Index

A

a (Wavecar attribute) a() (Kpoint property) (Lattice property) (PeriodicSite property) (Plane property) ab_shift() (Interface property) abc() (Lattice property) abcd() (Plane property) abinitixc_to_libxc (XcFunc attribute) AbinitTimer (class in pymatgen.io.abinit.abitimer) AbinitTimerParser (class in pymatgen.io.abinit.abitimer) AbinitTimerParserError AbinitTimerSection (class in pymatgen.io.abinit.abitimer) AbivarAble (class in pymatgen.io.abinit.abiobjects) abs_cap() (in module pymatgen.util.num) AbstractChemenvAlgorithm (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) AbstractChemenvError AbstractChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) AbstractComparator (class in pymatgen.analysis.structure_matcher) AbstractDiffractionPatternCalculator (class in pymatgen.analysis.diffraction.core) AbstractDrone (class in pymatgen.apps.borg.hive) AbstractElectrode (class in pymatgen.apps.battery.battery_abc) AbstractEnvironmentNode (class in pymatgen.analysis.chemenv.connectivity.environment_nodes) AbstractFeffInputSet (class in pymatgen.io.feff.sets) AbstractGeometry (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) AbstractInput (class in pymatgen.io.abinit.inputs) AbstractMolAtomMapper (class in pymatgen.analysis.molecule_matcher) AbstractRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) AbstractStructureFilter (class in pymatgen.alchemy.filters) AbstractTransformation (class in pymatgen.transformations.transformation_abc) AbstractVoltagePair (class in pymatgen.apps.battery.battery_abc) AC (AbstractChemenvStrategy attribute) (DetailedVoronoiContainer attribute) (DistanceAngleAreaNbSetWeight attribute) Ac (Element attribute) AC (StructureEnvironments attribute) AconvaspError actual_kpoints (Vasprun attribute) actual_kpoints_weights (Vasprun attribute) add() (EntrySet method) add_abiobjects() (BasicAbinitInput method) add_adsorbate() (AdsorbateSiteFinder method) add_adsorbate_atom() (Slab method) add_bonds() (StructureConnectivity method) (StructureVis method) add_charges_from_oxi_state_guesses() (Composition method) add_cohp() (CohpPlotter method) add_cohp_dict() (CohpPlotter method) add_config_var() (in module pymatgen.cli.pmg_config) add_coord_geom() (ChemicalEnvironments method) add_densities() (in module pymatgen.electronic_structure.dos) add_dos() (DosPlotter method) (PhononDosPlotter method) add_dos_dict() (DosPlotter method) (PhononDosPlotter method) add_edge() (MoleculeGraph method) (StructureGraph method) add_edges() (StructureVis method) add_electrode() (VoltageProfilePlotter method) add_faces() (StructureVis method) add_fig_kwargs() (in module pymatgen.util.plotting) add_gg_gap() (in module pymatgen.io.abinit.helpers) add_hydrogen() (BabelMolAdaptor method) add_label_cycle() (CyclesPlotter method) add_line() (StructureVis method) add_m_list() (EwaldMinimizer method) add_neighbors_set() (StructureEnvironments method) add_option() (AdfKey method) add_oxidation_state_by_element() (SiteCollection method) add_oxidation_state_by_guess() (SiteCollection method) add_oxidation_state_by_site() (SiteCollection method) add_oxidation_state_by_site_fraction() (in module pymatgen.analysis.bond_valence) add_partial_sphere() (StructureVis method) add_picker() (StructureVis method) add_picker_fixed() (StructureVis method) add_polyhedron() (StructureVis method) add_site() (StructureVis method) add_site_property() (SiteCollection method) add_sites() (StructureConnectivity method) add_source() (StructureEnvironments.NeighborsSet method) add_spectra() (SpectrumPlotter method) add_spectrum() (SpectrumPlotter method) add_spin_by_element() (SiteCollection method) add_spin_by_site() (SiteCollection method) add_strategy_visualization_to_subplot() (SimplestChemenvStrategy method) add_subkey() (AdfKey method) add_tags() (StandardTransmuter method) add_text() (StructureVis method) add_triangle() (StructureVis method) AddAdsorbateTransformation (class in pymatgen.transformations.advanced_transformations) additional_condition() (SimplestChemenvStrategy property) AdditionalConditionInt (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) AdditionalConditions (class in pymatgen.analysis.chemenv.utils.defs_utils) addnew_from() (BasicMultiDataset method) AddSitePropertyTransformation (class in pymatgen.transformations.site_transformations) AdfInput (class in pymatgen.io.adf) AdfInputError AdfKey (class in pymatgen.io.adf) AdfOutput (class in pymatgen.io.adf) AdfOutputError AdfTask (class in pymatgen.io.adf) adsorb_both_surfaces() (AdsorbateSiteFinder method) adsorbates (SlabEntry attribute) AdsorbateSiteFinder (class in pymatgen.analysis.adsorption) affine_matrix (SymmOp attribute) AflowPrototypeMatcher (class in pymatgen.analysis.aflow_prototypes) AFM (Ordering attribute) Ag (Element attribute) AiidaStructureAdaptor() (in module pymatgen.io.aiida) Al (Element attribute) ALGO_BEST_FIRST (EwaldMinimizer attribute) (OrderDisorderedStructureTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) ALGO_COMPLETE (EwaldMinimizer attribute) (OrderDisorderedStructureTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) ALGO_ENUMERATE (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) ALGO_FAST (EwaldMinimizer attribute) (OrderDisorderedStructureTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) ALGO_TIME_LIMIT (EwaldMinimizer attribute) algorithm_type() (AbstractChemenvAlgorithm property) algorithms() (CoordinationGeometry property) aliases() (XcFunc class method) align_x() (in module pymatgen.analysis.interface) ALL (AdditionalConditions attribute) all_combinations_for_elements() (PseudoTable method) all_comp() (BalancedReaction property) all_distances() (in module pymatgen.util.coord) all_docs_with_tag() (YamlTokenizer method) all_energies() (Oszicar property) all_entries() (ComputedReaction property) (PourbaixDiagram property) all_entries_hulldata() (PhaseDiagram property) all_families (LibxcFunc attribute) all_input() (AbstractFeffInputSet method) (VaspInputSet property) all_kinds (LibxcFunc attribute) all_molecules() (XYZ property) all_slab_entries (SurfaceEnergyPlotter attribute) all_stable_entries() (DefectPhaseDiagram property) all_unstable_entries() (DefectPhaseDiagram property) all_yaml_docs() (YamlTokenizer method) AllCoordinationGeometries (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) allnc() (PseudoTable property) allocations_keys (Control attribute) ALLOWED_FUNCTIONS (AbstractRatioFunction attribute) (CSMFiniteRatioFunction attribute) (CSMInfiniteRatioFunction attribute) (DeltaCSMRatioFunction attribute) (RatioFunction attribute) ALLOWED_HINTS_TYPES (CoordinationGeometry.NeighborsSetsHints attribute) allowed_values (AdditionalConditionInt attribute) (AngleCutoffFloat attribute) (CSMFloat attribute) (DistanceCutoffFloat attribute) (StrategyOption attribute) allpaw() (PseudoTable property) almost_equals() (Composition method) along_c (WorkFunctionAnalyzer attribute) alpha (WulffShape attribute) alpha() (Lattice property) alphabetical_formula() (Composition property) (Ion property) alter_edge() (MoleculeGraph method) (StructureGraph method) alternate() (in module pymatgen.io.abinit.abitimer) Am (Element attribute) amount_tol (CompoundPhaseDiagram attribute) amount_tolerance (Composition attribute) analyze() (in module pymatgen.cli.pmg_analyze) (VoronoiAnalyzer method) analyze_localenv() (in module pymatgen.cli.pmg_structure) analyze_structures() (in module pymatgen.cli.pmg_structure) (VoronoiAnalyzer method) analyze_symmetry() (in module pymatgen.cli.pmg_structure) (TopographyAnalyzer method) ang() (NormalizedAngleDistanceNbSetWeight method) ang_to_bohr (in module pymatgen.core.units) anginvdist() (NormalizedAngleDistanceNbSetWeight method) anginvndist() (NormalizedAngleDistanceNbSetWeight method) angle_cutoff() (SimplestChemenvStrategy property) angle_plateau() (StructureEnvironments.NeighborsSet method) angle_sum() (AngleNbSetWeight method) angle_sumn() (AngleNbSetWeight method) AngleCutoffFloat (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) AngleNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) AnglePlateauNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) angles() (Lattice property) (StructureEnvironments.NeighborsSet property) angn() (NormalizedAngleDistanceNbSetWeight method) angninvdist() (NormalizedAngleDistanceNbSetWeight method) angninvndist() (NormalizedAngleDistanceNbSetWeight method) AnionCorrection (class in pymatgen.entries.compatibility) anisotropy() (WulffShape property) anonymized_formula() (Composition property) (Ion property) anticlockwise_sort() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) anticlockwise_sort_indices() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) aos (MolecularOrbitals attribute) aos_as_list() (MolecularOrbitals method) append() (BasicMultiDataset method) (Molecule method) (Structure method) append_filter() (TransformedStructure method) append_transformation() (StandardTransmuter method) (TransformedStructure method) append_transformed_structures() (StandardTransmuter method) apply_filter() (StandardTransmuter method) apply_operation() (Molecule method) (Structure method) apply_rotation_only() (SymmOp method) apply_scissor() (BandStructureSymmLine method) apply_strain() (Structure method) apply_tags() (MultiStructuresVis method) apply_to_structure() (Deformation method) apply_transformation() (AbstractTransformation method) (AddAdsorbateTransformation method) (AddSitePropertyTransformation method) (AutoOxiStateDecorationTransformation method) (ChargeBalanceTransformation method) (ChargedCellTransformation method) (ConventionalCellTransformation method) (CubicSupercellTransformation method) (DefectTransformation method) (DeformStructureTransformation method) (DiscretizeOccupanciesTransformation method) (DisorderOrderedTransformation method) (DopingTransformation method) (EnumerateStructureTransformation method) (GrainBoundaryTransformation method) (InsertSitesTransformation method) (InterfaceBuilder method) (MagOrderingTransformation method) (MultipleSubstitutionTransformation method) (OrderDisorderedStructureTransformation method) (OxidationStateDecorationTransformation method) (OxidationStateRemovalTransformation method) (PartialRemoveSitesTransformation method) (PartialRemoveSpecieTransformation method) (PerturbStructureTransformation method) (PrimitiveCellTransformation method) (RemoveSitesTransformation method) (RemoveSpeciesTransformation method) (ReplaceSiteSpeciesTransformation method) (RotationTransformation method) (ScaleToRelaxedTransformation method) (SlabTransformation method) (SQSTransformation method) (SubstituteSurfaceSiteTransformation method) (SubstitutionPredictorTransformation method) (SubstitutionTransformation method) (SupercellTransformation method) (SuperTransformation method) (TranslateSitesTransformation method) apply_transformations() (InterfaceBuilder method) AqueousCorrection (class in pymatgen.entries.compatibility) Ar (Element attribute) are_collinear() (Magmom static method) are_coops (IcohpCollection attribute) (IcohpValue attribute) are_coops() (IcohpCollection property) (IcohpValue property)

are_equal() (AbstractComparator method) (ElementComparator method) (FrameworkComparator method) (MoleculeStructureComparator method) (OccupancyComparator method) (OrderDisorderElementComparator method) (PointDefectComparator method) (SpeciesComparator method) (SpinComparator method) are_symmetrically_equivalent() (SpacegroupOperations method) are_symmetrically_related() (SymmOp method) area_frac_vs_chempot_plot() (SurfaceEnergyPlotter method) area_fraction_dict() (WulffShape property) argsorted_ref_separation_perm() (SeparationPlane property) ArrayWithUnit (class in pymatgen.core.units) As (Element attribute) as_base_units() (ArrayWithUnit property) (FloatWithUnit property) (Unit property) as_dict() (AbstractChemenvAlgorithm method) (AbstractChemenvStrategy method) (AbstractComparator method) (AdditionalConditionInt method) (AdfKey method) (AdfTask method) (AngleCutoffFloat method) (AngleNbSetWeight method) (AnglePlateauNbSetWeight method) (Author method) (BalancedReaction method) (BandStructure method) (BandStructureSymmLine method) (BasicAbinitInput method) (BoltztrapAnalyzer method) (BoltztrapRunner method) (BSVasprun method) (ChemicalEnvironments method) (CifParser method) (CNBiasNbSetWeight method) (Cohp method) (CompleteCohp method) (CompleteDos method) (CompletePhononDos method) (Composition method) (CompoundPhaseDiagram method) (ComputedEntry method) (ComputedReaction method) (ComputedStructureEntry method) (ConnectedComponent method) (ContainsSpecieFilter method) (Control method) (ConversionElectrode method) (ConversionVoltagePair method) (CoordinationGeometry method) (CoordinationGeometry.NeighborsSetsHints method) (CSMFloat method) (DefectEntry method) (DefectPhaseDiagram method) (DeltaCSMNbSetWeight method) (DeltaDistanceNbSetWeight method) (DetailedVoronoiContainer method) (DiffusionAnalyzer method) (DistanceAngleAreaNbSetWeight method) (DistanceCutoffFloat method) (DistanceNbSetWeight method) (DistancePlateauNbSetWeight method) (Dos method) (DummySpecie method) (Eels method) (Electrons method) (ElectronsAlgorithm method) (Element method) (Entry method) (EntrySet method) (EwaldElectrostaticModel method) (ExpEntry method) (ExplicitPermutationsAlgorithm property) (FermiDos method) (FiestaInput method) (FiestaRun method) (GaussianInput method) (GaussianOutput method) (GaussianToComputedEntryDrone method) (GrainBoundary method) (GrandPotentialPhaseDiagram method) (GrandPotPDEntry method) (HistoryNode method) (IMolecule method) (Incar method) (InchiMolAtomMapper method) (InsertionElectrode method) (Interface method) (Ion method) (IonEntry method) (IRDielectricTensor method) (IsingModel method) (IsomorphismMolAtomMapper method) (IStructure method) (Kpoint method) (Kpoints method) (KSampling method) (LammpsData method) (LammpsDump method) (Lattice method) (LibxcFunc method) (LightStructureEnvironments method) (LightStructureEnvironments.NeighborsSet method) (LMTOCtrl method) (LobsterBandStructureSymmLine method) (Lobsterin method) (MagSymmOp method) (MoleculeGraph method) (MoleculeMatcher method) (MoleculeStructureComparator method) (MultiEntry method) (MultiWeightsChemenvStrategy method) (MVLSlabSet method) (NbSetWeight method) (NEBAnalysis method) (NormalizedAngleDistanceNbSetWeight method) (NsitesModel method) (Nwchem2Fiesta method) (NwInput method) (NwTask method) (Oszicar method) (Outcar method) (PDEntry method) (PeriodicSite method) (PhaseDiagram method) (PhononBandStructure method) (PhononBandStructureSymmLine method) (PhononDos method) (Poscar method) (Potcar method) (PourbaixDiagram method) (PourbaixEntry method) (PPModel method) (Pseudo method) (PseudoTable method) (PWInput method) (QCOutput method) (Reaction method) (RelaxationMethod method) (RemoveExistingFilter method) (SelfCSMNbSetWeight method) (SeparationPlane property) (SimpleAbundanceChemenvStrategy method) (SimpleGraphCycle method) (SimplestChemenvStrategy method) (SimpleVaspToComputedEntryDrone method) (Site method) (Slab method) (SlabEntry method) (Smearing method) (Specie method) (SpecieProximityFilter method) (SpinMode method) (StrategyOption method) (StructureConnectivity method) (StructureEnvironments method) (StructureEnvironments.NeighborsSet method) (StructureGraph method) (StructureMatcher method) (StructureNL method) (Substitutor method) (SymmetrizedStructure method) (SymmetryModel method) (SymmOp method) (Tags method) (TargettedPenaltiedAbundanceChemenvStrategy method) (Tensor method) (TensorCollection method) (ThermoData method) (Trajectory method) (TransformedPDEntry method) (TransformedStructure method) (TranslateSitesTransformation method) (VaspInput method) (VaspInputSet method) (Vasprun method) (VaspToComputedEntryDrone method) (WeightedNbSetChemenvStrategy method) (XcFunc method) (Xmu method) (YamlDoc method) as_dict_summary() (InsertionElectrode method) as_entry() (BalancedReaction method) as_etsfreader() (in module pymatgen.io.abinit.netcdf) as_ncreader() (in module pymatgen.io.abinit.netcdf) as_phononwebsite() (PhononBandStructureSymmLine method) as_ppmodel() (PPModel class method) as_pseudo() (Pseudo class method) as_smearing() (Smearing class method) as_spinmode() (SpinMode class method) as_structure() (in module pymatgen.io.abinit.inputs) as_table() (PseudoTable class method) as_tmpfile() (Pseudo method) as_xyz_string() (SymmOp method) as_xyzt_string() (MagSymmOp method) AseAtomsAdaptor (class in pymatgen.io.ase) ask_yesno() (in module pymatgen.util.io_utils) asr_breaking() (PhononBandStructure method) assertArrayAlmostEqual() (PymatgenTest static method) assertArrayEqual() (PymatgenTest static method) assertDictsAlmostEqual() (PymatgenTest static method) assertMSONable() (PymatgenTest method) assertStrContentEqual() (PymatgenTest static method) assign_selective_dynamics() (AdsorbateSiteFinder method) assign_site_properties() (AdsorbateSiteFinder method) assimilate() (AbstractDrone method) (GaussianToComputedEntryDrone method) (SimpleVaspToComputedEntryDrone method) (VaspToComputedEntryDrone method) asxc() (XcFunc class method) asymmetry() (ElectricFieldGradient property) At (Element attribute) ATOM (AbstractEnvironmentNode attribute) atom_basis_labels (GaussianOutput attribute) atom_symbol() (AbstractEnvironmentNode property) atomic_background() (Eels property) atomic_mass (Element attribute) atomic_mass() (Element property) atomic_no() (PotcarSingle property) atomic_numbers() (SiteCollection property) atomic_orbitals (Element attribute) atomic_radius (Element attribute) atomic_radius() (Element property) atomic_radius_calculated (Element attribute) atomic_symbols (Vasprun attribute) AtomicFile (class in pymatgen.util.io_utils) Atoms (class in pymatgen.io.feff.inputs) atoms() (AbstractFeffInputSet property) (FEFFDictSet property) atoms_and_cell() (RelaxationMethod class method) atoms_only() (RelaxationMethod class method) atoms_string_from_file() (Atoms static method) attribute (PDEntry attribute) Au (Element attribute) Author (class in pymatgen.util.provenance) auto_load() (ChemEnvConfig class method) Automatic (Kpoints_supported_modes attribute) automatic (KSamplingModes attribute) automatic() (Kpoints static method) automatic_density() (Kpoints static method) (KSampling class method) automatic_density_by_vol() (Kpoints static method) automatic_gamma_density() (Kpoints static method) automatic_linemode() (Kpoints static method) AutoOxiStateDecorationTransformation (class in pymatgen.transformations.standard_transformations) AVAILABLE_RADIATION (XRDCalculator attribute) available_strategies (MagneticStructureEnumerator attribute) AVAILABLEKEYWORDS (Lobsterin attribute) ave_bulk_p (WorkFunctionAnalyzer attribute) ave_locpot (WorkFunctionAnalyzer attribute) average_anionic_radius (Element attribute) average_anionic_radius() (Element property) average_cationic_radius (Element attribute) average_cationic_radius() (Element property) average_coordination_number() (in module pymatgen.analysis.structure_analyzer) average_electroneg() (Composition property) average_ionic_radius (Element attribute) average_ionic_radius() (Element property) average_over_unit_sphere() (Tensor method) aweight() (NormalizedAngleDistanceNbSetWeight method) axis_off (WulffShape attribute)

B

B (Element attribute) b (Wavecar attribute) b() (Kpoint property) (Lattice property) (PeriodicSite property) (Plane property) b0() (EOSBase property) b0_GPa() (EOSBase property) b1() (EOSBase property) Ba (Element attribute) BabelMolAdaptor (class in pymatgen.io.babel) bad_sections() (ParallelEfficiency method) bader_analysis_from_objects() (in module pymatgen.command_line.bader_caller) bader_analysis_from_path() (in module pymatgen.command_line.bader_caller) BaderAnalysis (class in pymatgen.command_line.bader_caller) BadIncarWarning BadInputSetWarning BadPotcarWarning BalancedReaction (class in pymatgen.analysis.reaction_calculator) band_edges (MolecularOrbitals attribute) band_energy (Wavecar attribute) band_reorder() (PhononBandStructureSymmLine method) BandEdgeShiftingCorrection (class in pymatgen.analysis.defects.corrections) BandFillingCorrection (class in pymatgen.analysis.defects.corrections) Bandoverlaps (class in pymatgen.io.lobster) bands (BandStructure attribute) BandStructure (class in pymatgen.electronic_structure.bandstructure) BandStructureSymmLine (class in pymatgen.electronic_structure.bandstructure) bary_coords() (Simplex method) barycentric_coords() (in module pymatgen.util.coord) basename() (InputVariable property) (Pseudo property) BasicAbinitInput (class in pymatgen.io.abinit.inputs) BasicAbinitInputError BasicMultiDataset (class in pymatgen.io.abinit.inputs) basis_set (GaussianOutput attribute) BasisSetReader (class in pymatgen.io.fiesta) batch_write_input() (in module pymatgen.io.vasp.sets) batch_write_vasp_input() (in module pymatgen.alchemy.transmuters) BatteryAnalyzer (class in pymatgen.apps.battery.analyzer) bcc() (HighSymmKpath method) bctet1() (HighSymmKpath method) bctet2() (HighSymmKpath method) Be (Element attribute) BE_vs_clean_SE() (SurfaceEnergyPlotter method) BEGIN_TAG (AbinitTimerParser attribute) best_case() (EwaldMinimizer method) best_m_list() (EwaldMinimizer property) beta() (Lattice property) Bi (Element attribute)

Birch (class in pymatgen.analysis.eos) BirchMurnaghan (class in pymatgen.analysis.eos) Bk (Element attribute) block (Element attribute) block() (Element property) block_keys (AdfKey attribute) bohr2ang (ExcitingInput attribute) boiling_point (Element attribute) BoltztrapAnalyzer (class in pymatgen.electronic_structure.boltztrap) BoltztrapError BoltztrapPlotter (class in pymatgen.electronic_structure.plotter) BoltztrapRunner (class in pymatgen.electronic_structure.boltztrap) bond (CriticalPointType attribute) bond_orders (GaussianOutput attribute) BondDissociationEnergies (class in pymatgen.analysis.bond_dissociation) BOOLEANKEYWORDS (Lobsterin attribute) BorgQueen (class in pymatgen.apps.borg.queen) BornEffectiveCharge (class in pymatgen.analysis.piezo_sensitivity) bottom_grain() (GrainBoundary property) Br (Element attribute) break_bond() (IMolecule method) break_edge() (MoleculeGraph method) (StructureGraph method) brinell_hardness (Element attribute) BrunnerNN_real (class in pymatgen.analysis.local_env) BrunnerNN_reciprocal (class in pymatgen.analysis.local_env) BrunnerNN_relative (class in pymatgen.analysis.local_env) bs() (BoltztrapRunner property) bs_plot_data() (BSPlotter method) (PhononBSPlotter method) BSDOSPlotter (class in pymatgen.electronic_structure.plotter) bse_run() (FiestaRun method) BSEOutput (class in pymatgen.io.fiesta) BSPlotter (class in pymatgen.electronic_structure.plotter) BSPlotterProjected (class in pymatgen.electronic_structure.plotter) BSVasprun (class in pymatgen.io.vasp.outputs) buckingham_input() (GulpIO method) buckingham_potential() (GulpIO method) BuckinghamPotential (class in pymatgen.command_line.gulp_caller) build_bader() (in module pymatgen.cli.pmg_config) build_enum() (in module pymatgen.cli.pmg_config) build_new_entry() (BondDissociationEnergies method) build_slabs() (ReconstructionGenerator method) build_unique_fragments() (MoleculeGraph method) bulk_gform() (NanoscaleStability method) bulk_modulus (Element attribute) bulk_structure() (Defect property) (DefectEntry property) BVA_DISTANCE_SCALE_FACTORS (LocalGeometryFinder attribute) BVAnalyzer (class in pymatgen.analysis.bond_valence) BVAValencesNotFoundChemenvError

C

C (Element attribute) c() (Kpoint property) (Lattice property) (PeriodicSite property) (Plane property) Ca (Element attribute) cage (CriticalPointType attribute) cahill_thermalcond() (ElasticTensor method) calc() (Xmu property) calc_ionic() (in module pymatgen.analysis.ferroelectricity.polarization) calc_shiftk() (in module pymatgen.io.abinit.inputs) calculate() (SubstrateAnalyzer method) calculate_3D_elastic_energy() (SubstrateAnalyzer method) calculate_bv_sum() (in module pymatgen.analysis.bond_valence) calculate_bv_sum_unordered() (in module pymatgen.analysis.bond_valence) calculate_dimensionality_of_site() (in module pymatgen.analysis.dimensionality) calculate_energy() (BalancedReaction method) calculate_stress() (ElasticTensorExpansion method) (NthOrderElasticTensor method) calculate_vol() (in module pymatgen.analysis.defects.utils) calculate_weighted_avg() (in module pymatgen.analysis.local_env) calculated_reaction_energy() (ComputedReaction property) cart_coords() (Kpoint property) (SiteCollection property) cart_forces (GaussianOutput attribute) Cartesian (Kpoints_supported_modes attribute) categorize_functional_groups() (FunctionalGroupExtractor method) Cd (Element attribute) cder_data() (Waveder property) Ce (Element attribute) ce() (AbstractEnvironmentNode property) CE_NNBCES_NBCES_LIGANDS (AbstractEnvironmentNode attribute) ce_symbol() (AbstractEnvironmentNode property) (CoordinationGeometry property) center_of_mass() (IMolecule property) (Slab property) center_slab (SlabGenerator attribute) center_slab() (in module pymatgen.core.surface) Cf (Element attribute) change_z_shift() (Interface method) changebasis() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) Charge (class in pymatgen.io.lobster) charge (GaussianOutput attribute) Charge (in module pymatgen.core.units) charge (Outcar attribute) charge() (Defect property) (DefectEntry property) (IMolecule property) (Ion property) (IStructure property) (SiteCollection property) charge_distribution_df() (ChargeDensityAnalyzer property) CHARGE_NEUTRALITY_TOLERANCE (BVAnalyzer attribute) charge_transfer_from_file() (LDos static method) charge_transfer_to_string() (LDos method) ChargeBalanceFilter (class in pymatgen.alchemy.filters) ChargeBalanceTransformation (class in pymatgen.transformations.advanced_transformations) ChargedCellTransformation (class in pymatgen.transformations.standard_transformations) ChargeDensityAnalyzer (class in pymatgen.analysis.defects.utils) check_acc_bzt_bands() (BoltztrapAnalyzer static method) check_condition() (AdditionalConditions method) check_final_relaxed_structure_delocalized() (DefectCompatibility method) check_freysoldt_delocalized() (DefectCompatibility method) check_kumagai_delocalized() (DefectCompatibility method) check_params() (Incar method) check_volume() (TopographyAnalyzer method) chemenv_citations() (in module pymatgen.analysis.chemenv.utils.defs_utils) ChemEnvConfig (class in pymatgen.analysis.chemenv.utils.chemenv_config) ChemenvError ChemenvStrategyError chemical_shielding (Outcar attribute) chemical_symbols (ETSF_Reader attribute) chemical_system() (Composition property) ChemicalEnvironments (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) ChemicalPotential (class in pymatgen.core.composition) ChemicalShielding (class in pymatgen.analysis.nmr) ChemicalShielding.MarylandNotation (class in pymatgen.analysis.nmr) ChemicalShielding.MehringNotation (class in pymatgen.analysis.nmr) chempot_plot_addons() (SurfaceEnergyPlotter method) chempot_vs_gamma() (SurfaceEnergyPlotter method) chempot_vs_gamma_plot_one() (SurfaceEnergyPlotter method) chemsys() (EntrySet property) Chgcar (class in pymatgen.io.vasp.outputs) ChgcarPotential (class in pymatgen.analysis.path_finder) chi() (Xmu property) CifBlock (class in pymatgen.io.cif) CifFile (class in pymatgen.io.cif) CifParser (class in pymatgen.io.cif) CifTransmuter (class in pymatgen.alchemy.transmuters) CifWriter (class in pymatgen.io.cif) Cl (Element attribute) clarke_thermalcond() (ElasticTensor method) ClassTypeChemenvError clean() (in module pymatgen.io.abinit.helpers) clean_lines() (in module pymatgen.util.io_utils) cleaned_up_slab() (SlabEntry property) clear_environments() (LightStructureEnvironments method) close() (AtomicFile method) (NetcdfReader method) (YamlTokenizer method) closestsites() (in module pymatgen.analysis.defects.utils) cluster() (Atoms property) cluster_from_file() (Atoms static method) cluster_nodes() (ChargeDensityAnalyzer method) (TopographyAnalyzer method) cluster_sites() (in module pymatgen.symmetry.analyzer) Cm (Element attribute) cn() (AbstractGeometry property) CNBiasNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) Co (Element attribute) COD (class in pymatgen.ext.cod) coefficient_of_linear_thermal_expansion (Element attribute) coefficients() (Plane property) coeffs (Wavecar attribute) coeffs() (BalancedReaction property) Cohp (class in pymatgen.electronic_structure.cohp) Cohpcar (class in pymatgen.io.lobster) CohpPlotter (class in pymatgen.electronic_structure.plotter) coincidents() (GrainBoundary property) collinear() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) CollinearMagneticStructureAnalyzer (class in pymatgen.analysis.magnetism.analyzer) color_area (WulffShape attribute) color_dict (SurfaceEnergyPlotter attribute) color_palette_dict() (SurfaceEnergyPlotter method) color_set (WulffShape attribute) colours (StringColorizer attribute) combine_neb_plots() (in module pymatgen.analysis.transition_state) combine_slabs() (InterfaceBuilder method) CombinedData (class in pymatgen.io.lammps.data) combiplot() (CyclesPlotter method) comment (Poscar attribute) (Xdatcar attribute) comment() (BasicAbinitInput property) common_oxidation_states (Element attribute) common_oxidation_states() (Element property) compare_structures() (in module pymatgen.cli.pmg_structure) compare_sym_bands() (in module pymatgen.electronic_structure.boltztrap) Compatibility (class in pymatgen.entries.compatibility) CompatibilityError complete_dos() (Vasprun property) CompleteCohp (class in pymatgen.electronic_structure.cohp) CompleteDos (class in pymatgen.electronic_structure.dos) completedos (Doscar attribute) completedos() (Doscar property) CompletePhononDos (class in pymatgen.phonon.dos) compliance_tensor() (ElasticTensor property) ComplianceTensor (class in pymatgen.analysis.elasticity.elastic) Composition (class in pymatgen.core.composition) composition (MolecularOrbitals attribute) (PDEntry attribute)

