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=1e-05, 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]

Bson-serializable dict representation of the VoronoiContainer. :return: dictionary that is BSON-encodable

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

get_rdf_figure(isite, normalized=True, figsize=None, step_function=None)[source]
get_sadf_figure(isite, normalized=True, figsize=None, step_function=None)[source]
is_close_to(other, rtol=0.0, atol=1e-08)[source]
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]
neighbors(isite, distfactor, angfactor, additional_condition=None)[source]
neighbors_map(isite, distfactor, angfactor, additional_condition)[source]
neighbors_surfaces(isite, surface_calculation_type=None, max_dist=2.0)[source]
neighbors_surfaces_bounded(isite, surface_calculation_options=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

to_bson_voronoi_list2()[source]

Transforms the voronoi_list into a vlist + bson_nb_voro_list, that are BSON-encodable. :return: [vlist, bson_nb_voro_list], to be used in the as_dict method

voronoi_parameters_bounds_and_limits(isite, plot_type, max_dist)[source]
from_bson_voronoi_list(bson_nb_voro_list, structure)[source]

Returns the voronoi_list needed for the VoronoiContainer object from a bson-encoded 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 bson-encoded 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)