pymatgen namespace
Subpackages
- pymatgen.alchemy package
- Submodules
- pymatgen.alchemy.filters module
- pymatgen.alchemy.materials module
TransformedStructureTransformedStructure.append_filter()TransformedStructure.append_transformation()TransformedStructure.as_dict()TransformedStructure.extend_transformations()TransformedStructure.from_cif_str()TransformedStructure.from_dict()TransformedStructure.from_poscar_str()TransformedStructure.from_snl()TransformedStructure.get_vasp_input()TransformedStructure.redo_next_change()TransformedStructure.set_parameter()TransformedStructure.structuresTransformedStructure.to_snl()TransformedStructure.undo_last_change()TransformedStructure.was_modifiedTransformedStructure.write_vasp_input()
- pymatgen.alchemy.transmuters module
CifTransmuterPoscarTransmuterStandardTransmuterStandardTransmuter.transformed_structuresStandardTransmuter.add_tags()StandardTransmuter.append_transformation()StandardTransmuter.append_transformed_structures()StandardTransmuter.apply_filter()StandardTransmuter.extend_transformations()StandardTransmuter.from_structures()StandardTransmuter.redo_next_change()StandardTransmuter.set_parameter()StandardTransmuter.undo_last_change()StandardTransmuter.write_vasp_input()
batch_write_vasp_input()
- pymatgen.analysis namespace
- Subpackages
- pymatgen.analysis.chemenv package
- Subpackages
- pymatgen.analysis.chemenv.connectivity package
- pymatgen.analysis.chemenv.coordination_environments package
- Subpackages
- Submodules
- pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies module
AbstractChemenvStrategyAdditionalConditionIntAngleCutoffFloatAngleNbSetWeightAnglePlateauNbSetWeightCNBiasNbSetWeightCSMFloatDeltaCSMNbSetWeightDeltaDistanceNbSetWeightDistanceAngleAreaNbSetWeightDistanceCutoffFloatDistanceNbSetWeightDistancePlateauNbSetWeightMultiWeightsChemenvStrategyNbSetWeightNormalizedAngleDistanceNbSetWeightSelfCSMNbSetWeightSimpleAbundanceChemenvStrategySimplestChemenvStrategyStrategyOptionTargetedPenaltiedAbundanceChemenvStrategyWeightedNbSetChemenvStrategyget_effective_csm()set_info()
- pymatgen.analysis.chemenv.coordination_environments.coordination_geometries module
- pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module
- pymatgen.analysis.chemenv.coordination_environments.structure_environments module
- pymatgen.analysis.chemenv.coordination_environments.voronoi module
- pymatgen.analysis.chemenv.utils package
- Submodules
- pymatgen.analysis.chemenv.utils.chemenv_config module
- pymatgen.analysis.chemenv.utils.chemenv_errors module
- pymatgen.analysis.chemenv.utils.coordination_geometry_utils module
Planeanticlockwise_sort()anticlockwise_sort_indices()changebasis()collinear()diamond_functions()function_comparison()get_lower_and_upper_f()is_anion_cation_bond()matrixTimesVector()quarter_ellipsis_functions()rectangle_surface_intersection()rotateCoords()rotateCoordsOpt()separation_in_list()solid_angle()sort_separation()sort_separation_tuple()spline_functions()vectorsToMatrix()
- pymatgen.analysis.chemenv.utils.defs_utils module
- 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
- Subpackages
- pymatgen.analysis.diffraction package
- 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.elasticity package
- Submodules
- pymatgen.analysis.elasticity.elastic module
ComplianceTensorElasticTensorElasticTensor.agne_diffusive_thermalcond()ElasticTensor.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_if_unphysical()subs()
- pymatgen.analysis.elasticity.strain module
- pymatgen.analysis.elasticity.stress module
- pymatgen.analysis.ferroelectricity package
- 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()
calc_ionic()get_nearest_site()get_total_ionic_dipole()zval_dict_from_potcar()
- pymatgen.analysis.gb package
- pymatgen.analysis.interfaces package
- Submodules
- pymatgen.analysis.interfaces.coherent_interfaces module
- pymatgen.analysis.interfaces.substrate_analyzer module
- pymatgen.analysis.interfaces.zsl module
- pymatgen.analysis.magnetism package
- 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
HeisenbergMapperHeisenbergMapper.strategyHeisenbergMapper.sgraphsHeisenbergMapper.unique_site_idsHeisenbergMapper.wyckoff_idsHeisenbergMapper.nn_interactionsHeisenbergMapper.distsHeisenbergMapper.ex_matHeisenbergMapper.ex_paramsHeisenbergMapper.estimate_exchange()HeisenbergMapper.get_exchange()HeisenbergMapper.get_heisenberg_model()HeisenbergMapper.get_interaction_graph()HeisenbergMapper.get_low_energy_orderings()HeisenbergMapper.get_mft_temperature()
HeisenbergModelHeisenbergScreener
- 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.solar package
- pymatgen.analysis.structure_prediction package
- Submodules
- pymatgen.analysis.structure_prediction.dopant_predictor module
- pymatgen.analysis.structure_prediction.substitution_probability module
- pymatgen.analysis.structure_prediction.substitutor module
- pymatgen.analysis.structure_prediction.volume_predictor module
- pymatgen.analysis.topological package
- pymatgen.analysis.xas package
- pymatgen.analysis.chemenv 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.from_edges()MoleculeGraph.from_empty_graph()MoleculeGraph.from_local_env_strategy()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.from_edges()StructureGraph.from_empty_graph()StructureGraph.from_local_env_strategy()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_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
BrunnerNNRealBrunnerNNReciprocalBrunnerNNRelativeBrunnerNN_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()oxygen_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.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_decomp_and_e_above_hull()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()PatchedPhaseDiagram.remove_redundant_spaces()
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_plot()PhaseDiagram.get_reference_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.elementsPourbaixEntry.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()
QuasiharmonicDebyeApprox
- pymatgen.analysis.quasirrho module
- pymatgen.analysis.reaction_calculator module
BalancedReactionBalancedReaction.TOLERANCEBalancedReaction.all_compBalancedReaction.as_dict()BalancedReaction.as_entry()BalancedReaction.calculate_energy()BalancedReaction.coeffsBalancedReaction.elementsBalancedReaction.from_dict()BalancedReaction.from_str()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
AbstractComparatorElementComparatorFrameworkComparatorOccupancyComparatorOrderDisorderElementComparatorSiteOrderedIStructureSpeciesComparatorSpinComparatorStructureMatcherStructureMatcher.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.surface_analysis module
NanoscaleStabilitySlabEntrySlabEntry.miller_indexSlabEntry.labelSlabEntry.adsorbatesSlabEntry.clean_entrySlabEntry.ads_entries_dictSlabEntry.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.color_dictSurfaceEnergyPlotter.ucell_entrySurfaceEnergyPlotter.ref_entriesSurfaceEnergyPlotter.facet_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.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
- Subpackages
- pymatgen.apps package
- Subpackages
- pymatgen.apps.battery package
- Submodules
- pymatgen.apps.battery.analyzer module
- pymatgen.apps.battery.battery_abc module
AbstractElectrodeAbstractElectrode.voltage_pairsAbstractElectrode.working_ionAbstractElectrode.working_ion_entryAbstractElectrode.framework_formulaAbstractElectrode.frameworkAbstractElectrode.framework_formulaAbstractElectrode.get_average_voltage()AbstractElectrode.get_capacity_grav()AbstractElectrode.get_capacity_vol()AbstractElectrode.get_energy_density()AbstractElectrode.get_specific_energy()AbstractElectrode.get_sub_electrodes()AbstractElectrode.get_summary_dict()AbstractElectrode.max_delta_volumeAbstractElectrode.max_voltageAbstractElectrode.max_voltage_stepAbstractElectrode.min_voltageAbstractElectrode.normalization_massAbstractElectrode.normalization_volumeAbstractElectrode.num_stepsAbstractElectrode.voltage_pairsAbstractElectrode.working_ionAbstractElectrode.working_ion_entryAbstractElectrode.x_chargeAbstractElectrode.x_discharge
AbstractVoltagePairAbstractVoltagePair.voltageAbstractVoltagePair.mAhAbstractVoltagePair.mass_chargeAbstractVoltagePair.mass_dischargeAbstractVoltagePair.vol_chargeAbstractVoltagePair.vol_dischargeAbstractVoltagePair.frac_chargeAbstractVoltagePair.frac_dischargeAbstractVoltagePair.working_ion_entryAbstractVoltagePair.framework_formulaAbstractVoltagePair.frac_chargeAbstractVoltagePair.frac_dischargeAbstractVoltagePair.frameworkAbstractVoltagePair.framework_formulaAbstractVoltagePair.mAhAbstractVoltagePair.mass_chargeAbstractVoltagePair.mass_dischargeAbstractVoltagePair.vol_chargeAbstractVoltagePair.vol_dischargeAbstractVoltagePair.voltageAbstractVoltagePair.working_ionAbstractVoltagePair.working_ion_entryAbstractVoltagePair.x_chargeAbstractVoltagePair.x_discharge
- pymatgen.apps.battery.conversion_battery module
ConversionElectrodeConversionVoltagePairConversionVoltagePair.rxnConversionVoltagePair.voltageConversionVoltagePair.mAhConversionVoltagePair.vol_chargeConversionVoltagePair.vol_dischargeConversionVoltagePair.mass_chargeConversionVoltagePair.mass_dischargeConversionVoltagePair.frac_chargeConversionVoltagePair.frac_dischargeConversionVoltagePair.entries_chargeConversionVoltagePair.entries_dischargeConversionVoltagePair.working_ion_entryConversionVoltagePair.entries_chargeConversionVoltagePair.entries_dischargeConversionVoltagePair.from_steps()ConversionVoltagePair.rxn
- pymatgen.apps.battery.insertion_battery module
InsertionElectrodeInsertionElectrode.as_dict_legacy()InsertionElectrode.from_dict_legacy()InsertionElectrode.from_entries()InsertionElectrode.fully_charged_entryInsertionElectrode.fully_discharged_entryInsertionElectrode.get_all_entries()InsertionElectrode.get_max_instability()InsertionElectrode.get_max_muO2()InsertionElectrode.get_min_instability()InsertionElectrode.get_min_muO2()InsertionElectrode.get_stable_entries()InsertionElectrode.get_sub_electrodes()InsertionElectrode.get_summary_dict()InsertionElectrode.get_unstable_entries()InsertionElectrode.stable_entriesInsertionElectrode.unstable_entries
