:
indices = [int(x) for x in test.split()]
print(str(indices))
for isite in indices:
if isite < 0:
raise IndexError
se.plot_environments(isite, additional_condition=se.AC.ONLY_ACB)
break
except ValueError:
print('This is not a valid site')
except IndexError:
print('This site is out of the site range')
if no_vis:
test = input('Go to next structure ? ("y" to do so)')
if test == 'y':
break
continue
test = input('View structure with environments ? ("y" for the unit cell or "m" for a supercell or "n") : ')
if test in ['y', 'm']:
if test == 'm':
mydeltas = []
while True:
try:
test = input('Enter multiplicity (e.g. 3 2 2) : ')
nns = test.split()
for i0 in range(int(nns[0])):
for i1 in range(int(nns[1])):
for i2 in range(int(nns[2])):
mydeltas.append(np.array([1.0 * i0, 1.0 * i1, 1.0 * i2], np.float))
break
except (ValueError, IndexError):
print('Not a valid multiplicity')
else:
mydeltas = [np.zeros(3, np.float)]
if firsttime:
vis = StructureVis(show_polyhedron=False, show_unit_cell=True)
vis.show_help = False
firsttime = False
vis.set_structure(se.structure)
strategy.set_structure_environments(se)
for isite, site in enumerate(se.structure):
try:
ces = strategy.get_site_coordination_environments(site)
except NeighborsNotComputedChemenvError:
continue
if len(ces) == 0:
continue
ce = strategy.get_site_coordination_environment(site)
if ce is not None and ce[0] != UNCLEAR_ENVIRONMENT_SYMBOL:
for mydelta in mydeltas:
psite = PeriodicSite(site.species, site.frac_coords + mydelta, site.lattice,
properties=site.properties)
vis.add_site(psite)
neighbors = strategy.get_site_neighbors(psite)
draw_cg(vis, psite, neighbors, cg=lgf.allcg.get_geometry_from_mp_symbol(ce[0]),
perm=ce[1]['permutation'])
vis.show()
test = input('Go to next structure ? ("y" to do so) : ')
if test == 'y':
break
print('')