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) absorption_coefficient() (in module pymatgen.analysis.solar.slme) 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) activate_fast_minimization() (DftSet method) activate_hybrid() (DftSet method) activate_nonperiodic() (DftSet method) activate_robust_minimization() (DftSet method) activate_very_strict_minimization() (DftSet method) actual_kpoints (Vasprun attribute) actual_kpoints_weights (Vasprun attribute) add() (EntrySet method) (Section method) add_abiobjects() (BasicAbinitInput method) add_adsorbate() (AdsorbateSiteFinder method) add_adsorbate_atom() (Slab method) add_bonds() (StructureConnectivity method) (StructureVis method) add_bs() (BSPlotter 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_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.prototypes) AFM (Ordering attribute) Ag (Element attribute) 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 (OptimadeRester attribute) 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() (BasePhaseDiagram property) all_families() (LibxcFunc static method) all_input() (AbstractFeffInputSet method) (VaspInputSet property) all_kinds() (LibxcFunc static method) all_molecules() (XYZ property) all_nninfo (CrystalNN.NNData attribute) 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) allsqs (Sqs attribute) 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) (TransformedPDEntry 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 static method) anginvdist() (NormalizedAngleDistanceNbSetWeight static method) anginvndist() (NormalizedAngleDistanceNbSetWeight method) angle_cutoff() (SimplestChemenvStrategy property) angle_plateau() (StructureEnvironments.NeighborsSet method) angle_sum() (AngleNbSetWeight static 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) (KeywordList 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 static method) (MagOrderingTransformation method) (MonteCarloRattleTransformation 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_dataframe() (IStructure method) (XYZ method) 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) (CoordinationGeometry method) (CoordinationGeometry.NeighborsSetsHints method) (Cp2kOutput 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) (DummySpecies method) (Eels method) (Electrons method) (ElectronsAlgorithm method) (ElementBase method) (Entry method) (EntrySet method) (EwaldElectrostaticModel method) (EwaldSummation method) (ExpEntry method) (ExplicitPermutationsAlgorithm property) (FermiDos method) (FiestaInput method) (FiestaRun method) (GaussianInput method) (GaussianOutput method) (GaussianToComputedEntryDrone method) (GibbsComputedStructureEntry method) (GrainBoundary method) (GrandPotentialPhaseDiagram method) (GrandPotPDEntry method) (HeisenbergModel method) (HistoryNode method) (IMolecule method) (Incar method) (InchiMolAtomMapper method) (Interface method) (Ion method) (IonEntry method) (IRDielectricTensor method) (IsingModel method) (IsomorphismMolAtomMapper method) (IStructure method) (Keyword 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) (LobsterLightStructureEnvironments 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) (SpecieProximityFilter method) (Species 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_legacy() (InsertionElectrode method) as_dict_summary() (ConversionElectrode method) (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 class 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() (ElementBase property) atomic_no() (PotcarSingle property) atomic_numbers() (SiteCollection property) atomic_orbitals (Element attribute) (ElementBase attribute) atomic_radius() (ElementBase property) atomic_radius_calculated (Element attribute) (ElementBase 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() (ElementBase property) average_cationic_radius() (ElementBase property) average_coordination_number() (in module pymatgen.analysis.structure_analyzer) average_electroneg() (Composition property) average_ionic_radius() (ElementBase property) average_over_unit_sphere() (Tensor method) aweight() (NormalizedAngleDistanceNbSetWeight static 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 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.outputs) 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) BasePhaseDiagram (class in pymatgen.analysis.phase_diagram) 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() (KPathSetyawanCurtarolo method) bctet1() (KPathSetyawanCurtarolo method) bctet2() (KPathSetyawanCurtarolo method) Be (Element attribute) BE_vs_clean_SE() (SurfaceEnergyPlotter method) BEGIN_TAG (AbinitTimerParser attribute) best_case() (EwaldMinimizer method) best_m_list() (EwaldMinimizer property) bestsqs (Sqs attribute) beta() (Lattice property) Bh (Element attribute) Bi (Element attribute) Birch (class in pymatgen.analysis.eos) BirchMurnaghan (class in pymatgen.analysis.eos)

Bk (Element attribute) block() (ElementBase property) block_keys (AdfKey attribute) bohr2ang (ExcitingInput attribute) boiling_point (Element attribute) (ElementBase 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) bragg_angles() (TEMCalculator method) break_bond() (IMolecule method) break_edge() (MoleculeGraph method) (StructureGraph method) brinell_hardness (Element attribute) (ElementBase attribute) BrokenSymmetry (class in pymatgen.io.cp2k.inputs) BrunnerNN_real (class in pymatgen.analysis.local_env) BrunnerNN_reciprocal (class in pymatgen.analysis.local_env) BrunnerNN_relative (class in pymatgen.analysis.local_env) BruteForceOrderMatcher (class in pymatgen.analysis.molecule_matcher) 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 static 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 static method) bulk_modulus (Element attribute) (ElementBase attribute) bulk_structure() (Defect property) (DefectEntry property) BVA_DISTANCE_SCALE_FACTORS (LocalGeometryFinder attribute) BVAnalyzer (class in pymatgen.analysis.bond_valence) by_path() (Section method)

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_compounds (CorrectionCalculator attribute) 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_efermi() (Vasprun method) calculate_energy() (BalancedReaction method) calculate_ng() (DictSet method) calculate_stress() (ElasticTensorExpansion method) (NthOrderElasticTensor method) calculate_vol() (in module pymatgen.analysis.defects.utils) calculated_reaction_energy() (ComputedReaction property) calculated_reaction_energy_uncertainty() (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) Cell (class in pymatgen.io.cp2k.inputs) cell_intensity() (TEMCalculator method) cell_scattering_factors() (TEMCalculator method) CellOptSet (class in pymatgen.io.cp2k.sets) 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.outputs) 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) ChargeInsertionAnalyzer (class in pymatgen.analysis.defects.utils) check() (Section method) check_acc_bzt_bands() (BoltztrapAnalyzer static method) check_condition() (AdditionalConditions method) check_final_relaxed_structure_delocalized() (DefectCompatibility method) check_for_structure_changes() (in module pymatgen.io.qchem.outputs) 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 chemical_energy() (GrandPotPDEntry property) chemical_shielding (Outcar attribute) chemical_symbols() (ETSF_Reader method) 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.HaeberlenNotation (class in pymatgen.analysis.nmr) ChemicalShielding.MarylandNotation (class in pymatgen.analysis.nmr) ChemicalShielding.MehringNotation (class in pymatgen.analysis.nmr) chempot_plot_addons() (SurfaceEnergyPlotter static 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) ciffile() (CifWriter property) 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) 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) clusters (Sqs attribute) Cm (Element attribute) Cn (Element attribute) cn() (AbstractGeometry property) cn_nninfo (CrystalNN.NNData attribute) cn_weights (CrystalNN.NNData attribute) 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) (ElementBase attribute) coefficients() (Plane property) coeffs (Wavecar attribute) coeffs() (BalancedReaction property) Cohp (class in pymatgen.electronic_structure.cohp) Cohpcar (class in pymatgen.io.lobster.outputs) 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) 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() (ElementBase 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) completed() (Cp2kOutput property) 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() (Entry property) (GrandPotPDEntry property) (Ion property) (PourbaixEntry property) (SiteCollection property) (TransformedPDEntry property)

