pymatgen.analysis namespace
Subpackages
- 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.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.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.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
- pymatgen.analysis.chemenv.connectivity package
- Module contents
- Subpackages
- pymatgen.analysis.diffraction package
- Subpackages
- Submodules
- pymatgen.analysis.diffraction.core module
AbstractDiffractionPatternCalculatorAbstractDiffractionPatternCalculator.SCALED_INTENSITY_TOLAbstractDiffractionPatternCalculator.TWO_THETA_TOLAbstractDiffractionPatternCalculator.get_pattern()AbstractDiffractionPatternCalculator.get_plot()AbstractDiffractionPatternCalculator.plot_structures()AbstractDiffractionPatternCalculator.show_plot()
DiffractionPatternget_unique_families()
- pymatgen.analysis.diffraction.neutron module
- pymatgen.analysis.diffraction.tem module
TEMCalculatorTEMCalculator.bragg_angles()TEMCalculator.cell_intensity()TEMCalculator.cell_scattering_factors()TEMCalculator.electron_scattering_factors()TEMCalculator.generate_points()TEMCalculator.get_first_point()TEMCalculator.get_interplanar_angle()TEMCalculator.get_interplanar_spacings()TEMCalculator.get_pattern()TEMCalculator.get_plot_2d()TEMCalculator.get_plot_2d_concise()TEMCalculator.get_plot_coeffs()TEMCalculator.get_positions()TEMCalculator.get_s2()TEMCalculator.is_parallel()TEMCalculator.normalized_cell_intensity()TEMCalculator.tem_dots()TEMCalculator.wavelength_rel()TEMCalculator.x_ray_factors()TEMCalculator.zone_axis_filter()
- pymatgen.analysis.diffraction.xrd module
- pymatgen.analysis.diffraction.core module
- Module contents
- Subpackages
- pymatgen.analysis.elasticity package
- Subpackages
- Submodules
- pymatgen.analysis.elasticity.elastic module
ComplianceTensorElasticTensorElasticTensor.cahill_thermalcond()ElasticTensor.clarke_thermalcond()ElasticTensor.compliance_tensorElasticTensor.debye_temperature()ElasticTensor.directional_elastic_mod()ElasticTensor.directional_poisson_ratio()ElasticTensor.from_independent_strains()ElasticTensor.from_pseudoinverse()ElasticTensor.g_reussElasticTensor.g_voigtElasticTensor.g_vrhElasticTensor.get_structure_property_dict()ElasticTensor.green_kristoffel()ElasticTensor.homogeneous_poissonElasticTensor.k_reussElasticTensor.k_voigtElasticTensor.k_vrhElasticTensor.long_v()ElasticTensor.property_dictElasticTensor.snyder_ac()ElasticTensor.snyder_opt()ElasticTensor.snyder_total()ElasticTensor.trans_v()ElasticTensor.universal_anisotropyElasticTensor.y_mod
ElasticTensorExpansionElasticTensorExpansion.calculate_stress()ElasticTensorExpansion.energy_density()ElasticTensorExpansion.from_diff_fit()ElasticTensorExpansion.get_compliance_expansion()ElasticTensorExpansion.get_effective_ecs()ElasticTensorExpansion.get_ggt()ElasticTensorExpansion.get_gruneisen_parameter()ElasticTensorExpansion.get_heat_capacity()ElasticTensorExpansion.get_stability_criteria()ElasticTensorExpansion.get_strain_from_stress()ElasticTensorExpansion.get_symmetric_wallace_tensor()ElasticTensorExpansion.get_tgt()ElasticTensorExpansion.get_wallace_tensor()ElasticTensorExpansion.get_yield_stress()ElasticTensorExpansion.omega()ElasticTensorExpansion.orderElasticTensorExpansion.thermal_expansion_coeff()
NthOrderElasticTensordiff_fit()find_eq_stress()generate_pseudo()get_diff_coeff()get_strain_state_dict()get_symbol_list()raise_error_if_unphysical()subs()
- pymatgen.analysis.elasticity.strain module