InsertionVoltagePair
- pymatgen.apps.battery.plotter module
- pymatgen.apps.borg package
- pymatgen.apps.battery package
- Subpackages
- pymatgen.cli package
- Submodules
- pymatgen.cli.feff_plot_cross_section module
- pymatgen.cli.feff_plot_dos module
- pymatgen.cli.get_environment module
- pymatgen.cli.pmg module
- pymatgen.cli.pmg_analyze module
- pymatgen.cli.pmg_config module
- pymatgen.cli.pmg_plot module
- pymatgen.cli.pmg_potcar module
- pymatgen.cli.pmg_structure module
- pymatgen.command_line package
- Submodules
- pymatgen.command_line.bader_caller module
BaderAnalysisBaderAnalysis.dataBaderAnalysis.vacuum_volumeBaderAnalysis.vacuum_chargeBaderAnalysis.nelectronsBaderAnalysis.chgcarBaderAnalysis.atomic_densitiesBaderAnalysis.from_path()BaderAnalysis.get_charge()BaderAnalysis.get_charge_decorated_structure()BaderAnalysis.get_charge_transfer()BaderAnalysis.get_decorated_structure()BaderAnalysis.get_oxidation_state_decorated_structure()BaderAnalysis.get_partial_charge()BaderAnalysis.summary
bader_analysis_from_objects()bader_analysis_from_path()
- pymatgen.command_line.chargemol_caller module
- pymatgen.command_line.critic2_caller module
- pymatgen.command_line.enumlib_caller module
- pymatgen.command_line.gulp_caller module
- pymatgen.command_line.mcsqs_caller module
- pymatgen.command_line.vampire_caller module
- pymatgen.core package
- Submodules
- pymatgen.core.bonds module
- pymatgen.core.composition module
ChemicalPotentialCompositionComposition.add_charges_from_oxi_state_guesses()Composition.almost_equals()Composition.alphabetical_formulaComposition.amount_toleranceComposition.anonymized_formulaComposition.as_dict()Composition.average_electronegComposition.chargeComposition.charge_balancedComposition.charge_balanced_toleranceComposition.chemical_systemComposition.chemical_system_setComposition.contains_element_type()Composition.copy()Composition.element_compositionComposition.elementsComposition.formulaComposition.fractional_compositionComposition.from_dict()Composition.from_weight_dict()Composition.get_atomic_fraction()Composition.get_el_amt_dict()Composition.get_integer_formula_and_factor()Composition.get_reduced_composition_and_factor()Composition.get_reduced_formula_and_factor()Composition.get_wt_fraction()Composition.hill_formulaComposition.is_elementComposition.iupac_formulaComposition.num_atomsComposition.oxi_probComposition.oxi_state_guesses()Composition.ranked_compositions_from_indeterminate_formula()Composition.reduced_compositionComposition.reduced_formulaComposition.remove_charges()Composition.replace()Composition.special_formulasComposition.to_data_dictComposition.to_pretty_string()Composition.to_reduced_dictComposition.to_weight_dictComposition.total_electronsComposition.validComposition.weight
CompositionErrorreduce_formula()
- pymatgen.core.interface 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()
InterfaceInterface.as_dict()Interface.copy()Interface.filmInterface.film_indicesInterface.film_layersInterface.film_sitesInterface.film_terminationInterface.from_dict()Interface.from_slabs()Interface.gapInterface.get_shifts_based_on_adsorbate_sites()Interface.get_sorted_structure()Interface.in_plane_offsetInterface.substrateInterface.substrate_indicesInterface.substrate_layersInterface.substrate_sitesInterface.substrate_terminationInterface.vacuum_over_film
count_layers()fix_pbc()label_termination()symm_group_cubic()
- pymatgen.core.ion module
- pymatgen.core.lattice module
LatticeLattice.aLattice.abcLattice.alphaLattice.anglesLattice.as_dict()Lattice.bLattice.betaLattice.cLattice.copy()Lattice.cubic()Lattice.d_hkl()Lattice.dot()Lattice.find_all_mappings()Lattice.find_mapping()Lattice.from_dict()Lattice.from_parameters()Lattice.gammaLattice.get_all_distances()Lattice.get_brillouin_zone()Lattice.get_cartesian_coords()Lattice.get_distance_and_image()Lattice.get_frac_coords_from_lll()Lattice.get_fractional_coords()Lattice.get_lll_frac_coords()Lattice.get_lll_reduced_lattice()Lattice.get_miller_index_from_coords()Lattice.get_niggli_reduced_lattice()Lattice.get_points_in_sphere()Lattice.get_points_in_sphere_old()Lattice.get_points_in_sphere_py()Lattice.get_recp_symmetry_operation()Lattice.get_vector_along_lattice_directions()Lattice.get_wigner_seitz_cell()Lattice.hexagonal()Lattice.inv_matrixLattice.is_3d_periodicLattice.is_hexagonal()Lattice.is_orthogonalLattice.lengthsLattice.lll_inverseLattice.lll_mappingLattice.lll_matrixLattice.matrixLattice.metric_tensorLattice.monoclinic()Lattice.norm()Lattice.orthorhombic()Lattice.parametersLattice.params_dictLattice.pbcLattice.reciprocal_latticeLattice.reciprocal_lattice_crystallographicLattice.rhombohedral()Lattice.scale()Lattice.selling_dist()Lattice.selling_vectorLattice.tetragonal()Lattice.volume
find_neighbors()get_integer_index()get_points_in_spheres()
- pymatgen.core.libxcfunc module
LibxcFuncLibxcFunc.GGA_C_AM05LibxcFunc.GGA_C_APBELibxcFunc.GGA_C_BGCPLibxcFunc.GGA_C_FT97LibxcFunc.GGA_C_GAMLibxcFunc.GGA_C_HCTH_ALibxcFunc.GGA_C_LMLibxcFunc.GGA_C_LYPLibxcFunc.GGA_C_N12LibxcFunc.GGA_C_N12_SXLibxcFunc.GGA_C_OPTCLibxcFunc.GGA_C_OP_B88LibxcFunc.GGA_C_OP_G96LibxcFunc.GGA_C_OP_PBELibxcFunc.GGA_C_OP_PW91LibxcFunc.GGA_C_OP_XALPHALibxcFunc.GGA_C_P86LibxcFunc.GGA_C_PBELibxcFunc.GGA_C_PBEFELibxcFunc.GGA_C_PBEINTLibxcFunc.GGA_C_PBELOCLibxcFunc.GGA_C_PBE_JRGXLibxcFunc.GGA_C_PBE_SOLLibxcFunc.GGA_C_PW91LibxcFunc.GGA_C_Q2DLibxcFunc.GGA_C_REGTPSSLibxcFunc.GGA_C_REVTCALibxcFunc.GGA_C_RGE2LibxcFunc.GGA_C_SOGGA11LibxcFunc.GGA_C_SOGGA11_XLibxcFunc.GGA_C_SPBELibxcFunc.GGA_C_TCALibxcFunc.GGA_C_WILibxcFunc.GGA_C_WI0LibxcFunc.GGA_C_WLLibxcFunc.GGA_C_XPBELibxcFunc.GGA_C_ZPBEINTLibxcFunc.GGA_C_ZPBESOLLibxcFunc.GGA_K_ABSP1LibxcFunc.GGA_K_ABSP2LibxcFunc.GGA_K_APBELibxcFunc.GGA_K_APBEINTLibxcFunc.GGA_K_BALTINLibxcFunc.GGA_K_DKLibxcFunc.GGA_K_ERNZERHOFLibxcFunc.GGA_K_FR_B88LibxcFunc.GGA_K_FR_PW86LibxcFunc.GGA_K_GE2LibxcFunc.GGA_K_GOLDENLibxcFunc.GGA_K_GP85LibxcFunc.GGA_K_GRLibxcFunc.GGA_K_LC94LibxcFunc.GGA_K_LIEBLibxcFunc.GGA_K_LLPLibxcFunc.GGA_K_LUDENALibxcFunc.GGA_K_MEYERLibxcFunc.GGA_K_OL1LibxcFunc.GGA_K_OL2LibxcFunc.GGA_K_PEARSONLibxcFunc.GGA_K_PERDEWLibxcFunc.GGA_K_REVAPBELibxcFunc.GGA_K_REVAPBEINTLibxcFunc.GGA_K_TFVWLibxcFunc.GGA_K_THAKKARLibxcFunc.GGA_K_TW1LibxcFunc.GGA_K_TW2LibxcFunc.GGA_K_TW3LibxcFunc.GGA_K_TW4LibxcFunc.GGA_K_VJKSLibxcFunc.GGA_K_VSKLibxcFunc.GGA_K_VWLibxcFunc.GGA_K_YT65LibxcFunc.GGA_XC_B97_DLibxcFunc.GGA_XC_B97_GGA1LibxcFunc.GGA_XC_EDF1LibxcFunc.GGA_XC_HCTH_120LibxcFunc.GGA_XC_HCTH_147LibxcFunc.GGA_XC_HCTH_407LibxcFunc.GGA_XC_HCTH_407PLibxcFunc.GGA_XC_HCTH_93LibxcFunc.GGA_XC_HCTH_P14LibxcFunc.GGA_XC_HCTH_P76LibxcFunc.GGA_XC_KT2LibxcFunc.GGA_XC_MOHLYPLibxcFunc.GGA_XC_MOHLYP2LibxcFunc.GGA_XC_MPWLYP1WLibxcFunc.GGA_XC_OBLYP_DLibxcFunc.GGA_XC_OPBE_DLibxcFunc.GGA_XC_OPWLYP_DLibxcFunc.GGA_XC_PBE1WLibxcFunc.GGA_XC_PBELYP1WLibxcFunc.GGA_XC_TH1LibxcFunc.GGA_XC_TH2LibxcFunc.GGA_XC_TH3LibxcFunc.GGA_XC_TH4LibxcFunc.GGA_XC_TH_FCLibxcFunc.GGA_XC_TH_FCFOLibxcFunc.GGA_XC_TH_FCOLibxcFunc.GGA_XC_TH_FLLibxcFunc.GGA_XC_VV10LibxcFunc.GGA_XC_XLYPLibxcFunc.GGA_X_2D_B86LibxcFunc.GGA_X_2D_B86_MGCLibxcFunc.GGA_X_2D_B88LibxcFunc.GGA_X_2D_PBELibxcFunc.GGA_X_AIRYLibxcFunc.GGA_X_AK13LibxcFunc.GGA_X_AM05LibxcFunc.GGA_X_APBELibxcFunc.GGA_X_B86LibxcFunc.GGA_X_B86_MGCLibxcFunc.GGA_X_B86_RLibxcFunc.GGA_X_B88LibxcFunc.GGA_X_BAYESIANLibxcFunc.GGA_X_BGCPLibxcFunc.GGA_X_BPCCACLibxcFunc.GGA_X_C09XLibxcFunc.GGA_X_CAPLibxcFunc.GGA_X_DK87_R1LibxcFunc.GGA_X_DK87_R2LibxcFunc.GGA_X_EV93LibxcFunc.GGA_X_FT97_ALibxcFunc.GGA_X_FT97_BLibxcFunc.GGA_X_G96LibxcFunc.GGA_X_GAMLibxcFunc.GGA_X_HCTH_ALibxcFunc.GGA_X_HERMANLibxcFunc.GGA_X_HJS_B88LibxcFunc.GGA_X_HJS_B88_V2LibxcFunc.GGA_X_HJS_B97XLibxcFunc.GGA_X_HJS_PBELibxcFunc.GGA_X_HJS_PBE_SOLLibxcFunc.GGA_X_HTBSLibxcFunc.GGA_X_ITYHLibxcFunc.GGA_X_KT1LibxcFunc.GGA_X_LAGLibxcFunc.GGA_X_LAMBDA_CH_NLibxcFunc.GGA_X_LAMBDA_LO_NLibxcFunc.GGA_X_LAMBDA_OC2_NLibxcFunc.GGA_X_LBLibxcFunc.GGA_X_LBMLibxcFunc.GGA_X_LG93LibxcFunc.GGA_X_LV_RPW86LibxcFunc.GGA_X_MB88LibxcFunc.GGA_X_MPBELibxcFunc.GGA_X_MPW91LibxcFunc.GGA_X_N12LibxcFunc.GGA_X_OL2LibxcFunc.GGA_X_OPTB88_VDWLibxcFunc.GGA_X_OPTPBE_VDWLibxcFunc.GGA_X_OPTXLibxcFunc.GGA_X_PBELibxcFunc.GGA_X_PBEALibxcFunc.GGA_X_PBEFELibxcFunc.GGA_X_PBEINTLibxcFunc.GGA_X_PBEK1_VDWLibxcFunc.GGA_X_PBE_JSJRLibxcFunc.GGA_X_PBE_MOLLibxcFunc.GGA_X_PBE_RLibxcFunc.GGA_X_PBE_SOLLibxcFunc.GGA_X_PBE_TCALibxcFunc.GGA_X_PW86LibxcFunc.GGA_X_PW91LibxcFunc.GGA_X_Q2DLibxcFunc.GGA_X_RGE2LibxcFunc.GGA_X_RPBELibxcFunc.GGA_X_RPW86LibxcFunc.GGA_X_SFATLibxcFunc.GGA_X_SOGGALibxcFunc.GGA_X_SOGGA11LibxcFunc.GGA_X_SSBLibxcFunc.GGA_X_SSB_DLibxcFunc.GGA_X_SSB_SWLibxcFunc.GGA_X_VMT84_GELibxcFunc.GGA_X_VMT84_PBELibxcFunc.GGA_X_VMT_GELibxcFunc.GGA_X_VMT_PBELibxcFunc.GGA_X_WCLibxcFunc.GGA_X_WPBEHLibxcFunc.GGA_X_XPBELibxcFunc.HYB_GGA_XC_B1LYPLibxcFunc.HYB_GGA_XC_B1PW91LibxcFunc.HYB_GGA_XC_B1WCLibxcFunc.HYB_GGA_XC_B3LYPLibxcFunc.HYB_GGA_XC_B3LYP5LibxcFunc.HYB_GGA_XC_B3LYPsLibxcFunc.HYB_GGA_XC_B3P86LibxcFunc.HYB_GGA_XC_B3PW91LibxcFunc.HYB_GGA_XC_B97LibxcFunc.HYB_GGA_XC_B97_1LibxcFunc.HYB_GGA_XC_B97_1pLibxcFunc.HYB_GGA_XC_B97_2LibxcFunc.HYB_GGA_XC_B97_3LibxcFunc.HYB_GGA_XC_B97_KLibxcFunc.HYB_GGA_XC_BHANDHLibxcFunc.HYB_GGA_XC_BHANDHLYPLibxcFunc.HYB_GGA_XC_CAMY_B3LYPLibxcFunc.HYB_GGA_XC_CAMY_BLYPLibxcFunc.HYB_GGA_XC_CAM_B3LYPLibxcFunc.HYB_GGA_XC_CAP0LibxcFunc.HYB_GGA_XC_EDF2LibxcFunc.HYB_GGA_XC_HJS_B88LibxcFunc.HYB_GGA_XC_HJS_B97XLibxcFunc.HYB_GGA_XC_HJS_PBELibxcFunc.HYB_GGA_XC_HJS_PBE_SOLLibxcFunc.HYB_GGA_XC_HPBEINTLibxcFunc.HYB_GGA_XC_HSE03LibxcFunc.HYB_GGA_XC_HSE06LibxcFunc.HYB_GGA_XC_LCY_BLYPLibxcFunc.HYB_GGA_XC_LCY_PBELibxcFunc.HYB_GGA_XC_LC_VV10LibxcFunc.HYB_GGA_XC_LRC_WPBELibxcFunc.HYB_GGA_XC_LRC_WPBEHLibxcFunc.HYB_GGA_XC_MB3LYP_RC04LibxcFunc.HYB_GGA_XC_MPW3LYPLibxcFunc.HYB_GGA_XC_MPW3PWLibxcFunc.HYB_GGA_XC_MPWLYP1MLibxcFunc.HYB_GGA_XC_O3LYPLibxcFunc.HYB_GGA_XC_PBE0_13LibxcFunc.HYB_GGA_XC_PBEHLibxcFunc.HYB_GGA_XC_REVB3LYPLibxcFunc.HYB_GGA_XC_SB98_1aLibxcFunc.HYB_GGA_XC_SB98_1bLibxcFunc.HYB_GGA_XC_SB98_1cLibxcFunc.HYB_GGA_XC_SB98_2aLibxcFunc.HYB_GGA_XC_SB98_2bLibxcFunc.HYB_GGA_XC_SB98_2cLibxcFunc.HYB_GGA_XC_