Index

A

a (Wavecar attribute) a() (Kpoint property) (Lattice property) (PeriodicSite property) (Plane property) ab_shift() (Interface property) abc() (Lattice property) abcd() (Plane property) abi_extensions() (in module pymatgen.io.abinit.utils) abi_splitext() (in module pymatgen.io.abinit.utils) abinit_build (TaskManager attribute) AbinitBuild (class in pymatgen.io.abinit.tasks) abinitixc_to_libxc (XcFunc attribute) AbinitTask (class in pymatgen.io.abinit.tasks) AbinitTimer (class in pymatgen.io.abinit.abitimer) AbinitTimerParser (class in pymatgen.io.abinit.abitimer) AbinitTimerParserError AbinitTimerSection (class in pymatgen.io.abinit.abitimer) abiopen() (FileNode method) abivalidate_inputs() (Flow method) AbivarAble (class in pymatgen.io.abinit.abiobjects) abs_cap() (in module pymatgen.util.num) AbstractChemenvAlgorithm (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) AbstractChemenvError AbstractChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) AbstractComparator (class in pymatgen.analysis.structure_matcher) AbstractDiffractionPatternCalculator (class in pymatgen.analysis.diffraction.core) AbstractDrone (class in pymatgen.apps.borg.hive) AbstractElectrode (class in pymatgen.apps.battery.battery_abc) AbstractError (class in pymatgen.io.abinit.scheduler_error_parsers) AbstractErrorParser (class in pymatgen.io.abinit.scheduler_error_parsers) AbstractFeffInputSet (class in pymatgen.io.feff.sets) AbstractGeometry (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) AbstractMolAtomMapper (class in pymatgen.analysis.molecule_matcher) AbstractRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) AbstractStructureFilter (class in pymatgen.alchemy.filters) AbstractTransformation (class in pymatgen.transformations.transformation_abc) AbstractVoltagePair (class in pymatgen.apps.battery.battery_abc) AC (AbstractChemenvStrategy attribute) (DetailedVoronoiContainer attribute) (DistanceAngleAreaNbSetWeight attribute) Ac (Element attribute) AC (StructureEnvironments attribute) AconvaspError actual_kpoints (Vasprun attribute) actual_kpoints_weights (Vasprun attribute) add() (EntrySet method) add_adsorbate() (AdsorbateSiteFinder method) add_adsorbate_atom() (Slab method) add_bonds() (StructureVis method) add_charges_from_oxi_state_guesses() (Composition method) add_cohp() (CohpPlotter method) add_cohp_dict() (CohpPlotter method) add_comment() (ScriptEditor method) add_config_var() (in module pymatgen.cli.pmg_config) add_coord_geom() (ChemicalEnvironments method) add_densities() (in module pymatgen.electronic_structure.dos) add_deps() (Node method) 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_emptyline() (ScriptEditor method) add_error() (ParalHintsParser method) add_faces() (StructureVis method) add_fig_kwargs() (in module pymatgen.util.plotting) add_filechild() (FileNode method) add_flow() (PyFlowScheduler method) add_gg_gap() (in module pymatgen.io.abinit.helpers) add_hydrogen() (BabelMolAdaptor method) add_label_cycle() (CyclesPlotter method) add_line() (ScriptEditor method) (StructureVis method) add_lines() (ScriptEditor 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_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) AddSitePropertyTransformation (class in pymatgen.transformations.site_transformations) AdfInput (class in pymatgen.io.adf) AdfInputError AdfKey (class in pymatgen.io.adf) AdfOutput (class in pymatgen.io.adf) AdfOutputError AdfTask (class in pymatgen.io.adf) adsorb_both_surfaces() (AdsorbateSiteFinder method) adsorbates (SlabEntry attribute) AdsorbateSiteFinder (class in pymatgen.analysis.adsorption) affine_matrix (SymmOp attribute) AflowPrototypeMatcher (class in pymatgen.analysis.aflow_prototypes) AFM (Ordering attribute) Ag (Element attribute) AiidaStructureAdaptor() (in module pymatgen.io.aiida) Al (Element attribute) ALGO_BEST_FIRST (EwaldMinimizer attribute) (OrderDisorderedStructureTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) ALGO_COMPLETE (EwaldMinimizer attribute) (OrderDisorderedStructureTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) ALGO_ENUMERATE (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) ALGO_FAST (EwaldMinimizer attribute) (OrderDisorderedStructureTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) ALGO_TIME_LIMIT (EwaldMinimizer attribute) algorithm_type() (AbstractChemenvAlgorithm property) algorithms() (CoordinationGeometry property) aliases() (XcFunc class method) align_x() (in module pymatgen.analysis.interface) ALL (AdditionalConditions attribute) all_combinations_for_elements() (PseudoTable method) all_comp() (BalancedReaction property) all_distances() (in module pymatgen.util.coord) all_docs_with_tag() (YamlTokenizer method) all_done() (Work property) all_energies() (Oszicar property) all_entries() (ComputedReaction property) (PourbaixDiagram property) all_entries_hulldata() (PhaseDiagram property) all_families (LibxcFunc attribute) all_input() (AbstractFeffInputSet method) (VaspInputSet property) all_kinds (LibxcFunc attribute) all_molecules() (XYZ property) all_ok() (Flow property) all_slab_entries (SurfaceEnergyPlotter attribute) all_stable_entries() (DefectPhaseDiagram property) ALL_STATUS (Node attribute) all_status_strings() (Status class method) all_unstable_entries() (DefectPhaseDiagram property) all_yaml_docs() (YamlTokenizer method) AllCoordinationGeometries (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) allnc() (PseudoTable property) allocate() (Flow method) (Work method) allocated() (Flow property) allocations_keys (Control attribute) ALLOWED_FUNCTIONS (AbstractRatioFunction attribute) (CSMFiniteRatioFunction attribute) (CSMInfiniteRatioFunction attribute) (DeltaCSMRatioFunction attribute) (RatioFunction attribute) ALLOWED_HINTS_TYPES (CoordinationGeometry.NeighborsSetsHints attribute) allowed_values (AdditionalConditionInt attribute) (AngleCutoffFloat attribute) (CSMFloat attribute) (DistanceCutoffFloat attribute) (StrategyOption attribute) allpaw() (PseudoTable property) almost_equals() (Composition method) along_c (WorkFunctionAnalyzer attribute) alpha (WulffShape attribute) alpha() (Lattice property) alphabetical_formula() (Composition property) (Ion property) alter_edge() (MoleculeGraph method) (StructureGraph method) alternate() (in module pymatgen.io.abinit.abitimer) Am (Element attribute) amount_tol (CompoundPhaseDiagram attribute) amount_tolerance (Composition attribute) AnaddbTask (class in pymatgen.io.abinit.tasks) analyze() (in module pymatgen.cli.pmg_analyze) (VoronoiAnalyzer method) analyze_localenv() (in module pymatgen.cli.pmg_structure) analyze_structures() (in module pymatgen.cli.pmg_structure) (VoronoiAnalyzer method) analyze_symmetry() (in module pymatgen.cli.pmg_structure) (TopographyAnalyzer method) ang() (NormalizedAngleDistanceNbSetWeight method) ang_to_bohr (in module pymatgen.core.units) anginvdist() (NormalizedAngleDistanceNbSetWeight method) anginvndist() (NormalizedAngleDistanceNbSetWeight method) angle_cutoff() (SimplestChemenvStrategy property) angle_plateau() (StructureEnvironments.NeighborsSet method) angle_sum() (AngleNbSetWeight method) angle_sumn() (AngleNbSetWeight method) AngleCutoffFloat (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) AngleNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) AnglePlateauNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) angles() (Lattice property) (StructureEnvironments.NeighborsSet property) angn() (NormalizedAngleDistanceNbSetWeight method) angninvdist() (NormalizedAngleDistanceNbSetWeight method) angninvndist() (NormalizedAngleDistanceNbSetWeight method) AnionCorrection (class in pymatgen.entries.compatibility) anisotropy() (WulffShape property) anonymized_formula() (Composition property) (Ion property) anticlockwise_sort() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) anticlockwise_sort_indices() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) any2mb() (in module pymatgen.io.abinit.qutils) aos (MolecularOrbitals attribute) aos_as_list() (MolecularOrbitals method) append() (Molecule method) (Structure method) append_filter() (TransformedStructure method) append_transformation() (StandardTransmuter method) (TransformedStructure method) append_transformed_structures() (StandardTransmuter method) application_adapter_solutions() (AbstractError property) (MemoryCancelError property) (TimeCancelError property) apply_corrections() (SchedulerErrorHandler method) apply_filter() (StandardTransmuter method) apply_getters() (Dependency method) apply_operation() (Molecule method) (Structure method) apply_rotation_only() (SymmOp method) apply_scissor() (BandStructureSymmLine method) (LobsterBandStructureSymmLine method) apply_strain() (Structure method) apply_tags() (MultiStructuresVis method) apply_to_structure() (Deformation method) apply_transformation() (AbstractTransformation method) (AddAdsorbateTransformation method) (AddSitePropertyTransformation method) (AutoOxiStateDecorationTransformation method) (ChargeBalanceTransformation method) (ChargedCellTransformation method) (ConventionalCellTransformation method) (CubicSupercellTransformation method) (DefectTransformation method) (DeformStructureTransformation method) (DiscretizeOccupanciesTransformation method) (DisorderOrderedTransformation method) (DopingTransformation method) (EnumerateStructureTransformation method) (GrainBoundaryTransformation method) (InsertSitesTransformation method) (InterfaceBuilder method) (MagOrderingTransformation method) (MultipleSubstitutionTransformation method) (OrderDisorderedStructureTransformation method) (OxidationStateDecorationTransformation method) (OxidationStateRemovalTransformation method) (PartialRemoveSitesTransformation method) (PartialRemoveSpecieTransformation method) (PerturbStructureTransformation method) (PrimitiveCellTransformation method) (RemoveSitesTransformation method) (RemoveSpeciesTransformation method) (ReplaceSiteSpeciesTransformation method) (RotationTransformation method) (SQSTransformation method) (ScaleToRelaxedTransformation method) (SlabTransformation method) (SubstituteSurfaceSiteTransformation method) (SubstitutionPredictorTransformation method) (SubstitutionTransformation method) (SuperTransformation method) (SupercellTransformation 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_bool() (in module pymatgen.io.abinit.utils) as_condition() (Condition class method) as_dict() (AbstractChemenvAlgorithm method) (AbstractChemenvStrategy method) (AbstractComparator method) (AdditionalConditionInt method) (AdfKey method) (AdfTask method) (AngleCutoffFloat method) (AngleNbSetWeight method) (AnglePlateauNbSetWeight method) (Author method) (BSVasprun method) (BalancedReaction method) (BandStructure method) (BandStructureSymmLine method) (BoltztrapAnalyzer method) (BoltztrapRunner method) (CNBiasNbSetWeight method) (CSMFloat method) (ChemicalEnvironments method) (CifParser method) (Cohp method) (CompleteCohp method) (CompleteDos method) (CompletePhononDos method) (Composition method) (CompoundPhaseDiagram method) (ComputedEntry method) (ComputedReaction method) (ComputedStructureEntry method) (ContainsSpecieFilter method) (Control method) (ConversionElectrode method) (ConversionVoltagePair method) (CoordinationGeometry method) (CoordinationGeometry.NeighborsSetsHints method) (Correction method) (DefectEntry method) (DefectPhaseDiagram method) (DeltaCSMNbSetWeight method) (DeltaDistanceNbSetWeight method) (DetailedVoronoiContainer method) (DiffusionAnalyzer method) (DilatmxErrorHandler method) (DistanceAngleAreaNbSetWeight method) (DistanceCutoffFloat method) (DistanceNbSetWeight method) (DistancePlateauNbSetWeight method) (Dos method) (DummySpecie method) (Eels method) (Electrons method) (ElectronsAlgorithm method) (Element method) (EntrySet method) (EwaldElectrostaticModel method) (ExpEntry method) (ExplicitPermutationsAlgorithm property) (FermiDos method) (FiestaInput method) (Fiesta_run method) (Flow method) (GaussianInput method) (GaussianOutput method) (GaussianToComputedEntryDrone method) (GrainBoundary method) (GrandPotPDEntry method) (GrandPotentialPhaseDiagram method) (HistoryNode method) (HistoryRecord method) (IMolecule method) (IStructure method) (Incar method) (InchiMolAtomMapper method) (InsertionElectrode method) (Interface method) (Ion method) (IonEntry method) (IsingModel method) (IsomorphismMolAtomMapper method) (KSampling method) (Kpoint method) (Kpoints method) (LMTOCtrl method) (LammpsData method) (LammpsDump method) (Lattice method) (LibxcFunc method) (LightStructureEnvironments method) (LightStructureEnvironments.NeighborsSet method) (LobsterBandStructureSymmLine method) (Lobsterin method) (MVLSlabSet method) (MagSymmOp method) (MoleculeGraph method) (MoleculeMatcher method) (MoleculeStructureComparator method) (MultiEntry method) (MultiWeightsChemenvStrategy method) (NEBAnalysis method) (NbSetWeight method) (NodeResults method) (NormalizedAngleDistanceNbSetWeight method) (NsitesModel method) (NwInput method) (NwTask method) (Nwchem2Fiesta method) (Oszicar method) (Outcar method) (PDEntry method) (PPModel method) (PWInput method) (ParalHints method) (PeriodicSite method) (PhaseDiagram method) (PhononBandStructure method) (PhononBandStructureSymmLine method) (PhononDos method) (Poscar method) (Potcar method) (PourbaixDiagram method) (PourbaixEntry method) (Pseudo method) (PseudoTable method) (QCOutput method) (Reaction method) (RelaxationMethod method) (RemoveExistingFilter method) (SelfCSMNbSetWeight method) (SeparationPlane property) (SimpleAbundanceChemenvStrategy method) (SimpleVaspToComputedEntryDrone method) (SimplestChemenvStrategy method) (Site method) (Slab method) (SlabEntry method) (Smearing method) (Specie method) (SpecieProximityFilter method) (SpinMode method) (StrategyOption method) (StructureEnvironments method) (StructureEnvironments.NeighborsSet method) (StructureGraph method) (StructureMatcher method) (StructureNL method) (Substitutor method) (SymmOp method) (SymmetryModel method) (Tags method) (TargettedPenaltiedAbundanceChemenvStrategy method) (TaskManager method) (Tensor method) (TensorCollection method) (ThermoData method) (Trajectory method) (TransformedPDEntry method) (TransformedStructure method) (TranslateSitesTransformation method) (VaspInput method) (VaspInputSet method) (VaspToComputedEntryDrone method) (Vasprun method) (WeightedNbSetChemenvStrategy method) (XcFunc method) (Xmu method) (YamlDoc method) as_dict_summary() (InsertionElectrode method) as_entry() (BalancedReaction method) as_etsfreader() (in module pymatgen.io.abinit.netcdf) as_flow() (Flow class method) as_manager() (TaskManager class method) as_ncreader() (in module pymatgen.io.abinit.netcdf) as_node() (Node class method) 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_status() (Status class method) as_table() (PseudoTable class method) as_tmpfile() (Pseudo method) as_xyz_string() (SymmOp method) as_xyzt_string() (MagSymmOp method) asctime (HistoryRecord attribute) 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) assertMSONable() (PymatgenTest method) assign_selective_dynamics() (AdsorbateSiteFinder method) assign_site_properties() (AdsorbateSiteFinder method) assimilate() (AbstractDrone method) (GaussianToComputedEntryDrone method) (SimpleVaspToComputedEntryDrone method) (VaspToComputedEntryDrone method) asxc() (XcFunc class method) asymmetry() (ElectricFieldGradient property) At (Element attribute) atom_basis_labels (GaussianOutput attribute) atomic_background() (Eels property) atomic_mass (Element attribute) atomic_mass() (Element property) atomic_no() (PotcarSingle property) atomic_numbers() (SiteCollection property) atomic_orbitals (Element attribute) atomic_radius (Element attribute) atomic_radius() (Element property) atomic_radius_calculated (Element attribute) atomic_symbols (Vasprun attribute) AtomicFile (class in pymatgen.util.io_utils) Atoms (class in pymatgen.io.feff.inputs) atoms() (AbstractFeffInputSet property) (FEFFDictSet property) atoms_and_cell() (RelaxationMethod class method) atoms_only() (RelaxationMethod class method) atoms_string_from_file() (Atoms static method) attribute (PDEntry attribute) Au (Element attribute) Author (class in pymatgen.util.provenance) auto_load() (ChemEnvConfig class method) autodoc() (DBConnector class method) (PyFlowScheduler class method) (TaskManager 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) autoparal_run() (AbinitTask method) (OpticTask method) AVAILABLE_RADIATION (XRDCalculator attribute) available_strategies (MagneticStructureEnumerator attribute) AVAILABLEKEYWORDS (Lobsterin attribute) ave_bulk_p (WorkFunctionAnalyzer attribute) ave_locpot (WorkFunctionAnalyzer attribute) average_anionic_radius (Element attribute) average_anionic_radius() (Element property) average_cationic_radius (Element attribute) average_cationic_radius() (Element property) average_coordination_number() (in module pymatgen.analysis.structure_analyzer) average_electroneg() (Composition property) average_ionic_radius (Element attribute) average_ionic_radius() (Element property) average_over_unit_sphere() (Tensor method) aweight() (NormalizedAngleDistanceNbSetWeight method) axis_off (WulffShape attribute)