composition_prediction() (SubstitutionPredictor method) CompositionEnergyAdjustment (class in pymatgen.entries.computed_entries) CompositionError CompoundPhaseDiagram (class in pymatgen.analysis.phase_diagram) compute_average_oxidation_state() (in module pymatgen.analysis.ewald) compute_coordination_environments() (LocalGeometryFinder method) compute_corrections() (CorrectionCalculator method) compute_defect_density() (in module pymatgen.analysis.defects.dilute_solution_model) compute_environments() (in module pymatgen.analysis.chemenv.utils.scripts_utils) compute_from_files() (CorrectionCalculator method) 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) ConstantEnergyAdjustment (class in pymatgen.entries.computed_entries) 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() (KPathSetyawanCurtarolo 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) convergence() (Cp2kOutput method) 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 (class in pymatgen.io.cp2k.inputs) 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 (Neighbor attribute) 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) correction() (ComputedEntry property) correction_per_atom() (ComputedEntry property) correction_uncertainty() (ComputedEntry property) correction_uncertainty_per_atom() (ComputedEntry property) CorrectionCalculator (class in pymatgen.entries.correction_calculator) corrections (CorrectionCalculator attribute) (GaussianOutput attribute) corrections_dict (CorrectionCalculator attribute) corrections_std_error (CorrectionCalculator attribute) CorrectionsList (class in pymatgen.entries.compatibility) 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) cp2k_version() (Cp2kOutput property) Cp2kInput (class in pymatgen.io.cp2k.inputs) Cp2kInputSet (class in pymatgen.io.cp2k.sets) Cp2kOutput (class in pymatgen.io.cp2k.outputs) cpuwall_histogram() (AbinitTimer method) Cr (Element attribute) create_saturated_interstitial_structure() (in module pymatgen.analysis.defects.core) create_slab_label() (SlabEntry property) create_subsys() (Cp2kInputSet method) Critic2Analysis (class in pymatgen.command_line.critic2_caller) Critic2Caller (class in pymatgen.command_line.critic2_caller) Critic2NN (class in pymatgen.analysis.local_env) critical_temperature (Element attribute) (ElementBase 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) CrystalNN.NNData (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) Cube (class in pymatgen.io.cube) cubic() (KPathSetyawanCurtarolo 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) (Unk attribute) (Wavederf attribute) data() (ElementBase property) (Unk property) dataset() (InputVariable property) Davidson (class in pymatgen.io.cp2k.inputs) Db (Element attribute) 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 attribute) 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) delta_sigma_iso (ChemicalShielding.HaeberlenNotation 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) (ElementBase 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 (class in pymatgen.io.cp2k.inputs) dft_task() (NwTask class method) DftPlusU (class in pymatgen.io.cp2k.inputs) DftSet (class in pymatgen.io.cp2k.sets) Diagonalization (class in pymatgen.io.cp2k.inputs) 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) directory (Sqs attribute) 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 attribute) 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.outputs) 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) Ds (Element attribute) dual_cv_simp (WulffShape attribute) DummySpecie (class in pymatgen.core.periodic_table) DummySpecies (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 attribute) (OrbitalDescription attribute) e0() (EOSBase property) E_Density_Cube (class in pymatgen.io.cp2k.inputs) 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) (ElementBase attribute) ElectricFieldGradient (class in pymatgen.analysis.nmr) electron_configuration() (PotcarSingle property) electron_scattering_factors() (TEMCalculator method) electronic_steps (Oszicar attribute) electronic_structure (Element attribute) (ElementBase attribute) electronic_structure() (ElementBase property) 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) (Species property) element_composition() (Composition property) ElementBase (class in pymatgen.core.periodic_table) 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) (GrandPotPDEntry property) (PDEntry property) (PourbaixEntry property) energy_at_conditions() (PourbaixEntry method) energy_density() (ElasticTensorExpansion method) (NthOrderElasticTensor method) energy_per_atom() (Entry property) (PourbaixEntry property) EnergyAdjustment (class in pymatgen.entries.computed_entries) EnergyModel (class in pymatgen.analysis.energy_models) EnergyTrend (class in pymatgen.analysis.ferroelectricity.polarization) ensemble_center() (AdsorbateSiteFinder class method) entries_charge (ConversionVoltagePair attribute), [1] entries_discharge (ConversionVoltagePair attribute), [1] entropy() (PhononDos method) Entry (class in pymatgen.entries)