- pymatgen.analysis.elasticity.stress module
- pymatgen.analysis.elasticity.elastic module
- Module contents
- Subpackages
- pymatgen.analysis.ferroelectricity package
- Subpackages
- Submodules
- pymatgen.analysis.ferroelectricity.polarization module
EnergyTrendPolarizationPolarization.from_outcars_and_structures()Polarization.get_lattice_quanta()Polarization.get_pelecs_and_pions()Polarization.get_polarization_change()Polarization.get_polarization_change_norm()Polarization.get_same_branch_polarization_data()Polarization.max_spline_jumps()Polarization.same_branch_splines()Polarization.smoothness()
PolarizationLatticecalc_ionic()get_total_ionic_dipole()zval_dict_from_potcar()
- pymatgen.analysis.ferroelectricity.polarization module
- Module contents
- Subpackages
- pymatgen.analysis.gb package
- Subpackages
- Submodules
- pymatgen.analysis.gb.grain module
GrainBoundaryGrainBoundaryGeneratorGrainBoundaryGenerator.enum_possible_plane_cubic()GrainBoundaryGenerator.enum_sigma_cubic()GrainBoundaryGenerator.enum_sigma_hex()GrainBoundaryGenerator.enum_sigma_ort()GrainBoundaryGenerator.enum_sigma_rho()GrainBoundaryGenerator.enum_sigma_tet()GrainBoundaryGenerator.gb_from_parameters()GrainBoundaryGenerator.get_ratio()GrainBoundaryGenerator.get_rotation_angle_from_sigma()GrainBoundaryGenerator.get_trans_mat()GrainBoundaryGenerator.reduce_mat()GrainBoundaryGenerator.slab_from_csl()GrainBoundaryGenerator.vec_to_surface()
fix_pbc()symm_group_cubic()
- pymatgen.analysis.gb.grain module
- Module contents
- Subpackages
- pymatgen.analysis.interfaces package
- Subpackages
- Submodules
- pymatgen.analysis.interfaces.coherent_interfaces module
- pymatgen.analysis.interfaces.substrate_analyzer module
- pymatgen.analysis.interfaces.zsl module
- Module contents
- Subpackages
- pymatgen.analysis.magnetism package
- Subpackages
- Submodules
- pymatgen.analysis.magnetism.analyzer module
CollinearMagneticStructureAnalyzerCollinearMagneticStructureAnalyzer.get_exchange_group_info()CollinearMagneticStructureAnalyzer.get_ferromagnetic_structure()CollinearMagneticStructureAnalyzer.get_nonmagnetic_structure()CollinearMagneticStructureAnalyzer.get_structure_with_only_magnetic_atoms()CollinearMagneticStructureAnalyzer.get_structure_with_spin()CollinearMagneticStructureAnalyzer.is_magneticCollinearMagneticStructureAnalyzer.magmomsCollinearMagneticStructureAnalyzer.magnetic_species_and_magmomsCollinearMagneticStructureAnalyzer.matches_ordering()CollinearMagneticStructureAnalyzer.number_of_magnetic_sitesCollinearMagneticStructureAnalyzer.number_of_unique_magnetic_sites()CollinearMagneticStructureAnalyzer.orderingCollinearMagneticStructureAnalyzer.types_of_magnetic_specieCollinearMagneticStructureAnalyzer.types_of_magnetic_species
MagneticDeformationMagneticStructureEnumeratorOrderingOverwriteMagmomModemagnetic_deformation()
- pymatgen.analysis.magnetism.heisenberg module
- pymatgen.analysis.magnetism.jahnteller module
JahnTellerAnalyzerJahnTellerAnalyzer.get_analysis()JahnTellerAnalyzer.get_analysis_and_structure()JahnTellerAnalyzer.get_magnitude_of_effect_from_species()JahnTellerAnalyzer.get_magnitude_of_effect_from_spin_config()JahnTellerAnalyzer.is_jahn_teller_active()JahnTellerAnalyzer.mu_so()JahnTellerAnalyzer.tag_structure()
- pymatgen.analysis.magnetism.analyzer module
- Module contents
- Subpackages
- pymatgen.analysis.solar package
- pymatgen.analysis.structure_prediction package
- pymatgen.analysis.topological package
