pymatgen.analysis.chemenv.coordination_environments package
Subpackages
Submodules
- pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies module
AbstractChemenvStrategy
AbstractChemenvStrategy.AC
AbstractChemenvStrategy.DEFAULT_SYMMETRY_MEASURE_TYPE
AbstractChemenvStrategy.STRATEGY_DESCRIPTION
AbstractChemenvStrategy.STRATEGY_INFO_FIELDS
AbstractChemenvStrategy.STRATEGY_OPTIONS
AbstractChemenvStrategy.as_dict()
AbstractChemenvStrategy.equivalent_site_index_and_transform()
AbstractChemenvStrategy.from_dict()
AbstractChemenvStrategy.get_site_ce_fractions_and_neighbors()
AbstractChemenvStrategy.get_site_coordination_environment()
AbstractChemenvStrategy.get_site_coordination_environments()
AbstractChemenvStrategy.get_site_coordination_environments_fractions()
AbstractChemenvStrategy.get_site_neighbors()
AbstractChemenvStrategy.prepare_symmetries()
AbstractChemenvStrategy.set_option()
AbstractChemenvStrategy.set_structure_environments()
AbstractChemenvStrategy.setup_options()
AbstractChemenvStrategy.symmetry_measure_type
AbstractChemenvStrategy.uniquely_determines_coordination_environments
AdditionalConditionInt
AngleCutoffFloat
AngleNbSetWeight
AnglePlateauNbSetWeight
CNBiasNbSetWeight
CSMFloat
DeltaCSMNbSetWeight
DeltaCSMNbSetWeight.DEFAULT_EFFECTIVE_CSM_ESTIMATOR
DeltaCSMNbSetWeight.DEFAULT_SYMMETRY_MEASURE_TYPE
DeltaCSMNbSetWeight.DEFAULT_WEIGHT_ESTIMATOR
DeltaCSMNbSetWeight.SHORT_NAME
DeltaCSMNbSetWeight.as_dict()
DeltaCSMNbSetWeight.delta_cn_specifics()
DeltaCSMNbSetWeight.from_dict()
DeltaCSMNbSetWeight.weight()
DeltaDistanceNbSetWeight
DistanceAngleAreaNbSetWeight
DistanceAngleAreaNbSetWeight.AC
DistanceAngleAreaNbSetWeight.DEFAULT_SURFACE_DEFINITION
DistanceAngleAreaNbSetWeight.SHORT_NAME
DistanceAngleAreaNbSetWeight.as_dict()
DistanceAngleAreaNbSetWeight.from_dict()
DistanceAngleAreaNbSetWeight.rectangle_crosses_area()
DistanceAngleAreaNbSetWeight.w_area_has_intersection()
DistanceAngleAreaNbSetWeight.w_area_has_intersection_smoothstep()
DistanceAngleAreaNbSetWeight.w_area_intersection_nbsfh_fbs_onb0()
DistanceAngleAreaNbSetWeight.weight()
DistanceCutoffFloat
DistanceNbSetWeight
DistancePlateauNbSetWeight
MultiWeightsChemenvStrategy
MultiWeightsChemenvStrategy.DEFAULT_CE_ESTIMATOR
MultiWeightsChemenvStrategy.STRATEGY_DESCRIPTION
MultiWeightsChemenvStrategy.as_dict()
MultiWeightsChemenvStrategy.from_dict()
MultiWeightsChemenvStrategy.stats_article_weights_parameters()
MultiWeightsChemenvStrategy.uniquely_determines_coordination_environments
NbSetWeight
NormalizedAngleDistanceNbSetWeight
NormalizedAngleDistanceNbSetWeight.SHORT_NAME
NormalizedAngleDistanceNbSetWeight.ang()
NormalizedAngleDistanceNbSetWeight.anginvdist()
NormalizedAngleDistanceNbSetWeight.anginvndist()
NormalizedAngleDistanceNbSetWeight.angn()
NormalizedAngleDistanceNbSetWeight.angninvdist()
NormalizedAngleDistanceNbSetWeight.angninvndist()
NormalizedAngleDistanceNbSetWeight.as_dict()
NormalizedAngleDistanceNbSetWeight.aweight()
NormalizedAngleDistanceNbSetWeight.from_dict()
NormalizedAngleDistanceNbSetWeight.gweight()
NormalizedAngleDistanceNbSetWeight.invdist()
NormalizedAngleDistanceNbSetWeight.invndist()
NormalizedAngleDistanceNbSetWeight.weight()
SelfCSMNbSetWeight
SimpleAbundanceChemenvStrategy
SimpleAbundanceChemenvStrategy.DEFAULT_ADDITIONAL_CONDITION
SimpleAbundanceChemenvStrategy.DEFAULT_MAX_DIST
SimpleAbundanceChemenvStrategy.STRATEGY_DESCRIPTION
SimpleAbundanceChemenvStrategy.STRATEGY_OPTIONS
SimpleAbundanceChemenvStrategy.as_dict()