entry_charge (InsertionVoltagePair attribute) entry_dict_from_list() (in module pymatgen.analysis.surface_analysis) entry_discharge (InsertionVoltagePair attribute) 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 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) equiv_labels() (HighSymmKpath 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) estimate_nbands() (DictSet method) eta (ChemicalShielding.HaeberlenNotation attribute) 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) exp_compounds (CorrectionCalculator attribute) ExpEntry (class in pymatgen.entries.exp_entries) explain() (Compatibility static method) (CompositionEnergyAdjustment property) (ConstantEnergyAdjustment property) (CorrectionsList method) (EnergyAdjustment property) (TemperatureEnergyAdjustment property) 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) (KeywordList 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 attribute) 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.outputs) fcc() (KPathSetyawanCurtarolo 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() (BruteForceOrderMatcher method) (DeltaFactor method) (EOS method) (EOSBase method) (GeneticOrderMatcher method) (HungarianOrderMatcher method) (KabschMatcher 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) Fl (Element attribute) 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) ForceEval (class in pymatgen.io.cp2k.inputs) ForceField (class in pymatgen.io.lammps.data) forces() (EwaldSummation property) ForceSet (class in pymatgen.io.qchem.sets) format_formula() (in module pymatgen.util.plotting) format_list() (InputVariable method) format_list2d() (InputVariable static method) format_scalar() (InputVariable static method) formation_energy() (DefectEntry method) formation_energy_tol (BasePhaseDiagram attribute) formula() (Composition property) (Header property) (Ion property) (SiteCollection property) formula_double_format() (in module pymatgen.util.string) Fr (Element attribute) frac_charge (AbstractVoltagePair attribute), [1] (ConversionVoltagePair attribute) frac_coords() (IStructure property) (Kpoint property) (PeriodicSite property) frac_discharge (AbstractVoltagePair attribute), [1] (ConversionVoltagePair attribute) fractional_composition() (Composition property) fractions() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) fragment_and_process() (BondDissociationEnergies method) Fragmenter (class in pymatgen.analysis.fragmenter) framework (AbstractElectrode attribute) (AbstractVoltagePair attribute) framework() (AbstractElectrode property) (AbstractVoltagePair property) 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_chgcar() (Critic2Caller class method) from_cif_file() (Header static method) from_cif_string() (TransformedStructure static method) from_coefficients() (Plane class method) from_composition_and_entries() (ConversionElectrode class method) from_composition_and_pd() (ConversionElectrode class 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() (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) (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) (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) (DummySpecies class method) (Electrons class method) (ElectronsAlgorithm class method) (ElementBase static method) (EnergyModel class method) (EwaldSummation 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) (GibbsComputedStructureEntry class method) (GrainBoundary class method) (GrandPotentialPhaseDiagram class method) (GrandPotPDEntry class method) (HeisenbergModel class method) (HistoryNode static method) (IMolecule class method) (Incar class method) (InchiMolAtomMapper class method) (Interface class method) (Ion class method) (IonEntry class method) (IRDielectricTensor class method) (IsomorphismMolAtomMapper class method) (IStructure class method) (Keyword class method) (Kpoints class method) (KSampling class method) (LammpsData class method) (LammpsDump class method) (Lattice class method) (LibxcFunc static 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) (SpecieProximityFilter class method) (Species 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_dict_legacy() (InsertionElectrode 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_entries() (BasePhaseDiagram class method) (GibbsComputedStructureEntry class method) (InsertionElectrode class method) (InsertionVoltagePair 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) (Cp2kInput static 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) (Unk static 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_kpoints() (Kpoints class method) from_lammpsdata() (CombinedData class method) from_lengths_and_angles() (Lattice static method) from_lines() (Cp2kInput class method) from_Lobster() (LobsterLightStructureEnvironments class 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 class method) from_old_dict() (BandStructure 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_pd() (GibbsComputedStructureEntry class method) from_poscar_string() (TransformedStructure static method) from_preset() (CutOffDictNN static method) from_prev_calc() (MPHSEBSSet class method) (MPNonSCFSet class method) (MPScanStaticSet 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() (ElementBase static method) 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 class method) from_str() (IMolecule class method) (IStructure class method) (SiteCollection class method) from_stream() (Relaxation class method) (ScfCycle class method) from_string() (AdfKey static method) (BabelMolAdaptor static method) (BalancedReaction static method) (CifBlock class method) (CifFile class method) (CifParser static method) (Cp2kInput static method) (Cssr static method) (DummySpecies static method) (ExcitingInput static method) (FiestaInput class method) (FloatWithUnit class method) (GaussianInput static method) (Header static method) (Incar static method) (Keyword static method) (Kpoints static method) (Kpoints_supported_modes static method) (LammpsDump class method) (LMTOCtrl class method) (NwInput class method) (Poscar static method) (PWInput static method) (QCInput class method) (Species 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() (ElementBase static method) full_electronic_structure() (ElementBase 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) gauss_smear() (in module pymatgen.io.cp2k.outputs) 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_points() (TEMCalculator static 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) generic_groupby() (in module pymatgen.analysis.defects.utils) GeneticOrderMatcher (class in pymatgen.analysis.molecule_matcher) genrecip() (in module pymatgen.analysis.defects.utils) geometrically_equidistant() (CNBiasNbSetWeight class method) get() (Section 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_adjustments() (Compatibility method) (CorrectionsList method) (MaterialsProject2020Compatibility method) (MaterialsProjectAqueousCompatibility method) get_all_anonymous_mappings() (StructureMatcher method) get_all_chempots() (BasePhaseDiagram 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() (IsayevNN method) (NearNeighbors method) (VoronoiNN method) get_all_possible_basis_combinations() (in module pymatgen.io.lobster.inputs) get_all_possible_basis_functions() (Lobsterin static 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) (JarvisAtomsAdaptor static method) get_aux_basis() (in module pymatgen.io.cp2k.utils) 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_basis() (Lobsterin static method) get_basis_and_potential() (in module pymatgen.io.cp2k.utils) 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_decorated_structure() (BaderAnalysis method) get_charge_transfer() (BaderAnalysis method) get_chempot_correction() (InterfacialReactivity static method) get_chempot_range_map() (BasePhaseDiagram method) get_chempot_range_map_plot() (PDPlotter method) get_chempot_range_stability_phase() (BasePhaseDiagram 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() (BasePhaseDiagram 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_continuous_path() (HighSymmKpath static method) get_contour_pd_plot() (PDPlotter method) 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() (CorrectionsList method) get_cost_per_kg() (CostAnalyzer method) get_cost_per_mol() (CostAnalyzer method) get_covalent_bonds() (IMolecule method) get_critical_compositions() (BasePhaseDiagram method) get_critical_original_kink_ratio() (InterfacialReactivity method) get_critical_point_for_site() (Critic2Analysis method) get_crystal_field_spin() (Species 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_database_version() (MPRester method) get_dataframe() (AbinitTimer method) get_decomp_and_e_above_hull() (BasePhaseDiagram method) get_decomp_and_phase_separation_energy() (BasePhaseDiagram method) get_decomposition() (BasePhaseDiagram 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_dir_indir_gap() (in module pymatgen.analysis.solar.slme) get_direct_band_gap() (BandStructure method) get_direct_band_gap_dict() (BandStructure method) get_disconnected_fragments() (MoleculeGraph 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() (BasePhaseDiagram 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() (BasePhaseDiagram 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 static 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() (BasePhaseDiagram 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() (CorrectionsList 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_filepath() (in module pymatgen.command_line.bader_caller) get_film_indices() (Interface method) get_first_point() (TEMCalculator method) get_form_energy() (BasePhaseDiagram method) get_form_energy_per_atom() (BasePhaseDiagram 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_heisenberg_model() (HeisenbergMapper method) get_help() (VaspDoc class method) get_heteroatoms() (FunctionalGroupExtractor method) get_high_accuracy_voronoi_nodes() (in module pymatgen.io.zeopp) get_hull_energy() (BasePhaseDiagram 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_incar_tags() (VaspDoc class method) get_info_cohps_to_neighbors() (LobsterNeighbors method) get_info_icohps_between_neighbors() (LobsterNeighbors method) get_info_icohps_to_neighbors() (LobsterNeighbors method) get_integer_formula_and_factor() (Composition method) get_integer_index() (in module pymatgen.core.lattice) get_integrated_cohp_in_energy_range() (in module pymatgen.electronic_structure.cohp) get_integrated_diff() (VolumetricData method) get_interaction_graph() (HeisenbergMapper method) get_interface_reactions() (MPRester method) get_interplanar_angle() (TEMCalculator static method) get_interplanar_spacings() (TEMCalculator 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() (in module pymatgen.ext.jhu) (KPathBase method) get_labels() (ChargeInsertionAnalyzer method) (WorkFunctionAnalyzer method) get_lattice() (CifParser method) get_lattice_quanta() (Polarization method) get_lattice_type() (SpacegroupAnalyzer method) get_light_structure_environment() (LobsterNeighbors 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_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 class method) get_niggli_reduced_lattice() (Lattice method) get_nmr_quadrupole_moment() (Species 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) (IsayevNN method) (JmolNN method) (LobsterNeighbors 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_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_orderings() (IStructure 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) (TEMCalculator 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_phase_separation_energy() (BasePhaseDiagram method) 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_2d() (TEMCalculator method) get_plot_2d_concise() (TEMCalculator method) get_plot_coeffs() (TEMCalculator static method) get_plot_data() (VoltageProfilePlotter method) get_plotly() (WulffShape method) get_plotly_figure() (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_positions() (TEMCalculator method) get_potcar_file_hash() (PotcarSingle method) get_potcar_hash() (PotcarSingle method) get_potcars() (Vasprun method) get_potential_shift() (KumagaiCorrection static 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_primitive_standard_structure() (SpacegroupAnalyzer method) get_primitive_structure() (IStructure method) get_principal_axis() (HungarianOrderMatcher static 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 static 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() (TEMCalculator 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() (Species 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_spin_state_decorated_structure() (BaderAnalysis 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) (Cp2kInput method) (Incar method) (Keyword method) (KeywordList method) (LammpsBox method) (LammpsData method) (LMTOCtrl method) (Poscar method) (Section method) (Tags method) (Xdatcar method) get_structure() (AseAtomsAdaptor static method) (Control method) (JarvisAtomsAdaptor static 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_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) (OptimadeRester method) get_structures_with_filter() (OptimadeRester method) get_sub_electrodes() (AbstractElectrode method) (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() (AbstractElectrode method) (ConversionElectrode method) (DiffusionAnalyzer method) (InsertionElectrode 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_ticks_old() (BSPlotter method) get_total_ionic_dipole() (in module pymatgen.analysis.ferroelectricity.polarization) get_trajectory() (Vasprun method) get_trans_mat() (GrainBoundaryGenerator static method) get_transformation() (StructureMatcher method) get_transition_chempots() (BasePhaseDiagram method) get_tri_area() (in module pymatgen.analysis.wulff) get_type() (LocalStructOrderParams method) get_unique_families() (in module pymatgen.analysis.diffraction.core) get_unique_site_indices() (in module pymatgen.io.cp2k.utils) 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_magmom_struct() (in module pymatgen.io.vasp.sets) 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_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_volume_and_charge_for_site() (Critic2Analysis method) get_volumetricdata_density() (Wavefunction method) get_volumetricdata_imaginary() (Wavefunction method) get_volumetricdata_real() (Wavefunction 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() (BasePhaseDiagram method) gf_sisso() (GibbsComputedStructureEntry 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) GibbsComputedStructureEntry (class in pymatgen.entries.computed_entries) Global (class in pymatgen.io.cp2k.inputs) 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) graph_residual_error() (CorrectionCalculator method) graph_residual_error_per_species() (CorrectionCalculator method) green_kristoffel() (ElasticTensor method) green_lagrange_strain() (Deformation property) grid_off (WulffShape attribute) Grosspop (class in pymatgen.io.lobster.outputs) ground_state_term_symbol() (ElementBase property) GroundStateScfCycle (class in pymatgen.io.abinit.abiinspect) group() (ElementBase 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 static method)

