pymatgen.analysis namespace
Subpackages
- pymatgen.analysis.chemenv package
- Subpackages
- pymatgen.analysis.chemenv.connectivity package
- Subpackages
- Submodules
- pymatgen.analysis.chemenv.connectivity.connected_components module
ConnectedComponent
ConnectedComponent.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.graph
ConnectedComponent.is_0d
ConnectedComponent.is_1d
ConnectedComponent.is_2d
ConnectedComponent.is_3d
ConnectedComponent.is_periodic
ConnectedComponent.make_supergraph()
ConnectedComponent.periodicity
ConnectedComponent.periodicity_vectors
ConnectedComponent.show_graph()
draw_network()
make_supergraph()
- pymatgen.analysis.chemenv.connectivity.connectivity_finder module
- pymatgen.analysis.chemenv.connectivity.environment_nodes module
AbstractEnvironmentNode
AbstractEnvironmentNode.ATOM
AbstractEnvironmentNode.CE_NNBCES_NBCES_LIGANDS
AbstractEnvironmentNode.COORDINATION_ENVIRONMENT
AbstractEnvironmentNode.DEFAULT_EXTENSIONS
AbstractEnvironmentNode.LIGANDS_ARRANGEMENT
AbstractEnvironmentNode.NEIGHBORING_CES
AbstractEnvironmentNode.NEIGHBORING_COORDINATION_ENVIRONMENTS
AbstractEnvironmentNode.NEIGHBORS_LIGANDS_ARRANGEMENT
AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE
AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT
AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_CES
AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS
AbstractEnvironmentNode.atom_symbol
AbstractEnvironmentNode.ce
AbstractEnvironmentNode.ce_symbol
AbstractEnvironmentNode.coordination_environment
AbstractEnvironmentNode.everything_equal()
AbstractEnvironmentNode.isite
AbstractEnvironmentNode.mp_symbol
EnvironmentNode
get_environment_node()
- pymatgen.analysis.chemenv.connectivity.structure_connectivity module
StructureConnectivity
StructureConnectivity.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
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.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.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.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()
- 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
Plane
Plane.TEST_2D_POINTS
Plane.a
Plane.abcd
Plane.b
Plane.c
Plane.coefficients
Plane.crosses_origin
Plane.d
Plane.distance_to_origin
Plane.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
AdditionalConditions
AdditionalConditions.ALL
AdditionalConditions.CONDITION_DESCRIPTION
AdditionalConditions.NONE
AdditionalConditions.NO_AC
AdditionalConditions.NO_ADDITIONAL_CONDITION
AdditionalConditions.NO_E2SEB
AdditionalConditions.NO_ELEMENT_TO_SAME_ELEMENT_BONDS
AdditionalConditions.ONLY_ACB
AdditionalConditions.ONLY_ACB_AND_NO_E2SEB
AdditionalConditions.ONLY_ANION_CATION_BONDS
AdditionalConditions.ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS
AdditionalConditions.ONLY_E2OB
AdditionalConditions.ONLY_ELEMENT_TO_OXYGEN_BONDS
AdditionalConditions.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
AbstractDiffractionPatternCalculator
AbstractDiffractionPatternCalculator.SCALED_INTENSITY_TOL
AbstractDiffractionPatternCalculator.TWO_THETA_TOL
AbstractDiffractionPatternCalculator.get_pattern()
AbstractDiffractionPatternCalculator.get_plot()
AbstractDiffractionPatternCalculator.plot_structures()
AbstractDiffractionPatternCalculator.show_plot()
DiffractionPattern
get_unique_families()
- pymatgen.analysis.diffraction.neutron module
- pymatgen.analysis.diffraction.tem module
TEMCalculator
TEMCalculator.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
ComplianceTensor
ElasticTensor
ElasticTensor.cahill_thermalcond()
ElasticTensor.clarke_thermalcond()
ElasticTensor.compliance_tensor
ElasticTensor.debye_temperature()