B

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

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

C

C (Element attribute) c() (Kpoint property) (Lattice property) (PeriodicSite property) (Plane property) Ca (Element attribute) cage (CriticalPointType attribute) cahill_thermalcond() (ElasticTensor method) calc() (Xmu property) calc_ionic() (in module pymatgen.analysis.ferroelectricity.polarization) calculate() (SubstrateAnalyzer method) calculate_3D_elastic_energy() (SubstrateAnalyzer method) calculate_bv_sum() (in module pymatgen.analysis.bond_valence) calculate_bv_sum_unordered() (in module pymatgen.analysis.bond_valence) calculate_dimensionality_of_site() (in module pymatgen.analysis.dimensionality) calculate_energy() (BalancedReaction method) calculate_stress() (ElasticTensorExpansion method) (NthOrderElasticTensor method) calculate_vol() (in module pymatgen.analysis.defects.utils) calculate_weighted_avg() (in module pymatgen.analysis.local_env) calculated_reaction_energy() (ComputedReaction property) callback() (PyFlowScheduler method) can_change_physics (DilatmxErrorHandler attribute) cancel() (Flow method) (TaskManager method) cart_coords() (Kpoint property) (SiteCollection property) cart_forces (GaussianOutput attribute) Cartesian (Kpoints_supported_modes attribute) categorize_functional_groups() (FunctionalGroupExtractor method) cbk_qptdm_workflow() (G0W0WithQptdmFlow method) Cd (Element attribute) cder_data() (Waveder property) Ce (Element attribute) ce_symbol() (CoordinationGeometry property) center_of_mass() (IMolecule property) (Slab property) center_slab (SlabGenerator attribute) center_slab() (in module pymatgen.core.surface) Cf (Element attribute) change_z_shift() (Interface method) changebasis() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) Charge (class in pymatgen.io.lobster) charge (GaussianOutput attribute) Charge (in module pymatgen.core.units) charge (Outcar attribute) charge() (Defect property) (DefectEntry property) (IMolecule property) (IStructure property) (Ion property) (SiteCollection property) charge_distribution_df() (ChargeDensityAnalyzer property) CHARGE_NEUTRALITY_TOLERANCE (BVAnalyzer attribute) charge_transfer_from_file() (LDos static method) charge_transfer_to_string() (LDos method) ChargeBalanceFilter (class in pymatgen.alchemy.filters) ChargeBalanceTransformation (class in pymatgen.transformations.advanced_transformations) ChargedCellTransformation (class in pymatgen.transformations.standard_transformations) ChargeDensityAnalyzer (class in pymatgen.analysis.defects.utils) check() (SchedulerErrorHandler method) check_acc_bzt_bands() (BoltztrapAnalyzer static method) check_condition() (AdditionalConditions method) check_dependencies() (Flow method) check_final_relaxed_structure_delocalized() (DefectCompatibility method) check_for_structure_changes() (in module pymatgen.io.qchem.outputs) check_freysoldt_delocalized() (DefectCompatibility method) check_input() (in module pymatgen.analysis.defects.dilute_solution_model) check_kumagai_delocalized() (DefectCompatibility method) check_mappings() (in module pymatgen.core.units) check_params() (Incar method) check_pid_file() (Flow method) check_spectator() (in module pymatgen.io.abinit.nodes) check_status() (FileNode method) (Flow method) (Node method) (Work method) check_volume() (TopographyAnalyzer method) chemenv_citations() (in module pymatgen.analysis.chemenv.utils.defs_utils) ChemEnvConfig (class in pymatgen.analysis.chemenv.utils.chemenv_config) ChemenvError ChemenvStrategyError chemical_shielding (Outcar attribute) chemical_symbols (ETSF_Reader attribute) chemical_system() (Composition property) ChemicalEnvironments (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) ChemicalPotential (class in pymatgen.core.composition) ChemicalShielding (class in pymatgen.analysis.nmr) ChemicalShielding.MarylandNotation (class in pymatgen.analysis.nmr) ChemicalShielding.MehringNotation (class in pymatgen.analysis.nmr) chempot_plot_addons() (SurfaceEnergyPlotter method) chempot_vs_gamma() (SurfaceEnergyPlotter method) chempot_vs_gamma_plot_one() (SurfaceEnergyPlotter method) chemsys() (EntrySet property) Chgcar (class in pymatgen.io.vasp.outputs) ChgcarPotential (class in pymatgen.analysis.path_finder) chi() (Xmu property) chmod() (File method) chroot() (Flow method) (Work method) chunks() (Work method) CifBlock (class in pymatgen.io.cif) CifFile (class in pymatgen.io.cif) CifParser (class in pymatgen.io.cif) CifTransmuter (class in pymatgen.alchemy.transmuters) CifWriter (class in pymatgen.io.cif) Cl (Element attribute) clarke_thermalcond() (ElasticTensor method) ClassTypeChemenvError clean() (Directory method) (in module pymatgen.io.abinit.helpers) clean_lines() (in module pymatgen.util.io_utils) cleaned_up_slab() (SlabEntry property) cleanup() (PyFlowScheduler method) clear_environments() (LightStructureEnvironments method) close() (AtomicFile method) (NetcdfReader method) (YamlTokenizer method) closestsites() (in module pymatgen.analysis.defects.utils) cluster() (Atoms property) cluster_from_file() (Atoms static method) cluster_nodes() (ChargeDensityAnalyzer method) (TopographyAnalyzer method) cluster_sites() (in module pymatgen.symmetry.analyzer) Cm (Element attribute) cn() (AbstractGeometry property) CNBiasNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) Co (Element attribute) COD (class in pymatgen.ext.cod) coefficient_of_linear_thermal_expansion (Element attribute) coefficients() (Plane property) coeffs (Wavecar attribute) coeffs() (BalancedReaction property) Cohp (class in pymatgen.electronic_structure.cohp) Cohpcar (class in pymatgen.io.lobster) CohpPlotter (class in pymatgen.electronic_structure.plotter) coincidents() (GrainBoundary property) collinear() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) CollinearMagneticStructureAnalyzer (class in pymatgen.analysis.magnetism.analyzer) color_area (WulffShape attribute) color_dict (SurfaceEnergyPlotter attribute) color_hex (Node attribute) color_opts() (Status property) color_palette_dict() (SurfaceEnergyPlotter method) color_rgb (AnaddbTask attribute) (DdkTask attribute) (ElasticTask attribute) (EphTask attribute) (FileNode attribute) (Node attribute) (NscfTask attribute) (OpticTask attribute) (PhononTask attribute) (RelaxTask attribute) (ScfTask attribute) (SigmaTask attribute) color_set (WulffShape attribute) colored() (Status property) colours (StringColorizer attribute) combine_neb_plots() (in module pymatgen.analysis.transition_state) combine_slabs() (InterfaceBuilder method) CombinedData (class in pymatgen.io.lammps.data) combiplot() (CyclesPlotter method) comment (Poscar attribute) (Xdatcar attribute) common_oxidation_states (Element attribute) common_oxidation_states() (Element property) compare_structures() (in module pymatgen.cli.pmg_structure) compare_sym_bands() (in module pymatgen.electronic_structure.boltztrap) compare_version() (AbinitBuild method)