H

H (Element attribute) haeberlen_values() (ChemicalShielding property) 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) HeisenbergModel (class in pymatgen.analysis.magnetism.heisenberg) HeisenbergScreener (class in pymatgen.analysis.magnetism.heisenberg) helmholtz_free_energy() (PhononDos method) hessian (GaussianOutput attribute) hex() (KPathSetyawanCurtarolo 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 method) 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) Hs (Element attribute) hubbards() (Vasprun property) HungarianOrderMatcher (class in pymatgen.analysis.molecule_matcher) 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) HybridCellOptSet (class in pymatgen.io.cp2k.sets) HybridRelaxSet (class in pymatgen.io.cp2k.sets) HybridStaticSet (class in pymatgen.io.cp2k.sets)

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.outputs) icohplist() (Icohplist property) IcohpValue (class in pymatgen.electronic_structure.cohp) icohpvalue() (IcohpValue method) icsd_oxidation_states() (ElementBase property) id_generator() (in module pymatgen.util.convergence) identify_potcar() (PotcarSingle method) idos (Vasprun attribute) ik (Unk attribute), [1] 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) inc() (Section method) Incar (class in pymatgen.io.vasp.inputs) incar (Vasprun attribute) incar() (DictSet property) (MPNMRSet property) (MPNonSCFSet property) (MPScanStaticSet 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 method) index (ConnectedSite attribute) 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) initial_comp() (ConversionElectrode property) InputVariable (class in pymatgen.io.abinit.variable) insert() (Molecule method) (Section 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 static 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) (MonteCarloRattleTransformation 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() (ElementBase property) ionic_radius (Specie attribute) (Species attribute) ionic_radius() (Species 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() (ElementBase property) is_alkali() (ElementBase property) is_alkaline() (ElementBase 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() (ElementBase property) is_close_to() (ChemicalEnvironments method) (DetailedVoronoiContainer method) is_complete() (PseudoTable method) is_converged() (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) is_failed (AdfOutput attribute) is_fit_to_structure() (Tensor method) (TensorCollection method) is_gga_family() (LibxcFunc property) is_halogen() (ElementBase 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() (ElementBase property) is_laue() (SpacegroupAnalyzer method) is_lda_family() (LibxcFunc property) is_magnetic() (CollinearMagneticStructureAnalyzer property) is_metal() (BandStructure method) (Cp2kOutput property) (ElementBase property) is_metalloid() (ElementBase property) is_mgga_family() (LibxcFunc property) is_noble_gas() (ElementBase property) is_noncollinear (Unk attribute), [1] 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) (MonteCarloRattleTransformation 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_parallel() (TEMCalculator method) is_pcm (GaussianOutput attribute) is_periodic() (ConnectedComponent property) is_periodic_image() (PeriodicSite method) is_polar() (Slab method) is_post_transition_metal() (ElementBase property) is_quadrupolar() (ElementBase property) is_rare_earth_metal() (ElementBase 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() (ElementBase property) is_valid() (SiteCollection method) is_valid_bibtex() (in module pymatgen.util.provenance) is_valid_op() (PointGroupAnalyzer method) is_valid_symbol() (ElementBase static method) is_voigt_symmetric() (Tensor method) (TensorCollection method) is_x_kind() (LibxcFunc property) is_xc_kind() (LibxcFunc property) IsayevNN (class in pymatgen.analysis.local_env) isclose() (SOCSpillage static method) 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() (ElementBase property) IUPAC_symbol() (CoordinationGeometry property) IUPAC_symbol_str() (CoordinationGeometry property)

J

j (Orbital attribute) JahnTellerAnalyzer (class in pymatgen.analysis.magnetism.jahnteller) JarvisAtomsAdaptor (class in pymatgen.io.jarvis)

jimage (ConnectedSite attribute) 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) kabsch() (KabschMatcher static method) KabschMatcher (class in pymatgen.analysis.molecule_matcher) kappa (ChemicalShielding.MarylandNotation attribute) kb (in module pymatgen.core.units) key() (AdfKey property) keyPressEvent() (MultiStructuresInteractorStyle method) (StructureInteractorStyle method) Keyword (class in pymatgen.io.cp2k.inputs) keyword_line() (GulpIO static method) KeywordList (class in pymatgen.io.cp2k.inputs) keywords (PotcarSingle attribute) Kind (class in pymatgen.io.cp2k.inputs) kpath() (KPathBase property) KPathBase (class in pymatgen.symmetry.kpath) KPathLatimerMunro (class in pymatgen.symmetry.kpath) KPathSeek (class in pymatgen.symmetry.kpath) KPathSetyawanCurtarolo (class in pymatgen.symmetry.kpath)

Kpoint (class in pymatgen.electronic_structure.bandstructure) Kpoints (class in pymatgen.io.cp2k.inputs) (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 attribute) (OrbitalDescription attribute) l_local() (Pseudo property) l_max() (Pseudo property) La (Element attribute) label (FreqUnits attribute) (SlabEntry attribute) label() (Kpoint property) label_index() (HighSymmKpath property) LabelPoints() (KPathLatimerMunro static method) labels() (InterfacialReactivity method) LabelSymbol() (KPathLatimerMunro static 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) Lattice (class in pymatgen.core.lattice) lattice (WulffShape attribute) lattice() (IStructure property) (KPathBase 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.cp2k.inputs) 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 static 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) linear_slice() (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) (ElementBase 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) LobsterBandStructureSymmLine (class in pymatgen.electronic_structure.bandstructure) LobsterCompleteDos (class in pymatgen.electronic_structure.dos) Lobsterin (class in pymatgen.io.lobster.inputs) LobsterLightStructureEnvironments (class in pymatgen.io.lobster.lobsterenv) LobsterNeighbors (class in pymatgen.io.lobster.lobsterenv) Lobsterout (class in pymatgen.io.lobster.outputs) 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) (ElementBase 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) Lv (Element attribute)