TUNED_CAM_B3LYPLibxcFunc.HYB_GGA_XC_WB97LibxcFunc.HYB_GGA_XC_WB97XLibxcFunc.HYB_GGA_XC_WB97X_DLibxcFunc.HYB_GGA_XC_WB97X_VLibxcFunc.HYB_GGA_XC_X3LYPLibxcFunc.HYB_GGA_XC_mPW1KLibxcFunc.HYB_GGA_XC_mPW1PWLibxcFunc.HYB_GGA_X_N12_SXLibxcFunc.HYB_GGA_X_SOGGA11_XLibxcFunc.HYB_MGGA_XC_B86B95LibxcFunc.HYB_MGGA_XC_B88B95LibxcFunc.HYB_MGGA_XC_BB1KLibxcFunc.HYB_MGGA_XC_M05LibxcFunc.HYB_MGGA_XC_M05_2XLibxcFunc.HYB_MGGA_XC_M06LibxcFunc.HYB_MGGA_XC_M06_2XLibxcFunc.HYB_MGGA_XC_M06_HFLibxcFunc.HYB_MGGA_XC_M08_HXLibxcFunc.HYB_MGGA_XC_M08_SOLibxcFunc.HYB_MGGA_XC_M11LibxcFunc.HYB_MGGA_XC_MPW1B95LibxcFunc.HYB_MGGA_XC_MPWB1KLibxcFunc.HYB_MGGA_XC_PW6B95LibxcFunc.HYB_MGGA_XC_PW86B95LibxcFunc.HYB_MGGA_XC_PWB6KLibxcFunc.HYB_MGGA_XC_REVTPSSHLibxcFunc.HYB_MGGA_XC_TPSSHLibxcFunc.HYB_MGGA_XC_WB97M_VLibxcFunc.HYB_MGGA_XC_X1B95LibxcFunc.HYB_MGGA_XC_XB1KLibxcFunc.HYB_MGGA_X_DLDFLibxcFunc.HYB_MGGA_X_MN12_SXLibxcFunc.HYB_MGGA_X_MN15LibxcFunc.HYB_MGGA_X_MS2HLibxcFunc.HYB_MGGA_X_MVSHLibxcFunc.HYB_MGGA_X_SCAN0LibxcFunc.LDA_C_1D_CSCLibxcFunc.LDA_C_1D_LOOSLibxcFunc.LDA_C_2D_AMGBLibxcFunc.LDA_C_2D_PRMLibxcFunc.LDA_C_GLLibxcFunc.LDA_C_GOMBASLibxcFunc.LDA_C_HLLibxcFunc.LDA_C_ML1LibxcFunc.LDA_C_ML2LibxcFunc.LDA_C_OB_PWLibxcFunc.LDA_C_OB_PZLibxcFunc.LDA_C_PWLibxcFunc.LDA_C_PW_MODLibxcFunc.LDA_C_PW_RPALibxcFunc.LDA_C_PZLibxcFunc.LDA_C_PZ_MODLibxcFunc.LDA_C_RC04LibxcFunc.LDA_C_RPALibxcFunc.LDA_C_VWNLibxcFunc.LDA_C_VWN_1LibxcFunc.LDA_C_VWN_2LibxcFunc.LDA_C_VWN_3LibxcFunc.LDA_C_VWN_4LibxcFunc.LDA_C_VWN_RPALibxcFunc.LDA_C_WIGNERLibxcFunc.LDA_C_XALPHALibxcFunc.LDA_C_vBHLibxcFunc.LDA_K_LPLibxcFunc.LDA_K_TFLibxcFunc.LDA_XLibxcFunc.LDA_XC_KSDTLibxcFunc.LDA_XC_TETER93LibxcFunc.LDA_XC_ZLPLibxcFunc.LDA_X_1DLibxcFunc.LDA_X_2DLibxcFunc.MGGA_C_BC95LibxcFunc.MGGA_C_CC06LibxcFunc.MGGA_C_CSLibxcFunc.MGGA_C_DLDFLibxcFunc.MGGA_C_M05LibxcFunc.MGGA_C_M05_2XLibxcFunc.MGGA_C_M06LibxcFunc.MGGA_C_M06_2XLibxcFunc.MGGA_C_M06_HFLibxcFunc.MGGA_C_M06_LLibxcFunc.MGGA_C_M08_HXLibxcFunc.MGGA_C_M08_SOLibxcFunc.MGGA_C_M11LibxcFunc.MGGA_C_M11_LLibxcFunc.MGGA_C_MN12_LLibxcFunc.MGGA_C_MN12_SXLibxcFunc.MGGA_C_MN15LibxcFunc.MGGA_C_MN15_LLibxcFunc.MGGA_C_PKZBLibxcFunc.MGGA_C_REVTPSSLibxcFunc.MGGA_C_SCANLibxcFunc.MGGA_C_TPSSLibxcFunc.MGGA_C_TPSSLOCLibxcFunc.MGGA_C_VSXCLibxcFunc.MGGA_XC_B97M_VLibxcFunc.MGGA_XC_OTPSS_DLibxcFunc.MGGA_XC_TPSSLYP1WLibxcFunc.MGGA_XC_ZLPLibxcFunc.MGGA_X_2D_PRHG07LibxcFunc.MGGA_X_2D_PRHG07_PRP10LibxcFunc.MGGA_X_BJ06LibxcFunc.MGGA_X_BLOCLibxcFunc.MGGA_X_BR89LibxcFunc.MGGA_X_GVT4LibxcFunc.MGGA_X_LTALibxcFunc.MGGA_X_M05LibxcFunc.MGGA_X_M05_2XLibxcFunc.MGGA_X_M06LibxcFunc.MGGA_X_M06_2XLibxcFunc.MGGA_X_M06_HFLibxcFunc.MGGA_X_M06_LLibxcFunc.MGGA_X_M08_HXLibxcFunc.MGGA_X_M08_SOLibxcFunc.MGGA_X_M11LibxcFunc.MGGA_X_M11_LLibxcFunc.MGGA_X_MBEEFLibxcFunc.MGGA_X_MBEEFVDWLibxcFunc.MGGA_X_MK00LibxcFunc.MGGA_X_MK00BLibxcFunc.MGGA_X_MN12_LLibxcFunc.MGGA_X_MN15_LLibxcFunc.MGGA_X_MODTPSSLibxcFunc.MGGA_X_MS0LibxcFunc.MGGA_X_MS1LibxcFunc.MGGA_X_MS2LibxcFunc.MGGA_X_MVSLibxcFunc.MGGA_X_PKZBLibxcFunc.MGGA_X_REVTPSSLibxcFunc.MGGA_X_RPP09LibxcFunc.MGGA_X_SCANLibxcFunc.MGGA_X_TAU_HCTHLibxcFunc.MGGA_X_TB09LibxcFunc.MGGA_X_TPSSLibxcFunc.all_families()LibxcFunc.all_kinds()LibxcFunc.as_dict()LibxcFunc.from_dict()LibxcFunc.info_dictLibxcFunc.is_c_kindLibxcFunc.is_gga_familyLibxcFunc.is_hyb_gga_familyLibxcFunc.is_hyb_mgga_familyLibxcFunc.is_k_kindLibxcFunc.is_lda_familyLibxcFunc.is_mgga_familyLibxcFunc.is_x_kindLibxcFunc.is_xc_kindLibxcFunc.to_json()
- pymatgen.core.molecular_orbitals module
- pymatgen.core.operations module
MagSymmOpSymmOpSymmOp.affine_matrixSymmOp.apply_rotation_only()SymmOp.are_symmetrically_related()SymmOp.are_symmetrically_related_vectors()SymmOp.as_dict()SymmOp.as_xyz_str()SymmOp.from_axis_angle_and_translation()SymmOp.from_dict()SymmOp.from_origin_axis_angle()SymmOp.from_rotation_and_translation()SymmOp.from_xyz_str()SymmOp.inverseSymmOp.inversion()SymmOp.operate()SymmOp.operate_multi()SymmOp.reflection()SymmOp.rotation_matrixSymmOp.rotoreflection()SymmOp.transform_tensor()SymmOp.translation_vector
- pymatgen.core.periodic_table module
DummySpecieDummySpeciesElementElement.ZElement.symbolElement.long_nameElement.AElement.atomic_radius_calculatedElement.van_der_waals_radiusElement.mendeleev_noElement.electrical_resistivityElement.velocity_of_soundElement.reflectivityElement.refractive_indexElement.poissons_ratioElement.molar_volumeElement.electronic_structureElement.atomic_orbitalsElement.atomic_orbitals_eVElement.thermal_conductivityElement.boiling_pointElement.melting_pointElement.critical_temperatureElement.superconduction_temperatureElement.liquid_rangeElement.bulk_modulusElement.youngs_modulusElement.brinell_hardnessElement.rigidity_modulusElement.mineral_hardnessElement.vickers_hardnessElement.density_of_solidElement.coefficient_of_linear_thermal_expansionElement.ground_levelElement.ionization_energiesElement.AcElement.AgElement.AlElement.AmElement.ArElement.AsElement.AtElement.AuElement.BElement.BaElement.BeElement.BhElement.BiElement.BkElement.BrElement.CElement.CaElement.CdElement.CeElement.CfElement.ClElement.CmElement.CnElement.CoElement.CrElement.CsElement.CuElement.DElement.DbElement.DsElement.DyElement.ErElement.EsElement.EuElement.FElement.FeElement.FlElement.FmElement.FrElement.GaElement.GdElement.GeElement.HElement.HeElement.HfElement.HgElement.HoElement.HsElement.IElement.InElement.IrElement.KElement.KrElement.LaElement.LiElement.LrElement.LuElement.LvElement.McElement.MdElement.MgElement.MnElement.MoElement.MtElement.NElement.NaElement.NbElement.NdElement.NeElement.NhElement.NiElement.NoElement.NpElement.OElement.OgElement.OsElement.PElement.PaElement.PbElement.PdElement.PmElement.PoElement.PrElement.PtElement.PuElement.RaElement.RbElement.ReElement.RfElement.RgElement.RhElement.RnElement.RuElement.SElement.SbElement.ScElement.SeElement.SgElement.SiElement.SmElement.SnElement.SrElement.TElement.TaElement.TbElement.TcElement.TeElement.ThElement.TiElement.TlElement.TmElement.TsElement.UElement.VElement.WElement.XeElement.YElement.YbElement.ZnElement.Zr
ElementBaseElementBase.ZElementBase.symbolElementBase.long_nameElementBase.AElementBase.atomic_radius_calculatedElementBase.van_der_waals_radiusElementBase.mendeleev_noElementBase.electrical_resistivityElementBase.velocity_of_soundElementBase.reflectivityElementBase.refractive_indexElementBase.poissons_ratioElementBase.molar_volumeElementBase.electronic_structureElementBase.atomic_orbitalsElementBase.atomic_orbitals_eVElementBase.thermal_conductivityElementBase.boiling_pointElementBase.melting_pointElementBase.critical_temperatureElementBase.superconduction_temperatureElementBase.liquid_rangeElementBase.bulk_modulusElementBase.youngs_modulusElementBase.brinell_hardnessElementBase.rigidity_modulusElementBase.mineral_hardnessElementBase.vickers_hardnessElementBase.density_of_solidElementBase.coefficient_of_linear_thermal_expansionElementBase.ground_levelElementBase.ionization_energiesElementBase.XElementBase.as_dict()ElementBase.atomic_massElementBase.atomic_mass_numberElementBase.atomic_orbitals_eVElementBase.atomic_radiusElementBase.average_anionic_radiusElementBase.average_cationic_radiusElementBase.average_ionic_radiusElementBase.blockElementBase.common_oxidation_statesElementBase.dataElementBase.electron_affinityElementBase.electronic_structureElementBase.from_Z()ElementBase.from_dict()ElementBase.from_name()ElementBase.from_row_and_group()ElementBase.full_electronic_structureElementBase.ground_state_term_symbolElementBase.groupElementBase.icsd_oxidation_statesElementBase.ionic_radiiElementBase.ionization_energyElementBase.is_actinoidElementBase.is_alkaliElementBase.is_alkalineElementBase.is_chalcogenElementBase.is_halogenElementBase.is_lanthanoidElementBase.is_metalElementBase.is_metalloidElementBase.is_noble_gasElementBase.is_post_transition_metalElementBase.is_quadrupolarElementBase.is_radioactiveElementBase.is_rare_earthElementBase.is_rare_earth_metalElementBase.is_transition_metalElementBase.is_valid_symbol()ElementBase.iupac_orderingElementBase.max_oxidation_stateElementBase.min_oxidation_stateElementBase.n_electronsElementBase.nmr_quadrupole_momentElementBase.numberElementBase.oxidation_statesElementBase.print_periodic_table()ElementBase.rowElementBase.term_symbolsElementBase.valence
ElementTypeElementType.actinoidElementType.alkaliElementType.alkalineElementType.chalcogenElementType.d_blockElementType.f_blockElementType.halogenElementType.lanthanoidElementType.metalElementType.metalloidElementType.noble_gasElementType.p_blockElementType.post_transition_metalElementType.quadrupolarElementType.radioactiveElementType.rare_earth_metalElementType.s_blockElementType.transition_metal
SpecieSpeciesSpecies.STRING_MODESpecies.as_dict()Species.electronic_structureSpecies.elementSpecies.from_dict()Species.from_str()Species.full_electronic_structureSpecies.get_crystal_field_spin()Species.get_nmr_quadrupole_moment()Species.get_shannon_radius()Species.ionic_radiusSpecies.n_electronsSpecies.oxi_stateSpecies.spinSpecies.to_pretty_string()Species.valence
get_el_sp()
- pymatgen.core.sites module
PeriodicSitePeriodicSite.aPeriodicSite.as_dict()PeriodicSite.bPeriodicSite.cPeriodicSite.coordsPeriodicSite.distance()PeriodicSite.distance_and_image()PeriodicSite.distance_and_image_from_frac_coords()PeriodicSite.frac_coordsPeriodicSite.from_dict()PeriodicSite.is_periodic_image()PeriodicSite.latticePeriodicSite.to_unit_cell()PeriodicSite.xPeriodicSite.yPeriodicSite.z
Site
- pymatgen.core.spectrum module
- pymatgen.core.structure module
IMoleculeIMolecule.as_dict()IMolecule.break_bond()IMolecule.center_of_massIMolecule.chargeIMolecule.copy()IMolecule.from_dict()IMolecule.from_file()IMolecule.from_sites()IMolecule.from_str()IMolecule.get_boxed_structure()IMolecule.get_centered_molecule()IMolecule.get_covalent_bonds()IMolecule.get_distance()IMolecule.get_neighbors()IMolecule.get_neighbors_in_shell()IMolecule.get_sites_in_sphere()IMolecule.get_zmatrix()IMolecule.nelectronsIMolecule.spin_multiplicityIMolecule.to()