composition() (ConversionElectrode property) (Ion property) (PourbaixEntry property) (SiteCollection property) composition_prediction() (SubstitutionPredictor method) CompositionError CompoundPhaseDiagram (class in pymatgen.analysis.phase_diagram) compute_average_oxidation_state() (in module pymatgen.analysis.ewald) compute_coordination_environments() (LocalGeometryFinder method) compute_defect_density() (in module pymatgen.analysis.defects.dilute_solution_model) compute_environments() (in module pymatgen.analysis.chemenv.utils.scripts_utils) compute_md5() (Pseudo method) compute_offset_vectors() (in module pymatgen.optimization.neighbors) compute_partial_energy() (EwaldSummation method) compute_periodicity() (ConnectedComponent method) compute_periodicity_all_simple_paths_algorithm() (ConnectedComponent method) compute_periodicity_cycle_basis() (ConnectedComponent method) compute_structure_environments() (LocalGeometryFinder method) compute_sub_structure() (EwaldSummation method) compute_trigonometric_terms() (LocalStructOrderParams method) ComputedEntry (class in pymatgen.entries.computed_entries) ComputedReaction (class in pymatgen.analysis.reaction_calculator) ComputedStructureEntry (class in pymatgen.entries.computed_entries) conc_term() (PourbaixEntry property) concatenate() (Xdatcar method) CONDITION_DESCRIPTION (AdditionalConditions attribute) confab_conformers() (BabelMolAdaptor method) CONFIG (LobsterSet attribute) (MITRelaxSet attribute) (MPELNESSet attribute) (MPEXAFSSet attribute) (MPEXELFSSet attribute) (MPHSERelaxSet attribute) (MPMetalRelaxSet attribute) (MPRelaxSet attribute) (MPScanRelaxSet attribute) (MPXANESSet attribute) (MVLGWSet attribute) (MVLRelax52Set attribute) configure_pmg() (in module pymatgen.cli.pmg_config) ConnectedComponent (class in pymatgen.analysis.chemenv.connectivity.connected_components) ConnectedSite (class in pymatgen.analysis.graphs) connectivity_array() (VoronoiConnectivity property) ConnectivityFinder (class in pymatgen.analysis.chemenv.connectivity.connectivity_finder) Constraints (class in pymatgen.io.abinit.abiobjects) contains_element_type() (Composition method) contains_only_one_anion() (LightStructureEnvironments method) contains_only_one_anion_atom() (LightStructureEnvironments method) contains_peroxide() (in module pymatgen.analysis.structure_analyzer) ContainsSpecieFilter (class in pymatgen.alchemy.filters) continuous_symmetry_measure_cutoff() (SimplestChemenvStrategy property) contract() (in module pymatgen.io.abinit.abiobjects) Control (class in pymatgen.io.shengbte) CONV_FACT (EwaldSummation attribute) conventional() (HighSymmKpath property) ConventionalCellTransformation (class in pymatgen.transformations.standard_transformations) converge() (in module pymatgen.analysis.defects.utils) converged() (Vasprun property) converged_electronic() (Vasprun property) converged_ionic() (Vasprun property) ConversionElectrode (class in pymatgen.apps.battery.conversion_battery) conversions() (ArrayWithUnit method) ConversionVoltagePair (class in pymatgen.apps.battery.conversion_battery) convert_fmt() (in module pymatgen.cli.pmg_structure) convert_obatoms_to_molecule() (PackmolRunner method) convert_strain_to_deformation() (in module pymatgen.analysis.elasticity.strain) convert_to_ieee() (Tensor method) (TensorCollection method) coord_list_mapping() (in module pymatgen.util.coord) coord_list_mapping_pbc() (in module pymatgen.util.coord) (in module pymatgen.util.coord_cython) coordination() (VoronoiPolyhedron property) COORDINATION_ENVIRONMENT (AbstractEnvironmentNode attribute) coordination_environment() (AbstractEnvironmentNode property) (EnvironmentNode property) coordination_geometry_symmetry_measures() (LocalGeometryFinder method) coordination_geometry_symmetry_measures_fallback_random() (LocalGeometryFinder method) coordination_geometry_symmetry_measures_separation_plane() (LocalGeometryFinder method) coordination_geometry_symmetry_measures_separation_plane_optim() (LocalGeometryFinder method) coordination_geometry_symmetry_measures_sepplane_optim() (LocalGeometryFinder method) coordination_geometry_symmetry_measures_standard() (LocalGeometryFinder method) coordination_number() (AbstractGeometry property) (CoordinationGeometry property) coordination_sequence() (ConnectedComponent method) CoordinationGeometry (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) CoordinationGeometry.NeighborsSetsHints (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) coords() (PeriodicNeighbor property) (PeriodicSite property) (Simplex property) (StructureEnvironments.NeighborsSet property) copy() (Composition method) (Defect method) (DefectEntry method) (GrainBoundary method) (Interface method) (IStructure method) (Lattice method) (Molecule method) (Reaction method) (Slab method) (Spectrum method) (SymmetrizedStructure method) (Trajectory method) (VolumetricData method) correct_entry() (Correction method) (DefectCorrection method) Correction (class in pymatgen.entries.compatibility) corrections (GaussianOutput attribute) cosinus_step() (in module pymatgen.analysis.chemenv.utils.math_utils) CostAnalyzer (class in pymatgen.analysis.cost) CostDB (class in pymatgen.analysis.cost) CostDBCSV (class in pymatgen.analysis.cost) CostEntry (class in pymatgen.analysis.cost) coth() (in module pymatgen.phonon.dos) coupling_constant() (ElectricFieldGradient method) CovalentBond (class in pymatgen.core.bonds) CovalentBondNN (class in pymatgen.analysis.local_env) CovalentRadius (class in pymatgen.analysis.molecule_structure_comparator) cpuwall_histogram() (AbinitTimer method) Cr (Element attribute) create_saturated_interstitial_structure() (in module pymatgen.analysis.defects.core) create_slab_label() (SlabEntry property) Critic2Caller (class in pymatgen.command_line.critic2_caller) Critic2NN (class in pymatgen.analysis.local_env) Critic2Output (class in pymatgen.command_line.critic2_caller) critical_temp (VampireOutput attribute) critical_temperature (Element attribute) CriticalPoint (class in pymatgen.command_line.critic2_caller) CriticalPointType (class in pymatgen.command_line.critic2_caller) crosses_origin() (Plane property) crystal_keys (Control attribute) CrystalAIRester (class in pymatgen.ext.crystalsai) CrystalNN (class in pymatgen.analysis.local_env) Cs (Element attribute) cs_core_contribution (Outcar attribute) cs_g0_contribution (Outcar attribute) CSM_SKIP_SEPARATION_PLANE_ALGO (CoordinationGeometry attribute) CSMFiniteRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) CSMFloat (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) CSMInfiniteRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) Cssr (class in pymatgen.io.cssr) Cu (Element attribute) cubic() (HighSymmKpath method) (Lattice static method) CubicSupercellTransformation (class in pymatgen.transformations.advanced_transformations) CutOffDictNN (class in pymatgen.analysis.local_env) cv() (PhononDos method) CyclesPlotter (class in pymatgen.io.abinit.abiinspect)

D

d (OrbitalType attribute) d() (Plane property) D2DEScfCycle (class in pymatgen.io.abinit.abiinspect) d_hkl() (Lattice method) data (Dynmat attribute) (PotcarSingle attribute) (Procar attribute) (Wavederf attribute) data() (Element property) dataset() (InputVariable property) debug (WulffShape attribute) debye_integral() (QuasiharmonicDebyeApprox static method) debye_temperature() (ElasticTensor method) (QuasiharmonicDebyeApprox method) debye_temperature_from_sound_velocities() (ElasticTensor method) deepcopy() (AbstractInput method) (BasicMultiDataset method) DEFAULT_ADDITIONAL_CONDITION (SimpleAbundanceChemenvStrategy attribute) (SimplestChemenvStrategy attribute) DEFAULT_ANGLE_CUTOFF (SimplestChemenvStrategy attribute) DEFAULT_ANIMATED_MOVIE_OPTIONS (MultiStructuresVis attribute) DEFAULT_BVA_DISTANCE_SCALE_FACTOR (LocalGeometryFinder attribute) DEFAULT_CE_ESTIMATOR (MultiWeightsChemenvStrategy attribute) (WeightedNbSetChemenvStrategy attribute) DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF (SimplestChemenvStrategy attribute) DEFAULT_DIST_ANG_AREA_WEIGHT (MultiWeightsChemenvStrategy attribute) DEFAULT_DISTANCE_CUTOFF (SimplestChemenvStrategy attribute) DEFAULT_EFFECTIVE_CSM_ESTIMATOR (DeltaCSMNbSetWeight attribute) (SelfCSMNbSetWeight attribute) DEFAULT_EXTENSIONS (AbstractEnvironmentNode attribute) DEFAULT_MAX_DIST (SimpleAbundanceChemenvStrategy attribute) default_normalized_angle_tolerance (DetailedVoronoiContainer attribute) default_normalized_distance_tolerance (DetailedVoronoiContainer attribute) DEFAULT_PACKAGE_OPTIONS (ChemEnvConfig attribute) DEFAULT_SPG_ANALYZER_OPTIONS (LocalGeometryFinder attribute) DEFAULT_STATISTICS_FIELDS (LightStructureEnvironments attribute) DEFAULT_STRATEGY (LocalGeometryFinder attribute) DEFAULT_SURFACE_DEFINITION (DistanceAngleAreaNbSetWeight attribute) DEFAULT_SYMMETRY_MEASURE_TYPE (AbstractChemenvStrategy attribute) (DeltaCSMNbSetWeight attribute) (SelfCSMNbSetWeight attribute) DEFAULT_TARGET_ENVIRONMENTS (TargettedPenaltiedAbundanceChemenvStrategy attribute) default_voronoi_cutoff (DetailedVoronoiContainer attribute) DEFAULT_WEIGHT_ESTIMATOR (DeltaCSMNbSetWeight attribute) (SelfCSMNbSetWeight attribute) Defect (class in pymatgen.analysis.defects.core) defect_composition() (Defect property) (Interstitial property) (Substitution property) (Vacancy property) defect_concentration() (DefectEntry method) defect_concentrations() (DefectPhaseDiagram method) defect_types() (DefectPhaseDiagram property) DefectCompatibility (class in pymatgen.analysis.defects.defect_compatibility) DefectCorrection (class in pymatgen.analysis.defects.core) DefectEntry (class in pymatgen.analysis.defects.core) DefectGenerator (class in pymatgen.analysis.defects.generators) DefectPhaseDiagram (class in pymatgen.analysis.defects.thermodynamics) DefectTransformation (class in pymatgen.transformations.defect_transformations) defined_aliases (XcFunc attribute) Deformation (class in pymatgen.analysis.elasticity.strain) deformation() (MagneticDeformation property) DeformedStructureSet (class in pymatgen.analysis.elasticity.strain) DeformStructureTransformation (class in pymatgen.transformations.standard_transformations) delete_snl() (MPRester method) delocalization_analysis() (DefectCompatibility method) delta_cn_specifics() (DeltaCSMNbSetWeight class method) DELTA_MAX_OXIDATION_STATE (LightStructureEnvironments attribute) DeltaCSMNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DeltaCSMRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) DeltaDistanceNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DeltaFactor (class in pymatgen.analysis.eos) density() (IStructure property) density_of_solid (Element attribute) description (AdditionalConditionInt attribute) (HistoryNode attribute) description() (ConnectedComponent method) det() (SquareTensor property) DetailedVoronoiContainer (class in pymatgen.analysis.chemenv.coordination_environments.voronoi) determine_convergence() (in module pymatgen.util.convergence) determine_min_cell() (MagOrderingTransformation static method)

dev_principal_invariants() (Stress property) deviator_stress() (Stress property) dft_task() (NwTask class method) diamond_functions() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) DictSet (class in pymatgen.io.vasp.sets) dielectric() (Vasprun property) dieze_tag (GaussianOutput attribute) diff() (Incar method) (Lobsterin method) (MoleculeGraph method) (StructureGraph method) (Tags method) diff_fit() (in module pymatgen.analysis.elasticity.elastic) diff_incar() (in module pymatgen.cli.pmg) differences_wrt() (StructureEnvironments method) DiffractionPattern (class in pymatgen.analysis.diffraction.core) DiffusionAnalyzer (class in pymatgen.analysis.diffusion_analyzer) dipole() (Slab property) directional_elastic_mod() (ElasticTensor method) directional_poisson_ratio() (ElasticTensor method) disassemble() (LammpsData method) discard() (AtomicFile method) (EntrySet method) DiscretizeOccupanciesTransformation (class in pymatgen.transformations.standard_transformations) disordered_formula() (in module pymatgen.util.string) DisorderOrderedTransformation (class in pymatgen.transformations.advanced_transformations) display_help() (MultiStructuresVis method) (StructureVis method) display_info() (MultiStructuresVis method) display_warning() (MultiStructuresVis method) dist() (ConnectedSite property) distance() (PeriodicSite method) (Site method) distance_and_image() (PeriodicSite method) distance_and_image_from_frac_coords() (PeriodicSite method) distance_cutoff() (SimplestChemenvStrategy property) distance_from_point() (Site method) distance_matrix() (IStructure property) (SiteCollection property) distance_plateau() (StructureEnvironments.NeighborsSet method) distance_to_origin() (Plane property) distance_to_point() (Plane method) DISTANCE_TOLERANCE (SiteCollection attribute) DistanceAngleAreaNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DistanceCutoffFloat (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DistanceNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DistancePlateauNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) distances() (Plane method) (StructureEnvironments.NeighborsSet property) distances_indices_groups() (Plane method) distances_indices_sorted() (Plane method) distfactor_max() (CoordinationGeometry property) divisors() (in module pymatgen.analysis.chemenv.utils.math_utils) djrepo_path() (Pseudo property) DLSVolumePredictor (class in pymatgen.analysis.structure_prediction.volume_predictor) do_query() (in module pymatgen.cli.pmg_query) domain_vertices() (PourbaixPlotter method) DopingTransformation (class in pymatgen.transformations.advanced_transformations) DOS (class in pymatgen.electronic_structure.dos) Dos (class in pymatgen.electronic_structure.dos) Doscar (class in pymatgen.io.lobster) DosPlotter (class in pymatgen.electronic_structure.plotter) dot() (Lattice method) double_cap_hints() (CoordinationGeometry.NeighborsSetsHints method) down (Spin attribute) draw_cg() (in module pymatgen.analysis.chemenv.utils.scripts_utils) draw_graph_to_file() (MoleculeGraph method) (StructureGraph method) draw_network() (in module pymatgen.analysis.chemenv.connectivity.connected_components) drift (Outcar attribute) dual_cv_simp (WulffShape attribute) DummySpecie (class in pymatgen.core.periodic_table) dump_BSE_data_in_GW_run() (FiestaInput method) dump_TDDFT_data_in_GW_run() (FiestaInput method) dx2 (Orbital attribute) dxy (Orbital attribute) dxz (Orbital attribute) Dy (Element attribute) Dynmat (class in pymatgen.io.vasp.outputs) dyz (Orbital attribute) dz2 (Orbital attribute)

E

E() (Orbital property) (OrbitalDescription property) e0() (EOSBase property) e_fermi() (Xmu property) e_surf_list (WulffShape attribute) ebands_input() (in module pymatgen.io.abinit.inputs) EconNN (class in pymatgen.analysis.local_env) edge() (Xmu property) edge_weight_name() (MoleculeGraph property) (StructureGraph property) edge_weight_unit() (MoleculeGraph property) (StructureGraph property) edges() (CoordinationGeometry method) Eels (class in pymatgen.io.feff.outputs) efermi (BandStructure attribute) (Vasprun attribute) (Wavecar attribute) (WorkFunctionAnalyzer attribute) effective_radius() (WulffShape property) efg (Outcar attribute) Eigenval (class in pymatgen.io.vasp.outputs) eigenvalue_band_properties() (Eigenval property) (Vasprun property) eigenvalues (Eigenval attribute) (GaussianOutput attribute) (Vasprun attribute) eigenvectors (GaussianOutput attribute) eigenvectors_from_displacements() (in module pymatgen.phonon.bandstructure) eigvec_to_eigdispl() (in module pymatgen.io.phonopy) einsum_sequence() (Tensor method) elastic_centered_graph() (ConnectedComponent method) elastic_tensor (Outcar attribute) ElasticTensor (class in pymatgen.analysis.elasticity.elastic) ElasticTensorExpansion (class in pymatgen.analysis.elasticity.elastic) elec_neg (MolecularOrbitals attribute) electrical_resistivity (Element attribute) ElectricFieldGradient (class in pymatgen.analysis.nmr) electron_configuration() (PotcarSingle property) electronic_steps (Oszicar attribute) electronic_structure (Element attribute) Electrons (class in pymatgen.io.abinit.abiobjects) electrons (GaussianOutput attribute) ElectronsAlgorithm (class in pymatgen.io.abinit.abiobjects) Element (class in pymatgen.core.periodic_table) element() (PotcarSingle property) (Pseudo property) (Specie property) element_composition() (Composition property) ElementComparator (class in pymatgen.analysis.structure_matcher) elements (MolecularOrbitals attribute) elements() (BalancedReaction property) (Composition property) Elfcar (class in pymatgen.io.vasp.outputs) ellipticity() (CriticalPoint property) email (Author attribute) encut (Wavecar attribute) END_TAG (AbinitTimerParser attribute) endpoints_minima() (EnergyTrend method) energies (AdfOutput attribute) (Doscar attribute), [1], [2] (GaussianOutput attribute) energies() (Doscar property) (Eels property) (Xmu property) Energy (in module pymatgen.core.units) energy (PDEntry attribute) energy() (ComputedEntry property) (DefectEntry property) (Entry property) (PDEntry property) (PourbaixEntry property) energy_at_conditions() (PourbaixEntry method) energy_density() (ElasticTensorExpansion method) (NthOrderElasticTensor method) energy_per_atom() (Entry property) (PourbaixEntry property) EnergyModel (class in pymatgen.analysis.energy_models) EnergyTrend (class in pymatgen.analysis.ferroelectricity.polarization) ensemble_center() (AdsorbateSiteFinder method) entries_charge() (ConversionVoltagePair property) entries_discharge() (ConversionVoltagePair property) entropy() (PhononDos method)

Entry (class in pymatgen.entries) entry_dict_from_list() (in module pymatgen.analysis.surface_analysis) EntrySet (class in pymatgen.entries.entry_tools) enum_possible_plane_cubic() (GrainBoundaryGenerator static method) enum_sigma_cubic() (GrainBoundaryGenerator static method) enum_sigma_hex() (GrainBoundaryGenerator static method) enum_sigma_ort() (GrainBoundaryGenerator static method) enum_sigma_rho() (GrainBoundaryGenerator static method) enum_sigma_tet() (GrainBoundaryGenerator static method) enumerate_defectsites() (StructureMotifInterstitial method) EnumerateStructureTransformation (class in pymatgen.transformations.advanced_transformations) EnumError EnumlibAdaptor() (in module pymatgen.command_line.enumlib_caller) environment_subgraph() (StructureConnectivity method) EnvironmentNode (class in pymatgen.analysis.chemenv.connectivity.environment_nodes) environments_identified() (LightStructureEnvironments method) EOS (class in pymatgen.analysis.eos) EOSBase (class in pymatgen.analysis.eos) EOSError epsilon_ionic() (Vasprun property) epsilon_static() (Vasprun property) epsilon_static_wolfe() (Vasprun property) equivalent_site_index_and_transform() (AbstractChemenvStrategy method) EquivalentSiteSearchError Er (Element attribute) erase_info() (MultiStructuresVis method) erase_warning() (MultiStructuresVis method) Error (AbinitTimerParser attribute) error (AdfOutput attribute) Error (ArrayWithUnit attribute) (BasicAbinitInput attribute) (BasicMultiDataset attribute) (FloatWithUnit attribute) (NetcdfReader attribute) (Unit attribute) (YamlTokenizer attribute) errors (GaussianOutput attribute) Es (Element attribute) esp_task() (NwTask class method) estimate_band_connection() (in module pymatgen.phonon.bandstructure) estimate_exchange() (HeisenbergMapper method) eta() (EwaldSummation property) eta_from_seebeck() (in module pymatgen.electronic_structure.boltztrap) ETSF_Reader (class in pymatgen.io.abinit.netcdf) Eu (Element attribute) eV_to_k() (in module pymatgen.analysis.defects.utils) EV_TO_KJ_PER_MOL (InterfacialReactivity attribute) evaluate() (AbstractRatioFunction method) evaluate_wavefunc() (Wavecar method) everything_equal() (AbstractEnvironmentNode method) (EnvironmentNode method) EwaldElectrostaticModel (class in pymatgen.analysis.energy_models) EwaldMinimizer (class in pymatgen.analysis.ewald) EwaldSummation (class in pymatgen.analysis.ewald) ExcHamiltonian (class in pymatgen.io.abinit.abiobjects) ExcitationSpectrum (class in pymatgen.analysis.excitation) ExcitingInput (class in pymatgen.io.exciting.inputs) expand() (in module pymatgen.io.abinit.helpers) ExpEntry (class in pymatgen.entries.exp_entries) explain() (Compatibility method) explicit() (CNBiasNbSetWeight class method) explicit_path() (KSampling class method) ExplicitPermutationsAlgorithm (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) exponential() (in module pymatgen.util.convergence) export_msdt() (DiffusionAnalyzer method) extend() (BasicMultiDataset method) (Trajectory method) extend_structure_molecules() (CovalentBondNN property) (Critic2NN property) (CutOffDictNN property) (EconNN property) (JmolNN property) (MinimumDistanceNN property) (MinimumOKeeffeNN property) (NearNeighbors property) (OpenBabelNN property) extend_transformations() (StandardTransmuter method) (TransformedStructure method) extract_cluster() (SiteCollection method) extrapolate_reciprocal() (in module pymatgen.util.convergence) extrapolate_simple_reciprocal() (in module pymatgen.util.convergence) extrema_df() (ChargeDensityAnalyzer property) extremum_icohpvalue() (IcohpCollection method)

F

F (Element attribute) f (OrbitalType attribute) f0 (Orbital attribute) f0() (in module pymatgen.electronic_structure.dos) f1 (Orbital attribute) f2 (Orbital attribute) f3 (Orbital attribute) f_1 (Orbital attribute) f_2 (Orbital attribute) f_3 (Orbital attribute) faces() (CoordinationGeometry method) facets (WulffShape attribute) factor() (FreqUnits property) factors() (in module pymatgen.analysis.gb.grain) fake() (AbinitTimerSection class method) farid (PPModelModes attribute) fast_norm() (in module pymatgen.analysis.substrate_analyzer) Fatband (class in pymatgen.io.lobster) fcc() (HighSymmKpath method) Fe (Element attribute) FEFFDictSet (class in pymatgen.io.feff.sets) FeffParserError FermiDos (class in pymatgen.electronic_structure.dos) fft_mesh() (Wavecar method) FIELDS (AbinitTimerSection attribute) FiestaInput (class in pymatgen.io.fiesta) FiestaOutput (class in pymatgen.io.fiesta) FiestaRun (class in pymatgen.io.fiesta) filename (Eigenval attribute) (Wavecar attribute) filenames() (AbinitTimerParser property) filepath() (Pseudo property) film() (Interface property) film_sites() (Interface property) filter_fragment_entries() (BondDissociationEnergies method) FiM (Ordering attribute) final_energy (AdfOutput attribute) final_energy() (GaussianOutput property) (Oszicar property) (PWOutput property) (Vasprun property) final_structure (AdfOutput attribute) final_structure() (GaussianOutput property) find_adsorption_sites() (AdsorbateSiteFinder method) find_all_mappings() (Lattice method) find_clusters() (in module pymatgen.analysis.dimensionality) find_connected_atoms() (in module pymatgen.analysis.dimensionality) find_eq_stress() (in module pymatgen.analysis.elasticity.elastic) find_equivalent_sites() (SymmetrizedStructure method) find_in_coord_list() (in module pymatgen.util.coord) find_in_coord_list_pbc() (in module pymatgen.util.coord) find_mapping() (Lattice method) find_neighbors() (in module pymatgen.core.lattice) find_points_in_spheres() (in module pymatgen.optimization.neighbors) find_primitive() (SpacegroupAnalyzer method) find_rings() (MoleculeGraph method) find_rotation() (in module pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) find_scaling_factor() (in module pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) find_sections() (QCInput static method) find_stable_charges() (DefectPhaseDiagram method) find_stable_entry() (PourbaixDiagram method) find_structure() (MPRester method) find_surface_sites_by_height() (AdsorbateSiteFinder method) fine_structure() (Eels property) fit() (DeltaFactor method) (EOS method) (EOSBase method) (MoleculeMatcher method) (NumericalEOS method) (PolynomialEOS method) (StructureMatcher method) fit_anonymous() (StructureMatcher method) fit_arrhenius() (in module pymatgen.analysis.diffusion_analyzer) fit_error() (Plane method) fit_least_square_distance_error() (Plane method) fit_maximum_distance_error() (Plane method) fit_to_structure() (Tensor method) (TensorCollection method) fix_pbc() (in module pymatgen.analysis.gb.grain) flags_keys (Control attribute) FLOATKEYWORDS (Lobsterin attribute) FloatWithUnit (class in pymatgen.core.units) Fm (Element attribute) FM (Ordering attribute) fn (PymatgenTest attribute) fold_point() (in module pymatgen.electronic_structure.plotter) force_constants (Vasprun attribute) force_field (ForceField attribute) ForceConstantMatrix (class in pymatgen.analysis.piezo_sensitivity) ForceField (class in pymatgen.io.lammps.data) forces() (EwaldSummation property) format_formula() (in module pymatgen.util.plotting) format_list() (InputVariable method) format_list2d() (InputVariable method) format_scalar() (InputVariable method) formation_energy() (DefectEntry method) formation_energy_tol (PhaseDiagram attribute) formula() (Composition property) (Header property) (Ion property) (SiteCollection property) formula_double_format() (in module pymatgen.util.string) Fr (Element attribute) frac_charge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) frac_coords() (IStructure property) (Kpoint property) (PeriodicSite property) frac_discharge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) fractional_composition() (Composition property) fractions() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) fragment_and_process() (BondDissociationEnergies method) Fragmenter (class in pymatgen.analysis.fragmenter) FrameworkComparator (class in pymatgen.analysis.structure_matcher) FreeVolumePotential (class in pymatgen.analysis.path_finder) freq_type (AdfOutput attribute) freq_units() (in module pymatgen.phonon.plotter) FreqSet (class in pymatgen.io.qchem.sets) frequencies (AdfOutput attribute) (GaussianOutput attribute) frequencies() (Outcar property) FreqUnits (class in pymatgen.phonon.plotter) FreysoldtCorrection (class in pymatgen.analysis.defects.corrections) from_2points_and_origin() (Plane class method) from_3points() (Plane class method) from_abinit_ixc() (XcFunc class method) from_axis_angle_and_translation() (SymmOp static method) from_bonding() (Topology class method) from_bson_voronoi_list2() (in module pymatgen.analysis.chemenv.coordination_environments.voronoi) from_bulk_and_miller() (AdsorbateSiteFinder class method) from_cg() (AbstractGeometry class method) from_cif_file() (Header static method) from_cif_string() (TransformedStructure static method) from_coefficients() (Plane class method) from_composition_and_entries() (ConversionElectrode static method) from_composition_and_pd() (ConversionElectrode static method) from_computed_structure_entry() (SlabEntry static method) from_csv() (EntrySet class method) from_deformation() (Strain class method) from_description() (CNBiasNbSetWeight class method) from_dict (Element attribute) (LibxcFunc attribute) from_dict() (AbstractChemenvStrategy class method) (AbstractComparator class method) (AbstractMolAtomMapper class method) (AbstractRatioFunction class method) (AdditionalConditionInt class method) (AdfKey class method) (AdfTask class method) (AngleCutoffFloat class method) (AngleNbSetWeight class method) (AnglePlateauNbSetWeight class method) (Author static method) (BalancedReaction class method) (BandStructure class method) (BandStructureSymmLine class method) (BasicAbinitInput class method) (BoltztrapAnalyzer static method) (ChemicalEnvironments class method) (CNBiasNbSetWeight class method) (Cohp class method) (CompleteCohp class method) (CompleteDos class method) (CompletePhononDos class method) (Composition class method) (CompoundPhaseDiagram class method) (ComputedEntry class method) (ComputedReaction class method) (ComputedStructureEntry class method) (ConnectedComponent class method) (ContainsSpecieFilter class method) (Control class method) (ConversionElectrode class method) (ConversionVoltagePair class method) (CoordinationGeometry class method) (CoordinationGeometry.NeighborsSetsHints class method) (CSMFloat class method) (DefectEntry class method) (DefectPhaseDiagram class method) (DeltaCSMNbSetWeight class method) (DeltaDistanceNbSetWeight class method) (DetailedVoronoiContainer class method) (DiffusionAnalyzer class method) (DistanceAngleAreaNbSetWeight class method) (DistanceCutoffFloat class method) (DistanceNbSetWeight class method) (DistancePlateauNbSetWeight class method) (Dos class method) (DummySpecie class method) (Electrons class method) (ElectronsAlgorithm class method) (EnergyModel class method) (ExpEntry class method) (ExplicitPermutationsAlgorithm class method) (FermiDos class method) (FiestaInput class method) (FiestaRun class method) (ForceField class method) (GaussianInput class method) (GaussianToComputedEntryDrone class method) (GrainBoundary class method) (GrandPotentialPhaseDiagram class method) (GrandPotPDEntry class method) (HistoryNode static method) (IMolecule class method) (Incar class method) (InchiMolAtomMapper class method) (InsertionElectrode class method) (Interface class method) (Ion class method) (IonEntry class method) (IRDielectricTensor class method) (IsomorphismMolAtomMapper class method) (IStructure class method) (Kpoints class method) (KSampling class method) (LammpsData class method) (LammpsDump class method) (Lattice class method) (LightStructureEnvironments class method) (LightStructureEnvironments.NeighborsSet class method) (LMTOCtrl class method) (LobsterBandStructureSymmLine class method) (LobsterCompleteDos class method) (Lobsterin class method) (MagSymmOp class method) (MoleculeGraph class method) (MoleculeMatcher class method) (MoleculeStructureComparator class method) (MultiEntry class method) (MultiWeightsChemenvStrategy class method) (NormalizedAngleDistanceNbSetWeight class method) (Nwchem2Fiesta class method) (NwInput class method) (NwTask class method) (PDEntry class method) (PeriodicSite class method) (PhaseDiagram class method) (PhononBandStructure class method) (PhononBandStructureSymmLine class method) (PhononDos class method) (Poscar class method) (Potcar class method) (PourbaixDiagram class method) (PourbaixEntry class method) (PPModel static method) (Pseudo class method) (PseudoTable class method) (PWInput class method) (Reaction class method) (RelaxationMethod class method) (SelfCSMNbSetWeight class method) (SeparationPlane class method) (SimpleAbundanceChemenvStrategy class method) (SimpleGraphCycle class method) (SimplestChemenvStrategy class method) (SimpleVaspToComputedEntryDrone class method) (Site class method) (Slab class method) (SlabEntry class method) (Smearing static method) (Specie class method) (SpecieProximityFilter class method) (SpinMode class method) (StructureConnectivity class method) (StructureEnvironments class method) (StructureEnvironments.NeighborsSet class method) (StructureGraph class method) (StructureMatcher class method) (StructureNL class method) (Substitutor class method) (SymmetrizedStructure class method) (SymmOp class method) (Tags static method) (TargettedPenaltiedAbundanceChemenvStrategy class method) (Tensor class method) (TensorCollection class method) (ThermoData class method) (TransformedPDEntry class method) (TransformedStructure class method) (VaspInput class method) (VaspToComputedEntryDrone class method) (WeightedNbSetChemenvStrategy class method) (XcFunc class method)