Compatibility (class in pymatgen.entries.compatibility) CompatibilityError complete_dos() (Vasprun property) complete_ordering() (PartialRemoveSitesTransformation method) CompleteCohp (class in pymatgen.electronic_structure.cohp) CompleteDos (class in pymatgen.electronic_structure.dos) completedos (Doscar attribute) completedos() (Doscar property) CompletePhononDos (class in pymatgen.phonon.dos) compliance_tensor() (ElasticTensor property) ComplianceTensor (class in pymatgen.analysis.elasticity.elastic) Composition (class in pymatgen.core.composition) composition (MolecularOrbitals attribute) (PDEntry attribute) composition() (ConversionElectrode property) (Ion property) (PourbaixEntry property) (SiteCollection property) composition_prediction() (SubstitutionPredictor method) CompositionError CompoundPhaseDiagram (class in pymatgen.analysis.phase_diagram) compute_average_oxidation_state() (in module pymatgen.analysis.ewald) compute_coordination_environments() (LocalGeometryFinder method) compute_defect_density() (in module pymatgen.analysis.defects.dilute_solution_model) compute_environments() (in module pymatgen.analysis.chemenv.utils.scripts_utils) compute_md5() (Pseudo method) compute_partial_energy() (EwaldSummation 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 (class in pymatgen.io.abinit.utils) 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) (MPXANESSet attribute) (MVLGWSet attribute) (MVLRelax52Set attribute) configure_pmg() (in module pymatgen.cli.pmg_config) connect_signals() (Flow method) ConnectedSite (class in pymatgen.analysis.graphs) connecting_vars() (Dependency method) (Product method) connectivity_array() (VoronoiConnectivity property) Constraints (class in pymatgen.io.abinit.abiobjects) contains_element_type() (Composition method) contains_only_one_anion() (LightStructureEnvironments method) contains_only_one_anion_atom() (LightStructureEnvironments method) contains_peroxide() (in module pymatgen.analysis.structure_analyzer) ContainsSpecieFilter (class in pymatgen.alchemy.filters) continuous_symmetry_measure_cutoff() (SimplestChemenvStrategy property) contract() (in module pymatgen.io.abinit.abiobjects) Control (class in pymatgen.io.shengbte) CONV_FACT (EwaldSummation attribute) conventional() (HighSymmKpath property) ConventionalCellTransformation (class in pymatgen.transformations.standard_transformations) converge() (in module pymatgen.analysis.defects.utils) converged() (Vasprun property) converged_electronic() (Vasprun property) converged_ionic() (Vasprun property) ConversionElectrode (class in pymatgen.apps.battery.conversion_battery) conversions() (ArrayWithUnit method) ConversionVoltagePair (class in pymatgen.apps.battery.conversion_battery) convert_fmt() (in module pymatgen.cli.pmg_structure) convert_obatoms_to_molecule() (PackmolRunner method) convert_strain_to_deformation() (in module pymatgen.analysis.elasticity.strain) convert_to_ieee() (Tensor method) (TensorCollection method) coord_list_mapping() (in module pymatgen.util.coord) coord_list_mapping_pbc() (in module pymatgen.util.coord) (in module pymatgen.util.coord_cython) coordination() (VoronoiPolyhedron property) coordination_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) CoordinationGeometry (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) CoordinationGeometry.NeighborsSetsHints (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) coords() (PeriodicSite property) (Simplex property) (StructureEnvironments.NeighborsSet property) copy() (Composition method) (Defect method) (DefectEntry method) (GrainBoundary method) (IStructure method) (Interface method) (Lattice method) (Molecule method) (ParalHints method) (Reaction method) (Slab method) (Spectrum method) (Trajectory method) copy_abiext() (Directory method) copy_r() (Directory method) correct() (SchedulerErrorHandler method) correct_entry() (Correction method) (DefectCorrection method) corrected_compound_formulas() (EntryPostProcessor property) Correction (class in pymatgen.entries.compatibility) (class in pymatgen.io.abinit.events) corrections (GaussianOutput attribute) corrections() (Node property) CorrectorProtocolApplication (class in pymatgen.io.abinit.scheduler_error_parsers) CorrectorProtocolScheduler (class in pymatgen.io.abinit.scheduler_error_parsers) cosinus_step() (in module pymatgen.analysis.chemenv.utils.math_utils) CostAnalyzer (class in pymatgen.analysis.cost.cost) CostDB (class in pymatgen.analysis.cost.cost) CostDBCSV (class in pymatgen.analysis.cost.cost) CostEntry (class in pymatgen.analysis.cost.cost) coth() (in module pymatgen.phonon.dos) coupling_constant() (ElectricFieldGradient method) CovalentBond (class in pymatgen.core.bonds) CovalentBondNN (class in pymatgen.analysis.local_env) CovalentRadius (class in pymatgen.analysis.molecule_structure_comparator) cpuwall_histogram() (AbinitTimer method) Cr (Element attribute) create_saturated_interstitial_structure() (in module pymatgen.analysis.defects.core) create_slab_label() (SlabEntry property) create_tasks() (QptdmWork method) created (HistoryRecord attribute) Critic2Caller (class in pymatgen.command_line.critic2_caller) Critic2NN (class in pymatgen.analysis.local_env) Critic2Output (class in pymatgen.command_line.critic2_caller) critical() (NodeHistory method) CRITICAL_EVENTS (NscfTask attribute) (RelaxTask attribute) (ScfTask attribute) (SigmaTask attribute) critical_temp (VampireOutput attribute) critical_temperature (Element attribute) CriticalPoint (class in pymatgen.command_line.critic2_caller) CriticalPointType (class in pymatgen.command_line.critic2_caller) crosses_origin() (Plane property) crystal_keys (Control attribute) CrystalAIRester (class in pymatgen.ext.crystalsai) CrystalNN (class in pymatgen.analysis.local_env) Cs (Element attribute) cs_core_contribution (Outcar attribute) cs_g0_contribution (Outcar attribute) csm_skip_algo() (CoordinationGeometry property) CSM_SKIP_SEPARATION_PLANE_ALGO (CoordinationGeometry attribute) CSMFiniteRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) CSMFloat (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) CSMInfiniteRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) Cssr (class in pymatgen.io.cssr) Cu (Element attribute) cubic() (HighSymmKpath method) (Lattice static method) CubicSupercellTransformation (class in pymatgen.transformations.advanced_transformations) CutOffDictNN (class in pymatgen.analysis.local_env) cv() (PhononDos method) cycle_class (AbinitTask attribute) CyclesPlotter (class in pymatgen.io.abinit.abiinspect)

D

d (OrbitalType attribute) d() (Plane property) D2DEScfCycle (class in pymatgen.io.abinit.abiinspect) d_hkl() (Lattice method) data (Dynmat attribute) (PotcarSingle attribute) (Procar attribute) (Wavederf attribute) data() (Element property) db_insert() (Flow method) DBConnector (class in pymatgen.io.abinit.db) ddb_filepath() (AnaddbTask property) ddk_filepath() (AnaddbTask property) ddk_filepaths() (OpticTask property) DdkTask (class in pymatgen.io.abinit.tasks) debug (WulffShape attribute) debug() (Flow method) debye_integral() (QuasiharmonicDebyeApprox static method) debye_temperature() (ElasticTensor method) (QuasiharmonicDebyeApprox method) debye_temperature_from_sound_velocities() (ElasticTensor method) declare_var() (ScriptEditor method) declare_vars() (ScriptEditor method) decrease_mem() (CorrectorProtocolApplication method) deepcopy() (DBConnector method) (TaskManager 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_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_matrix() (Strain property) DeformedStructureSet (class in pymatgen.analysis.elasticity.strain) DeformStructureTransformation (class in pymatgen.transformations.standard_transformations) delete_snl() (MPRester method) delocalization_analysis() (DefectCompatibility method) delta_cn_specifics() (DeltaCSMNbSetWeight class method) DELTA_MAX_OXIDATION_STATE (LightStructureEnvironments attribute) DeltaCSMNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DeltaCSMRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) DeltaDistanceNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DeltaFactor (class in pymatgen.analysis.eos) density() (IStructure property) density_of_solid (Element attribute) Dependency (class in pymatgen.io.abinit.nodes) depends_on() (Node method) deps() (Node property) deps_status() (Node property) description (AdditionalConditionInt attribute) (HistoryNode attribute) det() (SquareTensor property) DetailedVoronoiContainer (class in pymatgen.analysis.chemenv.coordination_environments.voronoi) determine_convergence() (in module pymatgen.util.convergence)

determine_min_cell() (MagOrderingTransformation static method) dev_principal_invariants() (Stress property) deviator_stress() (Stress property) dft_task() (NwTask class method) diamond_functions() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) DictSet (class in pymatgen.io.vasp.sets) dielectric (Vasprun attribute) 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) DilatmxError (class in pymatgen.io.abinit.events) DilatmxErrorHandler (class in pymatgen.io.abinit.events) dipole() (Slab property) directional_elastic_mod() (ElasticTensor method) directional_poisson_ratio() (ElasticTensor method) Directory (class in pymatgen.io.abinit.utils) dirname() (File property) Dirviz (class in pymatgen.io.abinit.utils) disassemble() (LammpsData method) discard() (AtomicFile method) (EntrySet method) disconnect_signals() (Flow method) DiscretizeOccupanciesTransformation (class in pymatgen.transformations.standard_transformations) DiskError (class in pymatgen.io.abinit.scheduler_error_parsers) disordered_formula() (in module pymatgen.util.string) DisorderOrderedTransformation (class in pymatgen.transformations.advanced_transformations) display_help() (MultiStructuresVis method) (StructureVis method) display_info() (MultiStructuresVis method) display_warning() (MultiStructuresVis method) dist() (ConnectedSite property) distance() (Neighbor property) (PeriodicSite method) (Site method) distance_and_image() (PeriodicSite method) distance_and_image_from_frac_coords() (PeriodicSite method) distance_cutoff() (SimplestChemenvStrategy property) distance_from_point() (Site method) distance_matrix() (IStructure property) (SiteCollection property) distance_plateau() (StructureEnvironments.NeighborsSet method) distance_to_origin() (Plane property) distance_to_point() (Plane method) DISTANCE_TOLERANCE (SiteCollection attribute) DistanceAngleAreaNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DistanceCutoffFloat (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DistanceNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) DistancePlateauNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) distances() (Plane method) (StructureEnvironments.NeighborsSet property) distances_indices_groups() (Plane method) distances_indices_sorted() (Plane method) distfactor_max() (CoordinationGeometry property) divisors() (in module pymatgen.analysis.chemenv.utils.math_utils) djrepo_path() (Pseudo property) DLSVolumePredictor (class in pymatgen.analysis.structure_prediction.volume_predictor) do_query() (in module pymatgen.cli.pmg_query) domain_vertices() (PourbaixPlotter method) DopingTransformation (class in pymatgen.transformations.advanced_transformations) DOS (class in pymatgen.electronic_structure.dos) Dos (class in pymatgen.electronic_structure.dos) Doscar (class in pymatgen.io.lobster) DosPlotter (class in pymatgen.electronic_structure.plotter) dot() (Lattice method) double_cap_hints() (CoordinationGeometry.NeighborsSetsHints method) down (Spin attribute) draw_cg() (in module pymatgen.analysis.chemenv.utils.scripts_utils) draw_graph_to_file() (MoleculeGraph method) (StructureGraph method) drift (Outcar attribute) DteWork (class in pymatgen.io.abinit.works) dual_cv_simp (WulffShape attribute) DummySpecie (class in pymatgen.core.periodic_table) dump_BSE_data_in_GW_run() (FiestaInput method) dump_TDDFT_data_in_GW_run() (FiestaInput method) dx2 (Orbital attribute) dxy (Orbital attribute) dxz (Orbital attribute) Dy (Element attribute) Dynmat (class in pymatgen.io.vasp.outputs) dyz (Orbital attribute) dz2 (Orbital attribute)