- pymatgen.analysis.xas package
Submodules
- pymatgen.analysis.adsorption module
AdsorbateSiteFinderAdsorbateSiteFinder.add_adsorbate()AdsorbateSiteFinder.adsorb_both_surfaces()AdsorbateSiteFinder.assign_selective_dynamics()AdsorbateSiteFinder.assign_site_properties()AdsorbateSiteFinder.ensemble_center()AdsorbateSiteFinder.find_adsorption_sites()AdsorbateSiteFinder.find_surface_sites_by_height()AdsorbateSiteFinder.from_bulk_and_miller()AdsorbateSiteFinder.generate_adsorption_structures()AdsorbateSiteFinder.generate_substitution_structures()AdsorbateSiteFinder.get_extended_surface_mesh()AdsorbateSiteFinder.near_reduce()AdsorbateSiteFinder.subsurface_sites()AdsorbateSiteFinder.surface_sitesAdsorbateSiteFinder.symm_reduce()
get_mi_vec()get_rot()plot_slab()put_coord_inside()reorient_z()
- pymatgen.analysis.bond_dissociation module
- pymatgen.analysis.bond_valence module
- pymatgen.analysis.chempot_diagram module
ChemicalPotentialDiagramChemicalPotentialDiagram.border_hyperplanesChemicalPotentialDiagram.chemical_systemChemicalPotentialDiagram.domainsChemicalPotentialDiagram.el_refsChemicalPotentialDiagram.entry_dictChemicalPotentialDiagram.get_plot()ChemicalPotentialDiagram.hyperplane_entriesChemicalPotentialDiagram.hyperplanesChemicalPotentialDiagram.lims
get_2d_orthonormal_vector()get_centroid_2d()simple_pca()
- pymatgen.analysis.cost module
- pymatgen.analysis.dimensionality module
- pymatgen.analysis.disorder module
- pymatgen.analysis.energy_models module
- pymatgen.analysis.eos module
- pymatgen.analysis.ewald module
EwaldMinimizerEwaldMinimizer.ALGO_BEST_FIRSTEwaldMinimizer.ALGO_COMPLETEEwaldMinimizer.ALGO_FASTEwaldMinimizer.ALGO_TIME_LIMITEwaldMinimizer.add_m_list()EwaldMinimizer.best_case()EwaldMinimizer.best_m_listEwaldMinimizer.get_next_index()EwaldMinimizer.minimize_matrix()EwaldMinimizer.minimized_sumEwaldMinimizer.output_lists
EwaldSummationEwaldSummation.CONV_FACTEwaldSummation.as_dict()EwaldSummation.compute_partial_energy()EwaldSummation.compute_sub_structure()EwaldSummation.etaEwaldSummation.forcesEwaldSummation.from_dict()EwaldSummation.get_site_energy()EwaldSummation.point_energyEwaldSummation.point_energy_matrixEwaldSummation.real_space_energyEwaldSummation.real_space_energy_matrixEwaldSummation.reciprocal_space_energyEwaldSummation.reciprocal_space_energy_matrixEwaldSummation.total_energyEwaldSummation.total_energy_matrix
compute_average_oxidation_state()
- pymatgen.analysis.excitation module
- pymatgen.analysis.fragmenter module
- pymatgen.analysis.functional_groups module
- pymatgen.analysis.graphs module
ConnectedSiteMolGraphSplitErrorMoleculeGraphMoleculeGraph.add_edge()MoleculeGraph.alter_edge()MoleculeGraph.as_dict()MoleculeGraph.break_edge()MoleculeGraph.build_unique_fragments()MoleculeGraph.diff()MoleculeGraph.draw_graph_to_file()MoleculeGraph.edge_weight_nameMoleculeGraph.edge_weight_unitMoleculeGraph.find_rings()MoleculeGraph.from_dict()MoleculeGraph.get_connected_sites()MoleculeGraph.get_coordination_of_site()MoleculeGraph.get_disconnected_fragments()MoleculeGraph.insert_node()MoleculeGraph.isomorphic_to()MoleculeGraph.nameMoleculeGraph.remove_nodes()MoleculeGraph.replace_group()MoleculeGraph.set_node_attributes()MoleculeGraph.sort()MoleculeGraph.split_molecule_subgraphs()MoleculeGraph.substitute_group()MoleculeGraph.with_edges()MoleculeGraph.with_empty_graph()MoleculeGraph.with_local_env_strategy()