from_diff_fit() (ElasticTensorExpansion class method) (NthOrderElasticTensor class method) from_dir() (NEBAnalysis class method) (PseudoTable class method) from_directory() (FEFFDictSet static method) (VaspInput static method) from_edges() (SimpleGraphCycle class method) from_ff_and_topologies() (LammpsData class method) from_file() (BabelMolAdaptor static method) (ChargeDensityAnalyzer class method) (Chgcar static method) (CifFile class method) (CompleteCohp class method) (Control class method) (Cssr static method) (Eels static method) (Elfcar class method) (ExcitingInput static method) (FiestaInput class method) (ForceField class method) (GaussianInput static method) (Header static method) (IMolecule class method) (Incar static method) (IStructure class method) (Kpoints static method) (LammpsData class method) (LDos static method) (LMTOCtrl class method) (Lobsterin class method) (Locpot class method) (NwInput class method) (Poscar static method) (Potcar static method) (PotcarSingle static method) (Pseudo static method) (PWInput static method) (QCInput static method) (Relaxation class method) (ScfCycle class method) (SiteCollection class method) (Tags static method) (Trajectory class method) (Xmu static method) (Xr static method) (XYZ static method) (ZeoCssr static method) (ZeoVoronoiXYZ static method) from_filenames() (CifTransmuter static method) (PoscarTransmuter static method) from_files() (BoltztrapAnalyzer static method) (CombinedData class method) (DiffusionAnalyzer class method) (WorkFunctionAnalyzer static method) from_formula() (Ion class method) from_global_moment_and_saxis() (Magmom class method) from_graph() (ConnectedComponent class method) from_hdf5() (VolumetricData class method) from_independent_strains() (ElasticTensor class method) from_index_amount() (Deformation class method) (Strain class method) from_inputs() (BasicMultiDataset class method) from_lammpsdata() (CombinedData class method) from_lengths_and_angles() (Lattice static method) from_magnetic_spacegroup() (IStructure class method) from_maryland_notation() (ChemicalShielding class method) from_molecule() (NwTask class method) from_molecule_graph() (BabelMolAdaptor static method) from_moment_relative_to_crystal_axes() (Magmom class method) from_multi_jobs_file() (QCInput class method) from_name() (XcFunc class method) from_npoints() (Plane class method) from_npoints_least_square_distance() (Plane class method) from_npoints_maximum_distance() (Plane class method) from_object (ShiftMode attribute) from_old_dict() (BandStructure class method) (BandStructureSymmLine class method) (LobsterBandStructureSymmLine class method) from_origin_axis_angle() (SymmOp static method) from_origin_shift() (JonesFaithfulTransformation class method) from_outcars() (NEBAnalysis class method) from_outcars_and_structures() (Polarization class method) from_parameters() (Lattice class method) from_path() (BaderAnalysis class method) (Critic2Caller class method) from_poscar_string() (TransformedStructure static method) from_preset() (CutOffDictNN static method) from_prev_calc() (MPHSEBSSet class method) (MPNonSCFSet class method) (MPSOCSet class method) (MPStaticSet class method) (MVLGWSet class method) from_pseudoinverse() (ElasticTensor class method) from_rotation_and_translation() (SymmOp static method) from_rotation_and_translation_and_time_reversal() (MagSymmOp static method) from_row_and_group (Element attribute) from_scaling_factors() (SupercellTransformation static method) from_sites() (IMolecule class method) (IStructure class method) from_snl() (TransformedStructure class method) from_spacegroup() (IStructure class method) from_steps() (ConversionVoltagePair static method) from_str() (IMolecule class method) (IStructure class method) (SiteCollection class method) from_stream() (Relaxation class method) (ScfCycle class method) from_string (Kpoints_supported_modes attribute) from_string() (AdfKey static method) (BabelMolAdaptor static method) (BalancedReaction static method) (CifBlock class method) (CifFile class method) (CifParser static method) (Cssr static method) (DummySpecie static method) (ExcitingInput static method) (FiestaInput class method) (FloatWithUnit class method) (GaussianInput static method) (Header static method) (Incar static method) (Kpoints static method) (LammpsDump class method) (LMTOCtrl class method) (NwInput class method) (Poscar static method) (PWInput static method) (QCInput class method) (Specie static method) (Xr static method) (XSF class method) (XYZ static method) (ZeoCssr static method) (ZeoVoronoiXYZ static method) from_structure() (Control class method) (LammpsData class method) from_structure_environments() (LightStructureEnvironments class method) from_structures() (DiffusionAnalyzer class method) (StandardTransmuter static method) (StructureNL class method) (Trajectory class method) from_symbol_and_functional() (PotcarSingle static method) from_symmop() (MagSymmOp class method) from_transformation_string() (JonesFaithfulTransformation class method) from_type_name() (XcFunc class method) from_values_indices() (Tensor class method) from_vasp_voigt() (PiezoTensor class method) from_vaspruns() (DiffusionAnalyzer class method) from_voigt() (Tensor class method) (TensorCollection class method) from_xyz_string() (SymmOp static method) from_xyzt_string() (MagSymmOp static method) from_Z (Element attribute) full_electronic_structure (Element attribute) full_electronic_structure() (Element property) fully_charged_entry() (InsertionElectrode property) fully_discharged_entry() (InsertionElectrode property) func() (EOSBase method) function_comparison() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) functional (GaussianOutput attribute) functional() (PotcarSingle property) FUNCTIONAL_CHOICES (Potcar attribute) functional_class() (PotcarSingle property) functional_dir (PotcarSingle attribute) functional_tags (PotcarSingle attribute) FunctionalGroupExtractor (class in pymatgen.analysis.functional_groups)

G

g_reuss() (ElasticTensor property) g_voigt() (ElasticTensor property) g_vrh() (ElasticTensor property) Ga (Element attribute) Gamma (Kpoints_supported_modes attribute) gamma() (Lattice property) gamma_automatic() (Kpoints static method) gamma_centered() (KSampling class method) gamma_only() (KSampling class method) GammaCentered (ShiftMode attribute) GasCorrection (class in pymatgen.entries.compatibility) gaussian_smear() (StaticPotential method) GaussianInput (class in pymatgen.io.gaussian) GaussianOutput (class in pymatgen.io.gaussian) GaussianToComputedEntryDrone (class in pymatgen.apps.borg.hive) gb_from_parameters() (GrainBoundaryGenerator method) Gd (Element attribute) Ge (Element attribute) gen3d_conformer() (BabelMolAdaptor method) gen_potcar() (in module pymatgen.cli.pmg_potcar) gen_sl_transform_matricies() (in module pymatgen.analysis.substrate_analyzer) generate_adsorption_structures() (AdsorbateSiteFinder method) generate_all_slabs() (in module pymatgen.core.surface) generate_defect_structure() (Defect method) (Interstitial method) (Substitution method) (Vacancy method) generate_entry_label() (in module pymatgen.analysis.pourbaix_diagram) generate_full_symmops() (in module pymatgen.symmetry.analyzer) generate_interfaces() (InterfaceBuilder method) generate_potcar() (in module pymatgen.cli.pmg_potcar) generate_pseudo() (in module pymatgen.analysis.elasticity.elastic) generate_R_and_G_vecs() (in module pymatgen.analysis.defects.utils) generate_reciprocal_vectors_squared() (in module pymatgen.analysis.defects.utils) generate_sl_transformation_sets() (ZSLGenerator method) generate_substitution_structures() (AdsorbateSiteFinder method) generate_surface_vectors() (SubstrateAnalyzer method) generators (PointGroup attribute) (SpaceGroup attribute) genrecip() (in module pymatgen.analysis.defects.utils) geometrically_equidistant() (CNBiasNbSetWeight class method) get_00t_magmom_with_xyz_saxis() (Magmom method) get_13_bonds() (MoleculeStructureComparator static method) get_absorbing_atom_symbol_index() (in module pymatgen.io.feff.inputs) get_adjusted_fermi_level() (in module pymatgen.io.vasp.outputs) get_all_anonymous_mappings() (StructureMatcher method) get_all_chempots() (PhaseDiagram method) get_all_distances() (Lattice method) get_all_elementary_cycles() (in module pymatgen.analysis.chemenv.utils.graph_utils) get_all_entries() (InsertionElectrode method) get_all_functional_groups() (FunctionalGroupExtractor method) get_all_neighbors() (IStructure method) get_all_neighbors_old() (IStructure method) get_all_neighbors_py() (IStructure method) get_all_nn_info() (NearNeighbors method) (VoronoiNN method) get_all_simple_paths_edges() (in module pymatgen.analysis.chemenv.utils.graph_utils) get_all_substrates() (MPRester method) get_all_voronoi_polyhedra() (VoronoiNN method) get_allowed_species() (Substitutor method) get_alpha() (Elfcar method) get_analysis() (JahnTellerAnalyzer method) get_analysis_and_structure() (JahnTellerAnalyzer method) get_angle() (in module pymatgen.util.coord) (SiteCollection method) get_arrhenius_plot() (in module pymatgen.analysis.diffusion_analyzer) get_asum_FCM() (ForceConstantMatrix method) get_atom_map() (in module pymatgen.io.feff.inputs) get_atomic_fraction() (Composition method) get_atoms() (AseAtomsAdaptor static method) get_available_models() (CrystalAIRester method) get_average_along_axis() (VolumetricData method) get_average_eff_mass() (BoltztrapAnalyzer method) get_average_voltage() (AbstractElectrode method) get_ax3d_fig_plt() (in module pymatgen.util.plotting) get_ax_fig_plt() (in module pymatgen.util.plotting) get_axarray_fig_plt() (in module pymatgen.util.plotting) get_axis_grid() (VolumetricData method) get_band_gap() (BandStructure method) get_band_structure() (Vasprun method) get_band_structure_from_vasp_multiple_branches() (in module pymatgen.io.vasp.outputs) get_bandstructure() (Fatband method) get_bandstructure_by_material_id() (MPRester method) get_basic_functional_groups() (FunctionalGroupExtractor method) get_BEC_operations() (BornEffectiveCharge method) get_best_electronegativity_anonymous_mapping() (StructureMatcher method) get_bibtex_string() (CifParser method) get_bond_length() (in module pymatgen.core.bonds) get_bond_order() (CovalentBond method) (in module pymatgen.core.bonds) get_bonded_structure() (CovalentBondNN method) (Critic2NN method) (NearNeighbors method) (OpenBabelNN method) get_box_shift() (LammpsBox method) get_boxed_structure() (IMolecule method) get_branch() (BandStructureSymmLine method) (PhononBandStructureSymmLine method) get_brillouin_zone() (Lattice method) get_capacity_grav() (AbstractElectrode method) get_capacity_vol() (AbstractElectrode method) get_carrier_concentration() (BoltztrapAnalyzer method) get_cart_coords() (GaussianInput method) get_cartesian_coords() (Lattice method) get_cbm() (BandStructure method) get_cbm_vbm() (DOS method) (Dos method) get_celldm() (PWOutput method) get_center_of_arc() (in module pymatgen.analysis.chemenv.utils.math_utils) get_centered_molecule() (IMolecule method) get_central_site() (CoordinationGeometry method) get_charge() (BaderAnalysis method) get_charge_transfer() (BaderAnalysis method) get_chempot_correction() (InterfacialReactivity static method) get_chempot_range_map() (PhaseDiagram method) get_chempot_range_map_plot() (PDPlotter method) get_chempot_range_stability_phase() (PhaseDiagram method) get_chgint_plot() (in module pymatgen.cli.pmg_plot) get_chunks() (in module pymatgen.util.sequence) get_cn() (CrystalNN method) (NearNeighbors method) get_cn_dict() (CrystalNN method) (NearNeighbors method) get_cod_ids() (COD method) get_coeff() (BalancedReaction method) get_cohesive_energy() (MPRester method) get_cohp() (Cohp method) get_cohp_by_label() (CompleteCohp method) get_cohp_dict() (CohpPlotter method) get_complete_dos() (BoltztrapAnalyzer method) get_complete_ph_dos() (in module pymatgen.io.phonopy) get_complexity_factor() (BoltztrapAnalyzer method) get_compliance_expansion() (ElasticTensorExpansion method) get_composition_chempots() (PhaseDiagram method) get_compound_pd() (ReactionDiagram method) get_computed_entry() (Vasprun method) get_conductivity() (BoltztrapAnalyzer method) get_connected_components() (StructureConnectivity method) get_connected_sites() (MoleculeGraph method) (StructureGraph method) get_connections() (VoronoiConnectivity method) get_consistent_set_and_saxis() (Magmom static method) get_contour_pd_plot() (PDPlotter method) get_conv_struct() (in module pymatgen.command_line.aconvasp_caller) get_conventional_standard_structure() (SpacegroupAnalyzer method) get_conventional_to_primitive_transformation_matrix() (SpacegroupAnalyzer method) get_conversion_factor() (in module pymatgen.analysis.diffusion_analyzer) (Unit method) get_coordinating_elements_cns() (StructureMotifInterstitial method) get_coordination_environments() (StructureEnvironments method) get_coordination_number() (CoordinationGeometry method) get_coordination_of_site() (MoleculeGraph method) (StructureGraph method) get_coordination_symmetry_measures() (LocalGeometryFinder method) get_coordination_symmetry_measures_optim() (LocalGeometryFinder method) get_correction() (BandEdgeShiftingCorrection method) (BandFillingCorrection method) (Correction method) (DefectCorrection method) (FreysoldtCorrection method) (KumagaiCorrection method) (PotcarCorrection method) get_corrections_dict() (Compatibility method) get_cost_per_kg() (CostAnalyzer method) get_cost_per_mol() (CostAnalyzer method) get_covalent_bonds() (IMolecule method) get_critical_compositions() (PhaseDiagram method) get_critical_original_kink_ratio() (InterfacialReactivity method) get_critical_point_for_site() (Critic2Output method) get_crystal_field_spin() (Specie method) get_crystal_system() (SpacegroupAnalyzer method) get_csm() (StructureEnvironments method) get_csm_and_maps() (StructureEnvironments method) get_csms() (StructureEnvironments method) get_d() (in module pymatgen.core.surface) get_data() (BorgQueen method) (MPRester method) get_dataframe() (AbinitTimer method) get_decomp_and_e_above_hull() (PhaseDiagram method) get_decomposition() (PhaseDiagram method) get_decomposition_energy() (PourbaixDiagram method) get_default_basis_set() (AdfTask static method) get_default_geo() (AdfTask static method) get_default_scf() (AdfTask static method) get_default_units() (AdfTask static method) get_default_xc() (AdfTask static method) get_defectsite_multiplicity() (StructureMotifInterstitial method) get_deformation_matrix() (Strain method) get_delta() (in module pymatgen.analysis.chemenv.utils.graph_utils) get_delta_image() (in module pymatgen.analysis.chemenv.connectivity.structure_connectivity) get_densities() (Dos method) get_derivatives() (in module pymatgen.util.convergence) get_diff_coeff() (in module pymatgen.analysis.elasticity.elastic) get_dihedral() (SiteCollection method) get_dimensionality_cheon() (in module pymatgen.analysis.dimensionality) get_dimensionality_gorai() (in module pymatgen.analysis.dimensionality) get_dimensionality_larsen() (in module pymatgen.analysis.dimensionality) get_direct_band_gap() (BandStructure method) get_direct_band_gap_dict() (BandStructure method) get_displaced_structures() (in module pymatgen.io.phonopy) get_distance() (IMolecule method) (IStructure method) (SiteCollection method) get_distance_and_image() (Lattice method) get_doc() (Lobsterout method) (MPRester method) get_dopability_limits() (DefectPhaseDiagram method) get_dopants_from_shannon_radii() (in module pymatgen.analysis.structure_prediction.dopant_predictor) get_dopants_from_substitution_probabilities() (in module pymatgen.analysis.structure_prediction.dopant_predictor) get_doping() (FermiDos method) get_dos_by_material_id() (MPRester method) get_dos_dict() (DosPlotter method) (PhononDosPlotter method) get_dos_plot() (in module pymatgen.cli.pmg_plot) get_download_info() (MPRester method) get_drift_corrected_structures() (DiffusionAnalyzer method) get_e_above_hull() (PhaseDiagram method) get_effective_csm() (in module pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) get_effective_ecs() (ElasticTensorExpansion method) get_el_amount() (BalancedReaction method) get_el_amt_dict() (Composition method) get_el_sp() (in module pymatgen.core.periodic_table) get_element_dos() (CompleteDos method) (CompletePhononDos method) get_element_fraction() (PourbaixEntry method) get_element_profile() (PhaseDiagram method) get_element_spd_dos() (CompleteDos method) (LobsterCompleteDos method) get_elements_between_bands() (Wavederf method) get_elt_projected_plots() (BSPlotterProjected method) get_elt_projected_plots_color() (BSPlotterProjected method) get_energies() (in module pymatgen.cli.gaussian_analyzer) (in module pymatgen.cli.pmg_analyze) get_energy() (ChemicalPotential method) (EnergyModel method) (EwaldElectrostaticModel method) (GulpIO method) (IsingModel method) (NsitesModel method) (SymmetryModel method) get_energy_buckingham() (in module pymatgen.command_line.gulp_caller) get_energy_density() (AbstractElectrode method) get_energy_relax_structure_buckingham() (in module pymatgen.command_line.gulp_caller) get_energy_tersoff() (in module pymatgen.command_line.gulp_caller) get_entries() (CostDB method) (CostDBCSV method) (MPRester method) get_entries_in_chemsys() (MPRester method) get_entry_by_material_id() (MPRester method) get_environment_node() (in module pymatgen.analysis.chemenv.connectivity.environment_nodes) get_environments_figure() (StructureEnvironments method) get_equilibrium_reaction_energy() (PhaseDiagram method) get_equiv_transformations() (ZSLGenerator method) get_equivalent_atoms() (PointGroupAnalyzer method) get_equivalent_kpoints() (BandStructureSymmLine method) get_equivalent_qpoints() (PhononBandStructureSymmLine method) get_exchange() (HeisenbergMapper method) get_exchange_group_info() (CollinearMagneticStructureAnalyzer method) get_excitation_spectrum() (NwOutput method) get_exp_entry() (MPRester method) get_exp_thermo_data() (MPRester method) get_explanation_dict() (Compatibility method) get_extended_surface_mesh() (AdsorbateSiteFinder method) get_extrapolated_conductivity() (in module pymatgen.analysis.diffusion_analyzer) get_extrapolated_diffusivity() (in module pymatgen.analysis.diffusion_analyzer) get_extrema() (NEBAnalysis method) get_extreme() (BoltztrapAnalyzer method) get_facets() (in module pymatgen.analysis.phase_diagram) get_factors() (in module pymatgen.analysis.substrate_analyzer) get_FCM_operations() (ForceConstantMatrix method) get_fermi() (FermiDos method) get_fermi_interextrapolated() (FermiDos method) get_ferromagnetic_structure() (CollinearMagneticStructureAnalyzer method) get_film_indices() (Interface method) get_form_energy() (PhaseDiagram method) get_form_energy_per_atom() (PhaseDiagram method) get_frac_coords_from_lll() (Lattice method) get_fractional_coords() (Lattice method) get_framework_rms_plot() (DiffusionAnalyzer method) get_free_sphere_params() (in module pymatgen.io.zeopp) get_gap() (DOS method) (Dos method) get_gb_data() (MPRester method) get_geometries() (AllCoordinationGeometries method) get_geometry_from_IUCr_symbol() (AllCoordinationGeometries method) get_geometry_from_IUPAC_symbol() (AllCoordinationGeometries method) get_geometry_from_mp_symbol() (AllCoordinationGeometries method) get_geometry_from_name() (AllCoordinationGeometries method) get_ggt() (ElasticTensorExpansion method) get_grouped_indices() (Tensor method) get_gruneisen_parameter() (ElasticTensorExpansion method) get_hall() (SpacegroupAnalyzer method) get_hall_carrier_concentration() (BoltztrapAnalyzer method) get_hash() (AbstractComparator method) (ElementComparator method) (FrameworkComparator method) (OccupancyComparator method) (OrderDisorderElementComparator method) (SpeciesComparator method) (SpinComparator method) get_heat_capacity() (ElasticTensorExpansion method) get_heteroatoms() (FunctionalGroupExtractor method) get_high_accuracy_voronoi_nodes() (in module pymatgen.io.zeopp) get_hull_energy() (PhaseDiagram method) (PourbaixDiagram method) get_icohp() (Cohp method) get_icohp_by_label() (IcohpCollection method) get_icohp_dict_by_bondlengths() (IcohpCollection method) get_icohp_dict_of_site() (IcohpCollection method) get_ieee_rotation() (Tensor static method) get_implemented_geometries() (AllCoordinationGeometries method) get_integer_formula_and_factor() (Composition method) get_integer_index() (in module pymatgen.core.lattice) get_integrated_diff() (VolumetricData method) get_interaction_graph() (HeisenbergMapper method) get_interface_reactions() (MPRester method) get_interpolated_gap() (DOS method) (Dos method) get_interpolated_value() (Cohp method) (Dos method) (PhononDos method) (Spectrum method) get_ir_reciprocal_mesh() (SpacegroupAnalyzer method) get_ir_spectra() (IRDielectricTensor method) get_IST_operations() (InternalStrainTensor method) get_kinks() (InterfacialReactivity method) get_kpoint_degeneracy() (BandStructure method) get_kpoint_weights() (SpacegroupAnalyzer method) get_kpoints() (HighSymmKpath method) (in module pymatgen.ext.jhu) get_labels() (WorkFunctionAnalyzer method) get_lattice() (CifParser method) get_lattice_quanta() (Polarization method) get_lattice_type() (SpacegroupAnalyzer method) get_line_in_facet() (WulffShape method) get_linear_interpolated_value() (in module pymatgen.util.coord) get_linearly_independent_vectors() (in module pymatgen.analysis.chemenv.utils.math_utils) get_lines() (Atoms method) get_lll_frac_coords() (Lattice method) get_lll_reduced_lattice() (Lattice method) get_local_extrema() (ChargeDensityAnalyzer method) get_local_order_parameters() (NearNeighbors method) get_locpot_along_slab_plot() (WorkFunctionAnalyzer method) get_low_energy_orderings() (HeisenbergMapper method) get_lower_and_upper_f() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) get_lowest_decomposition() (CostAnalyzer method) get_magnetizations() (in module pymatgen.cli.pmg_analyze) get_magnitude_of_effect_from_species() (JahnTellerAnalyzer method) get_magnitude_of_effect_from_spin_config() (JahnTellerAnalyzer static method) get_magsymops() (CifParser method) get_mapping() (StructureMatcher method) get_materials_id_from_task_id() (MPRester method) get_materials_id_references() (MPRester method) get_materials_ids() (MPRester method) get_max_bond_distance() (JmolNN method) get_max_bond_lengths() (in module pymatgen.analysis.structure_analyzer) get_max_capgrav() (BatteryAnalyzer method) get_max_capvol() (BatteryAnalyzer method) get_max_instability() (InsertionElectrode method) get_max_muO2() (InsertionElectrode method) get_mft_temperature() (HeisenbergMapper method) get_mi_vec() (in module pymatgen.analysis.adsorption) get_miller_index_from_coords() (Lattice method) get_miller_index_from_site_indexes() (IStructure method) get_min_instability() (InsertionElectrode method) get_min_muO2() (InsertionElectrode method) get_minkowski_red() (in module pymatgen.command_line.aconvasp_caller) get_molecule() (AseAtomsAdaptor static method) get_molecule_hash() (AbstractMolAtomMapper method) (InchiMolAtomMapper method) (IsomorphismMolAtomMapper method) get_moment() (Magmom method) get_moment_relative_to_crystal_axes() (Magmom method) get_monolayer() (SlabEntry property) get_motif_type() (StructureMotifInterstitial method) get_mp_structure() (PymatgenTest class method) get_msd_plot() (DiffusionAnalyzer method) get_mu_bounds() (BoltztrapAnalyzer method) get_multiplicity() (Defect method) (Interstitial method) (Substitution method) (Vacancy method) get_nac_eigendisplacements_along_dir() (PhononBandStructure method) get_nac_frequencies_along_dir() (PhononBandStructure method) get_name() (CoordinationGeometry method) get_nearest_site() (PolarizationLattice method) get_neighb_voronoi_indices() (StructureEnvironments.NeighborsSet method) get_neighbor_list() (IStructure method) get_neighbors() (IMolecule method) (IStructure method) get_neighbors_in_shell() (IMolecule method) (IStructure method) get_neighbors_of_site_with_index() (in module pymatgen.analysis.local_env) get_neighbors_old() (IStructure method) get_next_index() (EwaldMinimizer method) get_niggli_reduced_lattice() (Lattice method) get_nmr_quadrupole_moment() (Specie method) get_nn() (NearNeighbors method) get_nn_data() (CrystalNN method) get_nn_images() (NearNeighbors method) get_nn_info() (BrunnerNN_real method) (BrunnerNN_reciprocal method) (BrunnerNN_relative method) (CovalentBondNN method) (Critic2NN method) (CrystalNN method) (CutOffDictNN method) (EconNN method) (JmolNN method) (MinimumDistanceNN method) (MinimumOKeeffeNN method) (MinimumVIRENN method) (NearNeighbors method) (OpenBabelNN method) (VoronoiNN method) get_nn_shell_info() (CovalentBondNN method) (NearNeighbors method) (OpenBabelNN method) get_no_mixing_energy() (InterfacialReactivity method) get_nonmagnetic_structure() (CollinearMagneticStructureAnalyzer method) get_noppmodel() (PPModel class method) get_not_implemented_geometries() (AllCoordinationGeometries method) get_num_division_kpoints() (in module pymatgen.command_line.aconvasp_caller) get_occupation() (Procar method) get_okeeffe_distance_prediction() (in module pymatgen.analysis.local_env) get_okeeffe_params() (in module pymatgen.analysis.local_env) get_op_value() (StructureMotifInterstitial method) get_orbital_derivative_between_states() (Waveder method) get_orbital_resolved_cohp() (CompleteCohp method) get_order_parameters() (LocalStructOrderParams method) get_oriented_slabs() (InterfaceBuilder method) get_ortho_axes() (in module pymatgen.analysis.interface) get_orthogonal_c_slab() (Slab method) get_oxi_state_decorated_structure() (BVAnalyzer method) get_oxidation_state_decorated_structure() (BaderAnalysis method) get_parameters() (LocalStructOrderParams method) get_parchg() (Wavecar method) get_pattern() (AbstractDiffractionPatternCalculator method) (NDCalculator method) (XRDCalculator method) get_pelecs_and_pions() (Polarization method) get_percentage_bond_dist_changes() (RelaxationAnalyzer method) get_percentage_lattice_parameter_changes() (RelaxationAnalyzer method) get_percentage_volume_change() (RelaxationAnalyzer method) get_perturbed_indices() (Deformation method) get_ph_bs_symm_line() (in module pymatgen.io.phonopy) get_ph_bs_symm_line_from_dict() (in module pymatgen.io.phonopy) get_ph_dos() (in module pymatgen.io.phonopy) get_phonon_band_structure_from_fc() (in module pymatgen.io.phonopy) get_phonon_band_structure_symm_line_from_fc() (in module pymatgen.io.phonopy) get_phonon_bandstructure_by_material_id() (MPRester method) get_phonon_ddb_by_material_id() (MPRester method) get_phonon_dos_by_material_id() (MPRester method) get_phonon_dos_from_fc() (in module pymatgen.io.phonopy) get_phonon_frequencies() (Dynmat method) get_phonopy_structure() (in module pymatgen.io.phonopy) get_piezo() (in module pymatgen.analysis.piezo_sensitivity) get_plot() (AbstractDiffractionPatternCalculator method) (BSDOSPlotter method) (BSPlotter method) (CohpPlotter method) (DosPlotter method) (NEBAnalysis method) (PDPlotter method) (PhononBSPlotter method) (PhononDosPlotter method) (SpectrumPlotter method) (VoltageProfilePlotter method) (WulffShape method)

