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_and_occu.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)
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):
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_and_occu.keys())[0].symbol
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)
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,
):
"""
Draw cg.
:param vis:
:param site:
:param neighbors:
:param cg:
:param perm:
:param perfect2local_map:
:param show_perfect:
:param csm_info:
:param symmetry_measure_type:
:param perfect_radius:
:param show_distorted:
:param faces_color_override:
:return:
"""
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"][f"translation_vector_{csm_suffix}"]
rot = csm_info["other_symmetry_measures"][f"rotation_matrix_{csm_suffix}"]
scale = csm_info["other_symmetry_measures"][f"scaling_factor_{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"][f"translation_vector_{csm_suffix}"]
rot = csm_info["other_symmetry_measures"][f"rotation_matrix_{csm_suffix}"]
scale = csm_info["other_symmetry_measures"][f"scaling_factor_{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,
)