E

E() (Orbital property) (OrbitalDescription property) e0() (EOSBase property) e_fermi() (Xmu property) e_surf_list (WulffShape attribute) 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) edit_file() (Editor method) edit_files() (Editor method) Editor (class in pymatgen.io.abinit.utils) Eels (class in pymatgen.io.feff.outputs) efermi (BandStructure attribute) (Vasprun attribute) (Wavecar attribute) (WorkFunctionAnalyzer attribute) effective_radius() (WulffShape property) efg (Outcar attribute) eigenvalue_band_properties() (Vasprun property) eigenvalues (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_tensor (Outcar attribute) ElasticTask (class in pymatgen.io.abinit.tasks) ElasticTensor (class in pymatgen.analysis.elasticity.elastic) ElasticTensorExpansion (class in pymatgen.analysis.elasticity.elastic) elec_neg (MolecularOrbitals attribute) electrical_resistivity (Element attribute) ElectricFieldGradient (class in pymatgen.analysis.nmr) electron_configuration() (PotcarSingle property) electronic_steps (Oszicar attribute) electronic_structure (Element attribute) Electrons (class in pymatgen.io.abinit.abiobjects) electrons (GaussianOutput attribute) ElectronsAlgorithm (class in pymatgen.io.abinit.abiobjects) Element (class in pymatgen.core.periodic_table) element() (PotcarSingle property) (Pseudo property) (Specie property) element_composition() (Composition property) ElementComparator (class in pymatgen.analysis.structure_matcher) elements (MolecularOrbitals attribute) elements() (BalancedReaction property) (Composition property) Elfcar (class in pymatgen.io.vasp.outputs) ellipticity() (CriticalPoint property) email (Author attribute) encut (Wavecar attribute) END_TAG (AbinitTimerParser attribute) endpoints_minima() (EnergyTrend method) energies (AdfOutput attribute) (Doscar attribute), [1] (GaussianOutput attribute) energies() (Doscar property) (Eels property) (Xmu property) Energy (in module pymatgen.core.units) energy (PDEntry attribute) energy() (ComputedEntry property) (DefectEntry property) (PourbaixEntry property) energy_at_conditions() (PourbaixEntry method) energy_density() (ElasticTensorExpansion method) (NthOrderElasticTensor method) energy_per_atom() (ComputedEntry property) (PDEntry property) (PourbaixEntry property) EnergyModel (class in pymatgen.analysis.energy_models) EnergyTrend (class in pymatgen.analysis.ferroelectricity.polarization) ensemble_center() (AdsorbateSiteFinder method) ENTRIES (TaskManager attribute) entries_charge() (ConversionVoltagePair property) entries_discharge() (ConversionVoltagePair property) entropy() (PhononDos method) entry_dict_from_list() (in module pymatgen.analysis.surface_analysis) EntryPostProcessor (class in pymatgen.entries.post_processors_abc) 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) enumerate_ordering() (PartialRemoveSitesTransformation method) EnumerateStructureTransformation (class in pymatgen.transformations.advanced_transformations) EnumError EnumlibAdaptor() (in module pymatgen.command_line.enumlib_caller) EOS (class in pymatgen.analysis.eos) EOSBase (class in pymatgen.analysis.eos) EOSError EphTask (class in pymatgen.io.abinit.tasks) epsilon_ionic (Vasprun attribute) epsilon_ionic() (Vasprun property) epsilon_static (Vasprun attribute) epsilon_static() (Vasprun property) epsilon_static_wolfe (Vasprun attribute) epsilon_static_wolfe() (Vasprun property) equivalent_site_index_and_transform() (AbstractChemenvStrategy method) EquivalentSiteSearchError Er (Element attribute) erase_info() (MultiStructuresVis method) erase_warning() (MultiStructuresVis method) Error (AbinitTimerParser attribute) error (AdfOutput attribute) Error (ArrayWithUnit attribute) (EventsParser attribute) (FloatWithUnit attribute) (Flow attribute) (NetcdfReader attribute) (Node attribute) (ParalHints attribute) (ParalHintsParser attribute) (PyFlowScheduler attribute) (PyLauncher attribute) (Unit attribute) (YamlTokenizer attribute) error_definitions() (AbstractErrorParser property) (PBSErrorParser property) (SlurmErrorParser property) errored_tasks() (Flow property) errors (GaussianOutput attribute) Es (Element attribute) esp_task() (NwTask class method) estimate_band_connection() (in module pymatgen.phonon.bandstructure) estimate_exchange() (HeisenbergMapper method) estimated_start_time() (PbsProJob method) (QueueJob method) (SlurmJob method) eta() (EwaldSummation property) eta_from_seebeck() (in module pymatgen.electronic_structure.boltztrap) ETSF_Reader (class in pymatgen.io.abinit.netcdf) Eu (Element attribute) eV_to_k() (in module pymatgen.analysis.defects.utils) EV_TO_KJ_PER_MOL (InterfacialReactivity attribute) evaluate() (AbstractRatioFunction method) evaluate_rpn() (in module pymatgen.io.abinit.utils) evaluate_wavefunc() (Wavecar method) event_class (DilatmxErrorHandler attribute) event_handlers() (Node property) EventsParser (class in pymatgen.io.abinit.events) EwaldElectrostaticModel (class in pymatgen.analysis.energy_models) EwaldMinimizer (class in pymatgen.analysis.ewald) EwaldSummation (class in pymatgen.analysis.ewald) exceptions() (NodeResults property) ExcHamiltonian (class in pymatgen.io.abinit.abiobjects) ExcitationSpectrum (class in pymatgen.analysis.excitation) ExcitingInput (class in pymatgen.io.exciting.inputs) exclude_nodes() (CorrectorProtocolScheduler method) (TaskManager method) executable() (AbinitTask property) (AnaddbTask property) (OpticTask property) exists() (Directory property) (File property) expand() (in module pymatgen.io.abinit.helpers) ExpEntry (class in pymatgen.entries.exp_entries) explain() (Compatibility method) explicit() (CNBiasNbSetWeight class method) explicit_path() (KSampling class method) ExplicitPermutationsAlgorithm (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) exponential() (in module pymatgen.util.convergence) export_envar() (ScriptEditor method) export_envars() (ScriptEditor method) export_msdt() (DiffusionAnalyzer method) extend() (Trajectory method) extend_transformations() (StandardTransmuter method) (TransformedStructure method) extract_cluster() (SiteCollection method) extract_metadata() (AbstractErrorParser static method) extrapolate_reciprocal() (in module pymatgen.util.convergence) extrapolate_simple_reciprocal() (in module pymatgen.util.convergence) extrema_df() (ChargeDensityAnalyzer property) extremum_icohpvalue() (IcohpCollection method)

F

F (Element attribute) f (OrbitalType attribute) f0 (Orbital attribute) f0() (in module pymatgen.electronic_structure.dos) f1 (Orbital attribute) f2 (Orbital attribute) f3 (Orbital attribute) f_1 (Orbital attribute) f_2 (Orbital attribute) f_3 (Orbital attribute) faces() (CoordinationGeometry method) facets (WulffShape attribute) factor() (FreqUnits property) factors() (in module pymatgen.analysis.gb.grain) fake() (AbinitTimerSection class method) farid (PPModelModes attribute) fast_norm() (in module pymatgen.analysis.substrate_analyzer) fast_ordering() (PartialRemoveSitesTransformation method) Fatband (class in pymatgen.io.lobster) fcc() (HighSymmKpath method) Fe (Element attribute) FEFFDictSet (class in pymatgen.io.feff.sets) FeffParserError FermiDos (class in pymatgen.electronic_structure.dos) fetch_tasks_to_run() (PyLauncher method) fft_mesh() (Wavecar method) FIELDS (AbinitTimerSection attribute) Fiesta_run (class in pymatgen.io.fiesta) FiestaInput (class in pymatgen.io.fiesta) FiestaOutput (class in pymatgen.io.fiesta) File (class in pymatgen.io.abinit.utils) filechildren() (FileNode property) filename (HistoryRecord attribute) (Wavecar attribute) filenames() (AbinitTimerParser property) FileNode (class in pymatgen.io.abinit.nodes) filepath() (Product property) (Pseudo property) FilepathFixer (class in pymatgen.io.abinit.utils) filesfile_string() (AbinitTask property) (AnaddbTask property) (OpticTask 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) finalize() (Flow method) finalized() (Node property) find_1den_files() (Directory method) find_1wf_files() (Directory method) 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_deadlocks() (Flow method) 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_last_timden_file() (Directory method) find_mapping() (Lattice method) find_neighbors() (in module pymatgen.core.structure) find_optconf() (AbinitTask method) find_primitive() (SpacegroupAnalyzer method) find_rings() (MoleculeGraph method) find_rotation() (in module pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) find_scaling_factor() (in module pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) find_sections() (QCInput static method) find_stable_charges() (DefectPhaseDiagram method) find_stable_entry() (PourbaixDiagram method) find_structure() (MPRester method) find_surface_sites_by_height() (AdsorbateSiteFinder method) fine_structure() (Eels property) fit() (DeltaFactor method) (EOS method) (EOSBase method) (MoleculeMatcher method) (NumericalEOS method) (PolynomialEOS method) (StructureMatcher method) fit_anonymous() (StructureMatcher method) fit_arrhenius() (in module pymatgen.analysis.diffusion_analyzer) fit_error() (Plane method) fit_least_square_distance_error() (Plane method) fit_maximum_distance_error() (Plane method) fit_to_structure() (Tensor method) (TensorCollection method) fix_abicritical() (AbinitTask method) (Flow method) (OpticTask method) fix_ofiles() (RelaxTask method) fix_paths() (FilepathFixer method) fix_pbc() (in module pymatgen.analysis.gb.grain) fix_queue_critical() (AbinitTask method) (Flow method) (OpticTask method) flags_keys (Control attribute) FLOATKEYWORDS (Lobsterin attribute) FloatWithUnit (class in pymatgen.core.units) Flow (class in pymatgen.io.abinit.flows) flow() (PyFlowScheduler property) (Work property) Fm (Element attribute) FM (Ordering attribute) fn (PymatgenTest attribute) fold_point() (in module pymatgen.electronic_structure.plotter) force_constants (Vasprun attribute) force_field (ForceField attribute) ForceConstantMatrix (class in pymatgen.analysis.piezo_sensitivity) ForceField (class in pymatgen.io.lammps.data) forces() (EwaldSummation property) format_formula() (in module pymatgen.util.plotting) formation_energy() (DefectEntry method) formation_energy_tol (PhaseDiagram attribute) formula() (Composition property) (Header property) (Ion property) (SiteCollection property) formula_double_format() (in module pymatgen.util.string) Fr (Element attribute) frac_charge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) frac_coords() (IStructure property) (Kpoint property) (PeriodicSite property) frac_discharge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) fractional_composition() (Composition property) fractions() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) fragment_and_process() (BondDissociationEnergies method) Fragmenter (class in pymatgen.analysis.fragmenter) FrameworkComparator (class in pymatgen.analysis.structure_matcher) FreeVolumePotential (class in pymatgen.analysis.path_finder) freq_type (AdfOutput attribute) freq_units() (in module pymatgen.phonon.plotter) FreqSet (class in pymatgen.io.qchem.sets) frequencies (AdfOutput attribute) (GaussianOutput attribute) frequencies() (Outcar property) FreqUnits (class in pymatgen.phonon.plotter) FreysoldtCorrection (class in pymatgen.analysis.defects.corrections) from_2points_and_origin() (Plane class method) from_3points() (Plane class method) from_abinit_ixc() (XcFunc class method) from_axis_angle_and_translation() (SymmOp static method) from_bonding() (Topology class method) from_bson_voronoi_list() (in module pymatgen.analysis.chemenv.coordination_environments.voronoi) from_bson_voronoi_list2() (in module pymatgen.analysis.chemenv.coordination_environments.voronoi) from_bulk_and_miller() (AdsorbateSiteFinder class method) from_cg() (AbstractGeometry class method) from_cif_file() (Header static method) from_cif_string() (TransformedStructure static method) from_coefficients() (Plane class method) from_composition_and_entries() (ConversionElectrode static method) from_composition_and_pd() (ConversionElectrode static method) from_computed_structure_entry() (SlabEntry static method) from_csv() (EntrySet class method) from_deformation() (Strain class method) from_den_ddb_dvdb() (GKKPWork class method) from_description() (CNBiasNbSetWeight class method) from_dict (Element attribute) (LibxcFunc attribute) from_dict() (AbstractChemenvStrategy class method) (AbstractComparator class method) (AbstractMolAtomMapper class method) (AbstractRatioFunction class method) (AdditionalConditionInt class method) (AdfKey class method) (AdfTask class method) (AngleCutoffFloat class method) (AngleNbSetWeight class method) (AnglePlateauNbSetWeight class method) (Author static method) (BalancedReaction class method) (BandStructure class method) (BandStructureSymmLine class method) (BoltztrapAnalyzer static method) (CNBiasNbSetWeight class method) (CSMFloat class method) (ChemicalEnvironments 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) (ContainsSpecieFilter class method) (Control class method) (ConversionElectrode class method) (ConversionVoltagePair class method) (CoordinationGeometry class method) (CoordinationGeometry.NeighborsSetsHints class method) (Correction class method) (DefectEntry class method) (DefectPhaseDiagram class method) (DeltaCSMNbSetWeight class method) (DeltaDistanceNbSetWeight class method) (DetailedVoronoiContainer class method) (DiffusionAnalyzer class method) (DilatmxErrorHandler class method) (DistanceAngleAreaNbSetWeight class method) (DistanceCutoffFloat class method) (DistanceNbSetWeight class method) (DistancePlateauNbSetWeight class method) (Dos class method) (DummySpecie class method) (Electrons class method) (ElectronsAlgorithm class method) (EnergyModel class method) (ExpEntry class method) (ExplicitPermutationsAlgorithm class method) (FermiDos class method) (FiestaInput class method) (Fiesta_run class method) (Flow class method) (ForceField class method) (GaussianInput class method) (GaussianToComputedEntryDrone class method) (GrainBoundary class method) (GrandPotPDEntry class method) (GrandPotentialPhaseDiagram class method) (HistoryNode static method) (HistoryRecord class method) (IMolecule class method) (IStructure class method) (Incar class method) (InchiMolAtomMapper class method) (InsertionElectrode class method) (Interface class method) (Ion class method) (IonEntry class method) (IsomorphismMolAtomMapper class method) (KSampling class method) (Kpoints class method) (LMTOCtrl class method) (LammpsData class method) (LammpsDump class method) (Lattice class method) (LightStructureEnvironments class method) (LightStructureEnvironments.NeighborsSet 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) (NodeResults class method) (NormalizedAngleDistanceNbSetWeight class method) (NwInput class method) (NwTask class method) (Nwchem2Fiesta class method) (PDEntry class method) (PPModel static method) (PWInput class method) (ParalHints 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) (Pseudo class method) (PseudoTable class method) (Reaction class method) (RelaxationMethod class method) (SelfCSMNbSetWeight class method) (SeparationPlane class method) (SimpleAbundanceChemenvStrategy class method) (SimpleVaspToComputedEntryDrone class method) (SimplestChemenvStrategy class method) (Site class method) (Slab class method) (SlabEntry class method) (Smearing static method) (Specie class method) (SpecieProximityFilter class method) (SpinMode class method) (StructureEnvironments class method) (StructureEnvironments.NeighborsSet class method) (StructureGraph class method) (StructureMatcher class method) (StructureNL class method) (Substitutor class method) (SymmOp class method) (Tags static method) (TargettedPenaltiedAbundanceChemenvStrategy class method) (TaskManager class method) (Tensor class method) (TensorCollection class method) (ThermoData class method) (TransformedPDEntry class method) (TransformedStructure class method) (VaspInput class method) (VaspToComputedEntryDrone class method) (WeightedNbSetChemenvStrategy class method) (XcFunc class method)