get_plot_data() (VoltageProfilePlotter method) get_plotter() (IRDielectricTensor method) get_pmeshes() (CoordinationGeometry method) get_pmg_structure() (in module pymatgen.io.phonopy) get_point_group_operations() (SpacegroupAnalyzer method) get_point_group_symbol() (SpacegroupAnalyzer method) get_pointgroup() (PointGroupAnalyzer method) get_points_in_sphere() (Lattice method) get_points_in_sphere_old() (Lattice method) get_points_in_sphere_py() (Lattice method) get_points_in_spheres() (in module pymatgen.core.lattice) get_polarization_change() (Polarization method) get_polarization_change_norm() (Polarization method) get_potcar_file_hash() (PotcarSingle method) get_potcar_hash() (PotcarSingle method) get_potcars() (Vasprun method) get_potential_shift() (KumagaiCorrection method) get_pourbaix_domains() (PourbaixDiagram static method) get_pourbaix_entries() (MPRester method) get_pourbaix_plot() (PourbaixPlotter method) get_power_factor() (BoltztrapAnalyzer method) get_predicted_structure() (DLSVolumePredictor method) (RLSVolumePredictor method) get_prim_struct() (in module pymatgen.command_line.aconvasp_caller) get_primitive_standard_structure() (SpacegroupAnalyzer method) get_primitive_structure() (IStructure method) get_products() (InterfacialReactivity method) get_projected_plots_dots() (BSPlotterProjected method) get_projected_plots_dots_patom_pmorb() (BSPlotterProjected method) get_projection_on_elements() (BandStructure method) (LobsterBandStructureSymmLine method) (Procar method) get_projections_on_elements_and_orbitals() (BandStructure method) (LobsterBandStructureSymmLine method) get_prototypes() (AflowPrototypeMatcher method) get_pseudos_for_structure() (PseudoTable method) get_q2() (LocalStructOrderParams method) get_q4() (LocalStructOrderParams method) get_q6() (LocalStructOrderParams method) get_rand_BEC() (BornEffectiveCharge method) get_rand_FCM() (ForceConstantMatrix method) get_rand_IST() (InternalStrainTensor method) get_ratio() (GrainBoundaryGenerator method) get_rdf_figure() (DetailedVoronoiContainer method) get_reaction() (MPRester method) get_real_summation() (KumagaiCorrection method) get_reasonable_repetitions() (in module pymatgen.phonon.bandstructure) get_recip_summation() (KumagaiCorrection method) get_reconstructed_band_structure() (in module pymatgen.electronic_structure.bandstructure) get_recp_symmetry_operation() (Lattice method) get_reduced_composition_and_factor() (Composition method) get_reduced_formula_and_factor() (Composition method) get_reduced_structure() (IStructure method) get_refined_structure() (SpacegroupAnalyzer method) get_relaxed_structure() (GulpIO method) get_removals_int_oxid() (BatteryAnalyzer method) get_rms_anonymous() (StructureMatcher method) get_rms_dist() (StructureMatcher method) get_rmsd() (MoleculeMatcher method) get_rot() (in module pymatgen.analysis.adsorption) get_rotation_angle_from_sigma() (GrainBoundaryGenerator static method) get_s2_like_s1() (StructureMatcher method) get_sadf_figure() (DetailedVoronoiContainer method) get_same_branch_polarization_data() (Polarization method) get_scaled() (SquareTensor method) get_scan_plot() (GaussianOutput method), [1] get_section() (AbinitTimer method) get_sections() (AbinitTimerParser method) get_seebeck() (BoltztrapAnalyzer method) get_seebeck_eff_mass() (BoltztrapAnalyzer method) get_self_interaction() (KumagaiCorrection method) get_shannon_radius() (Specie method) get_shared_symmetry_operations() (in module pymatgen.symmetry.site_symmetries) get_shear_reduced_slab() (in module pymatgen.analysis.interface) get_site_ce_fractions_and_neighbors() (AbstractChemenvStrategy method) get_site_coordination_environment() (AbstractChemenvStrategy method) (SimpleAbundanceChemenvStrategy method) (SimplestChemenvStrategy method) (TargettedPenaltiedAbundanceChemenvStrategy method) (WeightedNbSetChemenvStrategy method) get_site_coordination_environments() (AbstractChemenvStrategy method) (SimpleAbundanceChemenvStrategy method) (SimplestChemenvStrategy method) (WeightedNbSetChemenvStrategy method) get_site_coordination_environments_fractions() (AbstractChemenvStrategy method) (SimplestChemenvStrategy method) (WeightedNbSetChemenvStrategy method) get_site_dos() (CompleteDos method) (CompletePhononDos method) get_site_energy() (EwaldSummation method) get_site_info_for_specie_allces() (LightStructureEnvironments method) get_site_info_for_specie_ce() (LightStructureEnvironments method) get_site_neighbors() (AbstractChemenvStrategy method) (SimpleAbundanceChemenvStrategy method) (SimplestChemenvStrategy method) (WeightedNbSetChemenvStrategy method) get_site_orbital_dos() (CompleteDos method) (LobsterCompleteDos method) get_site_spd_dos() (CompleteDos method) get_site_symmetries() (in module pymatgen.symmetry.site_symmetries) get_site_t2g_eg_resolved_dos() (CompleteDos method) (LobsterCompleteDos method) get_sitej() (VoronoiConnectivity method) get_sites_in_sphere() (IMolecule method) (IStructure method) get_slab() (SlabGenerator method) get_slab_regions() (in module pymatgen.core.surface) get_slabs() (SlabGenerator method) get_smeared_densities() (Dos method) (PhononDos method) get_sorted_structure() (GrainBoundary method) (Interface method) (IStructure method) (Slab method) get_space_group_info() (IStructure method) get_space_group_number() (SpacegroupAnalyzer method) get_space_group_operations() (SpacegroupAnalyzer method) get_space_group_symbol() (SpacegroupAnalyzer method) get_spd_dos() (CompleteDos method) (LobsterCompleteDos method) get_special_carbon() (FunctionalGroupExtractor method) get_specific_energy() (AbstractElectrode method) get_spectre_plot() (GaussianOutput method) get_spectrum() (IRDielectricTensor method) get_stability() (MPRester method) get_stability_criteria() (ElasticTensorExpansion method) get_stable_entries() (InsertionElectrode method) get_stable_entry() (PourbaixDiagram method) get_stable_entry_at_u() (SurfaceEnergyPlotter method) get_stable_FCM() (ForceConstantMatrix method) get_statistics() (LightStructureEnvironments method) get_strain_from_stress() (ElasticTensorExpansion method) get_strain_state_dict() (in module pymatgen.analysis.elasticity.elastic) get_string() (CombinedData method) (Incar method) (LammpsBox method) (LammpsData method) (LMTOCtrl method) (Poscar method) (Tags method) (Xdatcar method) get_structure() (AseAtomsAdaptor static method) (Control method) (LocalGeometryFinder method) (PymatgenTest class method) (Trajectory method) get_structure_by_formula() (COD method) get_structure_by_id() (COD method) get_structure_by_material_id() (MPRester method) get_structure_components() (in module pymatgen.analysis.dimensionality) get_structure_connectivity() (ConnectivityFinder method) get_structure_from_dict() (in module pymatgen.io.phonopy) get_structure_from_mp() (in module pymatgen) get_structure_from_prev_run() (in module pymatgen.io.vasp.sets) get_structure_property_dict() (ElasticTensor method) get_structure_with_charges() (Charge method) get_structure_with_nodes() (ChargeDensityAnalyzer method) (TopographyAnalyzer method) get_structure_with_only_magnetic_atoms() (CollinearMagneticStructureAnalyzer method) get_structure_with_spin() (CollinearMagneticStructureAnalyzer method) get_structure_with_total_grosspop() (Grosspop method) get_structures() (CifParser method) (MPRester method) get_sub_electrodes() (ConversionElectrode method) (InsertionElectrode method) get_subgraphs_as_molecules() (StructureGraph method) get_subset_in_chemsys() (EntrySet method) get_substrates() (MPRester method) get_suggested_saxis() (Magmom static method) get_summary_dict() (ConversionElectrode method) (DiffusionAnalyzer method) (InterfaceBuilder method) (QuasiharmonicDebyeApprox method) get_summed_cohp_by_label_and_orbital_list() (CompleteCohp method) get_summed_cohp_by_label_list() (CompleteCohp method) get_summed_icohp_by_label_list() (IcohpCollection method) get_supercell_matrix() (StructureMatcher method) get_surface_data() (MPRester method) get_surface_equilibrium() (SurfaceEnergyPlotter method) get_surface_sites() (Slab method) get_sym_eq_kpoints() (BandStructure method) get_symbol_cn_mapping() (AllCoordinationGeometries method) get_symbol_dict() (Tensor method) get_symbol_list() (in module pymatgen.analysis.elasticity.elastic) get_symbol_name_mapping() (AllCoordinationGeometries method) get_symm_bands() (BoltztrapAnalyzer method) get_symmetric_site() (Slab method) get_symmetric_wallace_tensor() (ElasticTensorExpansion method) get_symmetrically_distinct_miller_indices() (in module pymatgen.core.surface) get_symmetrically_equivalent_miller_indices() (in module pymatgen.core.surface) get_symmetrized_FCM() (ForceConstantMatrix method) get_symmetrized_structure() (SpacegroupAnalyzer method) get_symmetry_dataset() (SpacegroupAnalyzer method) get_symmetry_operations() (PointGroupAnalyzer method) (SpacegroupAnalyzer method) get_symops() (CifParser method) get_task_data() (MPRester method) get_tasker2_slabs() (Slab method) get_tgt() (ElasticTensorExpansion method) get_thermal_conductivity() (BoltztrapAnalyzer method) get_ticks() (BSPlotter method) (PhononBSPlotter method) get_total_ionic_dipole() (in module pymatgen.analysis.ferroelectricity.polarization) get_trans_mat() (GrainBoundaryGenerator static method) get_transformation() (StructureMatcher method) get_transition_chempots() (PhaseDiagram method) get_tri_area() (in module pymatgen.analysis.wulff) get_type() (LocalStructOrderParams method) get_unique_families() (in module pymatgen.analysis.diffraction.core) get_unit_primitive_area() (SlabEntry property) get_unreconstructed_slabs() (ReconstructionGenerator method) get_unstable_entries() (InsertionElectrode method) get_unstable_FCM() (ForceConstantMatrix method) get_uvec() (in module pymatgen.core.tensors) get_v() (StaticPotential method) get_valences() (BVAnalyzer method) get_valid_paths() (AbstractDrone method) (GaussianToComputedEntryDrone method) (VaspToComputedEntryDrone method) get_value() (InputVariable method) get_values() (AbinitTimer method) get_vasp_input() (TransformedStructure method) (VaspInputSet method) get_vasp_kpoint_file_sym() (in module pymatgen.command_line.aconvasp_caller) get_vasprun_outcar() (in module pymatgen.io.vasp.sets) get_vbm() (BandStructure method) get_vector_along_lattice_directions() (Lattice method) get_void_volume_surfarea() (in module pymatgen.io.zeopp) get_voigt_dict() (Tensor static method) get_voronoi_nodes() (in module pymatgen.io.zeopp) get_voronoi_polyhedra() (VoronoiNN method) get_wallace_tensor() (ElasticTensorExpansion method) get_weights() (in module pymatgen.util.convergence) get_weights_of_nn_sites() (NearNeighbors method) get_wigner_seitz_cell() (Lattice method) get_wt_fraction() (Composition method) get_wulff_shape() (MPRester method) get_xas_data() (MPRester method) get_xrd_plot() (in module pymatgen.cli.pmg_plot) get_xyz_magmom_with_001_saxis() (Magmom method) get_yield_stress() (ElasticTensorExpansion method) get_z_ordered_elmap() (in module pymatgen.analysis.bond_valence) get_zmatrix() (GaussianInput method) get_zt() (BoltztrapAnalyzer method) getmu_vertices_stability_phase() (PhaseDiagram method) GGA_C_AM05 (LibxcFunc attribute) GGA_C_APBE (LibxcFunc attribute) GGA_C_BGCP (LibxcFunc attribute) GGA_C_FT97 (LibxcFunc attribute) GGA_C_GAM (LibxcFunc attribute) GGA_C_HCTH_A (LibxcFunc attribute) GGA_C_LM (LibxcFunc attribute) GGA_C_LYP (LibxcFunc attribute) GGA_C_N12 (LibxcFunc attribute) GGA_C_N12_SX (LibxcFunc attribute) GGA_C_OP_B88 (LibxcFunc attribute) GGA_C_OP_G96 (LibxcFunc attribute) GGA_C_OP_PBE (LibxcFunc attribute) GGA_C_OP_PW91 (LibxcFunc attribute) GGA_C_OP_XALPHA (LibxcFunc attribute) GGA_C_OPTC (LibxcFunc attribute) GGA_C_P86 (LibxcFunc attribute) GGA_C_PBE (LibxcFunc attribute) GGA_C_PBE_JRGX (LibxcFunc attribute) GGA_C_PBE_SOL (LibxcFunc attribute) GGA_C_PBEFE (LibxcFunc attribute) GGA_C_PBEINT (LibxcFunc attribute) GGA_C_PBELOC (LibxcFunc attribute) GGA_C_PW91 (LibxcFunc attribute) GGA_C_Q2D (LibxcFunc attribute) GGA_C_REGTPSS (LibxcFunc attribute) GGA_C_REVTCA (LibxcFunc attribute) GGA_C_RGE2 (LibxcFunc attribute) GGA_C_SOGGA11 (LibxcFunc attribute) GGA_C_SOGGA11_X (LibxcFunc attribute) GGA_C_SPBE (LibxcFunc attribute) GGA_C_TCA (LibxcFunc attribute) GGA_C_WI (LibxcFunc attribute) GGA_C_WI0 (LibxcFunc attribute) GGA_C_WL (LibxcFunc attribute) GGA_C_XPBE (LibxcFunc attribute) GGA_C_ZPBEINT (LibxcFunc attribute) GGA_C_ZPBESOL (LibxcFunc attribute) GGA_DEF (TaskType attribute) GGA_K_ABSP1 (LibxcFunc attribute) GGA_K_ABSP2 (LibxcFunc attribute) GGA_K_APBE (LibxcFunc attribute) GGA_K_APBEINT (LibxcFunc attribute) GGA_K_BALTIN (LibxcFunc attribute) GGA_K_DK (LibxcFunc attribute) GGA_K_ERNZERHOF (LibxcFunc attribute) GGA_K_FR_B88 (LibxcFunc attribute) GGA_K_FR_PW86 (LibxcFunc attribute) GGA_K_GE2 (LibxcFunc attribute) GGA_K_GOLDEN (LibxcFunc attribute) GGA_K_GP85 (LibxcFunc attribute) GGA_K_GR (LibxcFunc attribute) GGA_K_LC94 (LibxcFunc attribute) GGA_K_LIEB (LibxcFunc attribute) GGA_K_LLP (LibxcFunc attribute) GGA_K_LUDENA (LibxcFunc attribute) GGA_K_MEYER (LibxcFunc attribute) GGA_K_OL1 (LibxcFunc attribute) GGA_K_OL2 (LibxcFunc attribute) GGA_K_PEARSON (LibxcFunc attribute) GGA_K_PERDEW (LibxcFunc attribute) GGA_K_REVAPBE (LibxcFunc attribute) GGA_K_REVAPBEINT (LibxcFunc attribute) GGA_K_TFVW (LibxcFunc attribute) GGA_K_THAKKAR (LibxcFunc attribute) GGA_K_TW1 (LibxcFunc attribute) GGA_K_TW2 (LibxcFunc attribute) GGA_K_TW3 (LibxcFunc attribute) GGA_K_TW4 (LibxcFunc attribute) GGA_K_VJKS (LibxcFunc attribute) GGA_K_VSK (LibxcFunc attribute) GGA_K_VW (LibxcFunc attribute) GGA_K_YT65 (LibxcFunc attribute) GGA_LINE (TaskType attribute) GGA_OPT (TaskType attribute) GGA_STATIC (TaskType attribute) GGA_STATIC_DIEL (TaskType attribute) GGA_UNIFORM (TaskType attribute) GGA_X_2D_B86 (LibxcFunc attribute) GGA_X_2D_B86_MGC (LibxcFunc attribute) GGA_X_2D_B88 (LibxcFunc attribute) GGA_X_2D_PBE (LibxcFunc attribute) GGA_X_AIRY (LibxcFunc attribute) GGA_X_AK13 (LibxcFunc attribute) GGA_X_AM05 (LibxcFunc attribute) GGA_X_APBE (LibxcFunc attribute) GGA_X_B86 (LibxcFunc attribute) GGA_X_B86_MGC (LibxcFunc attribute) GGA_X_B86_R (LibxcFunc attribute) GGA_X_B88 (LibxcFunc attribute) GGA_X_BAYESIAN (LibxcFunc attribute) GGA_X_BGCP (LibxcFunc attribute) GGA_X_BPCCAC (LibxcFunc attribute) GGA_X_C09X (LibxcFunc attribute) GGA_X_CAP (LibxcFunc attribute) GGA_X_DK87_R1 (LibxcFunc attribute) GGA_X_DK87_R2 (LibxcFunc attribute) GGA_X_EV93 (LibxcFunc attribute) GGA_X_FT97_A (LibxcFunc attribute) GGA_X_FT97_B (LibxcFunc attribute) GGA_X_G96 (LibxcFunc attribute) GGA_X_GAM (LibxcFunc attribute) GGA_X_HCTH_A (LibxcFunc attribute) GGA_X_HERMAN (LibxcFunc attribute) GGA_X_HJS_B88 (LibxcFunc attribute) GGA_X_HJS_B88_V2 (LibxcFunc attribute) GGA_X_HJS_B97X (LibxcFunc attribute) GGA_X_HJS_PBE (LibxcFunc attribute) GGA_X_HJS_PBE_SOL (LibxcFunc attribute) GGA_X_HTBS (LibxcFunc attribute) GGA_X_ITYH (LibxcFunc attribute) GGA_X_KT1 (LibxcFunc attribute) GGA_X_LAG (LibxcFunc attribute) GGA_X_LAMBDA_CH_N (LibxcFunc attribute) GGA_X_LAMBDA_LO_N (LibxcFunc attribute) GGA_X_LAMBDA_OC2_N (LibxcFunc attribute) GGA_X_LB (LibxcFunc attribute) GGA_X_LBM (LibxcFunc attribute) GGA_X_LG93 (LibxcFunc attribute) GGA_X_LV_RPW86 (LibxcFunc attribute) GGA_X_MB88 (LibxcFunc attribute) GGA_X_MPBE (LibxcFunc attribute) GGA_X_MPW91 (LibxcFunc attribute) GGA_X_N12 (LibxcFunc attribute) GGA_X_OL2 (LibxcFunc attribute) GGA_X_OPTB88_VDW (LibxcFunc attribute) GGA_X_OPTPBE_VDW (LibxcFunc attribute) GGA_X_OPTX (LibxcFunc attribute) GGA_X_PBE (LibxcFunc attribute) GGA_X_PBE_JSJR (LibxcFunc attribute) GGA_X_PBE_MOL (LibxcFunc attribute) GGA_X_PBE_R (LibxcFunc attribute) GGA_X_PBE_SOL (LibxcFunc attribute) GGA_X_PBE_TCA (LibxcFunc attribute) GGA_X_PBEA (LibxcFunc attribute) GGA_X_PBEFE (LibxcFunc attribute) GGA_X_PBEINT (LibxcFunc attribute) GGA_X_PBEK1_VDW (LibxcFunc attribute) GGA_X_PW86 (LibxcFunc attribute) GGA_X_PW91 (LibxcFunc attribute) GGA_X_Q2D (LibxcFunc attribute) GGA_X_RGE2 (LibxcFunc attribute) GGA_X_RPBE (LibxcFunc attribute) GGA_X_RPW86 (LibxcFunc attribute) GGA_X_SFAT (LibxcFunc attribute) GGA_X_SOGGA (LibxcFunc attribute) GGA_X_SOGGA11 (LibxcFunc attribute) GGA_X_SSB (LibxcFunc attribute) GGA_X_SSB_D (LibxcFunc attribute) GGA_X_SSB_SW (LibxcFunc attribute) GGA_X_VMT84_GE (LibxcFunc attribute) GGA_X_VMT84_PBE (LibxcFunc attribute) GGA_X_VMT_GE (LibxcFunc attribute) GGA_X_VMT_PBE (LibxcFunc attribute) GGA_X_WC (LibxcFunc attribute) GGA_X_WPBEH (LibxcFunc attribute) GGA_X_XPBE (LibxcFunc attribute) GGA_XC_B97_D (LibxcFunc attribute) GGA_XC_B97_GGA1 (LibxcFunc attribute) GGA_XC_EDF1 (LibxcFunc attribute) GGA_XC_HCTH_120 (LibxcFunc attribute) GGA_XC_HCTH_147 (LibxcFunc attribute) GGA_XC_HCTH_407 (LibxcFunc attribute) GGA_XC_HCTH_407P (LibxcFunc attribute) GGA_XC_HCTH_93 (LibxcFunc attribute) GGA_XC_HCTH_P14 (LibxcFunc attribute) GGA_XC_HCTH_P76 (LibxcFunc attribute) GGA_XC_KT2 (LibxcFunc attribute) GGA_XC_MOHLYP (LibxcFunc attribute) GGA_XC_MOHLYP2 (LibxcFunc attribute) GGA_XC_MPWLYP1W (LibxcFunc attribute) GGA_XC_OBLYP_D (LibxcFunc attribute) GGA_XC_OPBE_D (LibxcFunc attribute) GGA_XC_OPWLYP_D (LibxcFunc attribute) GGA_XC_PBE1W (LibxcFunc attribute) GGA_XC_PBELYP1W (LibxcFunc attribute) GGA_XC_TH1 (LibxcFunc attribute) GGA_XC_TH2 (LibxcFunc attribute) GGA_XC_TH3 (LibxcFunc attribute) GGA_XC_TH4 (LibxcFunc attribute) GGA_XC_TH_FC (LibxcFunc attribute) GGA_XC_TH_FCFO (LibxcFunc attribute) GGA_XC_TH_FCO (LibxcFunc attribute) GGA_XC_TH_FL (LibxcFunc attribute) GGA_XC_VV10 (LibxcFunc attribute) GGA_XC_XLYP (LibxcFunc attribute) GGAU_DEF (TaskType attribute) GGAU_LINE (TaskType attribute) GGAU_OPT (TaskType attribute) GGAU_STATIC (TaskType attribute) GGAU_STATIC_DIEL (TaskType attribute) GGAU_UNIFORM (TaskType attribute) gibbs_binding_energy() (SlabEntry method) global_moment() (Magmom property) godby (PPModelModes attribute) good_sections() (ParallelEfficiency method) GPa_to_eV_A3 (NthOrderElasticTensor attribute) Gpoints (Wavecar attribute) GrainBoundary (class in pymatgen.analysis.gb.grain) GrainBoundaryGenerator (class in pymatgen.analysis.gb.grain) GrainBoundaryTransformation (class in pymatgen.transformations.advanced_transformations) gramschmidt() (in module pymatgen.analysis.local_env) GrandPotentialPhaseDiagram (class in pymatgen.analysis.phase_diagram) GrandPotPDEntry (class in pymatgen.analysis.phase_diagram) graph() (ConnectedComponent property) green_kristoffel() (ElasticTensor method) green_lagrange_strain() (Deformation property) grid_off (WulffShape attribute) Grosspop (class in pymatgen.io.lobster) ground_state_term_symbol() (Element property) GroundStateScfCycle (class in pymatgen.io.abinit.abiinspect) group (Element attribute) group() (Element property) group_by_types() (SiteCollection method) group_entries_by_structure() (in module pymatgen.entries.entry_tools) group_molecules() (MoleculeMatcher method) group_structures() (StructureMatcher method) gruneisen_parameter() (QuasiharmonicDebyeApprox method) gs_input() (in module pymatgen.io.abinit.inputs) GulpCaller (class in pymatgen.command_line.gulp_caller) GulpConvergenceError GulpError GulpIO (class in pymatgen.command_line.gulp_caller) gwcalctyp() (SelfEnergy property) gweight() (NormalizedAngleDistanceNbSetWeight method)

H

H (Element attribute) haeberlen_values() (ChemicalShielding property) HaeberlenNotation (ChemicalShielding attribute) halogen_list (MoleculeStructureComparator attribute) has_antibnd_states_below_efermi() (Cohp method) has_dojo_report() (Pseudo property) has_eigendisplacements() (PhononBandStructure property) has_errors() (CifParser property) has_good_quality_check_occupied_bands() (Bandoverlaps method) has_good_quality_maxDeviation() (Bandoverlaps method) has_hints() (Pseudo property) has_imaginary_freq() (PhononBandStructure method) has_materials_project_access() (ChemEnvConfig property) has_nac() (PhononBandStructure property) has_option() (AdfKey method) has_same_structures() (BasicMultiDataset property) has_subkey() (AdfKey method) have_consistent_saxis() (Magmom static method) have_equivalent_surfaces() (Slab method) He (Element attribute) Header (class in pymatgen.io.feff.inputs) header() (AbstractFeffInputSet method) (FEFFDictSet method) header_string_from_file() (Header static method) HeisenbergMapper (class in pymatgen.analysis.magnetism.heisenberg) HeisenbergScreener (class in pymatgen.analysis.magnetism.heisenberg) helmholtz_free_energy() (PhononDos method) hessian (GaussianOutput attribute) hex() (HighSymmKpath method) hexagonal() (Lattice static method) Hf (Element attribute) Hg (Element attribute) HighSymmKpath (class in pymatgen.symmetry.bandstructure) HilbertTransform (class in pymatgen.io.abinit.abiobjects) hill_formula() (Composition property) hint_for_accuracy() (Pseudo method) hints() (CoordinationGeometry.NeighborsSetsHints method) history (Relaxation attribute) HistoryNode (class in pymatgen.util.provenance) hkl_list (WulffShape attribute) hkl_transformation() (in module pymatgen.core.surface) hkl_tuple_to_str() (in module pymatgen.analysis.wulff) Ho (Element attribute) homogeneous_poisson() (ElasticTensor property) htmlify() (in module pymatgen.util.string) hubbards() (Vasprun property) HYB_GGA_X_N12_SX (LibxcFunc attribute) HYB_GGA_X_SOGGA11_X (LibxcFunc attribute) HYB_GGA_XC_B1LYP (LibxcFunc attribute) HYB_GGA_XC_B1PW91 (LibxcFunc attribute) HYB_GGA_XC_B1WC (LibxcFunc attribute) HYB_GGA_XC_B3LYP (LibxcFunc attribute) HYB_GGA_XC_B3LYP5 (LibxcFunc attribute) HYB_GGA_XC_B3LYPs (LibxcFunc attribute) HYB_GGA_XC_B3P86 (LibxcFunc attribute) HYB_GGA_XC_B3PW91 (LibxcFunc attribute) HYB_GGA_XC_B97 (LibxcFunc attribute) HYB_GGA_XC_B97_1 (LibxcFunc attribute) HYB_GGA_XC_B97_1p (LibxcFunc attribute) HYB_GGA_XC_B97_2 (LibxcFunc attribute) HYB_GGA_XC_B97_3 (LibxcFunc attribute) HYB_GGA_XC_B97_K (LibxcFunc attribute) HYB_GGA_XC_BHANDH (LibxcFunc attribute) HYB_GGA_XC_BHANDHLYP (LibxcFunc attribute) HYB_GGA_XC_CAM_B3LYP (LibxcFunc attribute)