StructureGraphStructureGraph.add_edge()StructureGraph.alter_edge()StructureGraph.as_dict()StructureGraph.break_edge()StructureGraph.diff()StructureGraph.draw_graph_to_file()StructureGraph.edge_weight_nameStructureGraph.edge_weight_unitStructureGraph.from_dict()StructureGraph.get_connected_sites()StructureGraph.get_coordination_of_site()StructureGraph.get_subgraphs_as_molecules()StructureGraph.insert_node()StructureGraph.nameStructureGraph.remove_nodes()StructureGraph.set_node_attributes()StructureGraph.sort()StructureGraph.substitute_group()StructureGraph.types_and_weights_of_connectionsStructureGraph.types_of_coordination_environments()StructureGraph.weight_statisticsStructureGraph.with_edges()StructureGraph.with_empty_graph()StructureGraph.with_local_env_strategy()
- pymatgen.analysis.hhi module
- pymatgen.analysis.interface module
- pymatgen.analysis.interface_reactions module
GrandPotentialInterfacialReactivityInterfacialReactivityInterfacialReactivity.EV_TO_KJ_PER_MOLInterfacialReactivity.get_chempot_correction()InterfacialReactivity.get_critical_original_kink_ratio()InterfacialReactivity.get_dataframe()InterfacialReactivity.get_kinks()InterfacialReactivity.labelsInterfacialReactivity.minimumInterfacialReactivity.plot()InterfacialReactivity.products
- pymatgen.analysis.local_env module
BrunnerNN_realBrunnerNN_reciprocalBrunnerNN_relativeCovalentBondNNCritic2NNCrystalNNCutOffDictNNEconNNIsayevNNJmolNNLocalStructOrderParamsLocalStructOrderParams.compute_trigonometric_terms()LocalStructOrderParams.get_order_parameters()LocalStructOrderParams.get_parameters()LocalStructOrderParams.get_q2()LocalStructOrderParams.get_q4()LocalStructOrderParams.get_q6()LocalStructOrderParams.get_type()LocalStructOrderParams.last_nneighLocalStructOrderParams.num_ops
MinimumDistanceNNMinimumOKeeffeNNMinimumVIRENNNearNeighborsNearNeighbors.extend_structure_moleculesNearNeighbors.get_all_nn_info()NearNeighbors.get_bonded_structure()NearNeighbors.get_cn()NearNeighbors.get_cn_dict()NearNeighbors.get_local_order_parameters()NearNeighbors.get_nn()NearNeighbors.get_nn_images()NearNeighbors.get_nn_info()NearNeighbors.get_nn_shell_info()NearNeighbors.get_weights_of_nn_sites()NearNeighbors.molecules_allowedNearNeighbors.structures_allowed
OpenBabelNNValenceIonicRadiusEvaluatorVoronoiNNget_neighbors_of_site_with_index()get_okeeffe_distance_prediction()get_okeeffe_params()gramschmidt()metal_edge_extender()site_is_of_motif_type()solid_angle()vol_tetra()
- pymatgen.analysis.molecule_matcher module
- pymatgen.analysis.molecule_structure_comparator module
- pymatgen.analysis.nmr module
ChemicalShieldingElectricFieldGradient
- pymatgen.analysis.path_finder module
- pymatgen.analysis.phase_diagram module
CompoundPhaseDiagramGrandPotPDEntryGrandPotentialPhaseDiagramPDEntryPDPlotterPatchedPhaseDiagramPatchedPhaseDiagram.all_entriesPatchedPhaseDiagram.min_entriesPatchedPhaseDiagram.el_refsPatchedPhaseDiagram.elementsPatchedPhaseDiagram.as_dict()PatchedPhaseDiagram.from_dict()PatchedPhaseDiagram.get_all_chempots()PatchedPhaseDiagram.get_chempot_range_map()PatchedPhaseDiagram.get_chempot_range_stability_phase()PatchedPhaseDiagram.get_composition_chempots()PatchedPhaseDiagram.get_critical_compositions()PatchedPhaseDiagram.get_decomposition()PatchedPhaseDiagram.get_element_profile()PatchedPhaseDiagram.get_equilibrium_reaction_energy()PatchedPhaseDiagram.get_pd_for_entry()PatchedPhaseDiagram.get_transition_chempots()PatchedPhaseDiagram.getmu_vertices_stability_phase()