IStructureIStructure.CellTypeIStructure.as_dataframe()IStructure.as_dict()IStructure.chargeIStructure.copy()IStructure.densityIStructure.distance_matrixIStructure.frac_coordsIStructure.from_dict()IStructure.from_file()IStructure.from_id()IStructure.from_magnetic_spacegroup()IStructure.from_sites()IStructure.from_spacegroup()IStructure.from_str()IStructure.get_all_neighbors()IStructure.get_all_neighbors_old()IStructure.get_all_neighbors_py()IStructure.get_distance()IStructure.get_miller_index_from_site_indexes()IStructure.get_neighbor_list()IStructure.get_neighbors()IStructure.get_neighbors_in_shell()IStructure.get_neighbors_old()IStructure.get_orderings()IStructure.get_primitive_structure()IStructure.get_reduced_structure()IStructure.get_sites_in_sphere()IStructure.get_sorted_structure()IStructure.get_space_group_info()IStructure.get_symmetric_neighbor_list()IStructure.interpolate()IStructure.is_3d_periodicIStructure.latticeIStructure.matches()IStructure.pbcIStructure.propertiesIStructure.to()IStructure.to_cell()IStructure.to_conventional()IStructure.to_primitive()IStructure.unset_charge()IStructure.volume
MoleculeNeighborPeriodicNeighborSiteCollectionSiteCollection.DISTANCE_TOLERANCESiteCollection.add_oxidation_state_by_element()SiteCollection.add_oxidation_state_by_guess()SiteCollection.add_oxidation_state_by_site()SiteCollection.add_site_property()SiteCollection.add_spin_by_element()SiteCollection.add_spin_by_site()SiteCollection.alphabetical_formulaSiteCollection.atomic_numbersSiteCollection.cart_coordsSiteCollection.chargeSiteCollection.chemical_systemSiteCollection.chemical_system_setSiteCollection.compositionSiteCollection.copy()SiteCollection.distance_matrixSiteCollection.elementsSiteCollection.extract_cluster()SiteCollection.formulaSiteCollection.from_ase_atoms()SiteCollection.from_file()SiteCollection.from_str()SiteCollection.get_angle()SiteCollection.get_dihedral()SiteCollection.get_distance()SiteCollection.group_by_types()SiteCollection.indices_from_symbol()SiteCollection.is_orderedSiteCollection.is_valid()SiteCollection.labelsSiteCollection.n_elemsSiteCollection.ntypespSiteCollection.num_sitesSiteCollection.reduced_formulaSiteCollection.relabel_sites()SiteCollection.remove_oxidation_states()SiteCollection.remove_site_property()SiteCollection.remove_spin()SiteCollection.replace_species()SiteCollection.site_propertiesSiteCollection.sitesSiteCollection.speciesSiteCollection.species_and_occuSiteCollection.symbol_setSiteCollection.to()SiteCollection.to_ase_atoms()SiteCollection.to_file()SiteCollection.types_of_specieSiteCollection.types_of_species
StructureStructure.append()Structure.apply_operation()Structure.apply_strain()Structure.calculate()Structure.from_prototype()Structure.insert()Structure.latticeStructure.make_supercell()Structure.merge_sites()Structure.perturb()Structure.relax()Structure.remove_sites()Structure.remove_species()Structure.replace()Structure.rotate_sites()Structure.scale_lattice()Structure.set_charge()Structure.sort()Structure.substitute()Structure.translate_sites()
StructureError
- pymatgen.core.surface module
ReconstructionGeneratorSlabSlab.add_adsorbate_atom()Slab.as_dict()Slab.center_of_massSlab.copy()Slab.dipoleSlab.from_dict()Slab.get_orthogonal_c_slab()Slab.get_sorted_structure()Slab.get_surface_sites()Slab.get_symmetric_site()Slab.get_tasker2_slabs()Slab.is_polar()Slab.is_symmetric()Slab.normalSlab.surface_areaSlab.symmetrically_add_atom()Slab.symmetrically_remove_atoms()
SlabGeneratorSlabGenerator.oriented_unit_cellSlabGenerator.parentSlabGenerator.lll_reduceSlabGenerator.center_slabSlabGenerator.slab_scale_factorSlabGenerator.miller_indexSlabGenerator.min_slab_sizeSlabGenerator.min_vac_sizeSlabGenerator.get_slab()SlabGenerator.get_slabs()SlabGenerator.move_to_other_side()SlabGenerator.nonstoichiometric_symmetrized_slab()SlabGenerator.repair_broken_bonds()
center_slab()generate_all_slabs()get_d()get_slab_regions()get_symmetrically_distinct_miller_indices()get_symmetrically_equivalent_miller_indices()hkl_transformation()miller_index_from_sites()
- pymatgen.core.tensors module
SquareTensorTensorTensor.as_dict()Tensor.average_over_unit_sphere()Tensor.convert_to_ieee()Tensor.einsum_sequence()Tensor.fit_to_structure()Tensor.from_dict()Tensor.from_values_indices()Tensor.from_voigt()Tensor.get_grouped_indices()Tensor.get_ieee_rotation()Tensor.get_symbol_dict()Tensor.get_voigt_dict()Tensor.is_fit_to_structure()Tensor.is_symmetric()Tensor.is_voigt_symmetric()Tensor.populate()Tensor.project()Tensor.rotate()Tensor.round()Tensor.structure_transform()Tensor.symbolTensor.symmetrizedTensor.transform()Tensor.voigtTensor.voigt_symmetrizedTensor.zeroed()
TensorCollectionTensorCollection.as_dict()TensorCollection.convert_to_ieee()TensorCollection.fit_to_structure()TensorCollection.from_dict()TensorCollection.from_voigt()TensorCollection.is_fit_to_structure()TensorCollection.is_symmetric()TensorCollection.is_voigt_symmetric()TensorCollection.ranksTensorCollection.rotate()TensorCollection.round()TensorCollection.symmetrizedTensorCollection.transform()TensorCollection.voigtTensorCollection.voigt_symmetrizedTensorCollection.zeroed()
TensorMappingget_uvec()symmetry_reduce()
- pymatgen.core.trajectory module
- pymatgen.core.units module
- pymatgen.core.xcfunc module
- pymatgen.electronic_structure package
- Submodules
- pymatgen.electronic_structure.bandstructure module
BandStructureBandStructure.kpointsBandStructure.lattice_recBandStructure.efermiBandStructure.is_spin_polarizedBandStructure.bandsBandStructure.nb_bandsBandStructure.structureBandStructure.projectionsBandStructure.as_dict()BandStructure.from_dict()BandStructure.from_old_dict()BandStructure.get_band_gap()BandStructure.get_cbm()BandStructure.get_direct_band_gap()BandStructure.get_direct_band_gap_dict()BandStructure.get_kpoint_degeneracy()BandStructure.get_projection_on_elements()BandStructure.get_projections_on_elements_and_orbitals()BandStructure.get_sym_eq_kpoints()BandStructure.get_vbm()BandStructure.is_metal()
BandStructureSymmLineKpointLobsterBandStructureSymmLineget_reconstructed_band_structure()
- pymatgen.electronic_structure.boltztrap module
BoltztrapAnalyzerBoltztrapAnalyzer.as_dict()BoltztrapAnalyzer.check_acc_bzt_bands()BoltztrapAnalyzer.from_dict()BoltztrapAnalyzer.from_files()BoltztrapAnalyzer.get_average_eff_mass()BoltztrapAnalyzer.get_carrier_concentration()BoltztrapAnalyzer.get_complete_dos()BoltztrapAnalyzer.get_complexity_factor()BoltztrapAnalyzer.get_conductivity()BoltztrapAnalyzer.get_extreme()BoltztrapAnalyzer.get_hall_carrier_concentration()BoltztrapAnalyzer.get_mu_bounds()BoltztrapAnalyzer.get_power_factor()BoltztrapAnalyzer.get_seebeck()BoltztrapAnalyzer.get_seebeck_eff_mass()BoltztrapAnalyzer.get_symm_bands()BoltztrapAnalyzer.get_thermal_conductivity()BoltztrapAnalyzer.get_zt()BoltztrapAnalyzer.parse_cond_and_hall()BoltztrapAnalyzer.parse_intrans()BoltztrapAnalyzer.parse_outputtrans()BoltztrapAnalyzer.parse_struct()BoltztrapAnalyzer.parse_transdos()
BoltztrapErrorBoltztrapRunnercompare_sym_bands()eta_from_seebeck()read_cube_file()seebeck_eff_mass_from_carr()seebeck_eff_mass_from_seebeck_carr()seebeck_spb()
- pymatgen.electronic_structure.boltztrap2 module
- pymatgen.electronic_structure.cohp module
CohpCompleteCohpCompleteCohp.are_coopsCompleteCohp.are_cobisCompleteCohp.efermiCompleteCohp.energiesCompleteCohp.structureCompleteCohp.cohpCompleteCohp.icohpCompleteCohp.all_cohpsCompleteCohp.orb_res_cohpCompleteCohp.as_dict()CompleteCohp.from_dict()CompleteCohp.from_file()CompleteCohp.get_cohp_by_label()CompleteCohp.get_orbital_resolved_cohp()CompleteCohp.get_summed_cohp_by_label_and_orbital_list()CompleteCohp.get_summed_cohp_by_label_list()
IcohpCollectionIcohpCollection.are_coopsIcohpCollection.are_cobisIcohpCollection.is_spin_polarizedIcohpCollection.are_cobisIcohpCollection.are_coopsIcohpCollection.extremum_icohpvalue()IcohpCollection.get_icohp_by_label()IcohpCollection.get_icohp_dict_by_bondlengths()IcohpCollection.get_icohp_dict_of_site()IcohpCollection.get_summed_icohp_by_label_list()IcohpCollection.is_spin_polarized
IcohpValueIcohpValue.energiesIcohpValue.densitiesIcohpValue.energies_are_cartesianIcohpValue.are_coopsIcohpValue.are_cobisIcohpValue.icohpIcohpValue.summed_icohpIcohpValue.num_bondsIcohpValue.are_cobisIcohpValue.are_coopsIcohpValue.icohpIcohpValue.icohpvalue()IcohpValue.icohpvalue_orbital()IcohpValue.is_spin_polarizedIcohpValue.num_bondsIcohpValue.summed_icohpIcohpValue.summed_orbital_icohp
get_integrated_cohp_in_energy_range()
- pymatgen.electronic_structure.core module
MagmomMagmom.are_collinear()Magmom.from_global_moment_and_saxis()Magmom.from_moment_relative_to_crystal_axes()Magmom.get_00t_magmom_with_xyz_saxis()Magmom.get_consistent_set_and_saxis()Magmom.get_moment()Magmom.get_moment_relative_to_crystal_axes()Magmom.get_suggested_saxis()Magmom.get_xyz_magmom_with_001_saxis()Magmom.global_momentMagmom.have_consistent_saxis()Magmom.projection
OrbitalOrbitalTypeSpin
- pymatgen.electronic_structure.dos module
CompleteDosCompleteDos.structureCompleteDos.pdosCompleteDos.as_dict()CompleteDos.fp_to_dict()CompleteDos.from_dict()CompleteDos.get_band_center()CompleteDos.get_band_filling()CompleteDos.get_band_kurtosis()CompleteDos.get_band_skewness()CompleteDos.get_band_width()CompleteDos.get_dos_fp()CompleteDos.get_dos_fp_similarity()CompleteDos.get_element_dos()CompleteDos.get_element_spd_dos()CompleteDos.get_hilbert_transform()CompleteDos.get_n_moment()CompleteDos.get_normalized()CompleteDos.get_site_dos()CompleteDos.get_site_orbital_dos()CompleteDos.get_site_spd_dos()CompleteDos.get_site_t2g_eg_resolved_dos()CompleteDos.get_spd_dos()CompleteDos.get_upper_band_edge()CompleteDos.spin_polarization
DOSDosDosFingerprintFermiDosLobsterCompleteDosadd_densities()f0()
- pymatgen.electronic_structure.plotter module
BSDOSPlotterBSPlotterBSPlotterProjectedBoltztrapPlotterBoltztrapPlotter.plot_carriers()BoltztrapPlotter.plot_complexity_factor_mu()BoltztrapPlotter.plot_conductivity_dop()BoltztrapPlotter.plot_conductivity_mu()BoltztrapPlotter.plot_conductivity_temp()BoltztrapPlotter.plot_dos()BoltztrapPlotter.plot_eff_mass_dop()BoltztrapPlotter.plot_eff_mass_temp()BoltztrapPlotter.plot_hall_carriers()BoltztrapPlotter.plot_power_factor_dop()BoltztrapPlotter.plot_power_factor_mu()BoltztrapPlotter.plot_power_factor_temp()BoltztrapPlotter.plot_seebeck_dop()BoltztrapPlotter.plot_seebeck_eff_mass_mu()BoltztrapPlotter.plot_seebeck_mu()BoltztrapPlotter.plot_seebeck_temp()BoltztrapPlotter.plot_zt_dop()BoltztrapPlotter.plot_zt_mu()BoltztrapPlotter.plot_zt_temp()