HYB_GGA_XC_CAMY_B3LYP (LibxcFunc attribute) HYB_GGA_XC_CAMY_BLYP (LibxcFunc attribute) HYB_GGA_XC_CAP0 (LibxcFunc attribute) HYB_GGA_XC_EDF2 (LibxcFunc attribute) HYB_GGA_XC_HJS_B88 (LibxcFunc attribute) HYB_GGA_XC_HJS_B97X (LibxcFunc attribute) HYB_GGA_XC_HJS_PBE (LibxcFunc attribute) HYB_GGA_XC_HJS_PBE_SOL (LibxcFunc attribute) HYB_GGA_XC_HPBEINT (LibxcFunc attribute) HYB_GGA_XC_HSE03 (LibxcFunc attribute) HYB_GGA_XC_HSE06 (LibxcFunc attribute) HYB_GGA_XC_LC_VV10 (LibxcFunc attribute) HYB_GGA_XC_LCY_BLYP (LibxcFunc attribute) HYB_GGA_XC_LCY_PBE (LibxcFunc attribute) HYB_GGA_XC_LRC_WPBE (LibxcFunc attribute) HYB_GGA_XC_LRC_WPBEH (LibxcFunc attribute) HYB_GGA_XC_MB3LYP_RC04 (LibxcFunc attribute) HYB_GGA_XC_mPW1K (LibxcFunc attribute) HYB_GGA_XC_mPW1PW (LibxcFunc attribute) HYB_GGA_XC_MPW3LYP (LibxcFunc attribute) HYB_GGA_XC_MPW3PW (LibxcFunc attribute) HYB_GGA_XC_MPWLYP1M (LibxcFunc attribute) HYB_GGA_XC_O3LYP (LibxcFunc attribute) HYB_GGA_XC_PBE0_13 (LibxcFunc attribute) HYB_GGA_XC_PBEH (LibxcFunc attribute) HYB_GGA_XC_REVB3LYP (LibxcFunc attribute) HYB_GGA_XC_SB98_1a (LibxcFunc attribute) HYB_GGA_XC_SB98_1b (LibxcFunc attribute) HYB_GGA_XC_SB98_1c (LibxcFunc attribute) HYB_GGA_XC_SB98_2a (LibxcFunc attribute) HYB_GGA_XC_SB98_2b (LibxcFunc attribute) HYB_GGA_XC_SB98_2c (LibxcFunc attribute) HYB_GGA_XC_TUNED_CAM_B3LYP (LibxcFunc attribute) HYB_GGA_XC_WB97 (LibxcFunc attribute) HYB_GGA_XC_WB97X (LibxcFunc attribute) HYB_GGA_XC_WB97X_D (LibxcFunc attribute) HYB_GGA_XC_WB97X_V (LibxcFunc attribute) HYB_GGA_XC_X3LYP (LibxcFunc attribute) HYB_MGGA_X_DLDF (LibxcFunc attribute) HYB_MGGA_X_MN12_SX (LibxcFunc attribute) HYB_MGGA_X_MN15 (LibxcFunc attribute) HYB_MGGA_X_MS2H (LibxcFunc attribute) HYB_MGGA_X_MVSH (LibxcFunc attribute) HYB_MGGA_X_SCAN0 (LibxcFunc attribute) HYB_MGGA_XC_B86B95 (LibxcFunc attribute) HYB_MGGA_XC_B88B95 (LibxcFunc attribute) HYB_MGGA_XC_BB1K (LibxcFunc attribute) HYB_MGGA_XC_M05 (LibxcFunc attribute) HYB_MGGA_XC_M05_2X (LibxcFunc attribute) HYB_MGGA_XC_M06 (LibxcFunc attribute) HYB_MGGA_XC_M06_2X (LibxcFunc attribute) HYB_MGGA_XC_M06_HF (LibxcFunc attribute) HYB_MGGA_XC_M08_HX (LibxcFunc attribute) HYB_MGGA_XC_M08_SO (LibxcFunc attribute) HYB_MGGA_XC_M11 (LibxcFunc attribute) HYB_MGGA_XC_MPW1B95 (LibxcFunc attribute) HYB_MGGA_XC_MPWB1K (LibxcFunc attribute) HYB_MGGA_XC_PW6B95 (LibxcFunc attribute) HYB_MGGA_XC_PW86B95 (LibxcFunc attribute) HYB_MGGA_XC_PWB6K (LibxcFunc attribute) HYB_MGGA_XC_REVTPSSH (LibxcFunc attribute) HYB_MGGA_XC_TPSSH (LibxcFunc attribute) HYB_MGGA_XC_WB97M_V (LibxcFunc attribute) HYB_MGGA_XC_X1B95 (LibxcFunc attribute) HYB_MGGA_XC_XB1K (LibxcFunc attribute) hybersten (PPModelModes attribute)

I

I (Element attribute) icohp (IcohpValue attribute) icohp() (IcohpValue property) IcohpCollection (class in pymatgen.electronic_structure.cohp) icohpcollection() (Icohplist property) Icohplist (class in pymatgen.io.lobster) icohplist() (Icohplist property) IcohpValue (class in pymatgen.electronic_structure.cohp) icohpvalue() (IcohpValue method) icsd_oxidation_states() (Element property) id_generator() (in module pymatgen.util.convergence) identify_potcar() (PotcarSingle method) idos (Vasprun attribute) images() (NEBPathfinder property) IMolecule (class in pymatgen.core.structure) In (Element attribute) in_array_list() (in module pymatgen.symmetry.groups) in_coord_list() (in module pymatgen.util.coord) in_coord_list_pbc() (in module pymatgen.util.coord) in_simplex() (Simplex method) Incar (class in pymatgen.io.vasp.inputs) incar (Vasprun attribute) incar() (DictSet property) (MPNMRSet property) (MPNonSCFSet property) (MPSOCSet property) (MPStaticSet property) (MVLGBSet property) (MVLGWSet property) (VaspInputSet property) InchiMolAtomMapper (class in pymatgen.analysis.molecule_matcher) inclvkb() (ExcHamiltonian property) ind_zero_freq (PhononDos attribute) indent() (ExcitingInput static method) index() (ConnectedSite property) indices_from_symbol() (SiteCollection method) indices_separate() (Plane method) info() (StructureEnvironments.NeighborsSet property) info_dict() (LibxcFunc property) infos_on_basis_set() (BasisSetReader method) infos_on_system() (FiestaInput property) init_3points() (Plane method) init_neighbors_sets() (StructureEnvironments method) InitializationChemenvError InputVariable (class in pymatgen.io.abinit.variable) insert() (Molecule method) (Structure method) insert_node() (MoleculeGraph method) (StructureGraph method) InsertionElectrode (class in pymatgen.apps.battery.insertion_battery) InsertionVoltagePair (class in pymatgen.apps.battery.insertion_battery) InsertSitesTransformation (class in pymatgen.transformations.site_transformations) install_software() (in module pymatgen.cli.pmg_config) int_number (SpaceGroup attribute) integer (AdditionalConditionInt attribute) Interface (class in pymatgen.analysis.interface) InterfaceBuilder (class in pymatgen.analysis.interface) InterfacialReactivity (class in pymatgen.analysis.interface_reactions) internal_energy() (PhononDos method) InternalStrainTensor (class in pymatgen.analysis.piezo_sensitivity) interpolate() (IStructure method) (NEBPathfinder method) Interstitial (class in pymatgen.analysis.defects.core) InterstitialGenerator (class in pymatgen.analysis.defects.generators) inv() (SquareTensor property) inv_matrix() (Lattice property) invdist() (NormalizedAngleDistanceNbSetWeight method) inverse() (AbstractTransformation property) (AddAdsorbateTransformation property) (AddSitePropertyTransformation property) (AutoOxiStateDecorationTransformation property) (ChargeBalanceTransformation property) (ChargedCellTransformation property) (ConventionalCellTransformation property) (CubicSupercellTransformation property) (DefectTransformation property) (DeformStructureTransformation property) (DiscretizeOccupanciesTransformation property) (DisorderOrderedTransformation property) (DopingTransformation property) (EnumerateStructureTransformation property) (GrainBoundaryTransformation property) (InsertSitesTransformation property) (JonesFaithfulTransformation property) (MagOrderingTransformation property) (MultipleSubstitutionTransformation property) (OrderDisorderedStructureTransformation property) (OxidationStateDecorationTransformation property) (OxidationStateRemovalTransformation property) (PartialRemoveSitesTransformation property) (PartialRemoveSpecieTransformation property) (PerturbStructureTransformation property) (PrimitiveCellTransformation property) (RemoveSitesTransformation property) (RemoveSpeciesTransformation property) (ReplaceSiteSpeciesTransformation property) (RotationTransformation property) (ScaleToRelaxedTransformation property) (SlabTransformation property) (SQSTransformation property) (SubstituteSurfaceSiteTransformation property) (SubstitutionPredictorTransformation property) (SubstitutionTransformation property) (SupercellTransformation property) (SuperTransformation property) (SymmOp property) (TranslateSitesTransformation property) inverse_smootherstep() (RatioFunction method) inverse_smoothstep() (RatioFunction method) inversion() (SymmOp static method) inversion_op (PointGroupAnalyzer attribute) invndist() (NormalizedAngleDistanceNbSetWeight method) Ion (class in pymatgen.core.ion) ion_ioncell_relax_input() (in module pymatgen.io.abinit.inputs) ion_or_solid_comp_object() (in module pymatgen.analysis.pourbaix_diagram) IonEntry (class in pymatgen.analysis.pourbaix_diagram) ionic_element_list (MoleculeStructureComparator attribute) ionic_radii (Element attribute) ionic_radii() (Element property) ionic_radius (Specie attribute) ionic_radius() (Specie property) ionic_steps (Vasprun attribute) IONMOV_DEFAULT (RelaxationMethod attribute) Ir (Element attribute) IRDielectricTensor (class in pymatgen.phonon.ir_spectra) is_0d() (ConnectedComponent property) is_1d() (ConnectedComponent property) is_2d() (ConnectedComponent property) is_3d() (ConnectedComponent property) is_a_valid_coordination_geometry() (AllCoordinationGeometries method) is_actinoid (Element attribute) is_actinoid() (Element property) is_alkali (Element attribute) is_alkali() (Element property) is_alkaline (Element attribute) is_alkaline() (Element property) is_already_analyzed() (in module pymatgen.core.surface) is_anion_cation_bond() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) is_block_key() (AdfKey method) is_bonded() (CovalentBond static method) is_c_kind() (LibxcFunc property) is_chalcogen() (Element property) is_close_to() (ChemicalEnvironments method) (DetailedVoronoiContainer method)

is_complete() (PseudoTable method) is_converged() (in module pymatgen.io.abinit.helpers) (WorkFunctionAnalyzer method) is_coord_subset() (in module pymatgen.util.coord) is_coord_subset_pbc() (in module pymatgen.util.coord) (in module pymatgen.util.coord_cython) is_element() (Composition property) (Entry property) (GrandPotPDEntry property) is_failed (AdfOutput attribute) is_fit_to_structure() (Tensor method) (TensorCollection method) is_gga_family() (LibxcFunc property) is_halogen (Element attribute) is_halogen() (Element property) is_hexagonal() (Lattice method) is_homogeneous() (KSampling property) is_hubbard() (Vasprun property) is_hyb_gga_family() (LibxcFunc property) is_hyb_mgga_family() (LibxcFunc property) is_image() (VoronoiPolyhedron method) is_implemented() (CoordinationGeometry method) is_in_list() (Plane method) is_in_plane() (Plane method) is_independent() (Deformation method) is_internal_crash (AdfOutput attribute) is_jahn_teller_active() (JahnTellerAnalyzer method) is_k_kind() (LibxcFunc property) is_lanthanoid (Element attribute) is_lanthanoid() (Element property) is_laue() (SpacegroupAnalyzer method) is_lda_family() (LibxcFunc property) is_magnetic() (CollinearMagneticStructureAnalyzer property) is_metal() (BandStructure method) (Element property) is_metalloid (Element attribute) is_metalloid() (Element property) is_mgga_family() (LibxcFunc property) is_noble_gas (Element attribute) is_noble_gas() (Element property) is_numeric() (in module pymatgen.io.adf) is_one_to_many() (AbstractTransformation property) (AddAdsorbateTransformation property) (AddSitePropertyTransformation property) (AutoOxiStateDecorationTransformation property) (ChargeBalanceTransformation property) (ChargedCellTransformation property) (ConventionalCellTransformation property) (CubicSupercellTransformation property) (DefectTransformation property) (DeformStructureTransformation property) (DiscretizeOccupanciesTransformation property) (DisorderOrderedTransformation property) (DopingTransformation property) (EnumerateStructureTransformation property) (GrainBoundaryTransformation property) (InsertSitesTransformation property) (MagOrderingTransformation property) (MultipleSubstitutionTransformation property) (OrderDisorderedStructureTransformation property) (OxidationStateDecorationTransformation property) (OxidationStateRemovalTransformation property) (PartialRemoveSitesTransformation property) (PartialRemoveSpecieTransformation property) (PerturbStructureTransformation property) (PrimitiveCellTransformation property) (RemoveSitesTransformation property) (RemoveSpeciesTransformation property) (ReplaceSiteSpeciesTransformation property) (RotationTransformation property) (ScaleToRelaxedTransformation property) (SlabTransformation property) (SQSTransformation property) (SubstituteSurfaceSiteTransformation property) (SubstitutionPredictorTransformation property) (SubstitutionTransformation property) (SupercellTransformation property) (SuperTransformation property) (TranslateSitesTransformation property) is_ordered() (Site property) (SiteCollection property) is_orthogonal() (Lattice property) is_pcm (GaussianOutput attribute) is_periodic() (ConnectedComponent property) is_periodic_image() (PeriodicSite method) is_polar() (Slab method) is_post_transition_metal (Element attribute) is_post_transition_metal() (Element property) is_quadrupolar() (Element property) is_rare_earth_metal (Element attribute) is_rare_earth_metal() (Element property) is_redox_active_intercalation() (in module pymatgen.apps.battery.analyzer) is_rotation() (SquareTensor method) is_same_plane_as() (Plane method) is_same_vectors() (ZSLGenerator method) is_spin (GaussianOutput attribute) is_spin() (Vasprun property) is_spin_polarized (BandStructure attribute) (Doscar attribute) (IcohpCollection attribute) is_spin_polarized() (Doscar property) (IcohpCollection property) (IcohpValue property) is_stopped (Outcar attribute) is_subgroup() (SymmetryGroup method) is_super_electrode() (ConversionElectrode method) is_supergroup() (SymmetryGroup method) is_symmetric() (Slab method) (Tensor method) (TensorCollection method) is_transition_metal (Element attribute) is_transition_metal() (Element property) is_valid() (SiteCollection method) is_valid_bibtex() (in module pymatgen.util.provenance) is_valid_op() (PointGroupAnalyzer method) is_valid_symbol (Element attribute) is_voigt_symmetric() (Tensor method) (TensorCollection method) is_x_kind() (LibxcFunc property) is_xc_kind() (LibxcFunc property) IsingModel (class in pymatgen.analysis.energy_models) isite() (AbstractEnvironmentNode property) isnc() (BasicAbinitInput property) (BasicMultiDataset property) (Pseudo property) isomorphic_to() (MoleculeGraph method) IsomorphismMolAtomMapper (class in pymatgen.analysis.molecule_matcher) ispaw() (BasicAbinitInput property) (BasicMultiDataset property) (Pseudo property) ispin (Eigenval attribute) IStructure (class in pymatgen.core.structure) itdensities() (Doscar property) items() (CyclesPlotter method) (TensorMapping method) iterative_symmetrize() (in module pymatgen.symmetry.analyzer) iterlines() (in module pymatgen.io.adf) IUCr_symbol() (CoordinationGeometry property) IUCr_symbol_str() (CoordinationGeometry property) iupac_formula() (Composition property) iupac_ordering (Element attribute) iupac_ordering() (Element property) IUPAC_symbol() (CoordinationGeometry property) IUPAC_symbol_str() (CoordinationGeometry property)

J

j() (Orbital property) JahnTellerAnalyzer (class in pymatgen.analysis.magnetism.jahnteller) jimage() (ConnectedSite property)

JmolNN (class in pymatgen.analysis.local_env) JonesFaithfulTransformation (class in pymatgen.symmetry.settings) json_pretty_dump() (in module pymatgen.util.serialization)

K

K (Element attribute) k_reuss() (ElasticTensor property) k_voigt() (ElasticTensor property) k_vrh() (ElasticTensor property) kappa() (ChemicalShielding.MarylandNotation property) key() (AdfKey property) keyPressEvent() (MultiStructuresInteractorStyle method) (StructureInteractorStyle method) keyword_line() (GulpIO method) keywords (PotcarSingle attribute) kpath() (HighSymmKpath property) Kpoint (class in pymatgen.electronic_structure.bandstructure) Kpoints (class in pymatgen.io.vasp.inputs) kpoints (Eigenval attribute) (Vasprun attribute) (Wavecar attribute)

kpoints() (DictSet property) (MITMDSet property) (MPHSEBSSet property) (MPMDSet property) (MPNonSCFSet property) (MPStaticSet property) (MVLGBSet property) (MVLGWSet property) (MVLSlabSet property) (VaspInputSet property) Kpoints_supported_modes (class in pymatgen.io.vasp.inputs) kpoints_weights (Eigenval attribute) Kr (Element attribute) KSampling (class in pymatgen.io.abinit.abiobjects) KSamplingModes (class in pymatgen.io.abinit.abiobjects) KumagaiCorrection (class in pymatgen.analysis.defects.corrections)

L

l() (Orbital property) (OrbitalDescription property) l_local() (Pseudo property) l_max() (Pseudo property) La (Element attribute) label (SlabEntry attribute) label() (FreqUnits property) (Kpoint property) labels() (InterfacialReactivity method) LammpsBox (class in pymatgen.io.lammps.data) LammpsData (class in pymatgen.io.lammps.data) LammpsDump (class in pymatgen.io.lammps.outputs) LammpsRun (class in pymatgen.io.lammps.inputs) LammpsRunner (class in pymatgen.io.lammps.utils) laplacian() (CriticalPoint property) last_etotal() (D2DEScfCycle property) (GroundStateScfCycle property) last_iteration() (ScfCycle property) last_nneigh() (LocalStructOrderParams property) latexify() (in module pymatgen.util.string) latexify_ion() (in module pymatgen.analysis.pourbaix_diagram) latexify_spacegroup() (in module pymatgen.util.string) Lattice (class in pymatgen.core.lattice) lattice (WulffShape attribute) lattice() (IStructure property) (Kpoint property) (PeriodicSite property) (Structure property) lattice_2_lmpbox() (in module pymatgen.io.lammps.data) lattice_from_abivars() (in module pymatgen.io.abinit.abiobjects) lattice_points_in_supercell() (in module pymatgen.util.coord) lattice_rec (BandStructure attribute) lattice_type() (PWOutput property) LDA_C_1D_CSC (LibxcFunc attribute) LDA_C_1D_LOOS (LibxcFunc attribute) LDA_C_2D_AMGB (LibxcFunc attribute) LDA_C_2D_PRM (LibxcFunc attribute) LDA_C_GL (LibxcFunc attribute) LDA_C_GOMBAS (LibxcFunc attribute) LDA_C_HL (LibxcFunc attribute) LDA_C_ML1 (LibxcFunc attribute) LDA_C_ML2 (LibxcFunc attribute) LDA_C_OB_PW (LibxcFunc attribute) LDA_C_OB_PZ (LibxcFunc attribute) LDA_C_PW (LibxcFunc attribute) LDA_C_PW_MOD (LibxcFunc attribute) LDA_C_PW_RPA (LibxcFunc attribute) LDA_C_PZ (LibxcFunc attribute) LDA_C_PZ_MOD (LibxcFunc attribute) LDA_C_RC04 (LibxcFunc attribute) LDA_C_RPA (LibxcFunc attribute) LDA_C_vBH (LibxcFunc attribute) LDA_C_VWN (LibxcFunc attribute) LDA_C_VWN_1 (LibxcFunc attribute) LDA_C_VWN_2 (LibxcFunc attribute) LDA_C_VWN_3 (LibxcFunc attribute) LDA_C_VWN_4 (LibxcFunc attribute) LDA_C_VWN_RPA (LibxcFunc attribute) LDA_C_WIGNER (LibxcFunc attribute) LDA_C_XALPHA (LibxcFunc attribute)

LDA_K_LP (LibxcFunc attribute) LDA_K_TF (LibxcFunc attribute) LDA_STATIC_DIEL (TaskType attribute) LDA_X (LibxcFunc attribute) LDA_X_1D (LibxcFunc attribute) LDA_X_2D (LibxcFunc attribute) LDA_XC_KSDT (LibxcFunc attribute) LDA_XC_TETER93 (LibxcFunc attribute) LDA_XC_ZLP (LibxcFunc attribute) LDos (class in pymatgen.io.feff.outputs) leftButtonPressEvent() (StructureInteractorStyle method) leftButtonReleaseEvent() (StructureInteractorStyle method) Length (in module pymatgen.core.units) length() (CovalentBond property) lengths() (Lattice property) lengths_and_angles() (Lattice property) Li (Element attribute) library_line() (GulpIO method) LibxcFunc (class in pymatgen.core.libxcfunc) LIGANDS_ARRANGEMENT (AbstractEnvironmentNode attribute) LightStructureEnvironments (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) LightStructureEnvironments.NeighborsSet (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) linden (PPModelModes attribute) line_intersection() (Simplex method) Line_mode (Kpoints_supported_modes attribute) linear_add() (VolumetricData method) LinearAssignment (class in pymatgen.optimization.linear_assignment) (class in pymatgen.optimization.linear_assignment_numpy) linearly_equidistant() (CNBiasNbSetWeight class method) lineno (YamlDoc attribute) link0 (GaussianOutput attribute) link_marked_atoms() (FunctionalGroupExtractor method) liquid_range (Element attribute) list_prediction() (SubstitutionPredictor method) LISTKEYWORDS (Lobsterin attribute) lll_inverse() (Lattice property) lll_mapping() (Lattice property) lll_matrix() (Lattice property) lll_reduce (SlabGenerator attribute) LMTOCopl (class in pymatgen.io.lmto) LMTOCtrl (class in pymatgen.io.lmto) load_data() (BorgQueen method) loadfn() (in module pymatgen) LobsterBandStructureSymmLine (class in pymatgen.electronic_structure.bandstructure) LobsterCompleteDos (class in pymatgen.electronic_structure.dos) Lobsterin (class in pymatgen.io.lobster) Lobsterout (class in pymatgen.io.lobster) LobsterSet (class in pymatgen.io.vasp.sets) LocalGeometryFinder (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) localopt() (BabelMolAdaptor method) LocalStructOrderParams (class in pymatgen.analysis.local_env) lockxyz (ExcitingInput attribute) lockxyz() (ExcitingInput property) Locpot (class in pymatgen.io.vasp.outputs) locpot_along_c (WorkFunctionAnalyzer attribute) long_name (Element attribute) long_v() (ElasticTensor method) lower_and_check_unique() (in module pymatgen.io.qchem.utils) lowest_energy_structure() (OrderDisorderedStructureTransformation property) Lr (Element attribute) Lu (Element attribute)

M

MAGIC (D2DEScfCycle attribute) (GroundStateScfCycle attribute) Magmom (class in pymatgen.electronic_structure.core) magmoms() (CollinearMagneticStructureAnalyzer property) magnetic_deformation() (in module pymatgen.analysis.magnetism.analyzer) magnetic_species_and_magmoms() (CollinearMagneticStructureAnalyzer property) MagneticDeformation (class in pymatgen.analysis.magnetism.analyzer) MagneticSpaceGroup (class in pymatgen.symmetry.maggroups) MagneticStructureEnumerator (class in pymatgen.analysis.magnetism.analyzer) magnetization (Outcar attribute) MagOrderingTransformation (class in pymatgen.transformations.advanced_transformations) MagOrderParameterConstraint (class in pymatgen.transformations.advanced_transformations) MagSymmOp (class in pymatgen.core.operations) mAh() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) main() (in module pymatgen.cli.feff_input_generation) (in module pymatgen.cli.feff_plot_cross_section) (in module pymatgen.cli.feff_plot_dos) (in module pymatgen.cli.gaussian_analyzer) (in module pymatgen.cli.get_environment) (in module pymatgen.cli.pmg) make3d() (BabelMolAdaptor method) make_FULL_BSE_Densities_folder() (FiestaInput method) make_interface() (InterfaceBuilder method) make_movie() (in module pymatgen.vis.structure_vtk) make_supercell() (Structure method) make_supercells_with_defects() (StructureMotifInterstitial method) make_supergraph() (ConnectedComponent method) (in module pymatgen.analysis.chemenv.connectivity.connected_components) make_symmetric_matrix_from_upper_tri() (in module pymatgen.util.num) maps (ForceField attribute) maps_and_surfaces() (DetailedVoronoiContainer method) maps_and_surfaces_bounded() (DetailedVoronoiContainer method) maryland_values() (ChemicalShielding property) Mass (in module pymatgen.core.units) mass_charge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) mass_discharge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) masses (ForceField attribute) masses() (Dynmat property) match_as_dict() (ZSLGenerator method) matches() (IStructure method) matches_ordering() (CollinearMagneticStructureAnalyzer method) material_formula() (Xmu property) MaterialsProjectAqueousCompatibility (class in pymatgen.entries.compatibility) MaterialsProjectCompatibility (class in pymatgen.entries.compatibility) matrix() (Lattice property) matrixTimesVector() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) max_cation_insertion() (BatteryAnalyzer property) max_cation_removal() (BatteryAnalyzer property) max_connectivity() (VoronoiConnectivity property) max_delta_volume() (AbstractElectrode property) max_electronegativity() (MolecularOrbitals method) max_oxidation_state (Element attribute) max_oxidation_state() (Element property) max_phfreq() (IRDielectricTensor property) max_spline_jump() (EnergyTrend method) max_spline_jumps() (Polarization method) max_voltage() (AbstractElectrode property) max_voltage_step() (AbstractElectrode property) maxlen (CifBlock attribute) maxloc() (in module pymatgen.util.num) mcl() (HighSymmKpath method) mclc1() (HighSymmKpath method) mclc2() (HighSymmKpath method) mclc3() (HighSymmKpath method) mclc4() (HighSymmKpath method) mclc5() (HighSymmKpath method) Mcsqs (class in pymatgen.io.atat) Md (Element attribute) md() (LammpsRun class method) md5 (Pseudo attribute) mean_estimator() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) mean_stress() (Stress property) measure() (in module pymatgen.util.convergence) mehring_values() (ChemicalShielding property) melting_point (Element attribute) Memory (in module pymatgen.core.units) mendeleev_no (Element attribute) merge_sites() (Structure method) merge_slabs() (in module pymatgen.analysis.interface) metal_edge_extender() (in module pymatgen.analysis.fragmenter) metallic_radius() (Element property) metric_tensor() (Lattice property) Mg (Element attribute) MGGA_C_BC95 (LibxcFunc attribute) MGGA_C_CC06 (LibxcFunc attribute) MGGA_C_CS (LibxcFunc attribute) MGGA_C_DLDF (LibxcFunc attribute) MGGA_C_M05 (LibxcFunc attribute) MGGA_C_M05_2X (LibxcFunc attribute) MGGA_C_M06 (LibxcFunc attribute) MGGA_C_M06_2X (LibxcFunc attribute) MGGA_C_M06_HF (LibxcFunc attribute) MGGA_C_M06_L (LibxcFunc attribute) MGGA_C_M08_HX (LibxcFunc attribute) MGGA_C_M08_SO (LibxcFunc attribute) MGGA_C_M11 (LibxcFunc attribute) MGGA_C_M11_L (LibxcFunc attribute) MGGA_C_MN12_L (LibxcFunc attribute) MGGA_C_MN12_SX (LibxcFunc attribute) MGGA_C_MN15 (LibxcFunc attribute) MGGA_C_MN15_L (LibxcFunc attribute) MGGA_C_PKZB (LibxcFunc attribute) MGGA_C_REVTPSS (LibxcFunc attribute) MGGA_C_SCAN (LibxcFunc attribute) MGGA_C_TPSS (LibxcFunc attribute) MGGA_C_TPSSLOC (LibxcFunc attribute) MGGA_C_VSXC (LibxcFunc attribute) MGGA_X_2D_PRHG07 (LibxcFunc attribute) MGGA_X_2D_PRHG07_PRP10 (LibxcFunc attribute) MGGA_X_BJ06 (LibxcFunc attribute) MGGA_X_BLOC (LibxcFunc attribute) MGGA_X_BR89 (LibxcFunc attribute) MGGA_X_GVT4 (LibxcFunc attribute) MGGA_X_LTA (LibxcFunc attribute) MGGA_X_M05 (LibxcFunc attribute) MGGA_X_M05_2X (LibxcFunc attribute) MGGA_X_M06 (LibxcFunc attribute) MGGA_X_M06_2X (LibxcFunc attribute) MGGA_X_M06_HF (LibxcFunc attribute) MGGA_X_M06_L (LibxcFunc attribute) MGGA_X_M08_HX (LibxcFunc attribute) MGGA_X_M08_SO (LibxcFunc attribute) MGGA_X_M11 (LibxcFunc attribute) MGGA_X_M11_L (LibxcFunc attribute) MGGA_X_MBEEF (LibxcFunc attribute) MGGA_X_MBEEFVDW (LibxcFunc attribute) MGGA_X_MK00 (LibxcFunc attribute) MGGA_X_MK00B (LibxcFunc attribute) MGGA_X_MN12_L (LibxcFunc attribute) MGGA_X_MN15_L (LibxcFunc attribute) MGGA_X_MODTPSS (LibxcFunc attribute) MGGA_X_MS0 (LibxcFunc attribute) MGGA_X_MS1 (LibxcFunc attribute)