ElasticTensor.directional_elastic_mod()
ElasticTensor.directional_poisson_ratio()
ElasticTensor.from_independent_strains()
ElasticTensor.from_pseudoinverse()
ElasticTensor.g_reuss
ElasticTensor.g_voigt
ElasticTensor.g_vrh
ElasticTensor.get_structure_property_dict()
ElasticTensor.green_kristoffel()
ElasticTensor.homogeneous_poisson
ElasticTensor.k_reuss
ElasticTensor.k_voigt
ElasticTensor.k_vrh
ElasticTensor.long_v()
ElasticTensor.property_dict
ElasticTensor.snyder_ac()
ElasticTensor.snyder_opt()
ElasticTensor.snyder_total()
ElasticTensor.trans_v()
ElasticTensor.universal_anisotropy
ElasticTensor.y_mod
ElasticTensorExpansion
ElasticTensorExpansion.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.order
ElasticTensorExpansion.thermal_expansion_coeff()
NthOrderElasticTensor
diff_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
EnergyTrend
Polarization
Polarization.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()
PolarizationLattice
calc_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
GrainBoundary
GrainBoundaryGenerator
GrainBoundaryGenerator.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
CollinearMagneticStructureAnalyzer
CollinearMagneticStructureAnalyzer.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_magnetic
CollinearMagneticStructureAnalyzer.magmoms
CollinearMagneticStructureAnalyzer.magnetic_species_and_magmoms
CollinearMagneticStructureAnalyzer.matches_ordering()
CollinearMagneticStructureAnalyzer.number_of_magnetic_sites
CollinearMagneticStructureAnalyzer.number_of_unique_magnetic_sites()
CollinearMagneticStructureAnalyzer.ordering
CollinearMagneticStructureAnalyzer.types_of_magnetic_specie
CollinearMagneticStructureAnalyzer.types_of_magnetic_species
MagneticDeformation
MagneticStructureEnumerator
Ordering
OverwriteMagmomMode
magnetic_deformation()
- pymatgen.analysis.magnetism.heisenberg module
- pymatgen.analysis.magnetism.jahnteller module
JahnTellerAnalyzer
JahnTellerAnalyzer.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
AdsorbateSiteFinder
AdsorbateSiteFinder.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_sites
AdsorbateSiteFinder.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
ChemicalPotentialDiagram
ChemicalPotentialDiagram.border_hyperplanes
ChemicalPotentialDiagram.chemical_system
ChemicalPotentialDiagram.domains
ChemicalPotentialDiagram.el_refs
ChemicalPotentialDiagram.entry_dict
ChemicalPotentialDiagram.get_plot()
ChemicalPotentialDiagram.hyperplane_entries
ChemicalPotentialDiagram.hyperplanes
ChemicalPotentialDiagram.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
EwaldMinimizer
EwaldMinimizer.ALGO_BEST_FIRST
EwaldMinimizer.ALGO_COMPLETE
EwaldMinimizer.ALGO_FAST
EwaldMinimizer.ALGO_TIME_LIMIT
EwaldMinimizer.add_m_list()
EwaldMinimizer.best_case()
EwaldMinimizer.best_m_list
EwaldMinimizer.get_next_index()
EwaldMinimizer.minimize_matrix()
EwaldMinimizer.minimized_sum
EwaldMinimizer.output_lists
EwaldSummation
EwaldSummation.CONV_FACT
EwaldSummation.as_dict()
EwaldSummation.compute_partial_energy()
EwaldSummation.compute_sub_structure()
EwaldSummation.eta
EwaldSummation.forces
EwaldSummation.from_dict()
EwaldSummation.get_site_energy()
EwaldSummation.point_energy
EwaldSummation.point_energy_matrix
EwaldSummation.real_space_energy
EwaldSummation.real_space_energy_matrix
EwaldSummation.reciprocal_space_energy
EwaldSummation.reciprocal_space_energy_matrix
EwaldSummation.total_energy
EwaldSummation.total_energy_matrix
compute_average_oxidation_state()
- pymatgen.analysis.excitation module
- pymatgen.analysis.fragmenter module
- pymatgen.analysis.functional_groups module
- pymatgen.analysis.graphs module
ConnectedSite
MolGraphSplitError