CohpPlotterDosPlotterfold_point()plot_brillouin_zone()plot_brillouin_zone_from_kpath()plot_ellipsoid()plot_fermi_surface()plot_labels()plot_lattice_vectors()plot_path()plot_points()plot_wigner_seitz()
- pymatgen.entries package
Entry- Submodules
- pymatgen.entries.compatibility module
- pymatgen.entries.computed_entries module
CompositionEnergyAdjustmentComputedEntryComputedEntry.as_dict()ComputedEntry.copy()ComputedEntry.correctionComputedEntry.correction_per_atomComputedEntry.correction_uncertaintyComputedEntry.correction_uncertainty_per_atomComputedEntry.energyComputedEntry.from_dict()ComputedEntry.normalize()ComputedEntry.uncorrected_energyComputedEntry.uncorrected_energy_per_atom
ComputedStructureEntryConstantEnergyAdjustmentEnergyAdjustmentGibbsComputedStructureEntryManualEnergyAdjustmentTemperatureEnergyAdjustment
- pymatgen.entries.correction_calculator module
CorrectionCalculatorCorrectionCalculator.speciesCorrectionCalculator.exp_compoundsCorrectionCalculator.calc_compoundsCorrectionCalculator.correctionsCorrectionCalculator.corrections_std_errorCorrectionCalculator.corrections_dictCorrectionCalculator.compute_corrections()CorrectionCalculator.compute_from_files()CorrectionCalculator.graph_residual_error()CorrectionCalculator.graph_residual_error_per_species()CorrectionCalculator.make_yaml()
- pymatgen.entries.entry_tools module
- pymatgen.entries.exp_entries module
- pymatgen.entries.mixing_scheme module
- pymatgen.ext namespace
- pymatgen.io namespace
- Subpackages
- pymatgen.io.abinit package
- Submodules
- pymatgen.io.abinit.abiobjects module
AbivarAbleConstraintsElectronsElectronsAlgorithmExcHamiltonianHilbertTransformKSamplingKSamplingModesModelDielectricFunctionPPModelPPModelModesRelaxationMethodScreeningSelfEnergySmearingSpinModeSpinModeTuplecontract()lattice_from_abivars()species_by_znucl()structure_from_abivars()structure_to_abivars()
- pymatgen.io.abinit.abitimer module
AbinitTimerAbinitTimer.cpuwall_histogram()AbinitTimer.get_dataframe()AbinitTimer.get_section()AbinitTimer.get_values()AbinitTimer.names_and_values()AbinitTimer.ncpusAbinitTimer.order_sections()AbinitTimer.pie()AbinitTimer.scatter_hist()AbinitTimer.sum_sections()AbinitTimer.to_csv()AbinitTimer.to_table()AbinitTimer.totable()
AbinitTimerParseErrorAbinitTimerParserAbinitTimerParser.BEGIN_TAGAbinitTimerParser.END_TAGAbinitTimerParser.ErrorAbinitTimerParser.filenamesAbinitTimerParser.get_sections()AbinitTimerParser.parse()AbinitTimerParser.pefficiency()AbinitTimerParser.plot_all()AbinitTimerParser.plot_efficiency()AbinitTimerParser.plot_pie()AbinitTimerParser.plot_stacked_hist()AbinitTimerParser.section_names()AbinitTimerParser.summarize()AbinitTimerParser.timers()AbinitTimerParser.walk()
AbinitTimerSectionParallelEfficiencyalternate()
- pymatgen.io.abinit.inputs module
AbstractInputBasicAbinitInputBasicAbinitInput.ErrorBasicAbinitInput.add_abiobjects()BasicAbinitInput.as_dict()BasicAbinitInput.commentBasicAbinitInput.from_dict()BasicAbinitInput.isncBasicAbinitInput.ispawBasicAbinitInput.new_with_vars()BasicAbinitInput.pop_irdvars()BasicAbinitInput.pop_tolerances()BasicAbinitInput.pseudosBasicAbinitInput.set_comment()BasicAbinitInput.set_gamma_sampling()BasicAbinitInput.set_kmesh()BasicAbinitInput.set_kpath()BasicAbinitInput.set_spin_mode()BasicAbinitInput.set_structure()BasicAbinitInput.structureBasicAbinitInput.to_str()BasicAbinitInput.vars
BasicAbinitInputErrorBasicMultiDatasetBasicMultiDataset.ErrorBasicMultiDataset.addnew_from()BasicMultiDataset.append()BasicMultiDataset.deepcopy()BasicMultiDataset.extend()BasicMultiDataset.from_inputs()BasicMultiDataset.has_same_structuresBasicMultiDataset.isncBasicMultiDataset.ispawBasicMultiDataset.ndtsetBasicMultiDataset.pseudosBasicMultiDataset.replicate_input()BasicMultiDataset.split_datasets()BasicMultiDataset.to_str()BasicMultiDataset.write()
ShiftModeas_structure()calc_shiftk()ebands_input()gs_input()ion_ioncell_relax_input()num_valence_electrons()
- pymatgen.io.abinit.netcdf module
- pymatgen.io.abinit.pseudos module
AbinitHeaderAbinitPseudoHintNcAbinitHeaderNcAbinitPseudoNcPseudoPawAbinitHeaderPawAbinitPseudoPawPseudoPawXmlSetupPawXmlSetup.ZPawXmlSetup.Z_valPawXmlSetup.ae_core_density()PawXmlSetup.ae_partial_waves()PawXmlSetup.l_localPawXmlSetup.l_maxPawXmlSetup.paw_radiusPawXmlSetup.plot_densities()PawXmlSetup.plot_projectors()PawXmlSetup.plot_waves()PawXmlSetup.projector_functions()PawXmlSetup.pseudo_core_density()PawXmlSetup.pseudo_partial_wavesPawXmlSetup.root()PawXmlSetup.summaryPawXmlSetup.supports_socPawXmlSetup.yield_figs()
PseudoPseudo.ZPseudo.Z_valPseudo.as_dict()Pseudo.as_pseudo()Pseudo.as_tmpfile()Pseudo.basenamePseudo.compute_md5()Pseudo.djrepo_pathPseudo.elementPseudo.filepathPseudo.from_dict()Pseudo.from_file()Pseudo.has_dojo_reportPseudo.has_hintsPseudo.hint_for_accuracy()Pseudo.isncPseudo.ispawPseudo.l_localPseudo.l_maxPseudo.md5()Pseudo.open_pspsfile()Pseudo.summaryPseudo.supports_socPseudo.symbolPseudo.to_str()Pseudo.type
PseudoParseErrorPseudoParserPseudoTablePseudoTable.all_combinations_for_elements()PseudoTable.allncPseudoTable.allpawPseudoTable.as_dict()PseudoTable.as_table()PseudoTable.from_dict()PseudoTable.from_dir()PseudoTable.get_pseudos_for_structure()PseudoTable.is_complete()PseudoTable.print_table()PseudoTable.pseudo_with_symbol()PseudoTable.pseudos_with_symbols()PseudoTable.select()PseudoTable.select_family()PseudoTable.select_rows()PseudoTable.select_symbols()PseudoTable.sort_by_z()PseudoTable.sorted()PseudoTable.to_table()PseudoTable.with_dojo_report()PseudoTable.zlist
RadialFunctionl2str()str2l()
- pymatgen.io.abinit.variable module
- pymatgen.io.aims package
- Subpackages
- Submodules
- pymatgen.io.aims.inputs module
AimsControlInAimsCubeAimsCube.typeAimsCube.originAimsCube.edgesAimsCube.pointsAimsCube.spin_stateAimsCube.kpointAimsCube.filenameAimsCube.formatAimsCube.elf_typeAimsCube.as_dict()AimsCube.control_blockAimsCube.edgesAimsCube.elf_typeAimsCube.filenameAimsCube.formatAimsCube.from_dict()AimsCube.kpointAimsCube.originAimsCube.pointsAimsCube.spin_stateAimsCube.type
AimsGeometryInAimsSpeciesFileSpeciesDefaults
- pymatgen.io.aims.outputs module
AimsOutputAimsOutput.aims_versionAimsOutput.all_forcesAimsOutput.as_dict()AimsOutput.band_gapAimsOutput.cbmAimsOutput.completedAimsOutput.direct_band_gapAimsOutput.fermi_energyAimsOutput.final_energyAimsOutput.final_structureAimsOutput.forcesAimsOutput.from_dict()AimsOutput.from_outfile()AimsOutput.from_str()AimsOutput.get_results_for_image()AimsOutput.initial_structureAimsOutput.metadataAimsOutput.n_imagesAimsOutput.stressAimsOutput.stressesAimsOutput.structure_summaryAimsOutput.structuresAimsOutput.vbm
- pymatgen.io.aims.parsers module
AimsOutCalcChunkAimsOutCalcChunk.E_fAimsOutCalcChunk.cbmAimsOutCalcChunk.convergedAimsOutCalcChunk.coordsAimsOutCalcChunk.dielectric_tensorAimsOutCalcChunk.dipoleAimsOutCalcChunk.direct_gapAimsOutCalcChunk.electronic_temperatureAimsOutCalcChunk.energyAimsOutCalcChunk.forcesAimsOutCalcChunk.free_energyAimsOutCalcChunk.gapAimsOutCalcChunk.hirshfeld_atomic_dipolesAimsOutCalcChunk.hirshfeld_chargesAimsOutCalcChunk.hirshfeld_dipoleAimsOutCalcChunk.hirshfeld_volumesAimsOutCalcChunk.initial_latticeAimsOutCalcChunk.initial_structureAimsOutCalcChunk.is_metallicAimsOutCalcChunk.k_point_weightsAimsOutCalcChunk.k_pointsAimsOutCalcChunk.latticeAimsOutCalcChunk.magmomAimsOutCalcChunk.mulliken_chargesAimsOutCalcChunk.mulliken_spinsAimsOutCalcChunk.n_atomsAimsOutCalcChunk.n_bandsAimsOutCalcChunk.n_electronsAimsOutCalcChunk.n_iterAimsOutCalcChunk.n_k_pointsAimsOutCalcChunk.n_spinsAimsOutCalcChunk.polarizationAimsOutCalcChunk.resultsAimsOutCalcChunk.speciesAimsOutCalcChunk.stressAimsOutCalcChunk.stressesAimsOutCalcChunk.structureAimsOutCalcChunk.vbmAimsOutCalcChunk.velocities
AimsOutChunkAimsOutHeaderChunkAimsOutHeaderChunk.aims_uuidAimsOutHeaderChunk.build_typeAimsOutHeaderChunk.c_compilerAimsOutHeaderChunk.c_compiler_flagsAimsOutHeaderChunk.commit_hashAimsOutHeaderChunk.electronic_temperatureAimsOutHeaderChunk.fortran_compilerAimsOutHeaderChunk.fortran_compiler_flagsAimsOutHeaderChunk.header_summaryAimsOutHeaderChunk.initial_chargesAimsOutHeaderChunk.initial_latticeAimsOutHeaderChunk.initial_magnetic_momentsAimsOutHeaderChunk.initial_structureAimsOutHeaderChunk.is_mdAimsOutHeaderChunk.is_relaxationAimsOutHeaderChunk.k_point_weightsAimsOutHeaderChunk.k_pointsAimsOutHeaderChunk.linesAimsOutHeaderChunk.linked_againstAimsOutHeaderChunk.metadata_summaryAimsOutHeaderChunk.n_atomsAimsOutHeaderChunk.n_bandsAimsOutHeaderChunk.n_electronsAimsOutHeaderChunk.n_k_pointsAimsOutHeaderChunk.n_spinsAimsOutHeaderChunk.version_number
AimsParseErrorParseErrorcheck_convergence()get_aims_out_chunks()get_header_chunk()get_lines()read_aims_header_info()read_aims_header_info_from_content()read_aims_output()read_aims_output_from_content()
- pymatgen.io.cp2k package
- Submodules
- pymatgen.io.cp2k.inputs module
AtomicMetadataAtomicMetadata.infoAtomicMetadata.elementAtomicMetadata.potentialAtomicMetadata.nameAtomicMetadata.alias_namesAtomicMetadata.filenameAtomicMetadata.versionAtomicMetadata.alias_namesAtomicMetadata.elementAtomicMetadata.filenameAtomicMetadata.get_hash()AtomicMetadata.get_str()AtomicMetadata.infoAtomicMetadata.nameAtomicMetadata.potentialAtomicMetadata.softmatch()AtomicMetadata.version
BandStructureBand_StructureBasisFileBasisInfoBasisInfo.electronsBasisInfo.coreBasisInfo.valenceBasisInfo.polarizationBasisInfo.diffuseBasisInfo.ccBasisInfo.pcBasisInfo.srBasisInfo.moloptBasisInfo.admmBasisInfo.lriBasisInfo.contractedBasisInfo.xcBasisInfo.admmBasisInfo.ccBasisInfo.contractedBasisInfo.coreBasisInfo.diffuseBasisInfo.electronsBasisInfo.from_str()BasisInfo.lriBasisInfo.moloptBasisInfo.pcBasisInfo.polarizationBasisInfo.softmatch()BasisInfo.srBasisInfo.valenceBasisInfo.xc
