pymatgen.analysis.chemenv.coordination_environments package
Subpackages
Submodules
- pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies module
AbstractChemenvStrategyAbstractChemenvStrategy.ACAbstractChemenvStrategy.DEFAULT_SYMMETRY_MEASURE_TYPEAbstractChemenvStrategy.STRATEGY_DESCRIPTIONAbstractChemenvStrategy.STRATEGY_INFO_FIELDSAbstractChemenvStrategy.STRATEGY_OPTIONSAbstractChemenvStrategy.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_typeAbstractChemenvStrategy.uniquely_determines_coordination_environments
AdditionalConditionIntAngleCutoffFloatAngleNbSetWeightAnglePlateauNbSetWeightCNBiasNbSetWeightCSMFloatDeltaCSMNbSetWeightDeltaCSMNbSetWeight.DEFAULT_EFFECTIVE_CSM_ESTIMATORDeltaCSMNbSetWeight.DEFAULT_SYMMETRY_MEASURE_TYPEDeltaCSMNbSetWeight.DEFAULT_WEIGHT_ESTIMATORDeltaCSMNbSetWeight.SHORT_NAMEDeltaCSMNbSetWeight.as_dict()DeltaCSMNbSetWeight.delta_cn_specifics()DeltaCSMNbSetWeight.from_dict()DeltaCSMNbSetWeight.weight()
DeltaDistanceNbSetWeightDistanceAngleAreaNbSetWeightDistanceAngleAreaNbSetWeight.ACDistanceAngleAreaNbSetWeight.DEFAULT_SURFACE_DEFINITIONDistanceAngleAreaNbSetWeight.SHORT_NAMEDistanceAngleAreaNbSetWeight.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()
DistanceCutoffFloatDistanceNbSetWeightDistancePlateauNbSetWeightMultiWeightsChemenvStrategyMultiWeightsChemenvStrategy.DEFAULT_CE_ESTIMATORMultiWeightsChemenvStrategy.STRATEGY_DESCRIPTIONMultiWeightsChemenvStrategy.as_dict()MultiWeightsChemenvStrategy.from_dict()MultiWeightsChemenvStrategy.stats_article_weights_parameters()MultiWeightsChemenvStrategy.uniquely_determines_coordination_environments
NbSetWeightNormalizedAngleDistanceNbSetWeightNormalizedAngleDistanceNbSetWeight.SHORT_NAMENormalizedAngleDistanceNbSetWeight.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()
SelfCSMNbSetWeightSimpleAbundanceChemenvStrategySimpleAbundanceChemenvStrategy.DEFAULT_ADDITIONAL_CONDITIONSimpleAbundanceChemenvStrategy.DEFAULT_MAX_DISTSimpleAbundanceChemenvStrategy.STRATEGY_DESCRIPTIONSimpleAbundanceChemenvStrategy.STRATEGY_OPTIONSSimpleAbundanceChemenvStrategy.as_dict()SimpleAbundanceChemenvStrategy.from_dict()SimpleAbundanceChemenvStrategy.get_site_coordination_environment()SimpleAbundanceChemenvStrategy.get_site_coordination_environments()SimpleAbundanceChemenvStrategy.get_site_neighbors()SimpleAbundanceChemenvStrategy.uniquely_determines_coordination_environments
SimplestChemenvStrategySimplestChemenvStrategy.DEFAULT_ADDITIONAL_CONDITIONSimplestChemenvStrategy.DEFAULT_ANGLE_CUTOFFSimplestChemenvStrategy.DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFFSimplestChemenvStrategy.DEFAULT_DISTANCE_CUTOFFSimplestChemenvStrategy.STRATEGY_DESCRIPTIONSimplestChemenvStrategy.STRATEGY_OPTIONSSimplestChemenvStrategy.add_strategy_visualization_to_subplot()SimplestChemenvStrategy.additional_conditionSimplestChemenvStrategy.angle_cutoffSimplestChemenvStrategy.as_dict()SimplestChemenvStrategy.continuous_symmetry_measure_cutoffSimplestChemenvStrategy.distance_cutoffSimplestChemenvStrategy.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
StrategyOptionTargettedPenaltiedAbundanceChemenvStrategyTargettedPenaltiedAbundanceChemenvStrategy.DEFAULT_TARGET_ENVIRONMENTSTargettedPenaltiedAbundanceChemenvStrategy.as_dict()TargettedPenaltiedAbundanceChemenvStrategy.from_dict()TargettedPenaltiedAbundanceChemenvStrategy.get_site_coordination_environment()TargettedPenaltiedAbundanceChemenvStrategy.uniquely_determines_coordination_environments
WeightedNbSetChemenvStrategyWeightedNbSetChemenvStrategy.DEFAULT_CE_ESTIMATORWeightedNbSetChemenvStrategy.STRATEGY_DESCRIPTIONWeightedNbSetChemenvStrategy.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