PhaseDiagramPhaseDiagram.dimPhaseDiagram.elementsPhaseDiagram.el_refsPhaseDiagram.all_entriesPhaseDiagram.qhull_entriesPhaseDiagram.qhull_dataPhaseDiagram.facetsPhaseDiagram.simplicesPhaseDiagram.all_entries_hulldataPhaseDiagram.as_dict()PhaseDiagram.formation_energy_tolPhaseDiagram.from_dict()PhaseDiagram.get_all_chempots()PhaseDiagram.get_chempot_range_map()PhaseDiagram.get_chempot_range_stability_phase()PhaseDiagram.get_composition_chempots()PhaseDiagram.get_critical_compositions()PhaseDiagram.get_decomp_and_e_above_hull()PhaseDiagram.get_decomp_and_hull_energy_per_atom()PhaseDiagram.get_decomp_and_phase_separation_energy()PhaseDiagram.get_decomposition()PhaseDiagram.get_e_above_hull()PhaseDiagram.get_element_profile()PhaseDiagram.get_equilibrium_reaction_energy()PhaseDiagram.get_form_energy()PhaseDiagram.get_form_energy_per_atom()PhaseDiagram.get_hull_energy()PhaseDiagram.get_hull_energy_per_atom()PhaseDiagram.get_phase_separation_energy()PhaseDiagram.get_reference_energy_per_atom()PhaseDiagram.get_transition_chempots()PhaseDiagram.getmu_vertices_stability_phase()PhaseDiagram.numerical_tolPhaseDiagram.pd_coords()PhaseDiagram.stable_entriesPhaseDiagram.unstable_entries
PhaseDiagramErrorReactionDiagramTransformedPDEntryTransformedPDEntryErrorget_facets()order_phase_diagram()tet_coord()triangular_coord()uniquelines()
- pymatgen.analysis.piezo module
- pymatgen.analysis.piezo_sensitivity module
- pymatgen.analysis.pourbaix_diagram module
IonEntryMultiEntryPourbaixDiagramPourbaixDiagram.all_entriesPourbaixDiagram.as_dict()PourbaixDiagram.find_stable_entry()PourbaixDiagram.from_dict()PourbaixDiagram.get_decomposition_energy()PourbaixDiagram.get_hull_energy()PourbaixDiagram.get_pourbaix_domains()PourbaixDiagram.get_stable_entry()PourbaixDiagram.process_multientry()PourbaixDiagram.stable_entriesPourbaixDiagram.unprocessed_entriesPourbaixDiagram.unstable_entries
PourbaixEntryPourbaixEntry.as_dict()PourbaixEntry.compositionPourbaixEntry.conc_termPourbaixEntry.energyPourbaixEntry.energy_at_conditions()PourbaixEntry.energy_per_atomPourbaixEntry.from_dict()PourbaixEntry.get_element_fraction()PourbaixEntry.nH2OPourbaixEntry.nPhiPourbaixEntry.namePourbaixEntry.normalization_factorPourbaixEntry.normalized_energyPourbaixEntry.normalized_energy_at_conditions()PourbaixEntry.npHPourbaixEntry.num_atomsPourbaixEntry.to_pretty_string()
PourbaixPlottergenerate_entry_label()ion_or_solid_comp_object()
- pymatgen.analysis.prototypes module
- pymatgen.analysis.quasiharmonic module
QuasiharmonicDebyeApproxQuasiharmonicDebyeApprox.debye_integral()QuasiharmonicDebyeApprox.debye_temperature()QuasiharmonicDebyeApprox.get_summary_dict()QuasiharmonicDebyeApprox.gruneisen_parameter()QuasiharmonicDebyeApprox.optimize_gibbs_free_energy()QuasiharmonicDebyeApprox.optimizer()QuasiharmonicDebyeApprox.thermal_conductivity()QuasiharmonicDebyeApprox.vibrational_free_energy()QuasiharmonicDebyeApprox.vibrational_internal_energy()
- pymatgen.analysis.reaction_calculator module
BalancedReactionBalancedReaction.TOLERANCEBalancedReaction.all_compBalancedReaction.as_dict()BalancedReaction.as_entry()BalancedReaction.calculate_energy()BalancedReaction.coeffsBalancedReaction.elementsBalancedReaction.from_dict()BalancedReaction.from_string()BalancedReaction.get_coeff()BalancedReaction.get_el_amount()BalancedReaction.normalize_to()BalancedReaction.normalize_to_element()BalancedReaction.normalized_reprBalancedReaction.normalized_repr_and_factor()BalancedReaction.productsBalancedReaction.reactants