from_diff_fit() (ElasticTensorExpansion class method) (NthOrderElasticTensor class method) from_dir() (NEBAnalysis class method) (PseudoTable class method) from_directory() (FEFFDictSet static method) (VaspInput static method) from_ff_and_topologies() (LammpsData class method) from_file() (BabelMolAdaptor static method) (ChargeDensityAnalyzer class method) (Chgcar static method) (CifFile class method) (CompleteCohp class method) (Control class method) (Cssr static method) (Eels static method) (Elfcar class method) (ExcitingInput static method) (FiestaInput class method) (ForceField class method) (GaussianInput static method) (Header static method) (IMolecule class method) (IStructure class method) (Incar static method) (Kpoints static method) (LDos static method) (LMTOCtrl class method) (LammpsData class method) (Lobsterin class method) (Locpot static method) (NwInput class method) (PWInput static method) (Poscar static method) (Potcar static method) (PotcarSingle static method) (Product class method) (Pseudo static method) (PyFlowScheduler class method) (QCInput static method) (Relaxation class method) (ScfCycle class method) (SiteCollection class method) (Tags static method) (TaskManager class method) (Trajectory class method) (XYZ static method) (Xmu static method) (Xr 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_hdf5() (VolumetricData class method) from_independent_strains() (ElasticTensor class method) from_index_amount() (Deformation class method) (Strain class method) from_input() (AbinitTask class method) from_inputs() (Flow class method) from_lammpsdata() (CombinedData class method) from_lengths_and_angles() (Lattice static method) from_magnetic_spacegroup() (IStructure class method) from_maryland_notation() (ChemicalShielding class method) from_molecule() (NwTask class method) from_molecule_graph() (BabelMolAdaptor static method) from_moment_relative_to_crystal_axes() (Magmom class method) from_mpi_omp_lists() (ParalHints class method) from_multi_jobs_file() (QCInput class method) from_name() (XcFunc class method) from_node() (NodeResults class method) from_npoints() (Plane class method) from_npoints_least_square_distance() (Plane class method) from_npoints_maximum_distance() (Plane class method) from_old_dict() (BandStructure class method) (BandStructureSymmLine class method) (LobsterBandStructureSymmLine class method) from_origin_axis_angle() (SymmOp static method) from_origin_shift() (JonesFaithfulTransformation class method) from_outcars() (NEBAnalysis class method) from_outcars_and_structures() (Polarization class method) from_parameters() (Lattice class method) from_path() (BaderAnalysis class method) (Critic2Caller class method) from_phononwfkq_work() (GKKPWork class method) from_poscar_string() (TransformedStructure static method) from_preset() (CutOffDictNN static method) from_prev_calc() (MPHSEBSSet class method) (MPNonSCFSet class method) (MPSOCSet class method) (MPStaticSet class method) (MVLGWSet class method) from_pseudoinverse() (ElasticTensor class method) from_qtype_and_id() (QueueJob static method) from_rotation_and_translation() (SymmOp static method) from_rotation_and_translation_and_time_reversal() (MagSymmOp static method) from_row_and_group (Element attribute) from_scaling_factors() (SupercellTransformation static method) from_scf_input() (PhononWork class method) from_scf_task() (BecWork class method) (DteWork class method) (PhononWfkqWork class method) (PhononWork class method) from_sites() (IMolecule class method) (IStructure class method) from_snl() (TransformedStructure class method) from_spacegroup() (IStructure class method) from_steps() (ConversionVoltagePair static method) from_str() (IMolecule class method) (IStructure class method) (SiteCollection class method) from_stream() (Relaxation class method) (ScfCycle class method) from_string (Kpoints_supported_modes attribute) from_string() (AdfKey static method) (BabelMolAdaptor static method) (BalancedReaction static method) (CifBlock class method) (CifFile class method) (CifParser static method) (Cssr static method) (DummySpecie static method) (ExcitingInput static method) (FiestaInput class method) (FloatWithUnit class method) (GaussianInput static method) (Header static method) (Incar static method) (JobStatus class method) (Kpoints static method) (LMTOCtrl class method) (LammpsDump class method) (NwInput class method) (PWInput static method) (Poscar static method) (PyFlowScheduler class method) (QCInput class method) (Specie static method) (Status class method) (TaskManager class method) (XSF class method) (XYZ static method) (Xr static method) (ZeoCssr static method) (ZeoVoronoiXYZ static method) from_structure() (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_user_config() (PyFlowScheduler class method) (TaskManager class method) from_values_indices() (Tensor class method) from_vasp_voigt() (PiezoTensor class method) from_vaspruns() (DiffusionAnalyzer class method) from_voigt() (Tensor class method) (TensorCollection class method) from_xyz_string() (SymmOp static method) from_xyzt_string() (MagSymmOp static method) from_Z (Element attribute) full_electronic_structure (Element attribute) full_electronic_structure() (Element property) FullQueueError (class in pymatgen.io.abinit.scheduler_error_parsers) fully_charged_entry() (InsertionElectrode property) fully_discharged_entry() (InsertionElectrode property) func() (EOSBase method) func_name (HistoryRecord attribute) 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