M

mag_type() (KPathLatimerMunro property) MAGIC (D2DEScfCycle attribute) (GroundStateScfCycle attribute) (ScfCycle 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 attribute), [1] (ConversionVoltagePair attribute) main() (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 static 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) make_yaml() (CorrectionCalculator method) ManualEnergyAdjustment (class in pymatgen.entries.computed_entries) 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 attribute), [1] (ConversionVoltagePair attribute) mass_discharge (AbstractVoltagePair attribute), [1] (ConversionVoltagePair attribute) masses (ForceField attribute) masses() (Dynmat property) match() (BruteForceOrderMatcher method) (GeneticOrderMatcher method) (HungarianOrderMatcher method) (KabschMatcher method) match_as_dict() (ZSLGenerator static method) matches() (IStructure method) matches_ordering() (CollinearMagneticStructureAnalyzer method) material_formula() (Xmu property) MaterialsProject2020Compatibility (class in pymatgen.entries.compatibility) MaterialsProjectAqueousCompatibility (class in pymatgen.entries.compatibility) MaterialsProjectCompatibility (class in pymatgen.entries.compatibility) matrix() (Lattice property) matrix_eigvals() (in module pymatgen.analysis.solar.slme) 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() (ElementBase 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) Mc (Element attribute) mcl() (KPathSetyawanCurtarolo method) mclc1() (KPathSetyawanCurtarolo method) mclc2() (KPathSetyawanCurtarolo method) mclc3() (KPathSetyawanCurtarolo method) mclc4() (KPathSetyawanCurtarolo method) mclc5() (KPathSetyawanCurtarolo method) Mcsqs (class in pymatgen.io.atat) Md (Element attribute) md() (LammpsRun class method) md5() (Pseudo method) mean_estimator() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) mean_stress() (Stress property) measure() (in module pymatgen.util.convergence) mehring_values() (ChemicalShielding property) melting_point (Element attribute) (ElementBase attribute) Memory (in module pymatgen.core.units) mendeleev_no (Element attribute) (ElementBase attribute) merge_sites() (Structure method) merge_slabs() (in module pymatgen.analysis.interface) metal_edge_extender() (in module pymatgen.analysis.local_env) metallic_radius() (ElementBase 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) Mgrid (class in pymatgen.io.cp2k.inputs) 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() (ElementBase property) min_slab_size (SlabGenerator attribute) min_vac_size (SlabGenerator attribute) min_voltage() (AbstractElectrode property) mineral_hardness (Element attribute) (ElementBase 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) MO_Cubes (class in pymatgen.io.cp2k.inputs) mode() (Smearing property) ModelDielectricFunction (class in pymatgen.io.abinit.abiobjects) MODELS (EOS attribute) modify_dft_print_iters() (DftSet method) module pymatgen pymatgen.alchemy pymatgen.alchemy.filters pymatgen.alchemy.materials pymatgen.alchemy.transmuters pymatgen.analysis pymatgen.analysis.adsorption pymatgen.analysis.bond_dissociation pymatgen.analysis.bond_valence pymatgen.analysis.chemenv pymatgen.analysis.chemenv.connectivity pymatgen.analysis.chemenv.connectivity.connected_components pymatgen.analysis.chemenv.connectivity.connectivity_finder pymatgen.analysis.chemenv.connectivity.environment_nodes pymatgen.analysis.chemenv.connectivity.structure_connectivity pymatgen.analysis.chemenv.coordination_environments pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies pymatgen.analysis.chemenv.coordination_environments.coordination_geometries pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder pymatgen.analysis.chemenv.coordination_environments.structure_environments pymatgen.analysis.chemenv.coordination_environments.voronoi pymatgen.analysis.chemenv.utils pymatgen.analysis.chemenv.utils.chemenv_config pymatgen.analysis.chemenv.utils.chemenv_errors pymatgen.analysis.chemenv.utils.coordination_geometry_utils pymatgen.analysis.chemenv.utils.defs_utils pymatgen.analysis.chemenv.utils.func_utils pymatgen.analysis.chemenv.utils.graph_utils pymatgen.analysis.chemenv.utils.math_utils pymatgen.analysis.chemenv.utils.scripts_utils pymatgen.analysis.cost pymatgen.analysis.defects pymatgen.analysis.defects.core pymatgen.analysis.defects.corrections pymatgen.analysis.defects.defect_compatibility pymatgen.analysis.defects.dilute_solution_model pymatgen.analysis.defects.generators pymatgen.analysis.defects.thermodynamics pymatgen.analysis.defects.utils pymatgen.analysis.diffraction pymatgen.analysis.diffraction.core pymatgen.analysis.diffraction.neutron pymatgen.analysis.diffraction.tem pymatgen.analysis.diffraction.xrd pymatgen.analysis.diffusion_analyzer pymatgen.analysis.dimensionality pymatgen.analysis.elasticity pymatgen.analysis.elasticity.elastic pymatgen.analysis.elasticity.strain pymatgen.analysis.elasticity.stress pymatgen.analysis.energy_models pymatgen.analysis.eos pymatgen.analysis.ewald pymatgen.analysis.excitation pymatgen.analysis.ferroelectricity pymatgen.analysis.ferroelectricity.polarization pymatgen.analysis.find_dimension pymatgen.analysis.fragmenter pymatgen.analysis.functional_groups pymatgen.analysis.gb pymatgen.analysis.gb.grain pymatgen.analysis.graphs pymatgen.analysis.hhi pymatgen.analysis.interface pymatgen.analysis.interface_reactions pymatgen.analysis.local_env pymatgen.analysis.magnetism pymatgen.analysis.magnetism.analyzer pymatgen.analysis.magnetism.heisenberg pymatgen.analysis.magnetism.jahnteller pymatgen.analysis.molecule_matcher pymatgen.analysis.molecule_structure_comparator pymatgen.analysis.nmr pymatgen.analysis.path_finder pymatgen.analysis.phase_diagram pymatgen.analysis.piezo pymatgen.analysis.piezo_sensitivity pymatgen.analysis.pourbaix_diagram pymatgen.analysis.prototypes pymatgen.analysis.quasiharmonic pymatgen.analysis.reaction_calculator pymatgen.analysis.solar pymatgen.analysis.solar.slme pymatgen.analysis.structure_analyzer pymatgen.analysis.structure_matcher pymatgen.analysis.structure_prediction pymatgen.analysis.structure_prediction.dopant_predictor pymatgen.analysis.structure_prediction.substitution_probability pymatgen.analysis.structure_prediction.substitutor pymatgen.analysis.structure_prediction.volume_predictor pymatgen.analysis.substrate_analyzer pymatgen.analysis.surface_analysis pymatgen.analysis.thermochemistry pymatgen.analysis.topological pymatgen.analysis.topological.spillage pymatgen.analysis.transition_state pymatgen.analysis.wulff pymatgen.analysis.xas pymatgen.analysis.xas.spectrum pymatgen.apps pymatgen.apps.battery pymatgen.apps.battery.analyzer pymatgen.apps.battery.battery_abc pymatgen.apps.battery.conversion_battery pymatgen.apps.battery.insertion_battery pymatgen.apps.battery.plotter pymatgen.apps.borg pymatgen.apps.borg.hive pymatgen.apps.borg.queen pymatgen.cli pymatgen.cli.feff_plot_cross_section pymatgen.cli.feff_plot_dos pymatgen.cli.gaussian_analyzer pymatgen.cli.get_environment pymatgen.cli.pmg pymatgen.cli.pmg_analyze pymatgen.cli.pmg_config pymatgen.cli.pmg_plot pymatgen.cli.pmg_potcar pymatgen.cli.pmg_query pymatgen.cli.pmg_structure pymatgen.command_line pymatgen.command_line.bader_caller pymatgen.command_line.critic2_caller pymatgen.command_line.enumlib_caller pymatgen.command_line.gulp_caller pymatgen.command_line.mcsqs_caller pymatgen.command_line.vampire_caller pymatgen.core pymatgen.core.bonds pymatgen.core.composition pymatgen.core.ion pymatgen.core.lattice pymatgen.core.libxcfunc pymatgen.core.molecular_orbitals pymatgen.core.operations pymatgen.core.periodic_table pymatgen.core.sites pymatgen.core.spectrum pymatgen.core.structure pymatgen.core.surface pymatgen.core.tensors pymatgen.core.trajectory pymatgen.core.units pymatgen.core.xcfunc pymatgen.dao pymatgen.electronic_structure pymatgen.electronic_structure.bandstructure pymatgen.electronic_structure.boltztrap pymatgen.electronic_structure.cohp pymatgen.electronic_structure.core pymatgen.electronic_structure.dos pymatgen.electronic_structure.plotter pymatgen.entries pymatgen.entries.compatibility pymatgen.entries.computed_entries pymatgen.entries.correction_calculator pymatgen.entries.entry_tools pymatgen.entries.exp_entries pymatgen.ext pymatgen.ext.cod pymatgen.ext.crystalsai pymatgen.ext.jhu pymatgen.ext.matproj pymatgen.ext.optimade pymatgen.io pymatgen.io.abinit pymatgen.io.abinit.abiinspect pymatgen.io.abinit.abiobjects pymatgen.io.abinit.abitimer pymatgen.io.abinit.inputs pymatgen.io.abinit.netcdf pymatgen.io.abinit.pseudos pymatgen.io.abinit.variable pymatgen.io.adf pymatgen.io.aiida pymatgen.io.ase pymatgen.io.atat pymatgen.io.babel pymatgen.io.cif pymatgen.io.cp2k pymatgen.io.cp2k.inputs pymatgen.io.cp2k.outputs pymatgen.io.cp2k.sets pymatgen.io.cp2k.utils pymatgen.io.cssr pymatgen.io.cube pymatgen.io.exciting pymatgen.io.exciting.inputs pymatgen.io.feff pymatgen.io.feff.inputs pymatgen.io.feff.outputs pymatgen.io.feff.sets pymatgen.io.fiesta pymatgen.io.gaussian pymatgen.io.jarvis pymatgen.io.lammps pymatgen.io.lammps.data pymatgen.io.lammps.inputs pymatgen.io.lammps.outputs pymatgen.io.lammps.utils pymatgen.io.lmto pymatgen.io.lobster pymatgen.io.lobster.inputs pymatgen.io.lobster.lobsterenv pymatgen.io.lobster.outputs pymatgen.io.nwchem pymatgen.io.phonopy pymatgen.io.prismatic pymatgen.io.pwscf pymatgen.io.qchem pymatgen.io.qchem.inputs pymatgen.io.qchem.outputs pymatgen.io.qchem.sets pymatgen.io.qchem.utils pymatgen.io.shengbte pymatgen.io.vasp pymatgen.io.vasp.help pymatgen.io.vasp.inputs pymatgen.io.vasp.outputs pymatgen.io.vasp.sets pymatgen.io.wannier90 pymatgen.io.xcrysden pymatgen.io.xr pymatgen.io.xyz pymatgen.io.zeopp pymatgen.optimization pymatgen.optimization.linear_assignment pymatgen.optimization.linear_assignment_numpy pymatgen.optimization.neighbors pymatgen.phonon pymatgen.phonon.bandstructure pymatgen.phonon.dos pymatgen.phonon.ir_spectra pymatgen.phonon.plotter pymatgen.settings pymatgen.symmetry pymatgen.symmetry.analyzer pymatgen.symmetry.bandstructure pymatgen.symmetry.groups pymatgen.symmetry.kpath pymatgen.symmetry.maggroups pymatgen.symmetry.settings pymatgen.symmetry.site_symmetries pymatgen.symmetry.structure pymatgen.transformations pymatgen.transformations.advanced_transformations pymatgen.transformations.defect_transformations pymatgen.transformations.site_transformations pymatgen.transformations.standard_transformations pymatgen.transformations.transformation_abc pymatgen.util pymatgen.util.convergence pymatgen.util.coord pymatgen.util.coord_cython pymatgen.util.io_utils pymatgen.util.num pymatgen.util.plotting pymatgen.util.provenance pymatgen.util.sequence pymatgen.util.serialization pymatgen.util.string pymatgen.util.testing pymatgen.util.typing pymatgen.vis pymatgen.vis.plotters pymatgen.vis.structure_chemview pymatgen.vis.structure_vtk