BrokenSymmetryCellCoordCp2kInputDOSDataFileDavidsonDftDftPlusUDiagonalizationEDensityCubeE_Density_CubeForceEvalGaussianTypeOrbitalBasisSetGaussianTypeOrbitalBasisSet.infoGaussianTypeOrbitalBasisSet.nsetGaussianTypeOrbitalBasisSet.nGaussianTypeOrbitalBasisSet.lmaxGaussianTypeOrbitalBasisSet.lminGaussianTypeOrbitalBasisSet.nshellGaussianTypeOrbitalBasisSet.exponentsGaussianTypeOrbitalBasisSet.coefficientsGaussianTypeOrbitalBasisSet.coefficientsGaussianTypeOrbitalBasisSet.exponentsGaussianTypeOrbitalBasisSet.from_str()GaussianTypeOrbitalBasisSet.get_keyword()GaussianTypeOrbitalBasisSet.get_str()GaussianTypeOrbitalBasisSet.infoGaussianTypeOrbitalBasisSet.lmaxGaussianTypeOrbitalBasisSet.lminGaussianTypeOrbitalBasisSet.nGaussianTypeOrbitalBasisSet.nexpGaussianTypeOrbitalBasisSet.nsetGaussianTypeOrbitalBasisSet.nshell
GlobalGthPotentialGthPotential.infoGthPotential.n_elecsGthPotential.r_locGthPotential.nexp_pplGthPotential.c_exp_pplGthPotential.radiiGthPotential.nprjGthPotential.nprj_ppnlGthPotential.hprj_ppnlGthPotential.c_exp_pplGthPotential.from_section()GthPotential.from_str()GthPotential.get_keyword()GthPotential.get_section()GthPotential.get_str()GthPotential.hprj_ppnlGthPotential.n_elecsGthPotential.nexp_pplGthPotential.nprjGthPotential.nprj_ppnlGthPotential.r_locGthPotential.radii
KeywordKeywordListKindKpointSetKpoint_SetKpointsLDOSMOCubesMO_CubesMgridOrbitalTransformationPBEPDOSPotentialFilePotentialInfoQSScfSectionSectionListSmearSubsysVHartreeCubeV_Hartree_CubeXCFunctionalXc_Functional
- pymatgen.io.cp2k.outputs module
Cp2kOutputCp2kOutput.as_dict()Cp2kOutput.band_structureCp2kOutput.calculation_typeCp2kOutput.chargeCp2kOutput.complete_dosCp2kOutput.completedCp2kOutput.convergence()Cp2kOutput.cp2k_versionCp2kOutput.is_hubbardCp2kOutput.is_metalCp2kOutput.is_moleculeCp2kOutput.multiplicityCp2kOutput.num_warningsCp2kOutput.parse_atomic_kind_info()Cp2kOutput.parse_bandstructure()Cp2kOutput.parse_cell_params()Cp2kOutput.parse_chi_tensor()Cp2kOutput.parse_cp2k_params()Cp2kOutput.parse_dft_params()Cp2kOutput.parse_dos()Cp2kOutput.parse_energies()Cp2kOutput.parse_files()Cp2kOutput.parse_forces()Cp2kOutput.parse_global_params()Cp2kOutput.parse_gtensor()Cp2kOutput.parse_hirshfeld()Cp2kOutput.parse_homo_lumo()Cp2kOutput.parse_hyperfine()Cp2kOutput.parse_initial_structure()Cp2kOutput.parse_input()Cp2kOutput.parse_ionic_steps()Cp2kOutput.parse_mo_eigenvalues()Cp2kOutput.parse_mulliken()Cp2kOutput.parse_nmr_shift()Cp2kOutput.parse_opt_steps()Cp2kOutput.parse_overlap_condition()Cp2kOutput.parse_plus_u_params()Cp2kOutput.parse_qs_params()Cp2kOutput.parse_raman()Cp2kOutput.parse_scf_opt()Cp2kOutput.parse_scf_params()Cp2kOutput.parse_stresses()Cp2kOutput.parse_structures()Cp2kOutput.parse_tddfpt()Cp2kOutput.parse_timing()Cp2kOutput.parse_total_numbers()Cp2kOutput.project_nameCp2kOutput.ran_successfully()Cp2kOutput.read_pattern()Cp2kOutput.read_table_pattern()Cp2kOutput.run_typeCp2kOutput.spin_polarized
parse_dos()parse_energy_file()parse_pdos()
- pymatgen.io.cp2k.sets module
CellOptSetCp2kValidationErrorDftSetDftSet.activate_epr()DftSet.activate_fast_minimization()DftSet.activate_hybrid()DftSet.activate_hyperfine()DftSet.activate_localize()DftSet.activate_motion()DftSet.activate_nmr()DftSet.activate_nonperiodic()DftSet.activate_polar()DftSet.activate_robust_minimization()DftSet.activate_spinspin()DftSet.activate_tddfpt()DftSet.activate_vdw_potential()DftSet.activate_very_strict_minimization()DftSet.create_subsys()DftSet.get_basis_and_potential()DftSet.get_cutoff_from_basis()DftSet.get_xc_functionals()DftSet.modify_dft_print_iters()DftSet.print_bandstructure()DftSet.print_dos()DftSet.print_e_density()DftSet.print_forces()DftSet.print_hirshfeld()DftSet.print_ldos()DftSet.print_mo()DftSet.print_mo_cubes()DftSet.print_mulliken()DftSet.print_pdos()DftSet.print_v_hartree()DftSet.set_charge()DftSet.validate()DftSet.write_basis_set_file()DftSet.write_potential_file()
HybridCellOptSetHybridRelaxSetHybridStaticSetRelaxSetStaticSet
- pymatgen.io.cp2k.utils module
- pymatgen.io.exciting package
- pymatgen.io.feff package
- Submodules
- pymatgen.io.feff.inputs module
- pymatgen.io.feff.outputs module
- pymatgen.io.feff.sets module
- pymatgen.io.lammps package
- Submodules
- pymatgen.io.lammps.data module
- pymatgen.io.lammps.generators module
BaseLammpsGeneratorBaseLammpsGenerator.templateBaseLammpsGenerator.calc_typeBaseLammpsGenerator.settingsBaseLammpsGenerator.keep_stagesBaseLammpsGenerator.calc_typeBaseLammpsGenerator.dataBaseLammpsGenerator.get_input_set()BaseLammpsGenerator.inputfileBaseLammpsGenerator.keep_stagesBaseLammpsGenerator.settingsBaseLammpsGenerator.template
LammpsMinimization
- pymatgen.io.lammps.inputs module
LammpsInputFileLammpsInputFile.add_commands()LammpsInputFile.add_stage()LammpsInputFile.append()LammpsInputFile.contains_command()LammpsInputFile.from_file()LammpsInputFile.from_str()LammpsInputFile.get_args()LammpsInputFile.get_str()LammpsInputFile.merge_stages()LammpsInputFile.ncommentsLammpsInputFile.nstagesLammpsInputFile.remove_command()LammpsInputFile.remove_stage()LammpsInputFile.rename_stage()LammpsInputFile.set_args()LammpsInputFile.stages_namesLammpsInputFile.write_file()
LammpsRunLammpsTemplateGenwrite_lammps_inputs()
- pymatgen.io.lammps.outputs module
- pymatgen.io.lammps.sets module
- pymatgen.io.lammps.utils module
- pymatgen.io.lobster package
- Submodules
- pymatgen.io.lobster.inputs module
LobsterinLobsterin.AVAILABLE_KEYWORDSLobsterin.BOOLEAN_KEYWORDSLobsterin.FLOAT_KEYWORDSLobsterin.LIST_KEYWORDSLobsterin.STRING_KEYWORDSLobsterin.as_dict()Lobsterin.diff()Lobsterin.from_dict()Lobsterin.from_file()Lobsterin.get_all_possible_basis_functions()Lobsterin.get_basis()Lobsterin.standard_calculations_from_vasp_files()Lobsterin.write_INCAR()Lobsterin.write_KPOINTS()Lobsterin.write_POSCAR_with_standard_primitive()Lobsterin.write_lobsterin()
get_all_possible_basis_combinations()
- pymatgen.io.lobster.lobsterenv module
ICOHPNeighborsInfoLobsterLightStructureEnvironmentsLobsterNeighborsLobsterNeighbors.anion_typesLobsterNeighbors.get_anion_types()LobsterNeighbors.get_info_cohps_to_neighbors()LobsterNeighbors.get_info_icohps_between_neighbors()LobsterNeighbors.get_info_icohps_to_neighbors()LobsterNeighbors.get_light_structure_environment()LobsterNeighbors.get_nn_info()LobsterNeighbors.molecules_allowedLobsterNeighbors.plot_cohps_of_neighbors()LobsterNeighbors.structures_allowed
- pymatgen.io.lobster.outputs module
BandoverlapsBwdfChargeCohpcarDoscarFatbandGrosspopIcohplistLobsterMatricesLobsteroutLobsterout.basis_functionsLobsterout.basis_typeLobsterout.charge_spillingLobsterout.dft_programLobsterout.elementsLobsterout.has_chargeLobsterout.has_cohpcarLobsterout.has_madelungLobsterout.has_coopcarLobsterout.has_cobicarLobsterout.has_doscarLobsterout.has_doscar_lsoLobsterout.has_projectionLobsterout.has_bandoverlapsLobsterout.has_density_of_energiesLobsterout.has_fatbandsLobsterout.has_grosspopulationLobsterout.has_polarizationLobsterout.info_linesLobsterout.info_orthonormalizationLobsterout.is_restart_from_projectionLobsterout.lobster_versionLobsterout.number_of_spinsLobsterout.number_of_threadsLobsterout.timingLobsterout.total_spillingLobsterout.warning_linesLobsterout.as_dict()Lobsterout.get_doc()
MadelungEnergiesNciCobiListPolarizationSitePotentialSitePotential.atomlistSitePotential.typesSitePotential.num_atomsSitePotential.sitepotentials_mullikenSitePotential.sitepotentials_loewdinSitePotential.madelungenergies_mullikenSitePotential.madelungenergies_loewdinSitePotential.ewald_splittingSitePotential.get_structure_with_site_potentials()SitePotential.madelungenergies_LoewdinSitePotential.madelungenergies_MullikenSitePotential.sitepotentials_LoewdinSitePotential.sitepotentials_Mulliken
Wavefunctionget_orb_from_str()
- pymatgen.io.pwmat package
- pymatgen.io.qchem package
- Submodules
- pymatgen.io.qchem.inputs module
QCInputQCInput.almo_template()QCInput.cdft_template()QCInput.find_sections()QCInput.from_file()QCInput.from_multi_jobs_file()QCInput.from_str()QCInput.geom_opt_template()QCInput.get_str()QCInput.molecule_template()QCInput.multi_job_string()QCInput.nbo_template()QCInput.opt_template()QCInput.pcm_nonels_template()QCInput.pcm_template()QCInput.plots_template()QCInput.read_almo()QCInput.read_cdft()QCInput.read_geom_opt()QCInput.read_molecule()QCInput.read_nbo()QCInput.read_opt()QCInput.read_pcm()QCInput.read_pcm_nonels()QCInput.read_plots()QCInput.read_rem()QCInput.read_scan()QCInput.read_smx()QCInput.read_solvent()QCInput.read_svp()QCInput.read_vdw()QCInput.rem_template()QCInput.scan_template()QCInput.smx_template()QCInput.solvent_template()QCInput.svp_template()QCInput.van_der_waals_template()QCInput.write_multi_job_file()
- pymatgen.io.qchem.outputs module
- pymatgen.io.qchem.sets module
- pymatgen.io.qchem.utils module
- pymatgen.io.vasp package
- Submodules
- pymatgen.io.vasp.help module
- pymatgen.io.vasp.inputs module
BadIncarWarningBadPoscarWarningIncarKpointsKpoints.as_dict()Kpoints.automatic()Kpoints.automatic_density()Kpoints.automatic_density_by_lengths()Kpoints.automatic_density_by_vol()Kpoints.automatic_gamma_density()Kpoints.automatic_linemode()Kpoints.copy()Kpoints.from_dict()Kpoints.from_file()Kpoints.from_str()Kpoints.gamma_automatic()Kpoints.kptsKpoints.monkhorst_automatic()Kpoints.styleKpoints.supported_modesKpoints.write_file()
KpointsSupportedModesOrbitalOrbitalDescriptionPmgVaspPspDirErrorPoscarPoscar.structurePoscar.commentPoscar.true_namesPoscar.selective_dynamicsPoscar.velocitiesPoscar.predictor_correctorPoscar.predictor_corrector_preamblePoscar.lattice_velocitiesPoscar.temperaturePoscar.as_dict()Poscar.from_dict()Poscar.from_file()Poscar.from_str()Poscar.get_str()Poscar.get_string()Poscar.lattice_velocitiesPoscar.natomsPoscar.predictor_correctorPoscar.predictor_corrector_preamblePoscar.selective_dynamicsPoscar.set_temperature()Poscar.site_symbolsPoscar.velocitiesPoscar.write_file()