MGGA_X_MS2 (LibxcFunc attribute) MGGA_X_MVS (LibxcFunc attribute) MGGA_X_PKZB (LibxcFunc attribute) MGGA_X_REVTPSS (LibxcFunc attribute) MGGA_X_RPP09 (LibxcFunc attribute) MGGA_X_SCAN (LibxcFunc attribute) MGGA_X_TAU_HCTH (LibxcFunc attribute) MGGA_X_TB09 (LibxcFunc attribute) MGGA_X_TPSS (LibxcFunc attribute) MGGA_XC_B97M_V (LibxcFunc attribute) MGGA_XC_OTPSS_D (LibxcFunc attribute) MGGA_XC_TPSSLYP1W (LibxcFunc attribute) MGGA_XC_ZLP (LibxcFunc attribute) micro_pyawk() (in module pymatgen.util.io_utils) miller_area (WulffShape attribute) miller_area_dict() (WulffShape property) miller_energy_dict() (WulffShape property) miller_index (Slab attribute) (SlabEntry attribute) (SlabGenerator attribute) miller_index_from_sites() (in module pymatgen.core.surface) miller_list (WulffShape attribute) min_cost() (LinearAssignment property) min_freq() (PhononBandStructure method) min_max_indexes() (in module pymatgen.util.num) min_oxidation_state (Element attribute) min_oxidation_state() (Element property) min_slab_size (SlabGenerator attribute) min_vac_size (SlabGenerator attribute) min_voltage() (AbstractElectrode property) mineral_hardness (Element attribute) minimize_matrix() (EwaldMinimizer method) minimized_sum() (EwaldMinimizer property) minimum() (InterfacialReactivity method) minimum_geometries() (ChemicalEnvironments method) minimum_geometry() (ChemicalEnvironments method) MinimumDistanceNN (class in pymatgen.analysis.local_env) MinimumOKeeffeNN (class in pymatgen.analysis.local_env) MinimumVIRENN (class in pymatgen.analysis.local_env) minloc() (in module pymatgen.util.num) MITAqueousCompatibility (class in pymatgen.entries.compatibility) MITCompatibility (class in pymatgen.entries.compatibility) MITMDSet (class in pymatgen.io.vasp.sets) MITNEBSet (class in pymatgen.io.vasp.sets) MITRelaxSet (class in pymatgen.io.vasp.sets) MixedPotential (class in pymatgen.analysis.path_finder) Mn (Element attribute) Mo (Element attribute) MO_coefficients (GaussianOutput attribute) mode() (Smearing property) ModelDielectricFunction (class in pymatgen.io.abinit.abiobjects) MODELS (EOS attribute) modify_lattice() (Structure method) MODULE_DIR (PymatgenTest attribute) molar_volume (Element attribute) molecular_orbital (GaussianOutput attribute) MolecularOrbitals (class in pymatgen.core.molecular_orbitals) Molecule (class in pymatgen.core.structure) molecule() (FiestaInput property) (GaussianInput property) (NwInput property) (XYZ property) molecule_template() (QCInput static method) MoleculeGraph (class in pymatgen.analysis.graphs) MoleculeMatcher (class in pymatgen.analysis.molecule_matcher) molecules_allowed() (BrunnerNN_real property) (BrunnerNN_reciprocal property) (BrunnerNN_relative property) (CovalentBondNN property) (Critic2NN property) (CrystalNN property) (CutOffDictNN property) (EconNN property) (JmolNN property) (MinimumDistanceNN property) (MinimumOKeeffeNN property) (MinimumVIRENN property) (NearNeighbors property) (OpenBabelNN property) (VoronoiNN property) MoleculeStructureComparator (class in pymatgen.analysis.molecule_structure_comparator) MolGraphSplitError Monkhorst (Kpoints_supported_modes attribute) monkhorst (KSamplingModes attribute) monkhorst() (KSampling class method) monkhorst_automatic() (Kpoints static method) (KSampling class method) MonkhorstPack (ShiftMode attribute) monoclinic() (Lattice static method) monolayer_vs_BE() (SurfaceEnergyPlotter method) monotonic() (in module pymatgen.util.num) MonteCarloRattleTransformation() (in module pymatgen.transformations.advanced_transformations) mouseMoveEvent() (StructureInteractorStyle method) move_atoms() (RelaxationMethod property) move_cell() (RelaxationMethod property) move_to_other_side() (SlabGenerator method) mp_symbol() (AbstractEnvironmentNode property) (CoordinationGeometry property) MPEELSDictSet (class in pymatgen.io.feff.sets) MPELNESSet (class in pymatgen.io.feff.sets) MPEXAFSSet (class in pymatgen.io.feff.sets) MPEXELFSSet (class in pymatgen.io.feff.sets) MPHSEBSSet (class in pymatgen.io.vasp.sets) MPHSERelaxSet (class in pymatgen.io.vasp.sets) MPMDSet (class in pymatgen.io.vasp.sets) MPMetalRelaxSet (class in pymatgen.io.vasp.sets) MPNMRSet (class in pymatgen.io.vasp.sets) MPNonSCFSet (class in pymatgen.io.vasp.sets) MPRelaxSet (class in pymatgen.io.vasp.sets) MPRester (class in pymatgen.ext.matproj) MPRestError MPScanRelaxSet (class in pymatgen.io.vasp.sets) MPSOCSet (class in pymatgen.io.vasp.sets) MPStaticSet (class in pymatgen.io.vasp.sets) MPXANESSet (class in pymatgen.io.feff.sets) mu() (Xmu property) mu0() (Xmu property) mu_so() (JahnTellerAnalyzer static method) Mulliken_charges (GaussianOutput attribute) multi_curve_fit() (in module pymatgen.util.convergence) multi_job_string() (QCInput static method) multi_reciprocal_extra() (in module pymatgen.util.convergence) MultiEntry (class in pymatgen.analysis.pourbaix_diagram) MultiGraphCycle (class in pymatgen.analysis.chemenv.utils.graph_utils) multiple_outputs_from_file() (QCOutput static method) MultipleSubstitutionTransformation (class in pymatgen.transformations.advanced_transformations) multiplicity() (Defect property) (DefectEntry property) MultiStructuresInteractorStyle (class in pymatgen.vis.structure_vtk) MultiStructuresVis (class in pymatgen.vis.structure_vtk) MultiWeightsChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) Murnaghan (class in pymatgen.analysis.eos) MVLElasticSet (class in pymatgen.io.vasp.sets) MVLGBSet (class in pymatgen.io.vasp.sets) MVLGWSet (class in pymatgen.io.vasp.sets) MVLNPTMDSet (class in pymatgen.io.vasp.sets) MVLRelax52Set (class in pymatgen.io.vasp.sets) MVLScanRelaxSet (class in pymatgen.io.vasp.sets) MVLSlabSet (class in pymatgen.io.vasp.sets) my_solid_angle() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils)

N

N (Element attribute) n() (Orbital property) Na (Element attribute) Nads_in_slab() (SlabEntry property) name (Author attribute) (HistoryNode attribute) (IonEntry attribute) (PDEntry attribute) (XcFunc attribute) name() (Defect property) (DefectEntry property) (InputVariable property) (Interstitial property) (MoleculeGraph property) (MultiEntry property) (PourbaixEntry property) (StructureGraph property) (Substitution property) (Vacancy property) names_and_values() (AbinitTimer method) NanoscaleStability (class in pymatgen.analysis.surface_analysis) natoms() (Dynmat property) (Poscar property) (Xdatcar property) Nb (Element attribute) nb (Wavecar attribute) nb_bands (BandStructure attribute) nb_bands() (Wavederf property) nb_kpoints() (Wavederf property) nbands (Eigenval attribute) nbands() (Waveder property) NbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) ncpus() (AbinitTimer property) Nd (Element attribute) NDCalculator (class in pymatgen.analysis.diffraction.neutron) ndisps() (Dynmat property) ndtset() (BasicMultiDataset property) Ne (Element attribute) near_reduce() (AdsorbateSiteFinder method) NearNeighbors (class in pymatgen.analysis.local_env) NEBAnalysis (class in pymatgen.analysis.transition_state) NEBPathfinder (class in pymatgen.analysis.path_finder) neighb_coords() (LightStructureEnvironments.NeighborsSet property) (StructureEnvironments.NeighborsSet property) neighb_coordsOpt() (StructureEnvironments.NeighborsSet property) neighb_indices_and_images() (LightStructureEnvironments.NeighborsSet property) neighb_sites() (LightStructureEnvironments.NeighborsSet property) (StructureEnvironments.NeighborsSet property) neighb_sites_and_indices() (LightStructureEnvironments.NeighborsSet property) (StructureEnvironments.NeighborsSet property) Neighbor (class in pymatgen.core.structure) NEIGHBORING_CES (AbstractEnvironmentNode attribute) NEIGHBORING_COORDINATION_ENVIRONMENTS (AbstractEnvironmentNode attribute) neighbors() (DetailedVoronoiContainer method) NEIGHBORS_LIGANDS_ARRANGEMENT (AbstractEnvironmentNode attribute) neighbors_surfaces() (DetailedVoronoiContainer method) neighbors_surfaces_bounded() (DetailedVoronoiContainer method) NeighborsNotComputedChemenvError nelec() (BoltztrapRunner property) nelect (Eigenval attribute) nelect() (DictSet property) (Waveder property) nelectrons() (IMolecule property) (PotcarSingle property) net_magnetization() (Chgcar property) NetcdfReader (class in pymatgen.io.abinit.netcdf) new_with_vars() (BasicAbinitInput method) next() (YamlTokenizer method) next_doc_with_tag() (YamlTokenizer method) ngf (Outcar attribute) ngridpts (VolumetricData attribute) nH2O() (PourbaixEntry property) Ni (Element attribute) nionic_steps (Vasprun attribute) nk (Wavecar attribute) nkpoints() (Waveder property) nkpt (Eigenval attribute) NM (Ordering attribute)

nmr_quadrupole_moment() (Element property) NNData (CrystalNN attribute) No (Element attribute) NO_AC (AdditionalConditions attribute) NO_ADDITIONAL_CONDITION (AdditionalConditions attribute) NO_DEFAULT (class in pymatgen.io.abinit.netcdf) NO_E2SEB (AdditionalConditions attribute) NO_ELEMENT_TO_SAME_ELEMENT_BONDS (AdditionalConditions attribute) non_decreasing() (in module pymatgen.util.num) non_increasing() (in module pymatgen.util.num) NONE (AdditionalConditions attribute) none (OverwriteMagmomMode attribute) nonstoichiometric_symmetrized_slab() (SlabGenerator method) noppmodel (PPModelModes attribute) norm() (Lattice method) normal() (Slab property) normal_cdf_step() (in module pymatgen.analysis.chemenv.utils.math_utils) normal_modes (AdfOutput attribute) normalization_factor() (PourbaixEntry property) normalization_mass() (AbstractElectrode property) normalization_volume() (AbstractElectrode property) normalize (OverwriteMagmomMode attribute) normalize() (ComputedEntry method) (Entry method) (Spectrum method) (StaticPotential method) normalize_to() (BalancedReaction method) normalize_to_element() (BalancedReaction method) normalized_angles() (StructureEnvironments.NeighborsSet property) normalized_distances() (StructureEnvironments.NeighborsSet property) normalized_energy() (PourbaixEntry property) normalized_energy_at_conditions() (PourbaixEntry method) normalized_repr() (BalancedReaction property) normalized_repr_and_factor() (BalancedReaction method) NormalizedAngleDistanceNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) normalmode_eigenvals (Vasprun attribute) normalmode_eigenvecs (Vasprun attribute) nosmearing() (Smearing static method) now() (in module pymatgen.io.abinit.helpers) Np (Element attribute) npH() (PourbaixEntry property) nph_freqs() (IRDielectricTensor property) nPhi() (PourbaixEntry property) NsitesModel (class in pymatgen.analysis.energy_models) nspden() (Electrons property) nspecs() (Dynmat property) nspinor() (Electrons property) nsppol() (Electrons property) Nsurfs_ads_in_slab() (SlabEntry property) NthOrderElasticTensor (class in pymatgen.analysis.elasticity.elastic) ntypesp() (SiteCollection property) nucleus (CriticalPointType attribute) num_atoms() (Composition property) (PourbaixEntry property) num_basis_func (GaussianOutput attribute) num_bonds (IcohpValue attribute) num_bonds() (IcohpValue property) num_ops() (LocalStructOrderParams property) num_sites() (SiteCollection property) num_steps() (AbstractElectrode property) num_valence_electrons() (in module pymatgen.io.abinit.inputs) number (Element attribute) number() (Element property) NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE (AbstractEnvironmentNode attribute) NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT (AbstractEnvironmentNode attribute) number_of_magnetic_sites() (CollinearMagneticStructureAnalyzer property) NUMBER_OF_NEIGHBORING_CES (AbstractEnvironmentNode attribute) NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS (AbstractEnvironmentNode attribute) number_of_permutations() (CoordinationGeometry property) number_of_unique_magnetic_sites() (CollinearMagneticStructureAnalyzer method) NUMERIC_FIELDS (AbinitTimerSection attribute) numerical_tol (PhaseDiagram attribute) NumericalEOS (class in pymatgen.analysis.eos) Nwchem2Fiesta (class in pymatgen.io.fiesta) NwInput (class in pymatgen.io.nwchem) NwInputError NwOutput (class in pymatgen.io.nwchem) NwTask (class in pymatgen.io.nwchem)

O

O (Element attribute) obj_with_unit() (in module pymatgen.core.units) obtain_all_bond_lengths() (in module pymatgen.core.bonds) obtain_band_edges() (MolecularOrbitals method) occ() (Orbital property) occu_tol (Eigenval attribute) OccupancyComparator (class in pymatgen.analysis.structure_matcher) off_color (WulffShape attribute) offset_vector() (Interface property) omega() (ChemicalShielding.MarylandNotation property) (ElasticTensorExpansion method) on_wulff (WulffShape attribute) OneSymmetric (ShiftMode attribute) ONLY_ACB (AdditionalConditions attribute) ONLY_ACB_AND_NO_E2SEB (AdditionalConditions attribute) ONLY_ANION_CATION_BONDS (AdditionalConditions attribute) ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS (AdditionalConditions attribute) ONLY_E2OB (AdditionalConditions attribute) ONLY_ELEMENT_TO_OXYGEN_BONDS (AdditionalConditions attribute) open_pspsfile() (Pseudo method) open_ring() (in module pymatgen.analysis.fragmenter) openbabel_mol() (BabelMolAdaptor property) OpenBabelNN (class in pymatgen.analysis.local_env) operate() (SymmOp method) operate_magmom() (MagSymmOp method) operate_multi() (SymmOp method) operations (AdfTask attribute) (NwTask attribute) opt_template() (QCInput static method) OPTCELL_DEFAULT (RelaxationMethod attribute) optical_absorption_coeff() (Vasprun property) optimize_gibbs_free_energy() (QuasiharmonicDebyeApprox method) optimizer() (QuasiharmonicDebyeApprox method) OptSet (class in pymatgen.io.qchem.sets) Orbital (class in pymatgen.electronic_structure.core) (class in pymatgen.io.vasp.inputs) orbital_type() (Orbital property) OrbitalDescription (class in pymatgen.io.vasp.inputs) OrbitalType (class in pymatgen.electronic_structure.core) orc() (HighSymmKpath method) orcc() (HighSymmKpath method) orcf1() (HighSymmKpath method)

orcf2() (HighSymmKpath method) orcf3() (HighSymmKpath method) orci() (HighSymmKpath method) order (SpaceGroup attribute) order() (ElasticTensorExpansion property) (MultiGraphCycle method) (NthOrderElasticTensor property) (SimpleGraphCycle method) order_assimilation() (in module pymatgen.apps.borg.queen) order_phase_diagram() (in module pymatgen.analysis.phase_diagram) order_sections() (AbinitTimer method) OrderDisorderedStructureTransformation (class in pymatgen.transformations.standard_transformations) OrderDisorderElementComparator (class in pymatgen.analysis.structure_matcher) Ordering (class in pymatgen.analysis.magnetism.analyzer) ordering() (CollinearMagneticStructureAnalyzer property) oriented_unit_cell (SlabGenerator attribute) orthongonalize_structure() (StructureVis method) orthonormal_vectors() (Plane method) orthonormal_vectors_old() (Plane method) orthorhombic() (Lattice static method) Os (Element attribute) Oszicar (class in pymatgen.io.vasp.outputs) other_dielectric (Vasprun attribute) Outcar (class in pymatgen.io.vasp.outputs) output_lists() (EwaldMinimizer property) override_from_prev_calc() (MPHSEBSSet method) (MPNonSCFSet method) (MPSOCSet method) (MPStaticSet method) (MVLGWSet method) OverwriteMagmomMode (class in pymatgen.analysis.magnetism.analyzer) oxi_prob (Composition attribute) oxi_state (DummySpecie attribute) (Specie attribute) oxi_state() (DummySpecie property) (Specie property) oxi_state_guesses() (Composition method) oxidation_states (Element attribute) oxidation_states() (Element property) OxidationStateDecorationTransformation (class in pymatgen.transformations.standard_transformations) OxidationStateRemovalTransformation (class in pymatgen.transformations.standard_transformations) oxide_type() (in module pymatgen.analysis.structure_analyzer) OxideType (class in pymatgen.analysis.structure_analyzer)

P

P (Element attribute) p (OrbitalType attribute) P() (JonesFaithfulTransformation property) p() (JonesFaithfulTransformation property) p0_exponential() (in module pymatgen.util.convergence) p0_reciprocal() (in module pymatgen.util.convergence) p0_simple_2reciprocal() (in module pymatgen.util.convergence) p0_simple_4reciprocal() (in module pymatgen.util.convergence) p0_simple_5reciprocal() (in module pymatgen.util.convergence) p0_simple_reciprocal() (in module pymatgen.util.convergence) p0_single_reciprocal() (in module pymatgen.util.convergence) Pa (Element attribute) package_options_description() (ChemEnvConfig method) PackmolRunner (class in pymatgen.io.lammps.utils) parallel_assimilate() (BorgQueen method) ParallelEfficiency (class in pymatgen.io.abinit.abitimer) parameters (Vasprun attribute) parameters() (Lattice property) params_keys (Control attribute) parent (SlabGenerator attribute) parse() (AbinitTimerParser method) parse_author() (Author static method) parse_cond_and_hall() (BoltztrapAnalyzer static method) parse_criteria() (MPRester static method) parse_file() (VolumetricData static method) parse_functions (PotcarSingle attribute) parse_history_node() (HistoryNode static method) parse_intrans() (BoltztrapAnalyzer static method) parse_lammps_dumps() (in module pymatgen.io.lammps.outputs) parse_lammps_log() (in module pymatgen.io.lammps.outputs) parse_magmoms() (CifParser method) parse_outputtrans() (BoltztrapAnalyzer static method) parse_oxi_states() (CifParser method) parse_oxide() (OxideType method) parse_struct() (BoltztrapAnalyzer static method) parse_tddft() (NwOutput method) parse_transdos() (BoltztrapAnalyzer static method) parse_transformation_string() (JonesFaithfulTransformation static method) parse_view() (in module pymatgen.cli.pmg) parse_xyz() (CombinedData class method) PartialRemoveSitesTransformation (class in pymatgen.transformations.site_transformations) PartialRemoveSpecieTransformation (class in pymatgen.transformations.standard_transformations) path (KSamplingModes attribute) path_from_structure() (KSampling class method) Paths (class in pymatgen.io.feff.inputs) patterns (PWOutput attribute) pauling_stability_ratio() (CoordinationGeometry property) Pb (Element attribute) PBarSafe (class in pymatgen.util.sequence) pbc_diff() (in module pymatgen.util.coord) pbc_shortest_vectors() (in module pymatgen.util.coord) (in module pymatgen.util.coord_cython) pcm (GaussianOutput attribute) pcm_template() (QCInput static method) Pd (Element attribute) pd_coords() (PhaseDiagram method) pd_plot_data() (PDPlotter property) PDEntry (class in pymatgen.analysis.phase_diagram) pdos (CompleteDos attribute) (CompletePhononDos attribute) (Doscar attribute) (Vasprun attribute) pdos() (Doscar property) PDPlotter (class in pymatgen.analysis.phase_diagram) pefficiency() (AbinitTimerParser method) PenaltyFunctionError perform_all_corrections() (DefectCompatibility method) perform_band_edge_shifting() (DefectCompatibility method) perform_bandfill_corr() (BandFillingCorrection method) perform_bandfilling() (DefectCompatibility method) perform_es_corr() (FreysoldtCorrection method) (KumagaiCorrection method) perform_freysoldt() (DefectCompatibility method) perform_kumagai() (DefectCompatibility method) perform_pot_corr() (FreysoldtCorrection method) (KumagaiCorrection method) periodic_table_heatmap() (in module pymatgen.util.plotting) periodicity() (ConnectedComponent property) periodicity_vectors() (ConnectedComponent property) PeriodicNeighbor (class in pymatgen.core.structure) PeriodicSite (class in pymatgen.core.sites) permutations() (ExplicitPermutationsAlgorithm property) (SeparationPlane property) perpendicular_bisector() (Plane class method) persistent_id() (PmgPickler method) persistent_load() (PmgUnpickler method) perturb() (Molecule method) (Structure method) PerturbStructureTransformation (class in pymatgen.transformations.standard_transformations) PhaseDiagram (class in pymatgen.analysis.phase_diagram) PhaseDiagramError PhononBandStructure (class in pymatgen.phonon.bandstructure) PhononBandStructureSymmLine (class in pymatgen.phonon.bandstructure) PhononBSPlotter (class in pymatgen.phonon.plotter) PhononDos (class in pymatgen.phonon.dos) PhononDosPlotter (class in pymatgen.phonon.plotter) PhononScfCycle (class in pymatgen.io.abinit.abiinspect) pie() (AbinitTimer method) PiezoTensor (class in pymatgen.analysis.piezo) piola_kirchoff_1() (Stress method) piola_kirchoff_2() (Stress method) Plane (class in pymatgen.analysis.chemenv.utils.coordination_geometry_utils) plot() (DefectPhaseDiagram method) (EOSBase method) (FreysoldtCorrection method) (in module pymatgen.cli.pmg_plot) (InterfacialReactivity method) (IRDielectricTensor method) (KumagaiCorrection method) (Relaxation method) (ScfCycle method) plot_all() (AbinitTimerParser method) plot_all_stability_map() (NanoscaleStability method) plot_ax() (EOSBase method) plot_brillouin() (BSPlotter method) (PhononBSPlotter method) plot_brillouin_zone() (in module pymatgen.electronic_structure.plotter) plot_brillouin_zone_from_kpath() (in module pymatgen.electronic_structure.plotter) plot_carriers() (BoltztrapPlotter method) plot_chempot_range_map() (PDPlotter method) plot_compare() (BSPlotter method) (PhononBSPlotter method) plot_complexity_factor_mu() (BoltztrapPlotter method) plot_conductivity_dop() (BoltztrapPlotter method) plot_conductivity_mu() (BoltztrapPlotter method) plot_conductivity_temp() (BoltztrapPlotter method) plot_csm_and_maps() (StructureEnvironments method) plot_cv() (ThermoPlotter method) plot_dos() (BoltztrapPlotter method) plot_eff_mass_dop() (BoltztrapPlotter method) plot_eff_mass_temp() (BoltztrapPlotter method) plot_efficiency() (AbinitTimerParser method) plot_element_profile() (PDPlotter method) plot_ellipsoid() (in module pymatgen.electronic_structure.plotter) plot_entropy() (ThermoPlotter method) plot_entry_stability() (PourbaixPlotter method) plot_environments() (StructureEnvironments method) plot_fermi_surface() (in module pymatgen.electronic_structure.plotter) plot_hall_carriers() (BoltztrapPlotter method) plot_helmholtz_free_energy() (ThermoPlotter method) plot_images() (NEBPathfinder method) plot_internal_energy() (ThermoPlotter method) plot_labels() (in module pymatgen.electronic_structure.plotter) plot_lattice_vectors() (in module pymatgen.electronic_structure.plotter) plot_msd() (DiffusionAnalyzer method) plot_one_stability_map() (NanoscaleStability method) plot_path() (in module pymatgen.electronic_structure.plotter) plot_pie() (AbinitTimerParser method) plot_points() (in module pymatgen.electronic_structure.plotter) plot_power_factor_dop() (BoltztrapPlotter method) plot_power_factor_mu() (BoltztrapPlotter method) plot_power_factor_temp() (BoltztrapPlotter method) plot_seebeck_dop() (BoltztrapPlotter method) plot_seebeck_eff_mass_mu() (BoltztrapPlotter method) plot_seebeck_mu() (BoltztrapPlotter method) plot_seebeck_temp() (BoltztrapPlotter method) plot_slab() (in module pymatgen.analysis.adsorption) plot_stacked_hist() (AbinitTimerParser method) plot_structures() (AbstractDiffractionPatternCalculator method) plot_thermodynamic_properties() (ThermoPlotter method) plot_vor_analysis() (VoronoiAnalyzer static method) plot_wigner_seitz() (in module pymatgen.electronic_structure.plotter) plot_zt_dop() (BoltztrapPlotter method) plot_zt_mu() (BoltztrapPlotter method) plot_zt_temp() (BoltztrapPlotter method) plottable_from_outfile() (in module pymatgen.io.abinit.abiinspect) Pm (Element attribute) pmg_pickle_dump() (in module pymatgen.util.serialization) pmg_pickle_load() (in module pymatgen.util.serialization) pmg_serialize() (in module pymatgen.util.serialization) PmgPickler (class in pymatgen.util.serialization) PmgUnpickler (class in pymatgen.util.serialization) Po (Element attribute) point_energy() (EwaldSummation property) point_energy_matrix() (EwaldSummation property) point_from_bary_coords() (Simplex method) PointDefectComparator (class in pymatgen.analysis.structure_matcher) PointGroup (class in pymatgen.symmetry.groups) PointGroupAnalyzer (class in pymatgen.symmetry.analyzer) PointGroupOperations (class in pymatgen.symmetry.analyzer) points_wcs_csc() (AbstractGeometry method) points_wcs_ctwcc() (AbstractGeometry method) points_wcs_ctwocc() (AbstractGeometry method) points_wocs_csc() (AbstractGeometry method) points_wocs_ctwcc() (AbstractGeometry method) points_wocs_ctwocc() (AbstractGeometry method) poissons_ratio (Element attribute) polar_decomposition() (SquareTensor method) Polarization (class in pymatgen.analysis.ferroelectricity.polarization) PolarizationLattice (class in pymatgen.analysis.ferroelectricity.polarization) Polymer (class in pymatgen.io.lammps.utils) PolynomialEOS (class in pymatgen.analysis.eos) pop_irdvars() (BasicAbinitInput method) pop_tolerances() (BasicAbinitInput method) pop_vars() (AbstractInput method) populate() (Tensor method) Poscar (class in pymatgen.io.vasp.inputs) poscar() (DictSet property) (MITNEBSet property) (VaspInputSet property) poscars() (MITNEBSet property) PoscarTransmuter (class in pymatgen.alchemy.transmuters) position_atol (Site attribute) pot_dict_from_string() (Potential static method) pot_string_from_file() (Potential static method) Potcar (class in pymatgen.io.vasp.inputs) potcar() (VaspInputSet property) potcar_symbols (Vasprun attribute) potcar_symbols() (VaspInputSet property) PotcarCorrection (class in pymatgen.entries.compatibility) PotcarSingle (class in pymatgen.io.vasp.inputs) Potential (class in pymatgen.io.feff.inputs) potential() (AbstractFeffInputSet property) (FEFFDictSet property) potential_type() (PotcarSingle property) PourbaixDiagram (class in pymatgen.analysis.pourbaix_diagram) PourbaixEntry (class in pymatgen.analysis.pourbaix_diagram) PourbaixPlotter (class in pymatgen.analysis.pourbaix_diagram) PourierTarantola (class in pymatgen.analysis.eos) power2_decreasing_exp() (CSMFiniteRatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) (RatioFunction method) power2_inverse_decreasing() (CSMInfiniteRatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) (RatioFunction method) power2_inverse_power2_decreasing() (CSMInfiniteRatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) (RatioFunction method) power2_inverse_powern_decreasing() (in module pymatgen.analysis.chemenv.utils.math_utils) power2_tangent_decreasing() (in module pymatgen.analysis.chemenv.utils.math_utils) power3_step() (in module pymatgen.analysis.chemenv.utils.math_utils) powern_decreasing() (in module pymatgen.analysis.chemenv.utils.math_utils) powern_parts_step() (in module pymatgen.analysis.chemenv.utils.math_utils) PPModel (class in pymatgen.io.abinit.abiobjects) PPModelModes (class in pymatgen.io.abinit.abiobjects) Pr (Element attribute) pred_from_comp() (Substitutor method) pred_from_list() (Substitutor method) pred_from_structures() (Substitutor method) predict() (DLSVolumePredictor method) (RLSVolumePredictor method) predict_mp() (CrystalAIRester method) predict_structure() (CrystalAIRester method) predictor_corrector (Poscar attribute) predictor_corrector() (Poscar property) predictor_corrector_preamble (Poscar attribute) prepare_symmetries() (AbstractChemenvStrategy method) PRESETS (LocalGeometryFinder attribute) pretty_plot() (in module pymatgen.util.plotting) pretty_plot_two_axis() (in module pymatgen.util.plotting) pretty_polyfit_plot() (in module pymatgen.util.plotting) pretty_print() (AllCoordinationGeometries method) prim() (HighSymmKpath property) prim_rec() (HighSymmKpath property) prime_factors() (in module pymatgen.analysis.chemenv.utils.math_utils) PrimitiveCellTransformation (class in pymatgen.transformations.standard_transformations) principal_axis_system() (ChemicalShielding property) (ElectricFieldGradient property) principal_invariants() (SquareTensor property) print_and_raise_error() (in module pymatgen.util.convergence) print_gnuplot_header() (in module pymatgen.io.abinit.helpers) print_links() (StructureConnectivity method) print_periodic_table (Element attribute) print_plot_line() (in module pymatgen.util.convergence) print_stats() (TopographyAnalyzer method) print_table() (PseudoTable method) print_tree() (NetcdfReader method) Prismatic (class in pymatgen.io.prismatic) proc_dir() (in module pymatgen.cli.pmg_potcar) proc_val() (Incar static method) (PWInput method) (Tags static method) Procar (class in pymatgen.io.vasp.outputs) process_entries() (Compatibility method) process_entry() (Compatibility method) (DefectCompatibility method) process_multientry() (PourbaixDiagram static method) process_parsed_coords() (in module pymatgen.io.qchem.utils) products() (BalancedReaction property)