SimpleAbundanceChemenvStrategy.from_dict()
SimpleAbundanceChemenvStrategy.get_site_coordination_environment()
SimpleAbundanceChemenvStrategy.get_site_coordination_environments()
SimpleAbundanceChemenvStrategy.get_site_neighbors()
SimpleAbundanceChemenvStrategy.uniquely_determines_coordination_environments
SimplestChemenvStrategy
SimplestChemenvStrategy.DEFAULT_ADDITIONAL_CONDITION
SimplestChemenvStrategy.DEFAULT_ANGLE_CUTOFF
SimplestChemenvStrategy.DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF
SimplestChemenvStrategy.DEFAULT_DISTANCE_CUTOFF
SimplestChemenvStrategy.STRATEGY_DESCRIPTION
SimplestChemenvStrategy.STRATEGY_OPTIONS
SimplestChemenvStrategy.add_strategy_visualization_to_subplot()
SimplestChemenvStrategy.additional_condition
SimplestChemenvStrategy.angle_cutoff
SimplestChemenvStrategy.as_dict()
SimplestChemenvStrategy.continuous_symmetry_measure_cutoff
SimplestChemenvStrategy.distance_cutoff
SimplestChemenvStrategy.from_dict()
SimplestChemenvStrategy.get_site_coordination_environment()
SimplestChemenvStrategy.get_site_coordination_environments()
SimplestChemenvStrategy.get_site_coordination_environments_fractions()
SimplestChemenvStrategy.get_site_neighbors()
SimplestChemenvStrategy.uniquely_determines_coordination_environments
StrategyOption
TargettedPenaltiedAbundanceChemenvStrategy
TargettedPenaltiedAbundanceChemenvStrategy.DEFAULT_TARGET_ENVIRONMENTS
TargettedPenaltiedAbundanceChemenvStrategy.as_dict()
TargettedPenaltiedAbundanceChemenvStrategy.from_dict()
TargettedPenaltiedAbundanceChemenvStrategy.get_site_coordination_environment()
TargettedPenaltiedAbundanceChemenvStrategy.uniquely_determines_coordination_environments
WeightedNbSetChemenvStrategy
WeightedNbSetChemenvStrategy.DEFAULT_CE_ESTIMATOR
WeightedNbSetChemenvStrategy.STRATEGY_DESCRIPTION
WeightedNbSetChemenvStrategy.as_dict()
WeightedNbSetChemenvStrategy.from_dict()
WeightedNbSetChemenvStrategy.get_site_coordination_environment()
WeightedNbSetChemenvStrategy.get_site_coordination_environments()
WeightedNbSetChemenvStrategy.get_site_coordination_environments_fractions()
WeightedNbSetChemenvStrategy.get_site_neighbors()
WeightedNbSetChemenvStrategy.uniquely_determines_coordination_environments
get_effective_csm()
set_info()
- pymatgen.analysis.chemenv.coordination_environments.coordination_geometries module
AbstractChemenvAlgorithm
AllCoordinationGeometries
AllCoordinationGeometries.get_geometries()
AllCoordinationGeometries.get_geometry_from_IUCr_symbol()
AllCoordinationGeometries.get_geometry_from_IUPAC_symbol()
AllCoordinationGeometries.get_geometry_from_mp_symbol()
AllCoordinationGeometries.get_geometry_from_name()
AllCoordinationGeometries.get_implemented_geometries()
AllCoordinationGeometries.get_not_implemented_geometries()
AllCoordinationGeometries.get_symbol_cn_mapping()
AllCoordinationGeometries.get_symbol_name_mapping()
AllCoordinationGeometries.is_a_valid_coordination_geometry()
AllCoordinationGeometries.pretty_print()
CoordinationGeometry
CoordinationGeometry.CSM_SKIP_SEPARATION_PLANE_ALGO
CoordinationGeometry.IUCr_symbol
CoordinationGeometry.IUCr_symbol_str
CoordinationGeometry.IUPAC_symbol
CoordinationGeometry.IUPAC_symbol_str
CoordinationGeometry.NeighborsSetsHints
CoordinationGeometry.NeighborsSetsHints.ALLOWED_HINTS_TYPES
CoordinationGeometry.NeighborsSetsHints.as_dict()
CoordinationGeometry.NeighborsSetsHints.double_cap_hints()
CoordinationGeometry.NeighborsSetsHints.from_dict()
CoordinationGeometry.NeighborsSetsHints.hints()