MODULE_DIR (PymatgenTest attribute) molar_volume (Element attribute) (ElementBase 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) (LobsterNeighbors 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 (class in 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) MPScanStaticSet (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) Mt (Element attribute) 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 attribute) Na (Element attribute) Nads_in_slab() (SlabEntry property) name (Author attribute) (HistoryNode attribute) (IonEntry attribute) (PDEntry attribute) name() (Defect property) (DefectEntry property) (InputVariable property) (Interstitial property) (MoleculeGraph property) (MultiEntry property) (PourbaixEntry property) (StructureGraph property) (Substitution property) (Vacancy property) (XcFunc method) names_and_values() (AbinitTimer method) NanoscaleStability (class in pymatgen.analysis.surface_analysis) natoms() (Dynmat property) (Poscar property) (Xdatcar property) natural_keys() (in module pymatgen.io.cp2k.utils) Nb (Element attribute) nb (Wavecar attribute) nb_bands (BandStructure attribute) nb_bands() (Wavederf property) nb_kpoints() (Wavederf property) nbands (Eigenval attribute) nbands() (Waveder property) nbnd (Unk attribute), [1] 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) next_num_with_prime_factors() (in module pymatgen.io.vasp.sets) ng (Unk attribute), [1] ngf (Outcar attribute) ngridpts (VolumetricData attribute) Nh (Element 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() (ElementBase property) nnattr (CriticalPointType 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() (CompositionEnergyAdjustment method) (ComputedEntry method) (ComputedStructureEntry method) (ConstantEnergyAdjustment method) (EnergyAdjustment method) (Entry method) (Spectrum method) (StaticPotential method) (TemperatureEnergyAdjustment method) normalize_to() (BalancedReaction method) normalize_to_element() (BalancedReaction method) normalized_angles() (StructureEnvironments.NeighborsSet property) normalized_cell_intensity() (TEMCalculator method) 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) 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) num_warnings() (Cp2kOutput property) number() (ElementBase 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 (BasePhaseDiagram 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) objective_function (Sqs attribute) obtain_all_bond_lengths() (in module pymatgen.core.bonds) obtain_band_edges() (MolecularOrbitals method) occ (Orbital attribute) occu_tol (Eigenval attribute) OccupancyComparator (class in pymatgen.analysis.structure_matcher) off_color (WulffShape attribute) offset_vector() (Interface property) Og (Element attribute) omega (ChemicalShielding.MarylandNotation attribute) omega() (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_structures (GaussianOutput attribute) opt_template() (QCInput static method) OPTCELL_DEFAULT (RelaxationMethod attribute) optical_absorption_coeff() (Vasprun property) optics() (in module pymatgen.analysis.solar.slme) OptimadeRester (class in pymatgen.ext.optimade) 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) OrbitalTransformation (class in pymatgen.io.cp2k.inputs) OrbitalType (class in pymatgen.electronic_structure.core) orc() (KPathSetyawanCurtarolo method) orcc() (KPathSetyawanCurtarolo method)

