def setup_neighbors(self, additional_conditions=None, valences=None):
"""
Compute the list of neighbors for each distfactor/angfactor set of parameters from the voronoi list. The set of
distfactor/angfactor parameters is a "square" of all combinations of distfactors with angfactors.
:param distfactors: list of distfactors
:param angfactors: list of angfactors
:param only_anion_cation_bonds: Allows only neighbors that are cations (resp. anions) when the current site is
an anion (resp. a cation).
:param valences: Valences of all the sites in the structure, needed to check the anion-cation bond when
only_anion_cation_bonds is set to True.
:raise: ChemenvError if only_anion_cation_bonds is set to True and valences are not given.
"""
if additional_conditions is None:
additional_conditions = self.AC.ALL
if (self.AC.ONLY_ACB in additional_conditions
or self.AC.ONLY_ACB_AND_NO_E2SEB) and valences is None:
raise ChemenvError(
'VoronoiContainer', 'setup_neighbors',
'Valences are not given while only_anion_cation_bonds are allowed. Cannot continue'
)
self.neighbors_lists = [None] * len(self.voronoi_list)
self.additional_conditions = additional_conditions
for ivoronoi, voronoi in enumerate(self.voronoi_list):
if voronoi is None:
continue
self.neighbors_lists[ivoronoi] = []
voronoi_ac = self._precompute_additional_conditions(
ivoronoi, voronoi, valences)
distance_conditions = self._precompute_distance_conditions(
ivoronoi, voronoi)
angle_conditions = self._precompute_angle_conditions(
ivoronoi, voronoi)
for idp, dp_dict in enumerate(
self.neighbors_weighted_distances[ivoronoi]):
self.neighbors_lists[ivoronoi].append([])
for iap, ap_dict in enumerate(
self.neighbors_weighted_angles[ivoronoi]):
self.neighbors_lists[ivoronoi][idp].append([])
for iac, ac in enumerate(self.additional_conditions):
nlist = [(ips, vals['index'], {
'weighted_distance':
vals['weighted_distance'],
'weighted_angle':
vals['weighted_angle'],
'distance':
vals['distance'],
'angle':
vals['angle']
}) for ips, (ps, vals) in enumerate(voronoi)
if (distance_conditions[idp][ips]) and (
angle_conditions[iap][ips]) and (
voronoi_ac[ac][ips])]
self.neighbors_lists[ivoronoi][idp][iap].append(nlist)
def materials_project_api_key(self):
if self.materials_project_configuration is None:
raise ChemenvError('ChemEnvConfig', 'materials_project_api_key',
'No api_key saved')
return self.materials_project_configuration['api_key']
def __init__(
self,
environments=None,
links=None,
environments_data=None,
links_data=None,
graph=None,
):
"""
Constructor for the ConnectedComponent object.
Args:
environments: Environments in the connected component.
links: Links between environments in the connected component.
environments_data: Data of environment nodes.
links_data: Data of links between environment nodes.
graph: Graph of the connected component.
Returns:
ConnectedComponent: Instance of this class
"""
self._periodicity_vectors = None
self._primitive_reduced_connected_subgraph = None
self._projected = False
if graph is None:
self._connected_subgraph = nx.MultiGraph()
if environments_data is None:
self._connected_subgraph.add_nodes_from(environments)
else:
for env in environments:
if env in environments_data:
self._connected_subgraph.add_node(env, **environments_data[env])
else:
self._connected_subgraph.add_node(env)
for edge in links:
env_node1 = edge[0]
env_node2 = edge[1]
if len(edge) == 2:
key = None
else:
key = edge[2]
if (not self._connected_subgraph.has_node(env_node1)) or (
not self._connected_subgraph.has_node(env_node2)
):
raise ChemenvError(
self.__class__,
"__init__",
"Trying to add edge with some unexisting node ...",
)
if links_data is not None:
if (env_node1, env_node2, key) in links_data:
edge_data = links_data[(env_node1, env_node2, key)]
elif (env_node2, env_node1, key) in links_data:
edge_data = links_data[(env_node2, env_node1, key)]
elif (env_node1, env_node2) in links_data:
edge_data = links_data[(env_node1, env_node2)]
elif (env_node2, env_node1) in links_data:
edge_data = links_data[(env_node2, env_node1)]
else:
edge_data = None
else:
edge_data = None
if edge_data:
self._connected_subgraph.add_edge(env_node1, env_node2, key, **edge_data)
else:
self._connected_subgraph.add_edge(env_node1, env_node2, key)
else:
# TODO: should check a few requirements here ?
self._connected_subgraph = graph