CoordinationGeometry.NeighborsSetsHints.single_cap_hints()
CoordinationGeometry.NeighborsSetsHints.triple_cap_hints()
CoordinationGeometry.algorithms
CoordinationGeometry.as_dict()
CoordinationGeometry.ce_symbol
CoordinationGeometry.coordination_number
CoordinationGeometry.distfactor_max
CoordinationGeometry.edges()
CoordinationGeometry.faces()
CoordinationGeometry.from_dict()
CoordinationGeometry.get_central_site()
CoordinationGeometry.get_coordination_number()
CoordinationGeometry.get_name()
CoordinationGeometry.get_pmeshes()
CoordinationGeometry.is_implemented()
CoordinationGeometry.mp_symbol
CoordinationGeometry.number_of_permutations
CoordinationGeometry.pauling_stability_ratio
CoordinationGeometry.ref_permutation()
CoordinationGeometry.set_permutations_safe_override()
CoordinationGeometry.solid_angles()
ExplicitPermutationsAlgorithm
SeparationPlane
- pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module
AbstractGeometry
AbstractGeometry.cn
AbstractGeometry.coordination_number
AbstractGeometry.from_cg()
AbstractGeometry.points_wcs_csc()
AbstractGeometry.points_wcs_ctwcc()
AbstractGeometry.points_wcs_ctwocc()
AbstractGeometry.points_wocs_csc()
AbstractGeometry.points_wocs_ctwcc()
AbstractGeometry.points_wocs_ctwocc()
LocalGeometryFinder
LocalGeometryFinder.BVA_DISTANCE_SCALE_FACTORS
LocalGeometryFinder.DEFAULT_BVA_DISTANCE_SCALE_FACTOR
LocalGeometryFinder.DEFAULT_SPG_ANALYZER_OPTIONS
LocalGeometryFinder.DEFAULT_STRATEGY
LocalGeometryFinder.PRESETS
LocalGeometryFinder.STRUCTURE_REFINEMENT_NONE
LocalGeometryFinder.STRUCTURE_REFINEMENT_REFINED
LocalGeometryFinder.STRUCTURE_REFINEMENT_SYMMETRIZED
LocalGeometryFinder.compute_coordination_environments()
LocalGeometryFinder.compute_structure_environments()
LocalGeometryFinder.coordination_geometry_symmetry_measures()
LocalGeometryFinder.coordination_geometry_symmetry_measures_fallback_random()
LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane()
LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane_optim()
LocalGeometryFinder.coordination_geometry_symmetry_measures_sepplane_optim()
LocalGeometryFinder.coordination_geometry_symmetry_measures_standard()
LocalGeometryFinder.get_coordination_symmetry_measures()
LocalGeometryFinder.get_coordination_symmetry_measures_optim()
LocalGeometryFinder.get_structure()
LocalGeometryFinder.set_structure()
LocalGeometryFinder.setup_explicit_indices_local_geometry()
LocalGeometryFinder.setup_local_geometry()
LocalGeometryFinder.setup_ordered_indices_local_geometry()
LocalGeometryFinder.setup_parameter()
LocalGeometryFinder.setup_parameters()
LocalGeometryFinder.setup_random_indices_local_geometry()
LocalGeometryFinder.setup_random_structure()
LocalGeometryFinder.setup_structure()
LocalGeometryFinder.setup_test_perfect_environment()
LocalGeometryFinder.update_nb_set_environments()
find_rotation()
find_scaling_factor()
symmetry_measure()
- pymatgen.analysis.chemenv.coordination_environments.structure_environments module
ChemicalEnvironments
LightStructureEnvironments
LightStructureEnvironments.DEFAULT_STATISTICS_FIELDS
LightStructureEnvironments.DELTA_MAX_OXIDATION_STATE
LightStructureEnvironments.NeighborsSet
LightStructureEnvironments.NeighborsSet.as_dict()
LightStructureEnvironments.NeighborsSet.from_dict()
LightStructureEnvironments.NeighborsSet.neighb_coords
LightStructureEnvironments.NeighborsSet.neighb_indices_and_images
LightStructureEnvironments.NeighborsSet.neighb_sites
LightStructureEnvironments.NeighborsSet.neighb_sites_and_indices
LightStructureEnvironments.as_dict()