project() (Tensor method) project_and_to2dim() (Plane method) project_and_to2dim_ordered_indices() (Plane method) projected_eigenvalues (Vasprun attribute) projection() (Magmom property) projectionpoints() (Plane method) projections (BandStructure attribute) properly_terminated (GaussianOutput attribute) property_dict() (ElasticTensor property) Pseudo (class in pymatgen.io.abinit.pseudos) pseudo_with_symbol() (PseudoTable method) pseudos() (BasicAbinitInput property) (BasicMultiDataset property) pseudos_with_symbols() (PseudoTable method) PseudoTable (class in pymatgen.io.abinit.pseudos) Pt (Element attribute) Pu (Element attribute) put_coord_inside() (in module pymatgen.analysis.adsorption) PWInput (class in pymatgen.io.pwscf) PWInputError PWOutput (class in pymatgen.io.pwscf) px (Orbital attribute) py (Orbital attribute) pybel_mol() (BabelMolAdaptor property) pymatgen (module) pymatgen.alchemy (module) pymatgen.alchemy.filters (module) pymatgen.alchemy.materials (module) pymatgen.alchemy.transmuters (module) pymatgen.analysis (module) pymatgen.analysis.adsorption (module) pymatgen.analysis.aflow_prototypes (module) pymatgen.analysis.bond_dissociation (module) pymatgen.analysis.bond_valence (module) pymatgen.analysis.chemenv (module) pymatgen.analysis.chemenv.connectivity (module) pymatgen.analysis.chemenv.connectivity.connected_components (module) pymatgen.analysis.chemenv.connectivity.connectivity_finder (module) pymatgen.analysis.chemenv.connectivity.environment_nodes (module) pymatgen.analysis.chemenv.connectivity.structure_connectivity (module) pymatgen.analysis.chemenv.coordination_environments (module) pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies (module) pymatgen.analysis.chemenv.coordination_environments.coordination_geometries (module) pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files (module) pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder (module) pymatgen.analysis.chemenv.coordination_environments.strategy_files (module) pymatgen.analysis.chemenv.coordination_environments.structure_environments (module) pymatgen.analysis.chemenv.coordination_environments.voronoi (module) pymatgen.analysis.chemenv.utils (module) pymatgen.analysis.chemenv.utils.chemenv_config (module) pymatgen.analysis.chemenv.utils.chemenv_errors (module) pymatgen.analysis.chemenv.utils.coordination_geometry_utils (module) 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) pymatgen.analysis.chemenv.utils.scripts_utils (module) pymatgen.analysis.cost (module) pymatgen.analysis.defects (module) pymatgen.analysis.defects.core (module) pymatgen.analysis.defects.corrections (module) pymatgen.analysis.defects.defect_compatibility (module) pymatgen.analysis.defects.dilute_solution_model (module) pymatgen.analysis.defects.generators (module) pymatgen.analysis.defects.thermodynamics (module) pymatgen.analysis.defects.utils (module) pymatgen.analysis.diffraction (module) pymatgen.analysis.diffraction.core (module) pymatgen.analysis.diffraction.neutron (module) pymatgen.analysis.diffraction.xrd (module) pymatgen.analysis.diffusion_analyzer (module) pymatgen.analysis.dimensionality (module) pymatgen.analysis.elasticity (module) pymatgen.analysis.elasticity.elastic (module) pymatgen.analysis.elasticity.strain (module) pymatgen.analysis.elasticity.stress (module) pymatgen.analysis.energy_models (module) pymatgen.analysis.eos (module) pymatgen.analysis.ewald (module) pymatgen.analysis.excitation (module) pymatgen.analysis.ferroelectricity (module) pymatgen.analysis.ferroelectricity.polarization (module) pymatgen.analysis.find_dimension (module) pymatgen.analysis.fragmenter (module) pymatgen.analysis.functional_groups (module) pymatgen.analysis.gb (module) pymatgen.analysis.gb.grain (module) pymatgen.analysis.graphs (module) pymatgen.analysis.hhi (module) pymatgen.analysis.interface (module) pymatgen.analysis.interface_reactions (module) pymatgen.analysis.local_env (module) pymatgen.analysis.magnetism (module) pymatgen.analysis.magnetism.analyzer (module) pymatgen.analysis.magnetism.heisenberg (module) pymatgen.analysis.magnetism.jahnteller (module) pymatgen.analysis.molecule_matcher (module) pymatgen.analysis.molecule_structure_comparator (module) pymatgen.analysis.nmr (module) pymatgen.analysis.path_finder (module) pymatgen.analysis.phase_diagram (module) pymatgen.analysis.piezo (module) pymatgen.analysis.piezo_sensitivity (module) pymatgen.analysis.pourbaix_diagram (module) pymatgen.analysis.quasiharmonic (module) pymatgen.analysis.reaction_calculator (module) pymatgen.analysis.structure_analyzer (module) pymatgen.analysis.structure_matcher (module) pymatgen.analysis.structure_prediction (module) 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.substrate_analyzer (module) pymatgen.analysis.surface_analysis (module) pymatgen.analysis.thermochemistry (module) pymatgen.analysis.transition_state (module) pymatgen.analysis.wulff (module) pymatgen.analysis.xas (module) pymatgen.analysis.xas.spectrum (module) pymatgen.apps (module) pymatgen.apps.battery (module) pymatgen.apps.battery.analyzer (module) pymatgen.apps.battery.battery_abc (module) pymatgen.apps.battery.conversion_battery (module) pymatgen.apps.battery.insertion_battery (module) pymatgen.apps.battery.plotter (module) pymatgen.apps.borg (module) pymatgen.apps.borg.hive (module) pymatgen.apps.borg.queen (module) pymatgen.cli (module) pymatgen.cli.feff_input_generation (module) pymatgen.cli.feff_plot_cross_section (module) pymatgen.cli.feff_plot_dos (module) pymatgen.cli.gaussian_analyzer (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_query (module) pymatgen.cli.pmg_structure (module) pymatgen.command_line (module) pymatgen.command_line.aconvasp_caller (module) pymatgen.command_line.bader_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 (module) pymatgen.core.bonds (module) pymatgen.core.composition (module) pymatgen.core.ion (module) pymatgen.core.lattice (module) pymatgen.core.libxcfunc (module) pymatgen.core.molecular_orbitals (module) pymatgen.core.operations (module) pymatgen.core.periodic_table (module) pymatgen.core.sites (module) pymatgen.core.spectrum (module) pymatgen.core.structure (module) pymatgen.core.surface (module) pymatgen.core.tensors (module) pymatgen.core.trajectory (module) pymatgen.core.units (module) pymatgen.core.xcfunc (module) pymatgen.dao (module) pymatgen.electronic_structure (module) pymatgen.electronic_structure.bandstructure (module) pymatgen.electronic_structure.boltztrap (module) pymatgen.electronic_structure.cohp (module) pymatgen.electronic_structure.core (module) pymatgen.electronic_structure.dos (module) pymatgen.electronic_structure.plotter (module) pymatgen.entries (module) pymatgen.entries.compatibility (module) pymatgen.entries.computed_entries (module) pymatgen.entries.entry_tools (module) pymatgen.entries.exp_entries (module) pymatgen.ext (module) pymatgen.ext.cod (module) pymatgen.ext.crystalsai (module) pymatgen.ext.jhu (module) pymatgen.ext.matproj (module) pymatgen.io (module) pymatgen.io.abinit (module) pymatgen.io.abinit.abiinspect (module) pymatgen.io.abinit.abiobjects (module) pymatgen.io.abinit.abitimer (module) pymatgen.io.abinit.helpers (module) pymatgen.io.abinit.inputs (module) pymatgen.io.abinit.netcdf (module) pymatgen.io.abinit.pseudos (module) pymatgen.io.abinit.variable (module) pymatgen.io.adf (module) pymatgen.io.aiida (module) pymatgen.io.ase (module) pymatgen.io.atat (module) pymatgen.io.babel (module) pymatgen.io.cif (module) pymatgen.io.cssr (module) pymatgen.io.exciting (module) pymatgen.io.exciting.inputs (module) pymatgen.io.feff (module) pymatgen.io.feff.inputs (module) pymatgen.io.feff.outputs (module) pymatgen.io.feff.sets (module) pymatgen.io.fiesta (module) pymatgen.io.gaussian (module) pymatgen.io.lammps (module) pymatgen.io.lammps.data (module) pymatgen.io.lammps.inputs (module) pymatgen.io.lammps.outputs (module) pymatgen.io.lammps.utils (module) pymatgen.io.lmto (module) pymatgen.io.lobster (module) pymatgen.io.nwchem (module) pymatgen.io.phonopy (module) pymatgen.io.prismatic (module) pymatgen.io.pwscf (module) pymatgen.io.qchem (module) pymatgen.io.qchem.inputs (module) pymatgen.io.qchem.outputs (module) pymatgen.io.qchem.sets (module) pymatgen.io.qchem.utils (module) pymatgen.io.shengbte (module) pymatgen.io.vasp (module) pymatgen.io.vasp.inputs (module) pymatgen.io.vasp.outputs (module) pymatgen.io.vasp.sets (module) pymatgen.io.xcrysden (module) pymatgen.io.xr (module) pymatgen.io.xyz (module) pymatgen.io.zeopp (module) pymatgen.optimization (module) pymatgen.optimization.linear_assignment (module) pymatgen.optimization.linear_assignment_numpy (module) pymatgen.optimization.neighbors (module) pymatgen.phonon (module) pymatgen.phonon.bandstructure (module) pymatgen.phonon.dos (module) pymatgen.phonon.ir_spectra (module) pymatgen.phonon.plotter (module) pymatgen.plugins (module) pymatgen.symmetry (module) pymatgen.symmetry.analyzer (module) pymatgen.symmetry.bandstructure (module) pymatgen.symmetry.groups (module) pymatgen.symmetry.maggroups (module) pymatgen.symmetry.settings (module) pymatgen.symmetry.site_symmetries (module) pymatgen.symmetry.structure (module) pymatgen.transformations (module) pymatgen.transformations.advanced_transformations (module) pymatgen.transformations.defect_transformations (module) pymatgen.transformations.site_transformations (module) pymatgen.transformations.standard_transformations (module) pymatgen.transformations.transformation_abc (module) pymatgen.util (module) pymatgen.util.convergence (module) pymatgen.util.coord (module) pymatgen.util.coord_cython (module) pymatgen.util.io_utils (module) pymatgen.util.num (module) pymatgen.util.plotting (module) pymatgen.util.provenance (module) pymatgen.util.sequence (module) pymatgen.util.serialization (module) pymatgen.util.string (module) pymatgen.util.testing (module) pymatgen.util.typing (module) pymatgen.vis (module) pymatgen.vis.plotters (module) pymatgen.vis.structure_chemview (module) pymatgen.vis.structure_vtk (module) pymatgen_mol() (BabelMolAdaptor property) PymatgenTest (class in pymatgen.util.testing) pz (Orbital attribute)

Q

QChemDictSet (class in pymatgen.io.qchem.sets) QCInput (class in pymatgen.io.qchem.inputs) QCOutput (class in pymatgen.io.qchem.outputs) QModel (class in pymatgen.analysis.defects.utils) quarter_ellipsis_functions() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils)

QuasiharmonicDebyeApprox (class in pymatgen.analysis.quasiharmonic) query() (COD method) (MPRester method) query_snl() (MPRester method) quick_view() (in module pymatgen.vis.structure_chemview)

R

Ra (Element attribute) radii() (ValenceIonicRadiusEvaluator property) radius (CovalentRadius attribute) raise_error_if_unphysical() (in module pymatgen.analysis.elasticity.elastic) rand_piezo() (in module pymatgen.analysis.piezo_sensitivity) ranked_compositions_from_indeterminate_formula() (Composition static method) ranks() (TensorCollection property) RatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) RatioFunctionError ratios() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) Rb (Element attribute) Rcut() (OrbitalDescription property) Rcut2() (OrbitalDescription property) Re (Element attribute) reactants() (BalancedReaction property) Reaction (class in pymatgen.analysis.reaction_calculator) ReactionDiagram (class in pymatgen.analysis.phase_diagram) ReactionError read_abinit_hdr() (ETSF_Reader method) read_abinit_xcfunc() (ETSF_Reader method) read_avg_core_poten() (Outcar method) read_chemical_shielding() (Outcar method) read_core_state_eigen() (Outcar method) read_corrections() (Outcar method) read_cs_core_contribution() (Outcar method) read_cs_g0_contribution() (Outcar method) read_cs_raw_symmetrized_tensors() (Outcar method) read_cube_file() (in module pymatgen.electronic_structure.boltztrap) read_dimvalue() (NetcdfReader method) read_elastic_tensor() (Outcar method) read_electrostatic_potential() (Outcar method) read_excitation_energies() (GaussianOutput method) read_extra_abivars() (in module pymatgen.io.abinit.helpers) read_fermi_contact_shift() (Outcar method) read_freq_dielectric() (Outcar method) read_grid_from_file() (in module pymatgen.io.abinit.helpers) read_igpar() (Outcar method) read_internal_strain_tensor() (Outcar method) read_keys() (NetcdfReader method) read_lcalcpol() (Outcar method) read_lepsilon() (Outcar method) read_lepsilon_ionic() (Outcar method) read_molecule() (QCInput static method) read_neb() (Outcar method) read_nmr_efg() (Outcar method) read_nmr_efg_tensor() (Outcar method) read_onsite_density_matrices() (Outcar method) read_opt() (QCInput static method) read_pattern() (in module pymatgen.io.qchem.utils) (Outcar method) (PWOutput method) read_pcm() (QCInput static method) read_piezo_tensor() (Outcar method) read_pseudo_zval() (Outcar method) read_rem() (QCInput static method) read_route_line() (in module pymatgen.io.gaussian) read_scan() (GaussianOutput method), [1] read_smx() (QCInput static method) read_solvent() (QCInput static method) read_structure() (ETSF_Reader method) read_table_pattern() (in module pymatgen.io.qchem.utils) (Outcar method) read_value() (NetcdfReader method) read_variable() (NetcdfReader method) read_varnames() (NetcdfReader method) real_space_energy() (EwaldSummation property) real_space_energy_matrix() (EwaldSummation property) Reciprocal (Kpoints_supported_modes attribute) reciprocal() (in module pymatgen.util.convergence) reciprocal_lattice() (Lattice property) reciprocal_lattice_crystallographic() (Lattice property) reciprocal_space_energy() (EwaldSummation property) reciprocal_space_energy_matrix() (EwaldSummation property) ReconstructionGenerator (class in pymatgen.core.surface) rectangle_crosses_area() (DistanceAngleAreaNbSetWeight method) rectangle_surface_intersection() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) redo_next_change() (StandardTransmuter method) (TransformedStructure method) redraw() (StructureVis method) reduce_formula() (in module pymatgen.core.composition) reduce_mat() (GrainBoundaryGenerator static method) reduce_vectors() (in module pymatgen.analysis.substrate_analyzer) reduced_composition() (Composition property) reduced_formula() (Composition property) (Ion property) ref_entries (SurfaceEnergyPlotter attribute) ref_permutation() (CoordinationGeometry method) ref_separation_perm() (SeparationPlane property)

refine_rotation() (SquareTensor method) refine_structure() (in module pymatgen.io.abinit.helpers) reflection() (SymmOp static method) reflectivity (Element attribute) refractive_index (Element attribute) rel_angle() (in module pymatgen.analysis.substrate_analyzer) rel_strain() (in module pymatgen.analysis.substrate_analyzer) relative_energies() (Xmu property) Relaxation (class in pymatgen.io.abinit.abiinspect) RelaxationAnalyzer (class in pymatgen.analysis.structure_analyzer) RelaxationMethod (class in pymatgen.io.abinit.abiobjects) rem_template() (QCInput static method) remove_bond() (BabelMolAdaptor method) remove_charges() (Composition method) remove_collisions() (ChargeDensityAnalyzer method) (TopographyAnalyzer method) remove_nodes() (MoleculeGraph method) (StructureGraph method) remove_non_ground_states() (EntrySet method) remove_option() (AdfKey method) remove_oxidation_states() (SiteCollection method) remove_site_property() (SiteCollection method) remove_sites() (Molecule method) (Structure method) remove_species() (Molecule method) (Structure method) remove_spin() (SiteCollection method) remove_subkey() (AdfKey method) remove_vars() (AbstractInput method) RemoveDuplicatesFilter (class in pymatgen.alchemy.filters) RemoveExistingFilter (class in pymatgen.alchemy.filters) RemoveSitesTransformation (class in pymatgen.transformations.site_transformations) RemoveSpeciesTransformation (class in pymatgen.transformations.standard_transformations) reorient_z() (in module pymatgen.analysis.adsorption) repair_broken_bonds() (SlabGenerator method) replace() (Structure method) replace_all (OverwriteMagmomMode attribute) replace_group() (MoleculeGraph method) replace_species() (SiteCollection method) ReplaceSiteSpeciesTransformation (class in pymatgen.transformations.site_transformations) replicate_input() (BasicMultiDataset class method) report() (PBarSafe method) required_params (Control attribute) rescale_field() (StaticPotential method) respect_sign (OverwriteMagmomMode attribute) respect_zero (OverwriteMagmomMode attribute) restore_site_properties() (PackmolRunner method) results() (EOSBase property) resumes (GaussianOutput attribute) Rh (Element attribute) rhl1() (HighSymmKpath method) rhl2() (HighSymmKpath method) rho_rec() (QModel method) rho_rec_limit0() (QModel property) rhombohedral() (Lattice static method) rigidity_modulus (Element attribute) ring (CriticalPointType attribute) RLSVolumePredictor (class in pymatgen.analysis.structure_prediction.volume_predictor) Rn (Element attribute) rotate() (Tensor method) (TensorCollection method) rotate_sites() (Molecule method) (Structure method) rotate_view() (StructureVis method) rotateCoords() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) rotateCoordsOpt() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) rotation_matrix() (SymmOp property) RotationTransformation (class in pymatgen.transformations.standard_transformations) rotor_conformer() (BabelMolAdaptor method) rotoreflection() (SymmOp static method) round() (Tensor method) (TensorCollection method) round_to_sigfigs() (in module pymatgen.util.num) route (GaussianOutput attribute) row (Element attribute) row() (Element property) Ru (Element attribute) run() (BoltztrapRunner method) (FiestaRun method) (GulpCaller method) (LammpsRunner method) (Nwchem2Fiesta method) (PackmolRunner method) run_aconvasp_command() (in module pymatgen.command_line.aconvasp_caller) run_mcsqs() (in module pymatgen.command_line.mcsqs_caller) run_stats (Outcar attribute) run_type (AdfOutput attribute) run_type() (Vasprun property) run_vasp() (VaspInput method) rxn() (ConversionVoltagePair property)

S

S (Element attribute) s (Orbital attribute) (OrbitalType attribute) s_name() (in module pymatgen.io.abinit.helpers) safe_separation_permutations() (SeparationPlane method) same_branch_splines() (Polarization method) satisfies_constraint() (MagOrderParameterConstraint method) save() (ChemEnvConfig method) (VoltageProfilePlotter method) save_data() (BorgQueen method) save_environments_figure() (StructureEnvironments method) save_plot() (BSPlotter method) (CohpPlotter method) (DosPlotter method) (PhononBSPlotter method) (PhononDosPlotter method) (SpectrumPlotter method) save_scan_plot() (GaussianOutput method), [1] save_spectre_plot() (GaussianOutput method) Sb (Element attribute) Sc (Element attribute) scale() (Lattice method) scale_and_clamp() (in module pymatgen.analysis.chemenv.utils.math_utils) scale_factor (Slab attribute) scale_lattice() (Structure method) SCALED_INTENSITY_TOL (AbstractDiffractionPatternCalculator attribute) scaled_wulff() (NanoscaleStability method) ScaleToRelaxedTransformation (class in pymatgen.transformations.standard_transformations) SCAN_OPT (TaskType attribute) scatter_hist() (AbinitTimer method) ScfCycle (class in pymatgen.io.abinit.abiinspect) sch_symbol (PointGroupAnalyzer attribute) (PointGroupOperations attribute) screened_energies (HeisenbergScreener attribute) screened_structures (HeisenbergScreener attribute) Screening (class in pymatgen.io.abinit.abiobjects) Se (Element attribute) se_analyzers (NanoscaleStability attribute) search_fragment_entries() (BondDissociationEnergies method) section_names() (AbinitTimerParser method) seebeck_eff_mass_from_carr() (in module pymatgen.electronic_structure.boltztrap) seebeck_eff_mass_from_seebeck_carr() (in module pymatgen.electronic_structure.boltztrap) seebeck_spb() (in module pymatgen.electronic_structure.boltztrap) seek() (YamlTokenizer method) select() (PseudoTable method) select_family() (PseudoTable method) select_rows() (PseudoTable method) select_symbols() (PseudoTable method) selective_dynamics (Poscar attribute) selective_dynamics() (Poscar property) SelfCSMNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) SelfEnergy (class in pymatgen.io.abinit.abiobjects) separation_in_list() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) SeparationPlane (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) serial_assimilate() (BorgQueen method) serialize_with_pickle() (PymatgenTest method) set_all_variables() (SurfaceEnergyPlotter method) set_animated_movie_options() (MultiStructuresVis method) set_auxiliary_basis_set() (FiestaInput method) set_BSE_options() (FiestaInput method) set_charge() (Defect method) (Structure method) set_charge_and_spin() (Molecule method) set_comment() (BasicAbinitInput method) set_gamma_sampling() (BasicAbinitInput method) set_GW_options() (FiestaInput method) set_info() (in module pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) set_kmesh() (BasicAbinitInput method) set_kpath() (BasicAbinitInput method) set_n_nlmo() (BasisSetReader method) set_node_attributes() (MoleculeGraph method) (StructureGraph method) set_option() (AbstractChemenvStrategy method) set_parameter() (StandardTransmuter method) (TransformedStructure method) set_permutations_safe_override() (CoordinationGeometry method) set_spin_mode() (BasicAbinitInput method) set_structure() (BasicAbinitInput method) (LocalGeometryFinder method) (MultiStructuresVis method) (StructureVis method) set_structure_environments() (AbstractChemenvStrategy method) set_structures() (MultiStructuresVis method) set_symbols() (Potcar method) set_temperature() (Poscar method) set_vars() (AbstractInput method) set_vars_ifnotin() (AbstractInput method) setup() (ChemEnvConfig method) setup_atom_environment_subgraph() (StructureConnectivity method) setup_atom_environments_subgraph() (StructureConnectivity method) setup_connectivity_description() (StructureConnectivity method) setup_environment_subgraph() (StructureConnectivity method) setup_environments_subgraph() (StructureConnectivity method) setup_explicit_indices_local_geometry() (LocalGeometryFinder method) setup_local_geometry() (LocalGeometryFinder method) setup_neighbors_distances_and_angles() (DetailedVoronoiContainer method) setup_options() (AbstractChemenvStrategy method) setup_ordered_indices_local_geometry() (LocalGeometryFinder method) setup_package_options() (ChemEnvConfig method) setup_parameter() (LocalGeometryFinder method) setup_parameters() (AbstractRatioFunction method) (ConnectivityFinder method) (LocalGeometryFinder method) setup_potcars() (in module pymatgen.cli.pmg_config) setup_random_indices_local_geometry() (LocalGeometryFinder method) setup_random_structure() (LocalGeometryFinder method) setup_spline() (NEBAnalysis method) setup_statistic_lists() (LightStructureEnvironments method) setup_structure() (LocalGeometryFinder method) setup_test_perfect_environment() (LocalGeometryFinder method) setup_voronoi_list() (DetailedVoronoiContainer method) sg_symbol_from_int_number() (in module pymatgen.symmetry.groups) shape_factor() (WulffShape property) shift (Slab attribute) shift_film() (Interface method) shift_film_along_surface_lattice() (Interface method) ShiftMode (class in pymatgen.io.abinit.inputs) SHORT_NAME (AngleNbSetWeight attribute) (AnglePlateauNbSetWeight attribute) (CNBiasNbSetWeight attribute) (DeltaCSMNbSetWeight attribute) (DeltaDistanceNbSetWeight attribute) (DistanceAngleAreaNbSetWeight attribute) (DistanceNbSetWeight attribute) (DistancePlateauNbSetWeight attribute) (NormalizedAngleDistanceNbSetWeight attribute) (SelfCSMNbSetWeight attribute) show() (BSPlotter method) (CohpPlotter method) (DosPlotter method) (PDPlotter method) (PhononBSPlotter method) (PhononDosPlotter method) (PourbaixPlotter method) (SpectrumPlotter method) (StructureVis method) (VoltageProfilePlotter method) (WulffShape method) show_area (WulffShape attribute) show_graph() (ConnectedComponent method) show_plot() (AbstractDiffractionPatternCalculator method) Si (Element attribute) sigma() (GrainBoundary property) sigma_11() (ChemicalShielding.MehringNotation property) sigma_22() (ChemicalShielding.MehringNotation property) sigma_33() (ChemicalShielding.MehringNotation property) sigma_from_site_prop() (GrainBoundary property) sigma_iso() (ChemicalShielding.MarylandNotation property) (ChemicalShielding.MehringNotation property) simple_2reciprocal() (in module pymatgen.util.convergence) simple_4reciprocal() (in module pymatgen.util.convergence) simple_5reciprocal() (in module pymatgen.util.convergence) simple_reciprocal() (in module pymatgen.util.convergence) SimpleAbundanceChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) SimpleChargeGenerator (class in pymatgen.analysis.defects.generators) SimpleGraphCycle (class in pymatgen.analysis.chemenv.utils.graph_utils) SimplestChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) SimpleVaspToComputedEntryDrone (class in pymatgen.apps.borg.hive) Simplex (class in pymatgen.util.coord) single_cap_hints() (CoordinationGeometry.NeighborsSetsHints method) single_reciprocal() (in module pymatgen.util.convergence) SinglePointSet (class in pymatgen.io.qchem.sets) Site (class in pymatgen.core.sites) site() (ConnectedSite property) (Defect property) (DefectEntry property) site_contains_environment() (LightStructureEnvironments method) site_has_clear_environment() (LightStructureEnvironments method) site_is_of_motif_type() (in module pymatgen.analysis.local_env) site_properties() (SiteCollection property) site_symbols() (Poscar property) (Xdatcar property) SiteCollection (class in pymatgen.core.structure) sites() (IMolecule property) (IStructure property) (SiteCollection property) Slab (class in pymatgen.core.surface) slab (WorkFunctionAnalyzer attribute) slab_from_csl() (GrainBoundaryGenerator static method) slab_scale_factor (SlabGenerator attribute) SlabEntry (class in pymatgen.analysis.surface_analysis) slabgen_params (ReconstructionGenerator attribute) SlabGenerator (class in pymatgen.core.surface) SlabTransformation (class in pymatgen.transformations.advanced_transformations) slideshow() (CyclesPlotter method) (Relaxation method) SlotPickleMixin (class in pymatgen.util.serialization) Sm (Element attribute) smear() (Spectrum method) Smearing (class in pymatgen.io.abinit.abiobjects) smootherstep() (CSMFiniteRatioFunction method) (DeltaCSMRatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) (RatioFunction method) smoothness() (EnergyTrend method) (Polarization method) smoothstep() (CSMFiniteRatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) (RatioFunction method) smx_template() (QCInput static method) Sn (Element attribute) snyder_ac() (ElasticTensor method) snyder_opt() (ElasticTensor method) snyder_total() (ElasticTensor method) solid_angle() (in module pymatgen.analysis.local_env) (in module pymatgen.analysis.structure_analyzer) solid_angles() (CoordinationGeometry method) SolidAngleError solute_defect_density() (in module pymatgen.analysis.defects.dilute_solution_model) solute_site_preference_finder() (in module pymatgen.analysis.defects.dilute_solution_model) solve_equilibrium_point() (NanoscaleStability method) solve_for_fermi_energy() (DefectPhaseDiagram method) solve_for_non_equilibrium_fermi_energy() (DefectPhaseDiagram method) solvent_template() (QCInput static method) sort() (MoleculeGraph method) (Structure method) (StructureGraph method)