ComputedReactionReactionReactionError
- pymatgen.analysis.structure_analyzer module
- pymatgen.analysis.structure_matcher module
AbstractComparatorElementComparatorFrameworkComparatorOccupancyComparatorOrderDisorderElementComparatorSpeciesComparatorSpinComparatorStructureMatcherStructureMatcher.as_dict()StructureMatcher.fit()StructureMatcher.fit_anonymous()StructureMatcher.from_dict()StructureMatcher.get_all_anonymous_mappings()StructureMatcher.get_best_electronegativity_anonymous_mapping()StructureMatcher.get_mapping()StructureMatcher.get_rms_anonymous()StructureMatcher.get_rms_dist()StructureMatcher.get_s2_like_s1()StructureMatcher.get_supercell_matrix()StructureMatcher.get_transformation()StructureMatcher.group_structures()
- pymatgen.analysis.substrate_analyzer module
- pymatgen.analysis.surface_analysis module
NanoscaleStabilitySlabEntrySlabEntry.miller_indexSlabEntry.labelSlabEntry.adsorbatesSlabEntry.Nads_in_slabSlabEntry.Nsurfs_ads_in_slabSlabEntry.as_dict()SlabEntry.cleaned_up_slabSlabEntry.create_slab_labelSlabEntry.from_computed_structure_entry()SlabEntry.from_dict()SlabEntry.get_monolayerSlabEntry.get_unit_primitive_areaSlabEntry.gibbs_binding_energy()SlabEntry.surface_areaSlabEntry.surface_energy()
SurfaceEnergyPlotterSurfaceEnergyPlotter.all_slab_entriesSurfaceEnergyPlotter.ucell_entrySurfaceEnergyPlotter.ref_entriesSurfaceEnergyPlotter.color_dictSurfaceEnergyPlotter.BE_vs_clean_SE()SurfaceEnergyPlotter.area_frac_vs_chempot_plot()SurfaceEnergyPlotter.chempot_plot_addons()SurfaceEnergyPlotter.chempot_vs_gamma()SurfaceEnergyPlotter.chempot_vs_gamma_plot_one()SurfaceEnergyPlotter.color_palette_dict()SurfaceEnergyPlotter.get_stable_entry_at_u()SurfaceEnergyPlotter.get_surface_equilibrium()SurfaceEnergyPlotter.monolayer_vs_BE()SurfaceEnergyPlotter.set_all_variables()SurfaceEnergyPlotter.stable_u_range_dict()SurfaceEnergyPlotter.surface_chempot_range_map()SurfaceEnergyPlotter.wulff_from_chempot()
WorkFunctionAnalyzerWorkFunctionAnalyzer.efermiWorkFunctionAnalyzer.locpot_along_cWorkFunctionAnalyzer.vacuum_locpotWorkFunctionAnalyzer.work_functionWorkFunctionAnalyzer.slabWorkFunctionAnalyzer.along_cWorkFunctionAnalyzer.ave_locpotWorkFunctionAnalyzer.sorted_sitesWorkFunctionAnalyzer.ave_bulk_pWorkFunctionAnalyzer.from_files()WorkFunctionAnalyzer.get_labels()WorkFunctionAnalyzer.get_locpot_along_slab_plot()WorkFunctionAnalyzer.is_converged()
entry_dict_from_list()sub_chempots()
- pymatgen.analysis.thermochemistry module
- pymatgen.analysis.transition_state module
- pymatgen.analysis.wulff module
WulffFacetWulffShapeWulffShape.debugWulffShape.alphaWulffShape.transparencyWulffShape.color_setWulffShape.grid_offWulffShape.axis_offWulffShape.show_areaWulffShape.off_colorWulffShape.structureWulffShape.miller_listWulffShape.hkl_listWulffShape.e_surf_listWulffShape.latticeWulffShape.facetsWulffShape.dual_cv_simpWulffShape.wulff_pt_listWulffShape.wulff_cv_simpWulffShape.on_wulffWulffShape.color_areaWulffShape.miller_areaWulffShape.anisotropyWulffShape.area_fraction_dictWulffShape.effective_radiusWulffShape.get_line_in_facet()WulffShape.get_plot()WulffShape.get_plotly()WulffShape.miller_area_dictWulffShape.miller_energy_dictWulffShape.shape_factorWulffShape.show()WulffShape.surface_areaWulffShape.tot_corner_sitesWulffShape.tot_edgesWulffShape.total_surface_energyWulffShape.volumeWulffShape.weighted_surface_energy
get_tri_area()hkl_tuple_to_str()
- pymatgen.analysis.xps module