LightStructureEnvironments.clear_environments()
LightStructureEnvironments.contains_only_one_anion()
LightStructureEnvironments.contains_only_one_anion_atom()
LightStructureEnvironments.environments_identified()
LightStructureEnvironments.from_dict()
LightStructureEnvironments.from_structure_environments()
LightStructureEnvironments.get_site_info_for_specie_allces()
LightStructureEnvironments.get_site_info_for_specie_ce()
LightStructureEnvironments.get_statistics()
LightStructureEnvironments.setup_statistic_lists()
LightStructureEnvironments.site_contains_environment()
LightStructureEnvironments.site_has_clear_environment()
LightStructureEnvironments.structure_contains_atom_environment()
LightStructureEnvironments.structure_has_clear_environments()
LightStructureEnvironments.uniquely_determines_coordination_environments
StructureEnvironments
StructureEnvironments.AC
StructureEnvironments.NeighborsSet
StructureEnvironments.NeighborsSet.add_source()
StructureEnvironments.NeighborsSet.angle_plateau()
StructureEnvironments.NeighborsSet.angles
StructureEnvironments.NeighborsSet.as_dict()
StructureEnvironments.NeighborsSet.coords
StructureEnvironments.NeighborsSet.distance_plateau()
StructureEnvironments.NeighborsSet.distances
StructureEnvironments.NeighborsSet.from_dict()
StructureEnvironments.NeighborsSet.get_neighb_voronoi_indices()
StructureEnvironments.NeighborsSet.info
StructureEnvironments.NeighborsSet.neighb_coords
StructureEnvironments.NeighborsSet.neighb_coordsOpt
StructureEnvironments.NeighborsSet.neighb_sites
StructureEnvironments.NeighborsSet.neighb_sites_and_indices
StructureEnvironments.NeighborsSet.normalized_angles
StructureEnvironments.NeighborsSet.normalized_distances
StructureEnvironments.NeighborsSet.source
StructureEnvironments.NeighborsSet.voronoi_grid_surface_points()
StructureEnvironments.add_neighbors_set()
StructureEnvironments.as_dict()
StructureEnvironments.differences_wrt()
StructureEnvironments.from_dict()
StructureEnvironments.get_coordination_environments()
StructureEnvironments.get_csm()
StructureEnvironments.get_csm_and_maps()
StructureEnvironments.get_csms()
StructureEnvironments.get_environments_figure()
StructureEnvironments.init_neighbors_sets()
StructureEnvironments.plot_csm_and_maps()
StructureEnvironments.plot_environments()
StructureEnvironments.save_environments_figure()
StructureEnvironments.update_coordination_environments()
StructureEnvironments.update_site_info()
- pymatgen.analysis.chemenv.coordination_environments.voronoi module
DetailedVoronoiContainer
DetailedVoronoiContainer.AC
DetailedVoronoiContainer.as_dict()
DetailedVoronoiContainer.default_normalized_angle_tolerance
DetailedVoronoiContainer.default_normalized_distance_tolerance
DetailedVoronoiContainer.default_voronoi_cutoff
DetailedVoronoiContainer.from_dict()
DetailedVoronoiContainer.get_rdf_figure()
DetailedVoronoiContainer.get_sadf_figure()
DetailedVoronoiContainer.is_close_to()
DetailedVoronoiContainer.maps_and_surfaces()
DetailedVoronoiContainer.maps_and_surfaces_bounded()
DetailedVoronoiContainer.neighbors()
DetailedVoronoiContainer.neighbors_surfaces()
DetailedVoronoiContainer.neighbors_surfaces_bounded()
DetailedVoronoiContainer.setup_neighbors_distances_and_angles()
DetailedVoronoiContainer.setup_voronoi_list()
DetailedVoronoiContainer.to_bson_voronoi_list2()
DetailedVoronoiContainer.voronoi_parameters_bounds_and_limits()
from_bson_voronoi_list2()
Module contents
Package for analyzing coordination environments.