sort_by_z() (PseudoTable method) sort_dict() (in module pymatgen.util.num) sort_separation() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) sort_separation_tuple() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) sort_sites_by_integrated_chg() (ChargeDensityAnalyzer method) sorted() (PseudoTable method) sorted_sites (WorkFunctionAnalyzer attribute) source() (StructureEnvironments.NeighborsSet property) (Xmu property) SpaceGroup (class in pymatgen.symmetry.groups) SpacegroupAnalyzer (class in pymatgen.symmetry.analyzer) SpacegroupOperations (class in pymatgen.symmetry.analyzer) spec() (Potcar property) special_formulas (Composition attribute) Specie (class in pymatgen.core.periodic_table) specie() (Site property) specie_potential_lines() (GulpIO method) SpecieProximityFilter (class in pymatgen.alchemy.filters) species() (Site property) (SiteCollection property) species_and_occu() (Site property) (SiteCollection property) species_string() (Site property) SpeciesComparator (class in pymatgen.analysis.structure_matcher) SpeciesMaxDistFilter (class in pymatgen.alchemy.filters) Spectrum (class in pymatgen.core.spectrum) SpectrumPlotter (class in pymatgen.vis.plotters) Spin (class in pymatgen.electronic_structure.core) spin_data() (VolumetricData property) spin_multiplicity (GaussianOutput attribute) spin_multiplicity() (IMolecule property) spin_polarization() (CompleteDos property) SpinComparator (class in pymatgen.analysis.structure_matcher) SpinMode (class in pymatgen.io.abinit.abiobjects) spline() (EnergyTrend method) spline_functions() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) SplineInputError split_datasets() (BasicMultiDataset method) split_molecule_subgraphs() (MoleculeGraph method) SQSTransformation (class in pymatgen.transformations.advanced_transformations) SquareTensor (class in pymatgen.core.tensors) Sr (Element attribute) stable_entries() (PhaseDiagram property) (PourbaixDiagram property) stable_u_range_dict() (SurfaceEnergyPlotter method) standard_calculations_from_vasp_files() (Lobsterin class method) standard_orientation (GaussianOutput attribute) standardize_structure() (in module pymatgen.io.vasp.sets) StandardTransmuter (class in pymatgen.alchemy.transmuters) StaticPotential (class in pymatgen.analysis.path_finder) stationary_type (GaussianOutput attribute) stats_article_weights_parameters() (MultiWeightsChemenvStrategy class method) stitch() (XAS method) store_conv_results() (in module pymatgen.io.abinit.helpers) str2float() (in module pymatgen.io.cif) str_delimited() (in module pymatgen.util.string) STR_FIELDS (AbinitTimerSection attribute) straceback() (in module pymatgen.io.abinit.abiinspect) Strain (class in pymatgen.analysis.elasticity.strain) strain_slabs() (in module pymatgen.analysis.interface) STRATEGY_DESCRIPTION (AbstractChemenvStrategy attribute) (MultiWeightsChemenvStrategy attribute) (SimpleAbundanceChemenvStrategy attribute) (SimplestChemenvStrategy attribute) (WeightedNbSetChemenvStrategy attribute) STRATEGY_INFO_FIELDS (AbstractChemenvStrategy attribute) STRATEGY_OPTIONS (AbstractChemenvStrategy attribute) (SimpleAbundanceChemenvStrategy attribute) (SimplestChemenvStrategy attribute) StrategyOption (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) stream_has_colours() (in module pymatgen.util.string) Stress (class in pymatgen.analysis.elasticity.stress) strictly_decreasing() (in module pymatgen.util.num) strictly_increasing() (in module pymatgen.util.num) string_relax() (NEBPathfinder static method) StringColorizer (class in pymatgen.util.string) STRINGKEYWORDS (Lobsterin attribute) structure (BandStructure attribute) Structure (class in pymatgen.core.structure) structure (CompleteDos attribute) (ExcitingInput attribute) (Poscar attribute) (VolumetricData attribute) (WulffShape attribute) structure() (BasicAbinitInput property) (DictSet property) (HighSymmKpath property) (LammpsData property) (ValenceIonicRadiusEvaluator property) structure_contains_atom_environment() (LightStructureEnvironments method) structure_from_abivars() (in module pymatgen.io.abinit.abiobjects) structure_from_ncdata() (in module pymatgen.io.abinit.netcdf) structure_from_string() (Mcsqs static method) structure_graph() (Critic2Output method) structure_has_clear_environments() (LightStructureEnvironments method) structure_lines() (GulpIO method) STRUCTURE_REFINEMENT_NONE (LocalGeometryFinder attribute) STRUCTURE_REFINEMENT_REFINED (LocalGeometryFinder attribute) STRUCTURE_REFINEMENT_SYMMETRIZED (LocalGeometryFinder attribute) structure_symmetry() (Header property) structure_to_abivars() (in module pymatgen.io.abinit.abiobjects) structure_transform() (Tensor method) StructureConnectivity (class in pymatgen.analysis.chemenv.connectivity.structure_connectivity) StructureEnvironments (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) StructureEnvironments.NeighborsSet (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) StructureError StructureGraph (class in pymatgen.analysis.graphs) StructureInteractorStyle (class in pymatgen.vis.structure_vtk) StructureMatcher (class in pymatgen.analysis.structure_matcher) StructureMotifInterstitial (class in pymatgen.analysis.defects.utils) StructureNL (class in pymatgen.util.provenance) structures (AdfOutput attribute) (GaussianOutput attribute) (in module pymatgen.command_line.enumlib_caller) (Xdatcar attribute) structures() (TransformedStructure property) (Vasprun property) structures_allowed() (BrunnerNN_real property) (BrunnerNN_reciprocal property) (BrunnerNN_relative property) (CovalentBondNN property) (Critic2NN property) (CrystalNN property) (CutOffDictNN property) (EconNN property) (JmolNN property) (MinimumDistanceNN property) (MinimumOKeeffeNN property) (MinimumVIRENN property) (NearNeighbors property) (OpenBabelNN property) (VoronoiNN property) STRUCTURES_DIR (PymatgenTest attribute) structures_input_orientation (GaussianOutput attribute) StructureVis (class in pymatgen.vis.structure_vtk) style() (Kpoints property) sub_chempots() (in module pymatgen.analysis.surface_analysis) sub_keys (AdfKey attribute) sub_spgrp() (in module pymatgen.io.cif) submit_snl() (MPRester method) submit_structures() (MPRester method) submit_vasp_directory() (MPRester method) subs() (in module pymatgen.analysis.elasticity.elastic) substitute() (Molecule method) (Structure method) substitute_group() (MoleculeGraph method) (StructureGraph method) SubstituteSurfaceSiteTransformation (class in pymatgen.transformations.advanced_transformations) Substitution (class in pymatgen.analysis.defects.core) SubstitutionGenerator (class in pymatgen.analysis.defects.generators) SubstitutionPredictor (class in pymatgen.analysis.structure_prediction.substitution_probability) SubstitutionPredictorTransformation (class in pymatgen.transformations.advanced_transformations) SubstitutionProbability (class in pymatgen.analysis.structure_prediction.substitution_probability) SubstitutionTransformation (class in pymatgen.transformations.standard_transformations) Substitutor (class in pymatgen.analysis.structure_prediction.substitutor) substrate() (Interface property) substrate_sites() (Interface property) SubstrateAnalyzer (class in pymatgen.analysis.substrate_analyzer) subsurface_sites() (AdsorbateSiteFinder method) suggest_charges() (DefectPhaseDiagram method) suggest_larger_supercells() (DefectPhaseDiagram method) sulfide_type() (in module pymatgen.analysis.structure_analyzer) sum_sections() (AbinitTimer method) summarize() (AbinitTimerParser method) summary() (BaderAnalysis property) (Pseudo property) summed_icohp() (IcohpValue property) SupercellTransformation (class in pymatgen.transformations.standard_transformations) superconduction_temperature (Element attribute) SuperTransformation (class in pymatgen.transformations.advanced_transformations) supported_modes (Kpoints attribute) SUPPORTED_MODES (MVLGWSet attribute) supported_properties (MPRester attribute) (Specie attribute) supported_task_properties (MPRester attribute) supported_units() (ArrayWithUnit property) (FloatWithUnit property) supports_soc() (Pseudo property) surface_area() (Slab property) (SlabEntry property) (WulffShape property) surface_chempot_range_map() (SurfaceEnergyPlotter method) surface_energy() (SlabEntry method) surface_sites() (AdsorbateSiteFinder property) SurfaceEnergyPlotter (class in pymatgen.analysis.surface_analysis) symbol (Deformation attribute) (Element attribute) (NthOrderElasticTensor attribute) (PointGroup attribute) (SpaceGroup attribute) (Strain attribute) (Stress attribute) (Tensor attribute) symbol() (DummySpecie property) (PotcarSingle property) (Pseudo property) symbol_set() (SiteCollection property) symbols() (Potcar property) symm_group_cubic() (in module pymatgen.analysis.gb.grain) symm_reduce() (AdsorbateSiteFinder method) Symmetric (ShiftMode attribute) symmetrically_add_atom() (Slab method) symmetrically_remove_atoms() (Slab method) symmetrize_molecule() (PointGroupAnalyzer method) symmetrized() (Tensor property) (TensorCollection property) SymmetrizedStructure (class in pymatgen.symmetry.structure) symmetry_measure() (in module pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) symmetry_measure_type() (AbstractChemenvStrategy property) symmetry_ops (PointGroup attribute) symmetry_ops() (SymmetryGroup property) symmetry_reduce() (in module pymatgen.core.tensors) SymmetryGroup (class in pymatgen.symmetry.groups) SymmetryModel (class in pymatgen.analysis.energy_models) SymmOp (class in pymatgen.core.operations) symprec (NanoscaleStability attribute) symsigma() (SelfEnergy property)

T

Ta (Element attribute) tag (YamlDoc attribute) tag_structure() (JahnTellerAnalyzer method) Tags (class in pymatgen.io.feff.inputs) tags() (AbstractFeffInputSet property) (FEFFDictSet property) TargettedPenaltiedAbundanceChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) TaskType (class in pymatgen.ext.matproj) Tb (Element attribute) Tc (Element attribute) tdensities (Doscar attribute) tdensities() (Doscar property) tdos (Doscar attribute) (Vasprun attribute) tdos() (Doscar property) Te (Element attribute) Temp (in module pymatgen.core.units) temperature (Poscar attribute) template_dir (LammpsRun attribute) Tensor (class in pymatgen.core.tensors) TensorCollection (class in pymatgen.core.tensors) TensorMapping (class in pymatgen.core.tensors) term_symbols() (Element property) tersoff_input() (GulpIO method) tersoff_potential() (GulpIO method) TersoffPotential (class in pymatgen.command_line.gulp_caller) test() (AbstractStructureFilter method) (ChargeBalanceFilter method) (ContainsSpecieFilter method) (RemoveDuplicatesFilter method) (RemoveExistingFilter method) (SpecieProximityFilter method) (SpeciesMaxDistFilter method) TEST_2D_POINTS (Plane attribute) TEST_FILES_DIR (PymatgenTest attribute) TEST_STRUCTURES (PymatgenTest attribute) tet() (HighSymmKpath method) tet_coord() (in module pymatgen.analysis.phase_diagram) tetragonal() (Lattice static method) text (YamlDoc attribute) text_notag() (YamlDoc property) Th (Element attribute) thankyou() (in module pymatgen.analysis.chemenv.utils.scripts_utils) theories (NwTask attribute) thermal_conductivity (Element attribute) thermal_conductivity() (QuasiharmonicDebyeApprox method) thermal_expansion_coeff() (ElasticTensorExpansion method) ThermoData (class in pymatgen.analysis.thermochemistry) ThermoPlotter (class in pymatgen.phonon.plotter) third_vect() (in module pymatgen.analysis.interface) Ti (Element attribute) Time (in module pymatgen.core.units) timers() (AbinitTimerParser method) title (ExcitingInput attribute) (GaussianOutput attribute) Tl (Element attribute) Tm (Element attribute) tmpfile_write() (PymatgenTest method) to() (ArrayWithUnit method) (FloatWithUnit method) (IMolecule method) (IStructure method) (SiteCollection method) to_abivars() (AbivarAble method) (Constraints method) (Electrons method) (ElectronsAlgorithm method) (ExcHamiltonian method) (HilbertTransform method) (KSampling method) (ModelDielectricFunction method) (PPModel method) (RelaxationMethod method) (Screening method) (SelfEnergy method) (Smearing method) (SpinMode method) to_bson_voronoi_list2() (DetailedVoronoiContainer method) to_csv() (AbinitTimer method) (EntrySet method) to_csvline() (AbinitTimerSection method)

to_data_dict() (Composition property) to_dict() (AbinitTimerSection method) to_displacements() (Trajectory method) to_file() (Control method) (ForceField method) to_hdf5() (VolumetricData method) to_input() (GaussianOutput method), [1] to_json() (AdfKey method) (AdfTask method) (LibxcFunc method) to_lattice() (LammpsBox method) to_positions() (Trajectory method) to_reduced_dict() (Composition property) (Ion property) to_snl() (TransformedStructure method) to_string() (AbstractInput method) (BasicAbinitInput method) (BasicMultiDataset method) (GaussianInput method) (Mcsqs method) (Prismatic method) (Pseudo method) (Relaxation method) (ScfCycle method) (XSF method) to_table() (AbinitTimer method) (PseudoTable method) to_tuple() (AbinitTimerSection method) to_unit_cell() (PeriodicSite method) TOLERANCE (BalancedReaction attribute) top_grain() (GrainBoundary property) TopographyAnalyzer (class in pymatgen.analysis.defects.utils) Topology (class in pymatgen.io.lammps.data) tot_corner_sites() (WulffShape property) tot_edges() (WulffShape property) totable() (AbinitTimer method) (ParallelEfficiency method) total_electrons() (Composition property) total_energy() (EwaldSummation property) total_energy_matrix() (EwaldSummation property) total_spectrum() (Eels property) total_surface_energy() (WulffShape property) Trajectory (class in pymatgen.core.trajectory) trans() (SquareTensor property) trans_v() (ElasticTensor method) transf_mat() (in module pymatgen.analysis.interface) transform() (Tensor method) (TensorCollection method) transform_coords() (JonesFaithfulTransformation method) transform_entries() (CompoundPhaseDiagram method) transform_lattice() (JonesFaithfulTransformation method) transform_symmop() (JonesFaithfulTransformation method) transform_tensor() (SymmOp method) transform_to_length() (CrystalNN static method) transformation_string() (JonesFaithfulTransformation property) transformation_to_string() (in module pymatgen.util.string) TransformedPDEntry (class in pymatgen.analysis.phase_diagram) TransformedStructure (class in pymatgen.alchemy.materials) translate_sites() (Molecule method) (Structure method) TranslateSitesTransformation (class in pymatgen.transformations.site_transformations) translation_vector() (SymmOp property) transparency (WulffShape attribute) tria() (HighSymmKpath method) triangular_coord() (in module pymatgen.analysis.phase_diagram) trib() (HighSymmKpath method) triple_cap_hints() (CoordinationGeometry.NeighborsSetsHints method) true_names (Poscar attribute) tune_for_gamma() (in module pymatgen.analysis.defects.utils) TWO_THETA_TOL (AbstractDiffractionPatternCalculator attribute) type (XcFunc attribute) type() (CriticalPoint property) (MagneticDeformation property) Type() (OrbitalDescription property) type() (Pseudo property) Type2() (OrbitalDescription property) typeidx_from_symbol() (ETSF_Reader method) types_and_weights_of_connections() (StructureGraph property) types_of_coordination_environments() (StructureGraph method) types_of_magnetic_specie() (CollinearMagneticStructureAnalyzer property) types_of_specie() (SiteCollection property)

U

U (Element attribute) ucell_entry (SurfaceEnergyPlotter attribute) UCorrection (class in pymatgen.entries.compatibility) UnconvergedVASPWarning undo_last_change() (StandardTransmuter method) (TransformedStructure method) unicodeify() (in module pymatgen.util.string) unicodeify_spacegroup() (in module pymatgen.util.string) unicodeify_species() (in module pymatgen.util.string) uniform_labels() (AbstractMolAtomMapper method) (InchiMolAtomMapper method) (IsomorphismMolAtomMapper method) uniquelines() (in module pymatgen.analysis.phase_diagram) uniquely_determines_coordination_environments() (AbstractChemenvStrategy property) (LightStructureEnvironments property) (MultiWeightsChemenvStrategy property) (SimpleAbundanceChemenvStrategy property) (SimplestChemenvStrategy property) (TargettedPenaltiedAbundanceChemenvStrategy property) (WeightedNbSetChemenvStrategy property) Unit (class in pymatgen.core.units) unit() (ArrayWithUnit property) (FloatWithUnit property) unit_type() (ArrayWithUnit property) (FloatWithUnit property)

UnitError unitized() (in module pymatgen.core.units) units() (InputVariable property) universal_anisotropy() (ElasticTensor property) Unknown (Ordering attribute) unprocessed_entries() (PourbaixDiagram property) unstable_entries() (PhaseDiagram property) (PourbaixDiagram property) unsym_cs_tensor (Outcar attribute) up (Spin attribute) update() (PBarSafe method) update_charge_from_potcar() (Vasprun method) update_coordination_environments() (StructureEnvironments method) update_nb_set_environments() (LocalGeometryFinder method) update_potcar_spec() (Vasprun method) update_site_info() (StructureEnvironments method) url (HistoryNode attribute) use_cg() (ExcHamiltonian property) use_direct_diago() (ExcHamiltonian property) use_haydock() (ExcHamiltonian property) use_hilbert() (Screening property) use_multiprocessing() (AbstractTransformation property) use_ppmodel() (SelfEnergy property)

V

V (Element attribute) v0() (EOSBase property) V_xx() (ElectricFieldGradient property) V_yy() (ElectricFieldGradient property) V_zz() (ElectricFieldGradient property) Vacancy (class in pymatgen.analysis.defects.core) VacancyGenerator (class in pymatgen.analysis.defects.generators) vacuum_locpot (WorkFunctionAnalyzer attribute) vacuum_thickness() (Interface property) valence() (Element property) ValenceIonicRadiusEvaluator (class in pymatgen.analysis.local_env) valences() (ValenceIonicRadiusEvaluator property) valid() (Composition property) validate() (MultiGraphCycle method) (SimpleGraphCycle method) values() (TensorMapping method) VampireCaller (class in pymatgen.command_line.vampire_caller) VampireOutput (class in pymatgen.command_line.vampire_caller) van_arkel_triangle() (in module pymatgen.util.plotting) van_der_waals_radius (Element attribute) vars() (AbstractInput property) (BasicAbinitInput property) VaspInput (class in pymatgen.io.vasp.inputs) VaspInputSet (class in pymatgen.io.vasp.sets) VaspParserError Vasprun (class in pymatgen.io.vasp.outputs) VaspToComputedEntryDrone (class in pymatgen.apps.borg.hive) vec_angle() (in module pymatgen.analysis.substrate_analyzer) vec_area() (in module pymatgen.analysis.substrate_analyzer) vec_to_surface() (GrainBoundaryGenerator static method) vectorsToMatrix() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) velocities (Poscar attribute) velocities() (Poscar property) velocity_of_sound (Element attribute) vibrational_free_energy() (QuasiharmonicDebyeApprox method) vibrational_internal_energy() (QuasiharmonicDebyeApprox method) vickers_hardness (Element attribute) Vinet (class in pymatgen.analysis.eos) visualize() (in module pymatgen.analysis.chemenv.utils.scripts_utils)

visualize_interface() (in module pymatgen.analysis.interface) (InterfaceBuilder method) visualize_superlattice() (in module pymatgen.analysis.interface) voigt() (Tensor property) (TensorCollection property) voigt_symmetrized() (Tensor property) (TensorCollection property) vol (Wavecar attribute) vol_charge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) vol_discharge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) vol_tetra() (in module pymatgen.analysis.local_env) voltage() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) voltage_pairs() (AbstractElectrode property) (ConversionElectrode property) (InsertionElectrode property) VoltageProfilePlotter (class in pymatgen.apps.battery.plotter) volume() (IStructure property) (LammpsBox property) (Lattice property) (Simplex property) (VoronoiPolyhedron property) (WulffShape property) VolumetricData (class in pymatgen.io.vasp.outputs) von_mises() (Stress property) von_mises_strain() (Strain property) voronoi_grid_surface_points() (StructureEnvironments.NeighborsSet method) voronoi_parameters_bounds_and_limits() (DetailedVoronoiContainer method) VoronoiAnalyzer (class in pymatgen.analysis.structure_analyzer) VoronoiConnectivity (class in pymatgen.analysis.structure_analyzer) VoronoiInterstitialGenerator (class in pymatgen.analysis.defects.generators) VoronoiNN (class in pymatgen.analysis.local_env) VoronoiParametersError VoronoiPolyhedron (class in pymatgen.analysis.defects.utils) vtk() (TopographyAnalyzer method)

W

W (Element attribute) w_area_has_intersection() (DistanceAngleAreaNbSetWeight method) w_area_has_intersection_smoothstep() (DistanceAngleAreaNbSetWeight method) w_area_intersection_nbsfh_fbs_onb0() (DistanceAngleAreaNbSetWeight method) walk() (AbinitTimerParser class method) walk_tree() (NetcdfReader method) was_modified() (TransformedStructure property) Wavecar (class in pymatgen.io.vasp.outputs) Waveder (class in pymatgen.io.vasp.outputs) Wavederf (class in pymatgen.io.vasp.outputs) wavenumber() (Xmu property) weight() (AngleNbSetWeight method) (AnglePlateauNbSetWeight method) (CNBiasNbSetWeight method) (Composition property) (ConnectedSite property) (DeltaCSMNbSetWeight method) (DeltaDistanceNbSetWeight method) (DistanceAngleAreaNbSetWeight method) (DistanceNbSetWeight method) (DistancePlateauNbSetWeight method) (NbSetWeight method) (NormalizedAngleDistanceNbSetWeight method) (SelfCSMNbSetWeight method) weight_statistics() (StructureGraph property) weighted_surface_energy() (WulffShape property) WeightedNbSetChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) weights (Procar attribute) welcome() (in module pymatgen.analysis.chemenv.utils.scripts_utils) with_dojo_report() (PseudoTable method) with_edges() (MoleculeGraph static method) (StructureGraph static method) with_empty_graph() (MoleculeGraph class method) (StructureGraph class method) with_local_env_strategy() (MoleculeGraph static method) (StructureGraph static method) work_function (WorkFunctionAnalyzer attribute) WorkFunctionAnalyzer (class in pymatgen.analysis.surface_analysis) working_ion() (AbstractElectrode property) (ConversionElectrode property) (ConversionVoltagePair property) (InsertionElectrode property) (InsertionVoltagePair property) working_ion_entry() (AbstractElectrode property) (AbstractVoltagePair property) (ConversionElectrode property) (ConversionVoltagePair property) (InsertionElectrode property) (InsertionVoltagePair property) write() (AbstractInput method) (BasicMultiDataset method) (QChemDictSet method) write_all_structures() (InterfaceBuilder method) write_def() (BoltztrapRunner method) write_energy() (BoltztrapRunner method) write_etree() (ExcitingInput method) write_file() (AdfInput method) (Atoms method) (BabelMolAdaptor method) (CifWriter method) (Cssr method) (ExcitingInput method) (FiestaInput method) (GaussianInput method) (Header method) (Incar method) (Kpoints method) (LammpsData method) (LMTOCtrl method) (NwInput method) (Paths method) (Poscar method) (Potcar method) (PotcarSingle method) (Potential method) (PWInput method) (QCInput method) (Tags method) (VolumetricData method) (Xdatcar method) (Xr method) (XYZ method)

write_image() (PDPlotter method) (StructureVis method) write_INCAR() (Lobsterin method) write_input() (AbstractFeffInputSet method) (BoltztrapRunner method) (DictSet method) (MITNEBSet method) (VaspInput method) (VaspInputSet method) write_inputs() (LammpsRun method) write_intrans() (BoltztrapRunner method) write_json() (IRDielectricTensor method) write_KPOINTS() (Lobsterin static method) write_lammps_inputs() (in module pymatgen.io.lammps.inputs) write_lobsterin() (Lobsterin method) write_multi_job_file() (QCInput static method) write_pdb() (PackmolRunner method) write_phononwebsite() (PhononBandStructureSymmLine method) write_POSCAR_with_standard_primitive() (Lobsterin static method) write_proj() (BoltztrapRunner method) write_string() (ExcitingInput method) write_struct() (BoltztrapRunner method) write_topology() (TopographyAnalyzer method) write_vasp_input() (StandardTransmuter method) (TransformedStructure method) write_Xdatcar() (Trajectory method) wulff_cv_simp (WulffShape attribute) wulff_from_chempot() (SurfaceEnergyPlotter method) wulff_gform_and_r() (NanoscaleStability method) wulff_pt_list (WulffShape attribute) WulffFacet (class in pymatgen.analysis.wulff) WulffShape (class in pymatgen.analysis.wulff)

X

X (DummySpecie attribute) (Element attribute) X() (DummySpecie property) (Element property) x() (PeriodicSite property) (Site property) XAS (class in pymatgen.analysis.xas.spectrum) XcFunc (class in pymatgen.core.xcfunc) Xdatcar (class in pymatgen.io.vasp.outputs) Xe (Element attribute)

XLABEL (DiffractionPattern attribute) (DOS attribute) (ExcitationSpectrum attribute) (Spectrum attribute) (XAS attribute) Xmu (class in pymatgen.io.feff.outputs) Xr (class in pymatgen.io.xr) XRDCalculator (class in pymatgen.analysis.diffraction.xrd) XSF (class in pymatgen.io.xcrysden) XYZ (class in pymatgen.io.xyz)

Y

Y (Element attribute) y() (PeriodicSite property) (Site property) y_mod() (ElasticTensor property) yaml_read_irred_perts() (in module pymatgen.io.abinit.abiinspect) yaml_read_kpoints() (in module pymatgen.io.abinit.abiinspect) YamlDoc (class in pymatgen.io.abinit.abiinspect) YamlTokenizer (class in pymatgen.io.abinit.abiinspect)

YamlTokenizerError Yb (Element attribute) YLABEL (DiffractionPattern attribute) (DOS attribute) (ExcitationSpectrum attribute) (Spectrum attribute) (XAS attribute) youngs_modulus (Element attribute)

Z

Z (DummySpecie attribute) (Element attribute) Z() (DummySpecie property) z() (PeriodicSite property) Z() (Pseudo property) z() (Site property) z_shift() (Interface property) Z_val() (Pseudo property) ZeoCssr (class in pymatgen.io.zeopp) ZeoVoronoiXYZ (class in pymatgen.io.zeopp)

zero_d_graph_to_molecule_graph() (in module pymatgen.analysis.dimensionality) zero_point_energy() (PhononDos method) zeroed() (Tensor method) (TensorCollection method) zlist() (PseudoTable property) Zn (Element attribute) zoom() (StructureVis method) Zr (Element attribute) ZSLGenerator (class in pymatgen.analysis.substrate_analyzer) zval_dict_from_potcar() (in module pymatgen.analysis.ferroelectricity.polarization)