g0w0_extended_work() (in module pymatgen.io.abinit.calculations) g0w0_flow() (in module pymatgen.io.abinit.flows) G0W0WithQptdmFlow (class in pymatgen.io.abinit.flows) G0W0Work (class in pymatgen.io.abinit.works) 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) GarbageCollector (class in pymatgen.io.abinit.nodes) GasCorrection (class in pymatgen.entries.compatibility) gaussian_smear() (StaticPotential method) GaussianInput (class in pymatgen.io.gaussian) GaussianOutput (class in pymatgen.io.gaussian) GaussianToComputedEntryDrone (class in pymatgen.apps.borg.hive) gb_from_parameters() (GrainBoundaryGenerator method) gc() (Node property) Gd (Element attribute) Ge (Element attribute) gen3d_conformer() (BabelMolAdaptor method) gen_potcar() (in module pymatgen.cli.pmg_potcar) gen_sl_transform_matricies() (in module pymatgen.analysis.substrate_analyzer) generate_adsorption_structures() (AdsorbateSiteFinder method) generate_all_slabs() (in module pymatgen.core.surface) generate_defect_structure() (Defect method) (Interstitial method) (Substitution method) (Vacancy method) generate_entry_label() (in module pymatgen.analysis.pourbaix_diagram) generate_full_symmops() (in module pymatgen.symmetry.analyzer) generate_interfaces() (InterfaceBuilder method) generate_potcar() (in module pymatgen.cli.pmg_potcar) generate_pseudo() (in module pymatgen.analysis.elasticity.elastic) generate_R_and_G_vecs() (in module pymatgen.analysis.defects.utils) generate_reciprocal_vectors_squared() (in module pymatgen.analysis.defects.utils) generate_sl_transformation_sets() (ZSLGenerator method) generate_substitution_structures() (AdsorbateSiteFinder method) generate_surface_vectors() (SubstrateAnalyzer method) generators (PointGroup attribute) (SpaceGroup attribute) genrecip() (in module pymatgen.analysis.defects.utils) geometrically_equidistant() (CNBiasNbSetWeight class method) get_00t_magmom_with_xyz_saxis() (Magmom method) get_13_bonds() (MoleculeStructureComparator static method) get_absorbing_atom_symbol_index() (in module pymatgen.io.feff.inputs) get_adjusted_fermi_level() (in module pymatgen.io.vasp.outputs) get_all_anonymous_mappings() (StructureMatcher method) get_all_chempots() (PhaseDiagram method) get_all_distances() (Lattice method) get_all_entries() (InsertionElectrode method) get_all_functional_groups() (FunctionalGroupExtractor method) get_all_neighbors() (IStructure method) get_all_neighbors_old() (IStructure method) get_all_nn_info() (NearNeighbors method) (VoronoiNN method) get_all_status() (Work method) get_all_substrates() (MPRester method) get_all_voronoi_polyhedra() (VoronoiNN method) get_allowed_species() (Substitutor method) get_alpha() (Elfcar method) get_analysis() (JahnTellerAnalyzer method) get_analysis_and_structure() (JahnTellerAnalyzer method) get_angle() (in module pymatgen.util.coord) (SiteCollection method) get_arrhenius_plot() (in module pymatgen.analysis.diffusion_analyzer) get_asum_FCM() (ForceConstantMatrix method) get_atom_map() (in module pymatgen.io.feff.inputs) get_atomic_fraction() (Composition method) get_atoms() (AseAtomsAdaptor static method) get_available_models() (CrystalAIRester method) get_average_along_axis() (VolumetricData method) get_average_eff_mass() (BoltztrapAnalyzer method) get_average_voltage() (AbstractElectrode method) get_ax3d_fig_plt() (in module pymatgen.util.plotting) get_ax_fig_plt() (in module pymatgen.util.plotting) get_axarray_fig_plt() (in module pymatgen.util.plotting) get_axis_grid() (VolumetricData method) get_band_gap() (BandStructure method) get_band_structure() (Vasprun method) get_band_structure_from_vasp_multiple_branches() (in module pymatgen.io.vasp.outputs) get_bandstructure() (Fatband method) get_bandstructure_by_material_id() (MPRester method) get_basic_functional_groups() (FunctionalGroupExtractor method) get_BEC_operations() (BornEffectiveCharge method) get_best_electronegativity_anonymous_mapping() (StructureMatcher method) get_bibtex_string() (CifParser method) get_bond_length() (in module pymatgen.core.bonds) get_bond_order() (CovalentBond method) (in module pymatgen.core.bonds) get_bonded_structure() (CovalentBondNN method) (Critic2NN method) (NearNeighbors method) (OpenBabelNN method) get_box_shift() (LammpsBox method) get_boxed_structure() (IMolecule method) get_branch() (BandStructureSymmLine method) (PhononBandStructureSymmLine method) get_brillouin_zone() (Lattice method) get_capacity_grav() (AbstractElectrode method) get_capacity_vol() (AbstractElectrode method) get_carrier_concentration() (BoltztrapAnalyzer method) get_cart_coords() (GaussianInput method) get_cartesian_coords() (Lattice method) get_cbm() (BandStructure method) get_cbm_vbm() (DOS method) (Dos method) get_celldm() (PWOutput method) get_center_of_arc() (in module pymatgen.analysis.chemenv.utils.math_utils) get_centered_molecule() (IMolecule method) get_central_site() (CoordinationGeometry method) get_charge() (BaderAnalysis method) get_charge_transfer() (BaderAnalysis method) get_chempot_correction() (InterfacialReactivity static method) get_chempot_range_map() (PhaseDiagram method) get_chempot_range_map_plot() (PDPlotter method) get_chempot_range_stability_phase() (PhaseDiagram method) get_chgint_plot() (in module pymatgen.cli.pmg_plot) get_children() (Node method) get_chunks() (in module pymatgen.util.sequence) get_cluster_graph() (Dirviz method) 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_collection() (DBConnector method) (TaskManager method) get_complete_dos() (BoltztrapAnalyzer method) get_complete_ph_dos() (in module pymatgen.io.phonopy) get_complexity_factor() (BoltztrapAnalyzer method) get_compliance_expansion() (ElasticTensorExpansion method) get_composition_chempots() (PhaseDiagram method) get_compound_pd() (ReactionDiagram method) get_computed_entry() (Vasprun method) get_conductivity() (BoltztrapAnalyzer method) get_connected_sites() (MoleculeGraph method) (StructureGraph method) get_connections() (VoronoiConnectivity method) get_consistent_set_and_saxis() (Magmom static method) get_contour_pd_plot() (PDPlotter method) get_conv_struct() (in module pymatgen.command_line.aconvasp_caller) get_conventional_standard_structure() (SpacegroupAnalyzer method) get_conventional_to_primitive_transformation_matrix() (SpacegroupAnalyzer method) get_conversion_factor() (in module pymatgen.analysis.diffusion_analyzer) (Unit method) get_coordinating_elements_cns() (StructureMotifInterstitial method) get_coordination_environments() (StructureEnvironments method) get_coordination_number() (CoordinationGeometry method) get_coordination_of_site() (MoleculeGraph method) (StructureGraph method) get_coordination_symmetry_measures() (LocalGeometryFinder method) get_coordination_symmetry_measures_optim() (LocalGeometryFinder method) get_correction() (BandEdgeShiftingCorrection method) (BandFillingCorrection method) (Correction method) (DefectCorrection method) (FreysoldtCorrection method) (KumagaiCorrection method) (PotcarCorrection method) get_corrections_dict() (Compatibility method) get_cost_per_kg() (CostAnalyzer method) get_cost_per_mol() (CostAnalyzer method) get_covalent_bonds() (IMolecule method) get_critical_compositions() (PhaseDiagram method) get_critical_original_kink_ratio() (InterfacialReactivity method) get_critical_point_for_site() (Critic2Output method) get_crystal_field_spin() (Specie method) get_crystal_system() (SpacegroupAnalyzer method) get_csm() (StructureEnvironments method) get_csm_and_maps() (StructureEnvironments method) get_csms() (StructureEnvironments method) get_d() (in module pymatgen.core.surface) get_data() (BorgQueen method) (MPRester method) get_dataframe() (AbinitTimer method) get_decomp_and_e_above_hull() (PhaseDiagram method) get_decomposition() (PhaseDiagram method) get_decomposition_energy() (PourbaixDiagram method) get_default_basis_set() (AdfTask static method) get_default_geo() (AdfTask static method) get_default_scf() (AdfTask static method) get_default_units() (AdfTask static method) get_default_xc() (AdfTask static method) get_defectsite_multiplicity() (StructureMotifInterstitial method) get_deformation_matrix() (Strain method) get_delta_etime() (PyFlowScheduler method) get_densities() (Dos method) get_derivatives() (in module pymatgen.util.convergence) get_dict_for_mongodb_queries() (Flow method) get_diff_coeff() (in module pymatgen.analysis.elasticity.elastic) get_dihedral() (SiteCollection method) get_dimensionality_cheon() (in module pymatgen.analysis.dimensionality) get_dimensionality_gorai() (in module pymatgen.analysis.dimensionality) get_dimensionality_larsen() (in module pymatgen.analysis.dimensionality) get_direct_band_gap() (BandStructure method) get_direct_band_gap_dict() (BandStructure method) get_displaced_structures() (in module pymatgen.io.phonopy) get_distance() (IMolecule method) (IStructure method) (SiteCollection method) get_distance_and_image() (Lattice method) get_doc() (Lobsterout method) (MPRester method) get_dopability_limits() (DefectPhaseDiagram method) get_dopants_from_shannon_radii() (in module pymatgen.analysis.structure_prediction.dopant_predictor) get_dopants_from_substitution_probabilities() (in module pymatgen.analysis.structure_prediction.dopant_predictor) get_doping() (FermiDos method) get_dos_by_material_id() (MPRester method) get_dos_dict() (DosPlotter method) (PhononDosPlotter method) get_dos_plot() (in module pymatgen.cli.pmg_plot) get_drift_corrected_structures() (DiffusionAnalyzer method) get_e_above_hull() (PhaseDiagram method) get_effective_csm() (in module pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) get_effective_ecs() (ElasticTensorExpansion method) get_el_amount() (BalancedReaction method) get_el_amt_dict() (Composition method) get_el_sp() (in module pymatgen.core.periodic_table) get_element_dos() (CompleteDos method) (CompletePhononDos method) get_element_fraction() (PourbaixEntry method) get_element_profile() (PhaseDiagram method) get_element_spd_dos() (CompleteDos method) (LobsterCompleteDos method) get_elements_between_bands() (Wavederf method) get_elt_projected_plots() (BSPlotterProjected method) get_elt_projected_plots_color() (BSPlotterProjected method) get_energies() (in module pymatgen.cli.gaussian_analyzer) (in module pymatgen.cli.pmg_analyze) get_energy() (ChemicalPotential method) (EnergyModel method) (EwaldElectrostaticModel method) (GulpIO method) (IsingModel method) (NsitesModel method) (SymmetryModel method) get_energy_buckingham() (in module pymatgen.command_line.gulp_caller) get_energy_density() (AbstractElectrode method) get_energy_relax_structure_buckingham() (in module pymatgen.command_line.gulp_caller) get_energy_tersoff() (in module pymatgen.command_line.gulp_caller) get_entries() (CostDB method) (CostDBCSV method) (MPRester method) get_entries_in_chemsys() (MPRester method) get_entry_by_material_id() (MPRester method) get_environments_figure() (StructureEnvironments method) get_equilibrium_reaction_energy() (PhaseDiagram method) get_equiv_transformations() (ZSLGenerator method) get_equivalent_atoms() (PointGroupAnalyzer method) get_equivalent_kpoints() (BandStructureSymmLine method) get_equivalent_qpoints() (PhononBandStructureSymmLine method) get_event_handler_classes() (in module pymatgen.io.abinit.events) get_exchange() (HeisenbergMapper method) get_exchange_group_info() (CollinearMagneticStructureAnalyzer method) get_excitation_spectrum() (NwOutput method) get_exp_entry() (MPRester method) get_exp_thermo_data() (MPRester method) get_explanation_dict() (Compatibility method) get_extended_surface_mesh() (AdsorbateSiteFinder method) get_extrapolated_conductivity() (in module pymatgen.analysis.diffusion_analyzer) get_extrapolated_diffusivity() (in module pymatgen.analysis.diffusion_analyzer) get_extrema() (NEBAnalysis method) get_extreme() (BoltztrapAnalyzer method) get_facets() (in module pymatgen.analysis.phase_diagram) get_factors() (in module pymatgen.analysis.substrate_analyzer) get_FCM_operations() (ForceConstantMatrix method) get_fermi() (FermiDos method) get_fermi_interextrapolated() (FermiDos method) get_ferromagnetic_structure() (CollinearMagneticStructureAnalyzer method) get_filepaths_and_exts() (Dependency method) get_film_indices() (Interface method) get_final_structure() (RelaxTask method) get_form_energy() (PhaseDiagram method) get_form_energy_per_atom() (PhaseDiagram method) get_frac_coords_from_lll() (Lattice method) get_fractional_coords() (Lattice method) get_framework_rms_plot() (DiffusionAnalyzer method) get_free_sphere_params() (in module pymatgen.io.zeopp) get_gap() (DOS method) (Dos method) get_gb_data() (MPRester method) get_geometries() (AllCoordinationGeometries method) get_geometry_from_IUCr_symbol() (AllCoordinationGeometries method) get_geometry_from_IUPAC_symbol() (AllCoordinationGeometries method) get_geometry_from_mp_symbol() (AllCoordinationGeometries method) get_geometry_from_name() (AllCoordinationGeometries method) get_ggt() (ElasticTensorExpansion method) get_graphviz() (Flow method) get_graphviz_dirtree() (Node method) get_grouped_indices() (Tensor method) get_gruneisen_parameter() (ElasticTensorExpansion method) get_hall() (SpacegroupAnalyzer method) get_hall_carrier_concentration() (BoltztrapAnalyzer method) get_hash() (AbstractComparator method) (ElementComparator method) (FrameworkComparator method) (OccupancyComparator method) (OrderDisorderElementComparator method) (SpeciesComparator method) (SpinComparator method) get_heat_capacity() (ElasticTensorExpansion method) get_heteroatoms() (FunctionalGroupExtractor method) get_high_accuracy_voronoi_nodes() (in module pymatgen.io.zeopp) get_hull_energy() (PhaseDiagram method) (PourbaixDiagram method) get_icohp() (Cohp method) get_icohp_by_label() (IcohpCollection method) get_icohp_dict_by_bondlengths() (IcohpCollection method) get_icohp_dict_of_site() (IcohpCollection method) get_ieee_rotation() (Tensor static method) get_implemented_geometries() (AllCoordinationGeometries method) get_info() (PbsProJob method) (QueueJob method) (SlurmJob method) get_integer_formula_and_factor() (Composition method) get_integer_index() (in module pymatgen.core.lattice) get_integrated_diff() (VolumetricData method) get_interaction_graph() (HeisenbergMapper method) get_interface_reactions() (MPRester method) get_interpolated_gap() (DOS method) (Dos method) get_interpolated_value() (Cohp method) (Dos method) (PhononDos method) (Spectrum method) get_ir_reciprocal_mesh() (SpacegroupAnalyzer method) get_IST_operations() (InternalStrainTensor method) get_kinks() (InterfacialReactivity method) get_kpoint_degeneracy() (BandStructure method) get_kpoint_weights() (SpacegroupAnalyzer method) get_kpoints() (HighSymmKpath method) (in module pymatgen.ext.jhu) get_labels() (WorkFunctionAnalyzer method) get_lattice() (CifParser method) get_lattice_quanta() (Polarization method) get_lattice_type() (SpacegroupAnalyzer method) get_line_in_facet() (WulffShape method) get_linear_interpolated_value() (in module pymatgen.util.coord) get_linearly_independent_vectors() (in module pymatgen.analysis.chemenv.utils.math_utils) get_lines() (Atoms method) get_lll_frac_coords() (Lattice method) get_lll_reduced_lattice() (Lattice method) get_local_extrema() (ChargeDensityAnalyzer method) get_local_order_parameters() (NearNeighbors method) get_locpot_along_slab_plot() (WorkFunctionAnalyzer method) get_low_energy_orderings() (HeisenbergMapper method) get_lower_and_upper_f() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) get_lowest_decomposition() (CostAnalyzer method) get_magnetizations() (in module pymatgen.cli.pmg_analyze) get_magnitude_of_effect_from_species() (JahnTellerAnalyzer method) get_magnitude_of_effect_from_spin_config() (JahnTellerAnalyzer static method) get_magsymops() (CifParser method) get_mapping() (StructureMatcher method) get_materials_id_from_task_id() (MPRester method) get_materials_id_references() (MPRester method) get_materials_ids() (MPRester method) get_max_bond_distance() (JmolNN method) get_max_bond_lengths() (in module pymatgen.analysis.structure_analyzer) get_max_capgrav() (BatteryAnalyzer method) get_max_capvol() (BatteryAnalyzer method) get_max_instability() (InsertionElectrode method) get_max_muO2() (InsertionElectrode method) get_mdf_robot() (BseMdfWork method) get_message() (HistoryRecord method) get_mft_temperature() (HeisenbergMapper method) get_mi_vec() (in module pymatgen.analysis.adsorption) get_miller_index_from_coords() (Lattice method) get_miller_index_from_site_indexes() (IStructure method) get_min_instability() (InsertionElectrode method) get_min_muO2() (InsertionElectrode method) get_minkowski_red() (in module pymatgen.command_line.aconvasp_caller) get_molecule_hash() (AbstractMolAtomMapper method) (InchiMolAtomMapper method) (IsomorphismMolAtomMapper method) get_moment() (Magmom method) get_moment_relative_to_crystal_axes() (Magmom method) get_mongo_info() (Flow 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_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_newnode_id() (in module pymatgen.io.abinit.nodes) get_next_index() (EwaldMinimizer method) get_niggli_reduced_lattice() (Lattice method) get_njobs_in_queue() (Flow method) (TaskManager method) get_nmr_quadrupole_moment() (Specie method) get_nn() (NearNeighbors method) get_nn_data() (CrystalNN method) get_nn_images() (NearNeighbors method) get_nn_info() (BrunnerNN_real method) (BrunnerNN_reciprocal method) (BrunnerNN_relative method) (CovalentBondNN method) (Critic2NN method) (CrystalNN method) (CutOffDictNN method) (EconNN method) (JmolNN method) (MinimumDistanceNN method) (MinimumOKeeffeNN method) (MinimumVIRENN method) (NearNeighbors method) (OpenBabelNN method) (VoronoiNN method) get_nn_shell_info() (CovalentBondNN method) (NearNeighbors method) (OpenBabelNN method) get_no_mixing_energy() (InterfacialReactivity method) get_nodes() (QueueJob method) get_nonmagnetic_structure() (CollinearMagneticStructureAnalyzer method) get_noppmodel() (PPModel class method) get_not_implemented_geometries() (AllCoordinationGeometries method) get_num_division_kpoints() (in module pymatgen.command_line.aconvasp_caller) get_occupation() (Procar method) get_okeeffe_distance_prediction() (in module pymatgen.analysis.local_env) get_okeeffe_params() (in module pymatgen.analysis.local_env) get_op_value() (StructureMotifInterstitial method) get_orbital_derivative_between_states() (Waveder method) get_orbital_resolved_cohp() (CompleteCohp method) get_order_parameters() (LocalStructOrderParams method) get_ordered_with_policy() (ParalHints 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_parents() (Node method) get_parser() (in module pymatgen.io.abinit.scheduler_error_parsers) get_pattern() (AbstractDiffractionPatternCalculator method) (NDCalculator method) (XRDCalculator method) get_pelecs_and_pions() (Polarization method) get_percentage_bond_dist_changes() (RelaxationAnalyzer method) get_percentage_lattice_parameter_changes() (RelaxationAnalyzer method) get_percentage_volume_change() (RelaxationAnalyzer method) get_perturbed_indices() (Deformation method) get_ph_bs_symm_line() (in module pymatgen.io.phonopy) get_ph_bs_symm_line_from_dict() (in module pymatgen.io.phonopy) get_ph_dos() (in module pymatgen.io.phonopy) get_phonon_bandstructure_by_material_id() (MPRester method) get_phonon_ddb_by_material_id() (MPRester method) get_phonon_dos_by_material_id() (MPRester method) get_phonon_frequencies() (Dynmat method) get_phonopy_structure() (in module pymatgen.io.phonopy) get_piezo() (in module pymatgen.analysis.piezo_sensitivity) get_plot() (AbstractDiffractionPatternCalculator method) (BSDOSPlotter method) (BSPlotter method) (CohpPlotter method) (DosPlotter method) (NEBAnalysis method) (PDPlotter method) (PhononBSPlotter method) (PhononDosPlotter method) (SpectrumPlotter method) (VoltageProfilePlotter method) (WulffShape method)