PotcarPotcarSinglePotcarSingle.dataPotcarSingle.keywordsPotcarSingle.atomic_noPotcarSingle.copy()PotcarSingle.electron_configurationPotcarSingle.elementPotcarSingle.from_file()PotcarSingle.from_symbol_and_functional()PotcarSingle.functionalPotcarSingle.functional_classPotcarSingle.functional_dirPotcarSingle.functional_tagsPotcarSingle.hash_sha256_from_filePotcarSingle.identify_potcar()PotcarSingle.identify_potcar_hash_based()PotcarSingle.is_validPotcarSingle.md5_computed_file_hashPotcarSingle.md5_header_hashPotcarSingle.nelectronsPotcarSingle.parse_functionsPotcarSingle.potential_typePotcarSingle.sha256_computed_file_hashPotcarSingle.symbolPotcarSingle.verify_potcar()PotcarSingle.write_file()
UnknownPotcarWarningVaspInput
- pymatgen.io.vasp.optics module
DielectricFunctionCalculatorDielectricFunctionCalculator.cderDielectricFunctionCalculator.cder_imagDielectricFunctionCalculator.cder_realDielectricFunctionCalculator.cshiftDielectricFunctionCalculator.deltaeDielectricFunctionCalculator.efermiDielectricFunctionCalculator.eigsDielectricFunctionCalculator.from_directory()DielectricFunctionCalculator.from_vasp_objects()DielectricFunctionCalculator.get_epsilon()DielectricFunctionCalculator.ismearDielectricFunctionCalculator.ispinDielectricFunctionCalculator.kweightsDielectricFunctionCalculator.nedosDielectricFunctionCalculator.plot_weighted_transition_data()DielectricFunctionCalculator.sigmaDielectricFunctionCalculator.volume
delta_func()delta_methfessel_paxton()epsilon_imag()get_delta()get_step()kramers_kronig()step_func()step_methfessel_paxton()
- pymatgen.io.vasp.outputs module
BSVasprunChgcarDynmatEigenvalElfcarKpointOptPropsKpointOptProps.actual_kpointsKpointOptProps.actual_kpoints_weightsKpointOptProps.dos_has_errorsKpointOptProps.efermiKpointOptProps.eigenvaluesKpointOptProps.idosKpointOptProps.kpointsKpointOptProps.pdosKpointOptProps.projected_eigenvaluesKpointOptProps.projected_magnetisationKpointOptProps.tdos
LocpotOszicarOutcarOutcar.magnetizationOutcar.chemical_shieldingOutcar.unsym_cs_tensorOutcar.cs_g0_contributionOutcar.cs_core_contributionOutcar.efgOutcar.chargeOutcar.is_stoppedOutcar.run_statsOutcar.elastic_tensorOutcar.driftOutcar.ngfOutcar.sampling_radiiOutcar.electrostatic_potentialOutcar.final_energy_contribsOutcar.efermiOutcar.filenameOutcar.final_energyOutcar.final_energy_wo_entrpOutcar.final_fr_energyOutcar.has_onsite_density_matricesOutcar.lcalcpolOutcar.lepsilonOutcar.nelectOutcar.spinOutcar.total_magOutcar.as_dict()Outcar.read_avg_core_poten()Outcar.read_chemical_shielding()Outcar.read_core_state_eigen()Outcar.read_corrections()Outcar.read_cs_core_contribution()Outcar.read_cs_g0_contribution()Outcar.read_cs_raw_symmetrized_tensors()Outcar.read_elastic_tensor()Outcar.read_electrostatic_potential()Outcar.read_fermi_contact_shift()Outcar.read_freq_dielectric()Outcar.read_igpar()Outcar.read_internal_strain_tensor()Outcar.read_lcalcpol()Outcar.read_lepsilon()Outcar.read_lepsilon_ionic()Outcar.read_neb()Outcar.read_nmr_efg()Outcar.read_nmr_efg_tensor()Outcar.read_onsite_density_matrices()Outcar.read_pattern()Outcar.read_piezo_tensor()Outcar.read_pseudo_zval()Outcar.read_table_pattern()
ProcarUnconvergedVASPWarningVaspParseErrorVasprunVasprun.ionic_stepsVasprun.tdosVasprun.idosVasprun.pdosVasprun.efermiVasprun.eigenvaluesVasprun.projected_eigenvaluesVasprun.projected_magnetisationVasprun.dielectric_dataVasprun.nionic_stepsVasprun.force_constantsVasprun.normalmode_eigenvalsVasprun.normalmode_eigenvecsVasprun.md_dataVasprun.incarVasprun.parametersVasprun.kpointsVasprun.actual_kpointsVasprun.actual_kpoints_weightsVasprun.atomic_symbolsVasprun.potcar_symbolsVasprun.kpoints_opt_propsVasprun.as_dict()Vasprun.calculate_efermi()Vasprun.complete_dosVasprun.complete_dos_normalizedVasprun.convergedVasprun.converged_electronicVasprun.converged_ionicVasprun.dielectricVasprun.eigenvalue_band_propertiesVasprun.epsilon_ionicVasprun.epsilonassetsVasprun.epsilonassets_wolfeVasprun.final_energyVasprun.get_band_structure()Vasprun.get_computed_entry()Vasprun.get_potcars()Vasprun.get_trajectory()Vasprun.hubbardsVasprun.is_hubbardVasprun.is_spinVasprun.md_n_stepsVasprun.optical_absorption_coeffVasprun.run_typeVasprun.structuresVasprun.update_charge_from_potcar()Vasprun.update_potcar_spec()
VolumetricDataWSWQWavecarWavederXdatcarget_adjusted_fermi_level()get_band_structure_from_vasp_multiple_branches()
- pymatgen.io.vasp.sets module
BadInputSetWarningDictSetLobsterSetMITMDSetMITNEBSetMITRelaxSetMPAbsorptionSetMPAbsorptionSet.CONFIGMPAbsorptionSet.SUPPORTED_MODESMPAbsorptionSet.copy_wavecarMPAbsorptionSet.force_gammaMPAbsorptionSet.incar_updatesMPAbsorptionSet.inherit_incarMPAbsorptionSet.kpoints_updatesMPAbsorptionSet.modeMPAbsorptionSet.nbandsMPAbsorptionSet.nbands_factorMPAbsorptionSet.nedosMPAbsorptionSet.nkredMPAbsorptionSet.reciprocal_density
MPHSEBSSetMPHSERelaxSetMPMDSetMPMetalRelaxSetMPNMRSetMPNonSCFSetMPNonSCFSet.CONFIGMPNonSCFSet.copy_chgcarMPNonSCFSet.dedosMPNonSCFSet.incar_updatesMPNonSCFSet.inherit_incarMPNonSCFSet.kpoints_line_densityMPNonSCFSet.kpoints_updatesMPNonSCFSet.modeMPNonSCFSet.nbands_factorMPNonSCFSet.nedosMPNonSCFSet.opticsMPNonSCFSet.reciprocal_densityMPNonSCFSet.small_gap_multiply
MPRelaxSetMPSOCSetMPScanRelaxSetMPScanStaticSetMPStaticSetMVLElasticSetMVLGBSetMVLGWSetMVLNPTMDSetMVLRelax52SetMVLScanRelaxSetMVLSlabSetMatPESStaticSetVaspInputGeneratorVaspInputSetVaspInputSet.as_dict()VaspInputSet.auto_ismearVaspInputSet.auto_ispinVaspInputSet.auto_kspacingVaspInputSet.auto_lrealVaspInputSet.auto_metal_kpointsVaspInputSet.bandgapVaspInputSet.bandgap_tolVaspInputSet.calculate_ng()VaspInputSet.config_dictVaspInputSet.constrain_total_magmomVaspInputSet.estimate_nbands()VaspInputSet.files_to_transferVaspInputSet.force_gammaVaspInputSet.from_directory()VaspInputSet.from_prev_calc()VaspInputSet.get_input_set()VaspInputSet.get_vasp_input()VaspInputSet.incarVaspInputSet.incar_updatesVaspInputSet.inherit_incarVaspInputSet.international_monoclinicVaspInputSet.kpointsVaspInputSet.kpoints_updatesVaspInputSet.nelectVaspInputSet.override_from_prev_calc()VaspInputSet.poscarVaspInputSet.potcarVaspInputSet.potcar_functionalVaspInputSet.potcar_symbolsVaspInputSet.prev_incarVaspInputSet.prev_kpointsVaspInputSet.reduce_structureVaspInputSet.sort_structureVaspInputSet.standardizeVaspInputSet.structureVaspInputSet.sym_precVaspInputSet.use_structure_chargeVaspInputSet.user_incar_settingsVaspInputSet.user_kpoints_settingsVaspInputSet.user_potcar_functionalVaspInputSet.user_potcar_settingsVaspInputSet.validate_magmomVaspInputSet.vdwVaspInputSet.write_input()
auto_kspacing()batch_write_input()get_structure_from_prev_run()get_valid_magmom_struct()get_vasprun_outcar()next_num_with_prime_factors()primes_less_than()standardize_structure()
- pymatgen.io.xtb package
- pymatgen.io.abinit package
- Submodules
- pymatgen.io.adf module
- pymatgen.io.ase module
- pymatgen.io.atat module
- pymatgen.io.babel module
BabelMolAdaptorBabelMolAdaptor.add_hydrogen()BabelMolAdaptor.confab_conformers()BabelMolAdaptor.from_file()BabelMolAdaptor.from_molecule_graph()BabelMolAdaptor.from_str()BabelMolAdaptor.gen3d_conformer()BabelMolAdaptor.localopt()BabelMolAdaptor.make3d()BabelMolAdaptor.openbabel_molBabelMolAdaptor.pybel_molBabelMolAdaptor.pymatgen_molBabelMolAdaptor.remove_bond()BabelMolAdaptor.rotor_conformer()BabelMolAdaptor.write_file()
- pymatgen.io.cif module
- pymatgen.io.common module
PMGDirVolumetricDataVolumetricData.structureVolumetricData.is_spin_polarizedVolumetricData.dimVolumetricData.dataVolumetricData.ngridptsVolumetricData.copy()VolumetricData.from_cube()VolumetricData.from_hdf5()VolumetricData.get_average_along_axis()VolumetricData.get_axis_grid()VolumetricData.get_integrated_diff()VolumetricData.linear_add()VolumetricData.linear_slice()VolumetricData.scale()VolumetricData.spin_dataVolumetricData.to_cube()VolumetricData.to_hdf5()VolumetricData.value_at()
- pymatgen.io.core module
- pymatgen.io.cssr module
- pymatgen.io.fiesta module
BSEOutputBasisSetReaderFiestaInputFiestaInput.as_dict()FiestaInput.dump_bse_data_in_gw_run()FiestaInput.dump_tddft_data_in_gw_run()FiestaInput.from_dict()FiestaInput.from_file()FiestaInput.from_str()FiestaInput.infos_on_systemFiestaInput.make_full_bse_densities_folder()FiestaInput.moleculeFiestaInput.set_auxiliary_basis_set()FiestaInput.set_bse_options()FiestaInput.set_gw_options()FiestaInput.write_file()
FiestaOutputFiestaRunNwchem2Fiesta
- pymatgen.io.gaussian module
GaussianInputGaussianOutputGaussianOutput.structuresGaussianOutput.structures_input_orientationGaussianOutput.opt_structuresGaussianOutput.energiesGaussianOutput.eigenvaluesGaussianOutput.MO_coefficientsGaussianOutput.cart_forcesGaussianOutput.frequenciesGaussianOutput.hessianGaussianOutput.properly_terminatedGaussianOutput.is_pcmGaussianOutput.is_spinGaussianOutput.stationary_typeGaussianOutput.correctionsGaussianOutput.functionalGaussianOutput.basis_setGaussianOutput.routeGaussianOutput.dieze_tagGaussianOutput.link0GaussianOutput.chargeGaussianOutput.spin_multiplicityGaussianOutput.num_basis_funcGaussianOutput.electronsGaussianOutput.pcmGaussianOutput.errorsGaussianOutput.Mulliken_chargesGaussianOutput.eigenvectorsGaussianOutput.molecular_orbitalGaussianOutput.atom_basis_labelsGaussianOutput.resumesGaussianOutput.titleGaussianOutput.standard_orientationGaussianOutput.bond_ordersGaussianOutput.to_input()GaussianOutput.read_scan()GaussianOutput.get_scan_plot()GaussianOutput.save_scan_plot()GaussianOutput.as_dict()GaussianOutput.final_energyGaussianOutput.final_structureGaussianOutput.get_scan_plot()GaussianOutput.get_spectre_plot()GaussianOutput.read_excitation_energies()GaussianOutput.read_scan()GaussianOutput.save_scan_plot()GaussianOutput.save_spectre_plot()GaussianOutput.to_input()
read_route_line()
- pymatgen.io.icet module
- pymatgen.io.jarvis module
- pymatgen.io.lmto module
- pymatgen.io.multiwfn module
- pymatgen.io.nwchem module
- pymatgen.io.openff module
- pymatgen.io.optimade module
- pymatgen.io.packmol module
- pymatgen.io.phonopy module
eigvec_to_eigdispl()get_complete_ph_dos()get_displaced_structures()get_gruneisen_ph_bs_symm_line()get_gruneisenparameter()get_gs_ph_bs_symm_line_from_dict()get_ph_bs_symm_line()get_ph_bs_symm_line_from_dict()get_ph_dos()get_phonon_band_structure_from_fc()get_phonon_band_structure_symm_line_from_fc()get_phonon_dos_from_fc()get_phonopy_structure()get_pmg_structure()get_structure_from_dict()get_thermal_displacement_matrices()