AbstractChemenvAlgorithmAllCoordinationGeometriesAllCoordinationGeometries.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()
CoordinationGeometryCoordinationGeometry.CSM_SKIP_SEPARATION_PLANE_ALGOCoordinationGeometry.IUCr_symbolCoordinationGeometry.IUCr_symbol_strCoordinationGeometry.IUPAC_symbolCoordinationGeometry.IUPAC_symbol_strCoordinationGeometry.NeighborsSetsHintsCoordinationGeometry.NeighborsSetsHints.ALLOWED_HINTS_TYPESCoordinationGeometry.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.algorithmsCoordinationGeometry.as_dict()CoordinationGeometry.ce_symbolCoordinationGeometry.coordination_numberCoordinationGeometry.distfactor_maxCoordinationGeometry.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_symbolCoordinationGeometry.number_of_permutationsCoordinationGeometry.pauling_stability_ratioCoordinationGeometry.ref_permutation()CoordinationGeometry.set_permutations_safe_override()CoordinationGeometry.solid_angles()
ExplicitPermutationsAlgorithmSeparationPlane
- pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module
AbstractGeometryAbstractGeometry.cnAbstractGeometry.coordination_numberAbstractGeometry.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()
LocalGeometryFinderLocalGeometryFinder.BVA_DISTANCE_SCALE_FACTORSLocalGeometryFinder.DEFAULT_BVA_DISTANCE_SCALE_FACTORLocalGeometryFinder.DEFAULT_SPG_ANALYZER_OPTIONSLocalGeometryFinder.DEFAULT_STRATEGYLocalGeometryFinder.PRESETSLocalGeometryFinder.STRUCTURE_REFINEMENT_NONELocalGeometryFinder.STRUCTURE_REFINEMENT_REFINEDLocalGeometryFinder.STRUCTURE_REFINEMENT_SYMMETRIZEDLocalGeometryFinder.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
ChemicalEnvironmentsLightStructureEnvironmentsLightStructureEnvironments.DEFAULT_STATISTICS_FIELDSLightStructureEnvironments.DELTA_MAX_OXIDATION_STATELightStructureEnvironments.NeighborsSetLightStructureEnvironments.NeighborsSet.as_dict()LightStructureEnvironments.NeighborsSet.from_dict()LightStructureEnvironments.NeighborsSet.neighb_coordsLightStructureEnvironments.NeighborsSet.neighb_indices_and_imagesLightStructureEnvironments.NeighborsSet.neighb_sitesLightStructureEnvironments.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
StructureEnvironmentsStructureEnvironments.ACStructureEnvironments.NeighborsSetStructureEnvironments.NeighborsSet.add_source()StructureEnvironments.NeighborsSet.angle_plateau()StructureEnvironments.NeighborsSet.anglesStructureEnvironments.NeighborsSet.as_dict()StructureEnvironments.NeighborsSet.coordsStructureEnvironments.NeighborsSet.distance_plateau()StructureEnvironments.NeighborsSet.distancesStructureEnvironments.NeighborsSet.from_dict()StructureEnvironments.NeighborsSet.get_neighb_voronoi_indices()StructureEnvironments.NeighborsSet.infoStructureEnvironments.NeighborsSet.neighb_coordsStructureEnvironments.NeighborsSet.neighb_coordsOptStructureEnvironments.NeighborsSet.neighb_sitesStructureEnvironments.NeighborsSet.neighb_sites_and_indicesStructureEnvironments.NeighborsSet.normalized_anglesStructureEnvironments.NeighborsSet.normalized_distancesStructureEnvironments.NeighborsSet.sourceStructureEnvironments.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
DetailedVoronoiContainerDetailedVoronoiContainer.ACDetailedVoronoiContainer.as_dict()DetailedVoronoiContainer.default_normalized_angle_toleranceDetailedVoronoiContainer.default_normalized_distance_toleranceDetailedVoronoiContainer.default_voronoi_cutoffDetailedVoronoiContainer.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.