MoleculeGraph
MoleculeGraph.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_name
MoleculeGraph.edge_weight_unit
MoleculeGraph.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.name
MoleculeGraph.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()
StructureGraph
StructureGraph.add_edge()
StructureGraph.alter_edge()
StructureGraph.as_dict()
StructureGraph.break_edge()
StructureGraph.diff()
StructureGraph.draw_graph_to_file()
StructureGraph.edge_weight_name
StructureGraph.edge_weight_unit
StructureGraph.from_dict()
StructureGraph.get_connected_sites()
StructureGraph.get_coordination_of_site()
StructureGraph.get_subgraphs_as_molecules()
StructureGraph.insert_node()
StructureGraph.name
StructureGraph.remove_nodes()
StructureGraph.set_node_attributes()
StructureGraph.sort()
StructureGraph.substitute_group()
StructureGraph.types_and_weights_of_connections
StructureGraph.types_of_coordination_environments()
StructureGraph.weight_statistics
StructureGraph.with_edges()
StructureGraph.with_empty_graph()
StructureGraph.with_local_env_strategy()
- pymatgen.analysis.hhi module
- pymatgen.analysis.interface module
- pymatgen.analysis.interface_reactions module
GrandPotentialInterfacialReactivity
InterfacialReactivity
InterfacialReactivity.EV_TO_KJ_PER_MOL
InterfacialReactivity.get_chempot_correction()
InterfacialReactivity.get_critical_original_kink_ratio()
InterfacialReactivity.get_dataframe()
InterfacialReactivity.get_kinks()
InterfacialReactivity.labels
InterfacialReactivity.minimum
InterfacialReactivity.plot()
InterfacialReactivity.products
- pymatgen.analysis.local_env module
BrunnerNN_real
BrunnerNN_reciprocal
BrunnerNN_relative
CovalentBondNN
Critic2NN
CrystalNN
CutOffDictNN
EconNN
IsayevNN
JmolNN
LocalStructOrderParams
LocalStructOrderParams.compute_trigonometric_terms()
LocalStructOrderParams.get_order_parameters()
LocalStructOrderParams.get_parameters()
LocalStructOrderParams.get_q2()
LocalStructOrderParams.get_q4()
LocalStructOrderParams.get_q6()
LocalStructOrderParams.get_type()
LocalStructOrderParams.last_nneigh
LocalStructOrderParams.num_ops
MinimumDistanceNN
MinimumOKeeffeNN
MinimumVIRENN
NearNeighbors
NearNeighbors.extend_structure_molecules
NearNeighbors.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_allowed
NearNeighbors.structures_allowed
OpenBabelNN
ValenceIonicRadiusEvaluator
VoronoiNN
get_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
ChemicalShielding
ElectricFieldGradient
- pymatgen.analysis.path_finder module
- pymatgen.analysis.phase_diagram module
CompoundPhaseDiagram
GrandPotPDEntry
GrandPotentialPhaseDiagram
PDEntry
PDPlotter
PatchedPhaseDiagram
PatchedPhaseDiagram.all_entries
PatchedPhaseDiagram.min_entries
PatchedPhaseDiagram.el_refs
PatchedPhaseDiagram.elements
PatchedPhaseDiagram.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()
PhaseDiagram
PhaseDiagram.dim
PhaseDiagram.elements
PhaseDiagram.el_refs
PhaseDiagram.all_entries
PhaseDiagram.qhull_entries
PhaseDiagram.qhull_data
PhaseDiagram.facets
PhaseDiagram.simplices
PhaseDiagram.all_entries_hulldata
PhaseDiagram.as_dict()
PhaseDiagram.formation_energy_tol
PhaseDiagram.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_tol
PhaseDiagram.pd_coords()
PhaseDiagram.stable_entries
PhaseDiagram.unstable_entries
PhaseDiagramError
ReactionDiagram
TransformedPDEntry
TransformedPDEntryError
get_facets()
order_phase_diagram()
tet_coord()
triangular_coord()
uniquelines()
- pymatgen.analysis.piezo module
- pymatgen.analysis.piezo_sensitivity module
- pymatgen.analysis.pourbaix_diagram module
IonEntry
MultiEntry
PourbaixDiagram
PourbaixDiagram.all_entries
PourbaixDiagram.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_entries