get_plot_data() (VoltageProfilePlotter method) get_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_polarization_change() (Polarization method) get_polarization_change_norm() (Polarization method) get_potcar_hash() (PotcarSingle method) get_potcars() (Vasprun method) get_potential_shift() (KumagaiCorrection method) get_pourbaix_domains() (PourbaixDiagram static method) get_pourbaix_entries() (MPRester method) get_pourbaix_plot() (PourbaixPlotter method) get_power_factor() (BoltztrapAnalyzer method) get_predicted_structure() (DLSVolumePredictor method) (RLSVolumePredictor method) get_prim_struct() (in module pymatgen.command_line.aconvasp_caller) get_primitive_standard_structure() (SpacegroupAnalyzer method) get_primitive_structure() (IStructure method) get_products() (InterfacialReactivity method) get_projected_plots_dots() (BSPlotterProjected method) get_projected_plots_dots_patom_pmorb() (BSPlotterProjected method) get_projection_on_elements() (BandStructure method) (LobsterBandStructureSymmLine method) (Procar method) get_projections_on_elements_and_orbitals() (BandStructure method) (LobsterBandStructureSymmLine method) get_prototypes() (AflowPrototypeMatcher method) get_pseudos_for_structure() (PseudoTable method) get_q2() (LocalStructOrderParams method) get_q4() (LocalStructOrderParams method) get_q6() (LocalStructOrderParams method) get_rand_BEC() (BornEffectiveCharge method) get_rand_FCM() (ForceConstantMatrix method) get_rand_IST() (InternalStrainTensor method) get_ratio() (GrainBoundaryGenerator method) get_rdf_figure() (DetailedVoronoiContainer method) get_reaction() (MPRester method) get_real_summation() (KumagaiCorrection method) get_reasonable_repetitions() (in module pymatgen.phonon.bandstructure) get_recip_summation() (KumagaiCorrection method) get_reconstructed_band_structure() (in module pymatgen.electronic_structure.bandstructure) get_recp_symmetry_operation() (Lattice method) get_reduced_composition_and_factor() (Composition method) get_reduced_formula_and_factor() (Composition method) get_reduced_structure() (IStructure method) get_refined_structure() (SpacegroupAnalyzer method) get_relaxed_structure() (GulpIO method) get_removals_int_oxid() (BatteryAnalyzer method) get_results() (AnaddbTask method) (DdkTask method) (FileNode method) (Flow method) (NscfTask method) (OpticTask method) (PhononTask method) (RelaxTask method) (ScfTask method) (SigmaTask method) get_rms_anonymous() (StructureMatcher method) get_rms_dist() (StructureMatcher method) get_rmsd() (MoleculeMatcher method) get_rot() (in module pymatgen.analysis.adsorption) get_rotation_angle_from_sigma() (GrainBoundaryGenerator static method) get_s2_like_s1() (StructureMatcher method) get_sadf_figure() (DetailedVoronoiContainer method) get_same_branch_polarization_data() (Polarization method) get_scaled() (SquareTensor method) get_scan_plot() (GaussianOutput method), [1] get_scissors_builder() (SigmaTask method) get_script_str() (ScriptEditor method) get_section() (AbinitTimer method) get_sections() (AbinitTimerParser method) get_seebeck() (BoltztrapAnalyzer method) get_seebeck_eff_mass() (BoltztrapAnalyzer method) get_self_interaction() (KumagaiCorrection method) get_shannon_radius() (Specie method) get_shared_symmetry_operations() (in module pymatgen.symmetry.site_symmetries) get_shear_reduced_slab() (in module pymatgen.analysis.interface) get_site_ce_fractions_and_neighbors() (AbstractChemenvStrategy method) get_site_coordination_environment() (AbstractChemenvStrategy method) (SimpleAbundanceChemenvStrategy method) (SimplestChemenvStrategy method) (TargettedPenaltiedAbundanceChemenvStrategy method) (WeightedNbSetChemenvStrategy method) get_site_coordination_environments() (AbstractChemenvStrategy method) (SimpleAbundanceChemenvStrategy method) (SimplestChemenvStrategy method) (WeightedNbSetChemenvStrategy method) get_site_coordination_environments_fractions() (AbstractChemenvStrategy method) (SimplestChemenvStrategy method) (WeightedNbSetChemenvStrategy method) get_site_dos() (CompleteDos method) (CompletePhononDos method) get_site_energy() (EwaldSummation method) get_site_info_for_specie_allces() (LightStructureEnvironments method) get_site_info_for_specie_ce() (LightStructureEnvironments method) get_site_neighbors() (AbstractChemenvStrategy method) (SimpleAbundanceChemenvStrategy method) (SimplestChemenvStrategy method) (WeightedNbSetChemenvStrategy method) get_site_orbital_dos() (CompleteDos method) (LobsterCompleteDos method) get_site_spd_dos() (CompleteDos method) get_site_symmetries() (in module pymatgen.symmetry.site_symmetries) get_site_t2g_eg_resolved_dos() (CompleteDos method) (LobsterCompleteDos method) get_sitej() (VoronoiConnectivity method) get_sites_in_sphere() (IMolecule method) (IStructure method) get_slab() (SlabGenerator method) get_slab_regions() (in module pymatgen.core.surface) get_slabs() (SlabGenerator method) get_smeared_densities() (Dos method) (PhononDos method) get_sorted_structure() (GrainBoundary method) (IStructure method) (Interface 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_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_stat() (File method) get_statistics() (LightStructureEnvironments method) get_stats() (QueueJob method) (SlurmJob method) get_strain_from_stress() (ElasticTensorExpansion method) get_strain_state_dict() (in module pymatgen.analysis.elasticity.elastic) get_string() (CombinedData method) (Incar method) (LMTOCtrl method) (LammpsBox method) (LammpsData method) (Poscar method) (Tags method) (Xdatcar method) get_structure() (AseAtomsAdaptor 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_from_dict() (in module pymatgen.io.phonopy) get_structure_from_mp() (in module pymatgen) get_structure_from_prev_run() (in module pymatgen.io.vasp.sets) get_structure_property_dict() (ElasticTensor method) get_structure_with_charges() (Charge method) get_structure_with_nodes() (ChargeDensityAnalyzer method) (TopographyAnalyzer method) get_structure_with_only_magnetic_atoms() (CollinearMagneticStructureAnalyzer method) get_structure_with_spin() (CollinearMagneticStructureAnalyzer method) get_structures() (CifParser method) (MPRester method) get_sub_electrodes() (ConversionElectrode method) (InsertionElectrode method) get_subgraphs_as_molecules() (StructureGraph method) get_subset_in_chemsys() (EntrySet method) get_substrates() (MPRester method) get_suggested_saxis() (Magmom static method) get_summary_dict() (ConversionElectrode method) (DiffusionAnalyzer method) (InterfaceBuilder method) (QuasiharmonicDebyeApprox method) get_summed_cohp_by_label_and_orbital_list() (CompleteCohp method) get_summed_cohp_by_label_list() (CompleteCohp method) get_summed_icohp_by_label_list() (IcohpCollection method) get_supercell_matrix() (StructureMatcher method) get_surface_data() (MPRester method) get_surface_equilibrium() (SurfaceEnergyPlotter method) get_surface_sites() (Slab method) get_sym_eq_kpoints() (BandStructure method) get_symbol_cn_mapping() (AllCoordinationGeometries method) get_symbol_dict() (Tensor method) get_symbol_list() (in module pymatgen.analysis.elasticity.elastic) get_symbol_name_mapping() (AllCoordinationGeometries method) get_symm_bands() (BoltztrapAnalyzer method) get_symm_data() (in module pymatgen.symmetry.groups) 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_task_scfcycles() (Flow method) get_tasker2_slabs() (Slab method) get_tgt() (ElasticTensorExpansion method) get_thermal_conductivity() (BoltztrapAnalyzer method) get_ticks() (BSPlotter method) (PhononBSPlotter method) get_total_ionic_dipole() (in module pymatgen.analysis.ferroelectricity.polarization) get_trans_mat() (GrainBoundaryGenerator static method) get_transformation() (StructureMatcher method) get_transition_chempots() (PhaseDiagram method) get_tri_area() (in module pymatgen.analysis.wulff) get_type() (LocalStructOrderParams method) get_unique_families() (in module pymatgen.analysis.diffraction.core) get_unit_primitive_area() (SlabEntry property) get_unreconstructed_slabs() (ReconstructionGenerator method) get_unstable_entries() (InsertionElectrode method) get_unstable_FCM() (ForceConstantMatrix method) get_uvec() (in module pymatgen.core.tensors) get_v() (StaticPotential method) get_valences() (BVAnalyzer method) get_valid_paths() (AbstractDrone method) (GaussianToComputedEntryDrone method) (VaspToComputedEntryDrone method) get_values() (AbinitTimer method) get_vars_dataframe() (Node method) get_vasp_input() (TransformedStructure method) (VaspInputSet method) get_vasp_kpoint_file_sym() (in module pymatgen.command_line.aconvasp_caller) get_vasprun_outcar() (in module pymatgen.io.vasp.sets) get_vbm() (BandStructure method) get_vector_along_lattice_directions() (Lattice method) get_void_volume_surfarea() (in module pymatgen.io.zeopp) get_voigt_dict() (Tensor static method) get_voronoi_nodes() (in module pymatgen.io.zeopp) get_voronoi_polyhedra() (VoronoiNN method) get_wallace_tensor() (ElasticTensorExpansion method) get_weights() (in module pymatgen.util.convergence) get_weights_of_nn_sites() (NearNeighbors method) get_wigner_seitz_cell() (Lattice method) get_wt_fraction() (Composition method) get_wulff_shape() (MPRester method) get_xas_data() (MPRester method) get_xrd_plot() (in module pymatgen.cli.pmg_plot) get_xyz_magmom_with_001_saxis() (Magmom method) get_yield_stress() (ElasticTensorExpansion method) get_z_ordered_elmap() (in module pymatgen.analysis.bond_valence) get_zmatrix() (GaussianInput method) get_zt() (BoltztrapAnalyzer method) getmu_vertices_stability_phase() (PhaseDiagram method) getsize() (File 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_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_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) gibbs_binding_energy() (SlabEntry method) gkk_filepath() (AnaddbTask property) GKKPWork (class in pymatgen.io.abinit.works) 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) graphviz_imshow() (Flow method) green_kristoffel() (ElasticTensor method) green_lagrange_strain() (Deformation property) grid_off (WulffShape attribute) gridfs_files() (NodeResults property) GridFsFile (class in pymatgen.io.abinit.nodes) Grosspop (class in pymatgen.io.lobster) ground_state_term_symbol() (Element property) GroundStateScfCycle (class in pymatgen.io.abinit.abiinspect) group (Element attribute) group() (Element property) group_by_types() (SiteCollection method) group_entries_by_structure() (in module pymatgen.entries.entry_tools) group_molecules() (MoleculeMatcher method) group_structures() (StructureMatcher method) groupby_status() (Flow method) groupby_task_class() (Flow method) gruneisen_parameter() (QuasiharmonicDebyeApprox method) GulpCaller (class in pymatgen.command_line.gulp_caller) GulpConvergenceError GulpError GulpIO (class in pymatgen.command_line.gulp_caller) gw_run() (Fiesta_run method) gwcalctyp() (SelfEnergy property) gweight() (NormalizedAngleDistanceNbSetWeight method)

