pymatgen.analysis.chemenv package
Subpackages
- pymatgen.analysis.chemenv.connectivity package
- Subpackages
- Submodules
- pymatgen.analysis.chemenv.connectivity.connected_components module
ConnectedComponentConnectedComponent.as_dict()ConnectedComponent.compute_periodicity()ConnectedComponent.compute_periodicity_all_simple_paths_algorithm()ConnectedComponent.compute_periodicity_cycle_basis()ConnectedComponent.coordination_sequence()ConnectedComponent.description()ConnectedComponent.elastic_centered_graph()ConnectedComponent.from_dict()ConnectedComponent.from_graph()ConnectedComponent.graphConnectedComponent.is_0dConnectedComponent.is_1dConnectedComponent.is_2dConnectedComponent.is_3dConnectedComponent.is_periodicConnectedComponent.make_supergraph()ConnectedComponent.periodicityConnectedComponent.periodicity_vectorsConnectedComponent.show_graph()
draw_network()make_supergraph()
- pymatgen.analysis.chemenv.connectivity.connectivity_finder module
- pymatgen.analysis.chemenv.connectivity.environment_nodes module
AbstractEnvironmentNodeAbstractEnvironmentNode.ATOMAbstractEnvironmentNode.CE_NNBCES_NBCES_LIGANDSAbstractEnvironmentNode.COORDINATION_ENVIRONMENTAbstractEnvironmentNode.DEFAULT_EXTENSIONSAbstractEnvironmentNode.LIGANDS_ARRANGEMENTAbstractEnvironmentNode.NEIGHBORING_CESAbstractEnvironmentNode.NEIGHBORING_COORDINATION_ENVIRONMENTSAbstractEnvironmentNode.NEIGHBORS_LIGANDS_ARRANGEMENTAbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CEAbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENTAbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_CESAbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTSAbstractEnvironmentNode.atom_symbolAbstractEnvironmentNode.ceAbstractEnvironmentNode.ce_symbolAbstractEnvironmentNode.coordination_environmentAbstractEnvironmentNode.everything_equal()AbstractEnvironmentNode.isiteAbstractEnvironmentNode.mp_symbol
EnvironmentNodeget_environment_node()
- pymatgen.analysis.chemenv.connectivity.structure_connectivity module
StructureConnectivityStructureConnectivity.add_bonds()StructureConnectivity.add_sites()StructureConnectivity.as_dict()StructureConnectivity.environment_subgraph()StructureConnectivity.from_dict()StructureConnectivity.get_connected_components()StructureConnectivity.print_links()StructureConnectivity.setup_atom_environment_subgraph()StructureConnectivity.setup_atom_environments_subgraph()StructureConnectivity.setup_connectivity_description()StructureConnectivity.setup_environment_subgraph()StructureConnectivity.setup_environments_subgraph()
get_delta_image()
- pymatgen.analysis.chemenv.connectivity.connected_components module
- Module contents
- Subpackages
- 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()
- pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies module
- Module contents
- pymatgen.analysis.chemenv.utils package
- Subpackages
- Submodules
- pymatgen.analysis.chemenv.utils.chemenv_config module
- pymatgen.analysis.chemenv.utils.chemenv_errors module
- pymatgen.analysis.chemenv.utils.coordination_geometry_utils module
PlanePlane.TEST_2D_POINTSPlane.aPlane.abcdPlane.bPlane.cPlane.coefficientsPlane.crosses_originPlane.dPlane.distance_to_originPlane.distance_to_point()Plane.distances()Plane.distances_indices_groups()Plane.distances_indices_sorted()Plane.fit_error()Plane.fit_least_square_distance_error()Plane.fit_maximum_distance_error()Plane.from_2points_and_origin()Plane.from_3points()Plane.from_coefficients()Plane.from_npoints()Plane.from_npoints_least_square_distance()Plane.from_npoints_maximum_distance()Plane.indices_separate()Plane.init_3points()Plane.is_in_list()Plane.is_in_plane()Plane.is_same_plane_as()Plane.orthonormal_vectors()Plane.perpendicular_bisector()Plane.project_and_to2dim()Plane.project_and_to2dim_ordered_indices()Plane.projectionpoints()
anticlockwise_sort()anticlockwise_sort_indices()changebasis()collinear()diamond_functions()function_comparison()get_lower_and_upper_f()is_anion_cation_bond()matrixTimesVector()my_solid_angle()quarter_ellipsis_functions()rectangle_surface_intersection()rotateCoords()rotateCoordsOpt()separation_in_list()sort_separation()sort_separation_tuple()spline_functions()vectorsToMatrix()
- pymatgen.analysis.chemenv.utils.defs_utils module
AdditionalConditionsAdditionalConditions.ALLAdditionalConditions.CONDITION_DESCRIPTIONAdditionalConditions.NONEAdditionalConditions.NO_ACAdditionalConditions.NO_ADDITIONAL_CONDITIONAdditionalConditions.NO_E2SEBAdditionalConditions.NO_ELEMENT_TO_SAME_ELEMENT_BONDSAdditionalConditions.ONLY_ACBAdditionalConditions.ONLY_ACB_AND_NO_E2SEBAdditionalConditions.ONLY_ANION_CATION_BONDSAdditionalConditions.ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDSAdditionalConditions.ONLY_E2OBAdditionalConditions.ONLY_ELEMENT_TO_OXYGEN_BONDSAdditionalConditions.check_condition()
chemenv_citations()
- pymatgen.analysis.chemenv.utils.func_utils module
- pymatgen.analysis.chemenv.utils.graph_utils module
- pymatgen.analysis.chemenv.utils.math_utils module
cosinus_step()divisors()get_center_of_arc()get_linearly_independent_vectors()normal_cdf_step()power2_decreasing_exp()power2_inverse_decreasing()power2_inverse_power2_decreasing()power2_inverse_powern_decreasing()power2_tangent_decreasing()power3_step()powern_decreasing()powern_parts_step()prime_factors()scale_and_clamp()smootherstep()smoothstep()
- pymatgen.analysis.chemenv.utils.scripts_utils module
- Module contents
- Subpackages
Module contents
Package for analyzing chemical environments.