- pymatgen.io.prismatic module
- pymatgen.io.pwscf module
- pymatgen.io.res module
AirssProviderAirssProvider.appearancesAirssProvider.as_dict()AirssProvider.energyAirssProvider.entryAirssProvider.from_file()AirssProvider.from_str()AirssProvider.get_airss_version()AirssProvider.get_castep_version()AirssProvider.get_cut_grid_gmax_fsbc()AirssProvider.get_func_rel_disp()AirssProvider.get_mpgrid_offset_nkpts_spacing()AirssProvider.get_pspots()AirssProvider.get_run_start_info()AirssProvider.integrated_absolute_spin_densityAirssProvider.integrated_spin_densityAirssProvider.pressureAirssProvider.seedAirssProvider.spacegroup_labelAirssProvider.volume
AirssTITLIonResResCELLResErrorResIOResParseErrorResParserResProviderResSFACResWriter
- pymatgen.io.shengbte module
- pymatgen.io.template module
- pymatgen.io.wannier90 module
- pymatgen.io.xcrysden module
- pymatgen.io.xr module
- pymatgen.io.xyz module
- pymatgen.io.zeopp module
- Subpackages
- pymatgen.optimization package
- pymatgen.phonon package
- Submodules
- pymatgen.phonon.bandstructure module
PhononBandStructurePhononBandStructure.as_dict()PhononBandStructure.asr_breaking()PhononBandStructure.from_dict()PhononBandStructure.get_gamma_point()PhononBandStructure.get_nac_eigendisplacements_along_dir()PhononBandStructure.get_nac_frequencies_along_dir()PhononBandStructure.has_eigendisplacementsPhononBandStructure.has_imaginary_freq()PhononBandStructure.has_imaginary_gamma_freq()PhononBandStructure.has_nacPhononBandStructure.max_freq()PhononBandStructure.min_freq()PhononBandStructure.width()
PhononBandStructureSymmLinePhononBandStructureSymmLine.as_dict()PhononBandStructureSymmLine.as_phononwebsite()PhononBandStructureSymmLine.band_reorder()PhononBandStructureSymmLine.from_dict()PhononBandStructureSymmLine.get_branch()PhononBandStructureSymmLine.get_equivalent_qpoints()PhononBandStructureSymmLine.write_phononwebsite()
eigenvectors_from_displacements()estimate_band_connection()get_reasonable_repetitions()
- pymatgen.phonon.dos module
CompletePhononDosPhononDosPhononDos.as_dict()PhononDos.cv()PhononDos.entropy()PhononDos.fp_to_dict()PhononDos.from_dict()PhononDos.get_dos_fp()PhononDos.get_dos_fp_similarity()PhononDos.get_interpolated_value()PhononDos.get_last_peak()PhononDos.get_smeared_densities()PhononDos.helmholtz_free_energy()PhononDos.ind_zero_freq()PhononDos.internal_energy()PhononDos.mae()PhononDos.r2_score()PhononDos.zero_point_energy()
PhononDosFingerprint
- pymatgen.phonon.gruneisen module
- pymatgen.phonon.ir_spectra module
- pymatgen.phonon.plotter module
- pymatgen.phonon.thermal_displacements module
ThermalDisplacementMatricesThermalDisplacementMatrices.BThermalDisplacementMatrices.U1U2U3ThermalDisplacementMatrices.UcifThermalDisplacementMatrices.UstarThermalDisplacementMatrices.betaThermalDisplacementMatrices.compute_directionality_quality_criterion()ThermalDisplacementMatrices.from_Ucif()ThermalDisplacementMatrices.from_cif_P1()ThermalDisplacementMatrices.from_structure_with_site_properties_Ucif()ThermalDisplacementMatrices.get_full_matrix()ThermalDisplacementMatrices.get_reduced_matrix()ThermalDisplacementMatrices.ratio_prolateThermalDisplacementMatrices.to_structure_with_site_properties_Ucif()ThermalDisplacementMatrices.visualize_directionality_quality_criterion()ThermalDisplacementMatrices.write_cif()
- pymatgen.symmetry package
- Submodules
- pymatgen.symmetry.analyzer module
PointGroupAnalyzerPointGroupOperationsSpacegroupAnalyzerSpacegroupAnalyzer.find_primitive()SpacegroupAnalyzer.get_conventional_standard_structure()SpacegroupAnalyzer.get_conventional_to_primitive_transformation_matrix()SpacegroupAnalyzer.get_crystal_system()SpacegroupAnalyzer.get_hall()SpacegroupAnalyzer.get_ir_reciprocal_mesh()SpacegroupAnalyzer.get_ir_reciprocal_mesh_map()SpacegroupAnalyzer.get_kpoint_weights()SpacegroupAnalyzer.get_lattice_type()SpacegroupAnalyzer.get_point_group_operations()SpacegroupAnalyzer.get_point_group_symbol()SpacegroupAnalyzer.get_primitive_standard_structure()SpacegroupAnalyzer.get_refined_structure()SpacegroupAnalyzer.get_space_group_number()SpacegroupAnalyzer.get_space_group_operations()SpacegroupAnalyzer.get_space_group_symbol()SpacegroupAnalyzer.get_symmetrized_structure()SpacegroupAnalyzer.get_symmetry_dataset()SpacegroupAnalyzer.get_symmetry_operations()SpacegroupAnalyzer.is_laue()
SpacegroupOperationsSymmetryUndeterminedErrorcluster_sites()generate_full_symmops()iterative_symmetrize()
- pymatgen.symmetry.bandstructure module
- pymatgen.symmetry.groups module
PointGroupSpaceGroupSpaceGroup.symbolSpaceGroup.int_numberSpaceGroup.generatorsSpaceGroup.orderSpaceGroup.SG_SYMBOLSSpaceGroup.SYMM_OPSSpaceGroup.abbrev_sg_mappingSpaceGroup.crystal_systemSpaceGroup.from_int_number()SpaceGroup.full_sg_mappingSpaceGroup.gen_matricesSpaceGroup.get_orbit()SpaceGroup.get_orbit_and_generators()SpaceGroup.get_settings()SpaceGroup.is_compatible()SpaceGroup.is_subgroup()SpaceGroup.is_supergroup()SpaceGroup.opSpaceGroup.sg_encodingSpaceGroup.symmetry_opsSpaceGroup.to_pretty_string()SpaceGroup.translations
SymmetryGroupin_array_list()sg_symbol_from_int_number()
- pymatgen.symmetry.kpath module
KPathBaseKPathLatimerMunroKPathSeekKPathSetyawanCurtaroloKPathSetyawanCurtarolo.bcc()KPathSetyawanCurtarolo.bctet1()KPathSetyawanCurtarolo.bctet2()KPathSetyawanCurtarolo.conventionalKPathSetyawanCurtarolo.cubic()KPathSetyawanCurtarolo.fcc()KPathSetyawanCurtarolo.hex()KPathSetyawanCurtarolo.mcl()KPathSetyawanCurtarolo.mclc1()KPathSetyawanCurtarolo.mclc2()KPathSetyawanCurtarolo.mclc3()KPathSetyawanCurtarolo.mclc4()KPathSetyawanCurtarolo.mclc5()KPathSetyawanCurtarolo.orc()KPathSetyawanCurtarolo.orcc()KPathSetyawanCurtarolo.orcf1()KPathSetyawanCurtarolo.orcf2()KPathSetyawanCurtarolo.orcf3()KPathSetyawanCurtarolo.orci()KPathSetyawanCurtarolo.primKPathSetyawanCurtarolo.prim_recKPathSetyawanCurtarolo.rhl1()KPathSetyawanCurtarolo.rhl2()KPathSetyawanCurtarolo.tet()KPathSetyawanCurtarolo.tria()KPathSetyawanCurtarolo.trib()
- pymatgen.symmetry.maggroups module
- pymatgen.symmetry.settings module
JonesFaithfulTransformationJonesFaithfulTransformation.PJonesFaithfulTransformation.from_origin_shift()JonesFaithfulTransformation.from_transformation_str()JonesFaithfulTransformation.inverseJonesFaithfulTransformation.pJonesFaithfulTransformation.parse_transformation_string()JonesFaithfulTransformation.transform_coords()JonesFaithfulTransformation.transform_lattice()JonesFaithfulTransformation.transform_symmop()JonesFaithfulTransformation.transformation_string
- pymatgen.symmetry.site_symmetries module
- pymatgen.symmetry.structure module
- pymatgen.transformations package
- Submodules
- pymatgen.transformations.advanced_transformations module
AddAdsorbateTransformationChargeBalanceTransformationCubicSupercellTransformationDisorderOrderedTransformationDopingTransformationEnumerateStructureTransformationGrainBoundaryTransformationMagOrderParameterConstraintMagOrderingTransformationMonteCarloRattleTransformationMultipleSubstitutionTransformationSQSTransformationSlabTransformationSubstituteSurfaceSiteTransformationSubstitutionPredictorTransformationSuperTransformationfind_codopant()
- pymatgen.transformations.site_transformations module
- pymatgen.transformations.standard_transformations module
AutoOxiStateDecorationTransformationChargedCellTransformationConventionalCellTransformationDeformStructureTransformationDiscretizeOccupanciesTransformationOrderDisorderedStructureTransformationOrderDisorderedStructureTransformation.ALGO_BEST_FIRSTOrderDisorderedStructureTransformation.ALGO_COMPLETEOrderDisorderedStructureTransformation.ALGO_FASTOrderDisorderedStructureTransformation.apply_transformation()OrderDisorderedStructureTransformation.is_one_to_manyOrderDisorderedStructureTransformation.lowest_energy_structure
OxidationStateDecorationTransformationOxidationStateRemovalTransformationPartialRemoveSpecieTransformationPerturbStructureTransformationPrimitiveCellTransformationRemoveSpeciesTransformationRotationTransformationScaleToRelaxedTransformationSubstitutionTransformationSupercellTransformation
- pymatgen.transformations.transformation_abc module
- pymatgen.util package
- Subpackages
- Submodules
- pymatgen.util.coord module
Simplexall_distances()barycentric_coords()coord_list_mapping()coord_list_mapping_pbc()find_in_coord_list()find_in_coord_list_pbc()get_angle()get_linear_interpolated_value()in_coord_list()in_coord_list_pbc()is_coord_subset()is_coord_subset_pbc()lattice_points_in_supercell()pbc_diff()pbc_shortest_vectors()
- pymatgen.util.coord_cython module
- pymatgen.util.due module
- pymatgen.util.graph_hashing module
- pymatgen.util.io_utils module
- pymatgen.util.joblib module
- pymatgen.util.misc module
- pymatgen.util.num module
- pymatgen.util.numba module
- pymatgen.util.plotting module
- pymatgen.util.provenance module
- pymatgen.util.string module
- pymatgen.util.typing module
- pymatgen.vis package
- Submodules
- pymatgen.vis.plotters module
- pymatgen.vis.structure_chemview module
- pymatgen.vis.structure_vtk module
MultiStructuresInteractorStyleMultiStructuresVisMultiStructuresVis.DEFAULT_ANIMATED_MOVIE_OPTIONSMultiStructuresVis.apply_tags()MultiStructuresVis.display_help()MultiStructuresVis.display_info()MultiStructuresVis.display_warning()MultiStructuresVis.erase_info()MultiStructuresVis.erase_warning()MultiStructuresVis.set_animated_movie_options()MultiStructuresVis.set_structure()MultiStructuresVis.set_structures()
StructureInteractorStyleStructureVisStructureVis.add_bonds()StructureVis.add_edges()StructureVis.add_faces()StructureVis.add_line()StructureVis.add_partial_sphere()StructureVis.add_picker()StructureVis.add_picker_fixed()StructureVis.add_polyhedron()StructureVis.add_site()StructureVis.add_text()StructureVis.add_triangle()StructureVis.display_help()StructureVis.orthogonalize_structure()StructureVis.redraw()StructureVis.rotate_view()StructureVis.set_structure()StructureVis.show()StructureVis.write_image()StructureVis.zoom()
make_movie()
Submodules
pymatgen.dao module
The dao for pymatgen.