PourbaixDiagram.unprocessed_entries
PourbaixDiagram.unstable_entries
PourbaixEntry
PourbaixEntry.as_dict()
PourbaixEntry.composition
PourbaixEntry.conc_term
PourbaixEntry.energy
PourbaixEntry.energy_at_conditions()
PourbaixEntry.energy_per_atom
PourbaixEntry.from_dict()
PourbaixEntry.get_element_fraction()
PourbaixEntry.nH2O
PourbaixEntry.nPhi
PourbaixEntry.name
PourbaixEntry.normalization_factor
PourbaixEntry.normalized_energy
PourbaixEntry.normalized_energy_at_conditions()
PourbaixEntry.npH
PourbaixEntry.num_atoms
PourbaixEntry.to_pretty_string()
PourbaixPlotter
generate_entry_label()
ion_or_solid_comp_object()
- pymatgen.analysis.prototypes module
- pymatgen.analysis.quasiharmonic module
QuasiharmonicDebyeApprox
QuasiharmonicDebyeApprox.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
BalancedReaction
BalancedReaction.TOLERANCE
BalancedReaction.all_comp
BalancedReaction.as_dict()
BalancedReaction.as_entry()
BalancedReaction.calculate_energy()
BalancedReaction.coeffs
BalancedReaction.elements
BalancedReaction.from_dict()
BalancedReaction.from_string()
BalancedReaction.get_coeff()
BalancedReaction.get_el_amount()
BalancedReaction.normalize_to()
BalancedReaction.normalize_to_element()
BalancedReaction.normalized_repr
BalancedReaction.normalized_repr_and_factor()
BalancedReaction.products
BalancedReaction.reactants
ComputedReaction
Reaction
ReactionError
- pymatgen.analysis.structure_analyzer module
- pymatgen.analysis.structure_matcher module
AbstractComparator
ElementComparator
FrameworkComparator
OccupancyComparator
OrderDisorderElementComparator
SpeciesComparator
SpinComparator
StructureMatcher
StructureMatcher.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
NanoscaleStability
SlabEntry
SlabEntry.miller_index
SlabEntry.label
SlabEntry.adsorbates
SlabEntry.Nads_in_slab
SlabEntry.Nsurfs_ads_in_slab
SlabEntry.as_dict()
SlabEntry.cleaned_up_slab
SlabEntry.create_slab_label
SlabEntry.from_computed_structure_entry()
SlabEntry.from_dict()
SlabEntry.get_monolayer
SlabEntry.get_unit_primitive_area
SlabEntry.gibbs_binding_energy()
SlabEntry.surface_area
SlabEntry.surface_energy()
SurfaceEnergyPlotter
SurfaceEnergyPlotter.all_slab_entries
SurfaceEnergyPlotter.ucell_entry
SurfaceEnergyPlotter.ref_entries
SurfaceEnergyPlotter.color_dict
SurfaceEnergyPlotter.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()
WorkFunctionAnalyzer
WorkFunctionAnalyzer.efermi
WorkFunctionAnalyzer.locpot_along_c
WorkFunctionAnalyzer.vacuum_locpot
WorkFunctionAnalyzer.work_function
WorkFunctionAnalyzer.slab
WorkFunctionAnalyzer.along_c
WorkFunctionAnalyzer.ave_locpot
WorkFunctionAnalyzer.sorted_sites
WorkFunctionAnalyzer.ave_bulk_p
WorkFunctionAnalyzer.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
WulffFacet
WulffShape
WulffShape.debug
WulffShape.alpha
WulffShape.transparency
WulffShape.color_set
WulffShape.grid_off
WulffShape.axis_off
WulffShape.show_area
WulffShape.off_color
WulffShape.structure
WulffShape.miller_list
WulffShape.hkl_list
WulffShape.e_surf_list
WulffShape.lattice
WulffShape.facets
WulffShape.dual_cv_simp
WulffShape.wulff_pt_list
WulffShape.wulff_cv_simp
WulffShape.on_wulff
WulffShape.color_area
WulffShape.miller_area
WulffShape.anisotropy
WulffShape.area_fraction_dict
WulffShape.effective_radius
WulffShape.get_line_in_facet()
WulffShape.get_plot()
WulffShape.get_plotly()
WulffShape.miller_area_dict
WulffShape.miller_energy_dict
WulffShape.shape_factor
WulffShape.show()
WulffShape.surface_area
WulffShape.tot_corner_sites
WulffShape.tot_edges
WulffShape.total_surface_energy
WulffShape.volume
WulffShape.weighted_surface_energy
get_tri_area()
hkl_tuple_to_str()
- pymatgen.analysis.xps module