def setup_voronoi_list(self, indices, voronoi_cutoff):
"""
Set up of the voronoi list of neighbours by calling qhull
:param indices: indices of the sites for which the Voronoi is needed
:param voronoi_cutoff: Voronoi cutoff for the search of neighbours
:raise RuntimeError: If an infinite vertex is found in the voronoi construction
"""
self.voronoi_list2 = [None] * len(self.structure)
logging.info('Getting all neighbors in structure')
struct_neighbors = self.structure.get_all_neighbors(voronoi_cutoff,
include_index=True)
t1 = time.clock()
logging.info('Setting up Voronoi list :')
for jj, isite in enumerate(indices):
logging.info(
' - Voronoi analysis for site #{:d} ({:d}/{:d})'.format(
isite, jj + 1, len(indices)))
site = self.structure[isite]
neighbors1 = [(site, 0.0, isite)]
neighbors1.extend(struct_neighbors[isite])
distances = [i[1] for i in sorted(neighbors1, key=lambda s: s[1])]
neighbors = [i[0] for i in sorted(neighbors1, key=lambda s: s[1])]
qvoronoi_input = [s.coords for s in neighbors]
voro = Voronoi(points=qvoronoi_input, qhull_options="o Fv")
all_vertices = voro.vertices
results2 = []
maxangle = 0.0
mindist = 10000.0
for iridge, ridge_points in enumerate(voro.ridge_points):
if 0 in ridge_points:
ridge_vertices_indices = voro.ridge_vertices[iridge]
if -1 in ridge_vertices_indices:
raise RuntimeError("This structure is pathological,"
" infinite vertex in the voronoi "
"construction")
ridge_point2 = max(ridge_points)
facets = [all_vertices[i] for i in ridge_vertices_indices]
sa = my_solid_angle(site.coords, facets)
maxangle = max([sa, maxangle])
mindist = min([mindist, distances[ridge_point2]])
for iii, sss in enumerate(self.structure):
if neighbors[ridge_point2].is_periodic_image(sss):
myindex = iii
break
results2.append({
'site': neighbors[ridge_point2],
'angle': sa,
'distance': distances[ridge_point2],
'index': myindex
})
for dd in results2:
dd['normalized_angle'] = dd['angle'] / maxangle
dd['normalized_distance'] = dd['distance'] / mindist
self.voronoi_list2[isite] = results2
t2 = time.clock()
logging.info('Voronoi list set up in {:.2f} seconds'.format(t2 - t1))
def setup_voronoi_list(self, indices, voronoi_cutoff):
"""
Set up of the voronoi list of neighbours by calling qhull
:param indices: indices of the sites for which the Voronoi is needed
:param voronoi_cutoff: Voronoi cutoff for the search of neighbours
:raise RuntimeError: If an infinite vertex is found in the voronoi construction
"""
self.voronoi_list2 = [None] * len(self.structure)
logging.info('Getting all neighbors in structure')
struct_neighbors = self.structure.get_all_neighbors(voronoi_cutoff, include_index=True)
t1 = time.clock()
logging.info('Setting up Voronoi list :')
for jj, isite in enumerate(indices):
logging.info(' - Voronoi analysis for site #{:d} ({:d}/{:d})'.format(isite, jj+1, len(indices)))
site = self.structure[isite]
neighbors1 = [(site, 0.0, isite)]
neighbors1.extend(struct_neighbors[isite])
distances = [i[1] for i in sorted(neighbors1, key=lambda s: s[1])]
neighbors = [i[0] for i in sorted(neighbors1, key=lambda s: s[1])]
qvoronoi_input = [s.coords for s in neighbors]
voro = Voronoi(points=qvoronoi_input, qhull_options="o Fv")
all_vertices = voro.vertices
results2 = []
maxangle = 0.0
mindist = 10000.0
for iridge, ridge_points in enumerate(voro.ridge_points):
if 0 in ridge_points:
ridge_vertices_indices = voro.ridge_vertices[iridge]
if -1 in ridge_vertices_indices:
raise RuntimeError("This structure is pathological,"
" infinite vertex in the voronoi "
"construction")
ridge_point2 = max(ridge_points)
facets = [all_vertices[i] for i in ridge_vertices_indices]
try:
sa = solid_angle(site.coords, facets)
except ValueError:
sa = my_solid_angle(site.coords, facets)
maxangle = max([sa, maxangle])
mindist = min([mindist, distances[ridge_point2]])
for iii, sss in enumerate(self.structure):
if neighbors[ridge_point2].is_periodic_image(sss):
myindex = iii
break
results2.append({'site': neighbors[ridge_point2],
'angle': sa,
'distance': distances[ridge_point2],
'index': myindex})
for dd in results2:
dd['normalized_angle'] = dd['angle'] / maxangle
dd['normalized_distance'] = dd['distance'] / mindist
self.voronoi_list2[isite] = results2
t2 = time.clock()
logging.info('Voronoi list set up in {:.2f} seconds'.format(t2-t1))
def setup_voronoi_list(self, indices, voronoi_cutoff):
"""
Set up of the voronoi list of neighbours by calling qhull.
Args:
indices: indices of the sites for which the Voronoi is needed.
voronoi_cutoff: Voronoi cutoff for the search of neighbours.
Raises:
RuntimeError: If an infinite vertex is found in the voronoi construction.
"""
self.voronoi_list2 = [None] * len(self.structure)
self.voronoi_list_coords = [None] * len(self.structure)
logging.debug("Getting all neighbors in structure")
struct_neighbors = self.structure.get_all_neighbors(voronoi_cutoff,
include_index=True)
t1 = time.process_time()
logging.debug("Setting up Voronoi list :")
for jj, isite in enumerate(indices):
logging.debug(
" - Voronoi analysis for site #{:d} ({:d}/{:d})".format(
isite, jj + 1, len(indices)))
site = self.structure[isite]
neighbors1 = [(site, 0.0, isite)]
neighbors1.extend(struct_neighbors[isite])
distances = [i[1] for i in sorted(neighbors1, key=lambda s: s[1])]
neighbors = [i[0] for i in sorted(neighbors1, key=lambda s: s[1])]
qvoronoi_input = [s.coords for s in neighbors]
voro = Voronoi(points=qvoronoi_input, qhull_options="o Fv")
all_vertices = voro.vertices
results2 = []
maxangle = 0.0
mindist = 10000.0
for iridge, ridge_points in enumerate(voro.ridge_points):
if 0 in ridge_points:
ridge_vertices_indices = voro.ridge_vertices[iridge]
if -1 in ridge_vertices_indices:
raise RuntimeError("This structure is pathological,"
" infinite vertex in the voronoi "
"construction")
ridge_point2 = max(ridge_points)
facets = [all_vertices[i] for i in ridge_vertices_indices]
sa = my_solid_angle(site.coords, facets)
maxangle = max([sa, maxangle])
mindist = min([mindist, distances[ridge_point2]])
for iii, sss in enumerate(self.structure):
if neighbors[ridge_point2].is_periodic_image(
sss, tolerance=1.0e-6):
myindex = iii
break
results2.append({
"site": neighbors[ridge_point2],
"angle": sa,
"distance": distances[ridge_point2],
"index": myindex,
})
for dd in results2:
dd["normalized_angle"] = dd["angle"] / maxangle
dd["normalized_distance"] = dd["distance"] / mindist
self.voronoi_list2[isite] = results2
self.voronoi_list_coords[isite] = np.array(
[dd["site"].coords for dd in results2])
t2 = time.process_time()
logging.debug("Voronoi list set up in {:.2f} seconds".format(t2 - t1))