orcf1() (KPathSetyawanCurtarolo method) orcf2() (KPathSetyawanCurtarolo method) orcf3() (KPathSetyawanCurtarolo method) orci() (KPathSetyawanCurtarolo 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) orth() (SOCSpillage static method) 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) overlap_so_spinpol() (SOCSpillage method) override_from_prev_calc() (MPHSEBSSet method) (MPNonSCFSet method) (MPScanStaticSet method) (MPSOCSet method) (MPStaticSet method) (MVLGWSet method) OverwriteMagmomMode (class in pymatgen.analysis.magnetism.analyzer) oxi_prob (Composition attribute) oxi_state (DummySpecies attribute) (Specie attribute) (Species attribute) oxi_state() (DummySpecies property) (Species property) oxi_state_guesses() (Composition method) oxidation_states() (ElementBase 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_atomic_kind_info() (Cp2kOutput method) parse_author() (Author static method) parse_cell_params() (Cp2kOutput method) parse_cond_and_hall() (BoltztrapAnalyzer static method) parse_cp2k_params() (Cp2kOutput method) parse_criteria() (MPRester static method) parse_dft_params() (Cp2kOutput method) parse_dielectric_data() (in module pymatgen.analysis.solar.slme) parse_dos() (Cp2kOutput method) (in module pymatgen.io.cp2k.outputs) parse_energies() (Cp2kOutput method) parse_energy_file() (in module pymatgen.io.cp2k.outputs) parse_file() (VolumetricData static method) parse_files() (Cp2kOutput method) parse_forces() (Cp2kOutput method) parse_functions (PotcarSingle attribute) parse_global_params() (Cp2kOutput method) parse_hirshfeld() (Cp2kOutput method) parse_history_node() (HistoryNode static method) parse_homo_lumo() (Cp2kOutput method) parse_initial_structure() (Cp2kOutput method) parse_input() (Cp2kOutput method) parse_intrans() (BoltztrapAnalyzer static method) parse_ionic_steps() (Cp2kOutput method) parse_lammps_dumps() (in module pymatgen.io.lammps.outputs) parse_lammps_log() (in module pymatgen.io.lammps.outputs) parse_magmoms() (CifParser static method) parse_mo_eigenvalues() (Cp2kOutput method) parse_mulliken() (Cp2kOutput method) parse_opt_steps() (Cp2kOutput method) parse_outputtrans() (BoltztrapAnalyzer static method) parse_oxi_states() (CifParser static method) parse_oxide() (OxideType method) parse_scf_opt() (Cp2kOutput method) parse_scf_params() (Cp2kOutput method) parse_stdout() (VampireCaller static method) parse_stresses() (Cp2kOutput method) parse_struct() (BoltztrapAnalyzer static method) parse_structures() (Cp2kOutput method) parse_tddft() (NwOutput method) parse_timing() (Cp2kOutput method) parse_total_numbers() (Cp2kOutput 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) path_lengths() (HighSymmKpath property) path_type() (HighSymmKpath property) 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) PBE (class in pymatgen.io.cp2k.inputs) pcm (GaussianOutput attribute) pcm_template() (QCInput static method) Pd (Element attribute) pd_coords() (BasePhaseDiagram method) pd_plot_data() (PDPlotter property) PDEntry (class in pymatgen.analysis.phase_diagram) PDOS (class in pymatgen.io.cp2k.inputs) pdos (CompleteDos attribute) (CompletePhononDos attribute) (Doscar attribute) (Vasprun attribute) pdos() (Doscar property) PDPlotter (class in pymatgen.analysis.phase_diagram) pefficiency() (AbinitTimerParser method) perform_all_corrections() (DefectCompatibility method) perform_band_edge_shifting() (DefectCompatibility static method) perform_bandfill_corr() (BandFillingCorrection method) perform_bandfilling() (DefectCompatibility static method) perform_es_corr() (FreysoldtCorrection method) (KumagaiCorrection method) perform_freysoldt() (DefectCompatibility static method) perform_kumagai() (DefectCompatibility static 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() (BruteForceOrderMatcher static method) (ExplicitPermutationsAlgorithm property) (GeneticOrderMatcher method) (HungarianOrderMatcher static method) (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) PESScanSet (class in pymatgen.io.qchem.sets) PhaseDiagram (class in pymatgen.analysis.phase_diagram) 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_cohps_of_neighbors() (LobsterNeighbors 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) plots_template() (QCInput static 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) (ElementBase 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() (KPathSetyawanCurtarolo property) prim_rec() (KPathSetyawanCurtarolo property) prime_factors() (in module pymatgen.analysis.chemenv.utils.math_utils) primes_less_than() (in module pymatgen.io.vasp.sets) 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_e_density() (DftSet method) print_forces() (Cp2kInputSet method) print_hartree_potential() (DftSet method) print_help() (VaspDoc method) print_jupyter_help() (VaspDoc method) print_ldos() (DftSet method) print_links() (StructureConnectivity method) print_mo() (DftSet method) print_mo_cubes() (DftSet method) print_motion() (Cp2kInputSet method) print_pdos() (DftSet method) print_periodic_table() (ElementBase static method) 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 static method) (Tags static method) Procar (class in pymatgen.io.vasp.outputs) process_entries() (Compatibility method) (MaterialsProjectAqueousCompatibility 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) project_name() (Cp2kOutput property) projected_eigenvalues (Vasprun attribute) projected_magnetisation (Vasprun attribute) projection() (Magmom property) projectionpoints() (Plane method) projections (BandStructure attribute) properly_terminated (GaussianOutput attribute) properties (Neighbor attribute) (PeriodicNeighbor 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.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.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.tem 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.prototypes module pymatgen.analysis.quasiharmonic module pymatgen.analysis.reaction_calculator module pymatgen.analysis.solar module pymatgen.analysis.solar.slme 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.topological module pymatgen.analysis.topological.spillage 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_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.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.correction_calculator 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.ext.optimade 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.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.cp2k module pymatgen.io.cp2k.inputs module pymatgen.io.cp2k.outputs module pymatgen.io.cp2k.sets module pymatgen.io.cp2k.utils module pymatgen.io.cssr module pymatgen.io.cube 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.jarvis 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.lobster.inputs module pymatgen.io.lobster.lobsterenv module pymatgen.io.lobster.outputs 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.help module pymatgen.io.vasp.inputs module pymatgen.io.vasp.outputs module pymatgen.io.vasp.sets module pymatgen.io.wannier90 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.settings module pymatgen.symmetry module pymatgen.symmetry.analyzer module pymatgen.symmetry.bandstructure module pymatgen.symmetry.groups module pymatgen.symmetry.kpath 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) QS (class in pymatgen.io.cp2k.inputs)

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) ran_successfully() (Cp2kOutput method) 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) ratios() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) Rb (Element attribute) Rcut (OrbitalDescription attribute) Rcut2 (OrbitalDescription attribute) 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_fermi_contact_shift() (Outcar method) read_freq_dielectric() (Outcar method) 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() (Cp2kOutput method) (in module pymatgen.io.qchem.utils) (Outcar method) (PWOutput method) read_pcm() (QCInput static method) read_piezo_tensor() (Outcar method) read_plots() (QCInput static method) read_pseudo_zval() (Outcar method) read_rem() (QCInput static method) read_route_line() (in module pymatgen.io.gaussian) read_scan() (GaussianOutput method), [1] (QCInput static method) read_smx() (QCInput static method) read_solvent() (QCInput static method) read_structure() (ETSF_Reader method) read_table_pattern() (Cp2kOutput method) (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) rec_lattice() (KPathBase 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) reflection() (SymmOp static method) reflectivity (Element attribute) (ElementBase attribute)

refractive_index (Element attribute) (ElementBase attribute) refresh_aliases() (OptimadeRester method) 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) RelaxSet (class in pymatgen.io.cp2k.sets) 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_keywords (Section attribute) required_params (Control attribute) required_sections (Section attribute) rescale_field() (StaticPotential method) respect_sign (OverwriteMagmomMode attribute) respect_zero (OverwriteMagmomMode attribute) restore_site_properties() (PackmolRunner method) results() (EOSBase property) resumes (GaussianOutput attribute) Rf (Element attribute) Rg (Element attribute) Rh (Element attribute) rhl1() (KPathSetyawanCurtarolo method) rhl2() (KPathSetyawanCurtarolo method) rho_rec() (QModel method) rho_rec_limit0() (QModel property) rhombohedral() (Lattice static method) rigidity_modulus (Element attribute) (ElementBase 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) rotation_matrix_vectors() (HungarianOrderMatcher static method) 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() (ElementBase property) Ru (Element attribute) run() (BoltztrapRunner method) (FiestaRun method) (GulpCaller method) (LammpsRunner method) (Nwchem2Fiesta method) (PackmolRunner method) run_mcsqs() (in module pymatgen.command_line.mcsqs_caller) run_stats (Outcar attribute) run_type (AdfOutput attribute) run_type() (Cp2kOutput property) (Vasprun property) run_vasp() (VaspInput method) rxn (ConversionVoltagePair attribute)

