pymatgen.analysis.chemenv.coordination_environments.voronoi module¶

class
DetailedVoronoiContainer
(structure=None, voronoi_list=None, voronoi_list2=None, voronoi_cutoff=10.0, isites=None, normalized_distance_tolerance=1e05, normalized_angle_tolerance=0.001, additional_conditions=None, valences=None, maximum_distance_factor=None, minimum_angle_factor=None)[source]¶ Bases:
monty.json.MSONable
Class used to store the full Voronoi of a given structure.
Constructor for the VoronoiContainer object. Either a structure is given, in which case the Voronoi is computed, or the different components of the VoronoiContainer are given (used in the from_dict method) :param structure: Structure for which the Voronoi is computed :param voronoi_list: List of voronoi polyhedrons for each site :param neighbors_list: list of neighbors for each site :param voronoi_cutoff: cutoff used for the voronoi :param isites: indices of sites for which the Voronoi has to be computed :raise: RuntimeError if the Voronoi cannot be constructed

AC
= <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>¶

as_dict
()[source]¶ Bsonserializable dict representation of the VoronoiContainer. :return: dictionary that is BSONencodable

default_voronoi_cutoff
= 10.0¶

classmethod
from_dict
(d)[source]¶ Reconstructs the VoronoiContainer object from a dict representation of the VoronoiContainer created using the as_dict method. :param d: dict representation of the VoronoiContainer object :return: VoronoiContainer object

maps_and_surfaces
(isite, surface_calculation_type=None, max_dist=2.0, additional_conditions=None)[source]¶

maps_and_surfaces_bounded
(isite, surface_calculation_options=None, additional_conditions=None)[source]¶

setup_neighbors_distances_and_angles
(indices)[source]¶ Initializes the angle and distance separations :param indices: indices of the sites for which the Voronoi is needed

setup_voronoi_list
(indices, voronoi_cutoff)[source]¶ 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


from_bson_voronoi_list
(bson_nb_voro_list, structure)[source]¶ Returns the voronoi_list needed for the VoronoiContainer object from a bsonencoded voronoi_list (composed of vlist and bson_nb_voro_list). :param vlist: List of voronoi objects :param bson_nb_voro_list: List of periodic sites involved in the Voronoi :return: The voronoi_list needed for the VoronoiContainer (with PeriodicSites as keys of the dictionary  not allowed in the BSON format)

from_bson_voronoi_list2
(bson_nb_voro_list2, structure)[source]¶ Returns the voronoi_list needed for the VoronoiContainer object from a bsonencoded voronoi_list (composed of vlist and bson_nb_voro_list). :param vlist: List of voronoi objects :param bson_nb_voro_list: List of periodic sites involved in the Voronoi :return: The voronoi_list needed for the VoronoiContainer (with PeriodicSites as keys of the dictionary  not allowed in the BSON format)