S

S (Element attribute) s (Orbital attribute) (OrbitalType attribute) 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) scan_template() (QCInput static method) scatter_hist() (AbinitTimer method) Scf (class in pymatgen.io.cp2k.inputs) 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 (class in pymatgen.io.cp2k.inputs) 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() (Section 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) (DftSet 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) set_volumetric_data() (Wavefunction 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 (Element attribute) 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 attribute) sigma_22 (ChemicalShielding.MehringNotation attribute) sigma_33 (ChemicalShielding.MehringNotation attribute) sigma_from_site_prop() (GrainBoundary property) sigma_iso (ChemicalShielding.HaeberlenNotation attribute) (ChemicalShielding.MarylandNotation attribute) (ChemicalShielding.MehringNotation attribute) silence() (Section method) 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 attribute) site() (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) site_weighted_spectrum() (in module pymatgen.analysis.xas.spectrum) 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) slme() (in module pymatgen.analysis.solar.slme) SlotPickleMixin (class in pymatgen.util.serialization) Sm (Element attribute) Smear (class in pymatgen.io.cp2k.inputs) 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) SOCSpillage (class in pymatgen.analysis.topological.spillage) 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 static method) SpecieProximityFilter (class in pymatgen.alchemy.filters) Species (class in pymatgen.core.periodic_table) species (CorrectionCalculator attribute) species() (Site property) (SiteCollection property) species_and_occu() (Site property) (SiteCollection property) species_by_znucl() (in module pymatgen.io.abinit.abiobjects) 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) spin_polarized() (Cp2kOutput 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) Sqs (class in pymatgen.command_line.mcsqs_caller) SQSTransformation (class in pymatgen.transformations.advanced_transformations) SquareTensor (class in pymatgen.core.tensors) Sr (Element attribute) stable_entries() (BasePhaseDiagram 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) StaticSet (class in pymatgen.io.cp2k.sets) stationary_type (GaussianOutput attribute) stats_article_weights_parameters() (MultiWeightsChemenvStrategy class method) stitch() (XAS method) 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_MODE (Species attribute) (Stringify attribute) string_relax() (NEBPathfinder static method) Stringify (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) (ComputedStructureEntry property) (DictSet property) (KPathBase 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() (Critic2Analysis method) structure_has_clear_environments() (LightStructureEnvironments method) structure_lines() (GulpIO static 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) (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) (LobsterNeighbors 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) 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) Subsys (class in pymatgen.io.cp2k.inputs) 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) (ElementBase attribute) SuperTransformation (class in pymatgen.transformations.advanced_transformations) supported_modes (Kpoints attribute) SUPPORTED_MODES (MVLGWSet attribute) supported_properties (MPRester attribute) (Species 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) (ElementBase attribute) (NthOrderElasticTensor attribute) (PointGroup attribute) (SpaceGroup attribute) (Strain attribute) (Stress attribute) (Tensor attribute) symbol() (DummySpecies 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) tem_dots() (TEMCalculator method) TEMCalculator (class in pymatgen.analysis.diffraction.tem) Temp (in module pymatgen.core.units) temperature (Poscar attribute) TemperatureEnergyAdjustment (class in pymatgen.entries.computed_entries) template_dir (LammpsRun attribute) Tensor (class in pymatgen.core.tensors) TensorCollection (class in pymatgen.core.tensors) TensorMapping (class in pymatgen.core.tensors) term_symbols() (ElementBase property) tersoff_input() (GulpIO method) tersoff_potential() (GulpIO static 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() (KPathSetyawanCurtarolo 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) (ElementBase 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) 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_html_string() (Stringify method) to_input() (GaussianOutput method), [1] to_json() (AdfKey method) (AdfTask method) (LibxcFunc method) to_latex_string() (Stringify method) (SymmetryGroup method) to_lattice() (LammpsBox method) to_matrix() (in module pymatgen.analysis.solar.slme) to_positions() (Trajectory method) to_pretty_string() (Composition method) (Ion method) (Species method) (Stringify 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_unicode_string() (Stringify 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) TransformedPDEntryError TransformedStructure (class in pymatgen.alchemy.materials) TransitionStateSet (class in pymatgen.io.qchem.sets) translate_sites() (Molecule method) (Structure method) TranslateSitesTransformation (class in pymatgen.transformations.site_transformations) translation_vector() (SymmOp property) transparency (WulffShape attribute) tria() (KPathSetyawanCurtarolo method) triangular_coord() (in module pymatgen.analysis.phase_diagram) trib() (KPathSetyawanCurtarolo method) triple_cap_hints() (CoordinationGeometry.NeighborsSetsHints method) true_names (Poscar attribute) Ts (Element attribute) tune_for_gamma() (in module pymatgen.analysis.defects.utils) TWO_THETA_TOL (AbstractDiffractionPatternCalculator attribute) type (MagneticDeformation attribute) Type (OrbitalDescription attribute) type() (CriticalPoint property) (Pseudo property) (XcFunc method) Type2 (OrbitalDescription attribute) 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_magnetic_species() (CollinearMagneticStructureAnalyzer property) types_of_specie() (SiteCollection property) types_of_species() (SiteCollection property)

U

U (Element attribute) ucell_entry (SurfaceEnergyPlotter attribute) UCorrection (class in pymatgen.entries.compatibility) uncertainty() (CompositionEnergyAdjustment property) (EnergyAdjustment property) (TemperatureEnergyAdjustment property) UnconvergedVASPWarning uncorrected_energy() (ComputedEntry property) uncorrected_energy_per_atom() (ComputedEntry property) undo_last_change() (StandardTransmuter method) (TransformedStructure method) uniform_labels() (AbstractMolAtomMapper method) (InchiMolAtomMapper method) (IsomorphismMolAtomMapper method) uniquelines() (in module pymatgen.analysis.phase_diagram) uniquely_determines_coordination_environments() (AbstractChemenvStrategy property) (LightStructureEnvironments property) (LobsterLightStructureEnvironments 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) Unk (class in pymatgen.io.wannier90) Unknown (Ordering attribute) UnknownPotcarWarning unprocessed_entries() (PourbaixDiagram property) unset() (Section method) unstable_entries() (BasePhaseDiagram property) (PourbaixDiagram property) unsym_cs_tensor (Outcar attribute) up (Spin attribute) update() (PBarSafe method) (Section 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_Hartree_Cube (class in pymatgen.io.cp2k.inputs) 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() (ElementBase property) ValenceIonicRadiusEvaluator (class in pymatgen.analysis.local_env) valences() (ValenceIonicRadiusEvaluator property) valid() (Composition property) validate() (MultiGraphCycle method) (SimpleGraphCycle method) value() (CompositionEnergyAdjustment property) (EnergyAdjustment property) (TemperatureEnergyAdjustment property) value_at() (VolumetricData 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) (ElementBase attribute) vars() (AbstractInput property) (BasicAbinitInput property) vasp_type (Wavecar attribute) VaspDoc (class in pymatgen.io.vasp.help) 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) (ElementBase attribute)

verbosity() (Keyword method) (KeywordList method) (Section method) vibrational_free_energy() (QuasiharmonicDebyeApprox method) vibrational_internal_energy() (QuasiharmonicDebyeApprox method) vickers_hardness (Element attribute) (ElementBase 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 attribute), [1] (ConversionVoltagePair attribute) vol_discharge (AbstractVoltagePair attribute), [1] (ConversionVoltagePair attribute) vol_tetra() (in module pymatgen.analysis.local_env) voltage (AbstractVoltagePair attribute), [1] (ConversionVoltagePair attribute) voltage_pairs (AbstractElectrode attribute) 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) 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) Wavefunction (class in pymatgen.io.lobster.outputs) wavelength_rel() (TEMCalculator method) wavenumber() (Xmu property) weight (ConnectedSite attribute) weight() (AngleNbSetWeight method) (AnglePlateauNbSetWeight method) (CNBiasNbSetWeight method) (Composition 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 attribute) working_ion() (AbstractElectrode property) (AbstractVoltagePair property) working_ion_entry (AbstractElectrode attribute), [1] (AbstractVoltagePair attribute), [1] (ConversionVoltagePair attribute) 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) (Cp2kInput 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) (Unk method) (VolumetricData method) (Wavefunction 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 static 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_unks() (Wavecar 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 (DummySpecies attribute) X() (DummySpecies property) (ElementBase property) x() (PeriodicSite property) (Site property) x_charge() (AbstractElectrode property) (AbstractVoltagePair property) x_discharge() (AbstractElectrode property) (AbstractVoltagePair property) x_ray_factors() (TEMCalculator method) XAS (class in pymatgen.analysis.xas.spectrum) XC_FUNCTIONAL (class in pymatgen.io.cp2k.inputs)

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) (ElementBase attribute)

Z

Z (DummySpecies attribute) (Element attribute) (ElementBase attribute) Z() (DummySpecies 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) zeta (ChemicalShielding.HaeberlenNotation attribute) zlist() (PseudoTable property) Zn (Element attribute) zone_axis_filter() (TEMCalculator method) zoom() (StructureVis method) Zr (Element attribute) ZSLGenerator (class in pymatgen.analysis.substrate_analyzer) zval_dict_from_potcar() (in module pymatgen.analysis.ferroelectricity.polarization)