H

H (Element attribute) haeberlen_values() (ChemicalShielding property) HaeberlenNotation (ChemicalShielding attribute) halogen_list (MoleculeStructureComparator attribute) handle_input_event() (DilatmxErrorHandler method) handle_task_event() (DilatmxErrorHandler method) has_abiext() (Directory method) has_antibnd_states_below_efermi() (Cohp method) has_chrooted() (Flow property) has_db() (Flow property) (TaskManager property) 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_mpi (AbinitBuild attribute) has_mpiio (AbinitBuild attribute) has_nac() (PhononBandStructure property) has_netcdf (AbinitBuild attribute) has_node_failures() (QueueJob property) has_omp (AbinitBuild attribute) has_omp() (TaskManager property) has_option() (AdfKey method) has_queue() (TaskManager property) has_scheduler() (Flow property) has_subkey() (AdfKey method) have_consistent_saxis() (Magmom static method) have_equivalent_surfaces() (Slab method) He (Element attribute) Header (class in pymatgen.io.feff.inputs) header() (AbstractFeffInputSet method) (FEFFDictSet method) header_string_from_file() (Header static method) HeisenbergMapper (class in pymatgen.analysis.magnetism.heisenberg) HeisenbergScreener (class in pymatgen.analysis.magnetism.heisenberg) helmholtz_free_energy() (PhononDos method) hessian (GaussianOutput attribute) hex() (HighSymmKpath method) hexagonal() (Lattice static method) Hf (Element attribute) Hg (Element attribute) HighSymmKpath (class in pymatgen.symmetry.bandstructure) HilbertTransform (class in pymatgen.io.abinit.abiobjects) hill_formula() (Composition property) hint_for_accuracy() (Pseudo method) hints() (CoordinationGeometry.NeighborsSetsHints method) history (Relaxation attribute) HistoryNode (class in pymatgen.util.provenance) HistoryRecord (class in pymatgen.io.abinit.nodes) hkl_list (WulffShape attribute) hkl_transformation() (in module pymatgen.core.surface) hkl_tuple_to_str() (in module pymatgen.analysis.wulff) Ho (Element attribute) homogeneous_poisson() (ElasticTensor property) htmlify() (in module pymatgen.util.string) hubbards() (Vasprun property) HYB_GGA_X_N12_SX (LibxcFunc attribute) HYB_GGA_X_SOGGA11_X (LibxcFunc attribute) HYB_GGA_XC_B1LYP (LibxcFunc attribute) HYB_GGA_XC_B1PW91 (LibxcFunc attribute) HYB_GGA_XC_B1WC (LibxcFunc attribute) HYB_GGA_XC_B3LYP (LibxcFunc attribute) HYB_GGA_XC_B3LYP5 (LibxcFunc attribute) HYB_GGA_XC_B3LYPs (LibxcFunc attribute) HYB_GGA_XC_B3P86 (LibxcFunc attribute) HYB_GGA_XC_B3PW91 (LibxcFunc attribute) HYB_GGA_XC_B97 (LibxcFunc attribute) HYB_GGA_XC_B97_1 (LibxcFunc attribute)

HYB_GGA_XC_B97_1p (LibxcFunc attribute) HYB_GGA_XC_B97_2 (LibxcFunc attribute) HYB_GGA_XC_B97_3 (LibxcFunc attribute) HYB_GGA_XC_B97_K (LibxcFunc attribute) HYB_GGA_XC_BHANDH (LibxcFunc attribute) HYB_GGA_XC_BHANDHLYP (LibxcFunc attribute) HYB_GGA_XC_CAM_B3LYP (LibxcFunc attribute) HYB_GGA_XC_CAMY_B3LYP (LibxcFunc attribute) HYB_GGA_XC_CAMY_BLYP (LibxcFunc attribute) HYB_GGA_XC_CAP0 (LibxcFunc attribute) HYB_GGA_XC_EDF2 (LibxcFunc attribute) HYB_GGA_XC_HJS_B88 (LibxcFunc attribute) HYB_GGA_XC_HJS_B97X (LibxcFunc attribute) HYB_GGA_XC_HJS_PBE (LibxcFunc attribute) HYB_GGA_XC_HJS_PBE_SOL (LibxcFunc attribute) HYB_GGA_XC_HPBEINT (LibxcFunc attribute) HYB_GGA_XC_HSE03 (LibxcFunc attribute) HYB_GGA_XC_HSE06 (LibxcFunc attribute) HYB_GGA_XC_LC_VV10 (LibxcFunc attribute) HYB_GGA_XC_LCY_BLYP (LibxcFunc attribute) HYB_GGA_XC_LCY_PBE (LibxcFunc attribute) HYB_GGA_XC_LRC_WPBE (LibxcFunc attribute) HYB_GGA_XC_LRC_WPBEH (LibxcFunc attribute) HYB_GGA_XC_MB3LYP_RC04 (LibxcFunc attribute) HYB_GGA_XC_mPW1K (LibxcFunc attribute) HYB_GGA_XC_mPW1PW (LibxcFunc attribute) HYB_GGA_XC_MPW3LYP (LibxcFunc attribute) HYB_GGA_XC_MPW3PW (LibxcFunc attribute) HYB_GGA_XC_MPWLYP1M (LibxcFunc attribute) HYB_GGA_XC_O3LYP (LibxcFunc attribute) HYB_GGA_XC_PBE0_13 (LibxcFunc attribute) HYB_GGA_XC_PBEH (LibxcFunc attribute) HYB_GGA_XC_REVB3LYP (LibxcFunc attribute) HYB_GGA_XC_SB98_1a (LibxcFunc attribute) HYB_GGA_XC_SB98_1b (LibxcFunc attribute) HYB_GGA_XC_SB98_1c (LibxcFunc attribute) HYB_GGA_XC_SB98_2a (LibxcFunc attribute) HYB_GGA_XC_SB98_2b (LibxcFunc attribute) HYB_GGA_XC_SB98_2c (LibxcFunc attribute) HYB_GGA_XC_TUNED_CAM_B3LYP (LibxcFunc attribute) HYB_GGA_XC_WB97 (LibxcFunc attribute) HYB_GGA_XC_WB97X (LibxcFunc attribute) HYB_GGA_XC_WB97X_D (LibxcFunc attribute) HYB_GGA_XC_WB97X_V (LibxcFunc attribute) HYB_GGA_XC_X3LYP (LibxcFunc attribute) HYB_MGGA_X_DLDF (LibxcFunc attribute) HYB_MGGA_X_MN12_SX (LibxcFunc attribute) HYB_MGGA_X_MN15 (LibxcFunc attribute) HYB_MGGA_X_MS2H (LibxcFunc attribute) HYB_MGGA_X_MVSH (LibxcFunc attribute) HYB_MGGA_X_SCAN0 (LibxcFunc attribute) HYB_MGGA_XC_B86B95 (LibxcFunc attribute) HYB_MGGA_XC_B88B95 (LibxcFunc attribute) HYB_MGGA_XC_BB1K (LibxcFunc attribute) HYB_MGGA_XC_M05 (LibxcFunc attribute) HYB_MGGA_XC_M05_2X (LibxcFunc attribute) HYB_MGGA_XC_M06 (LibxcFunc attribute) HYB_MGGA_XC_M06_2X (LibxcFunc attribute) HYB_MGGA_XC_M06_HF (LibxcFunc attribute) HYB_MGGA_XC_M08_HX (LibxcFunc attribute) HYB_MGGA_XC_M08_SO (LibxcFunc attribute) HYB_MGGA_XC_M11 (LibxcFunc attribute) HYB_MGGA_XC_MPW1B95 (LibxcFunc attribute) HYB_MGGA_XC_MPWB1K (LibxcFunc attribute) HYB_MGGA_XC_PW6B95 (LibxcFunc attribute) HYB_MGGA_XC_PW86B95 (LibxcFunc attribute) HYB_MGGA_XC_PWB6K (LibxcFunc attribute) HYB_MGGA_XC_REVTPSSH (LibxcFunc attribute) HYB_MGGA_XC_TPSSH (LibxcFunc attribute) HYB_MGGA_XC_WB97M_V (LibxcFunc attribute) HYB_MGGA_XC_X1B95 (LibxcFunc attribute) HYB_MGGA_XC_XB1K (LibxcFunc attribute) hybersten (PPModelModes attribute)

I

I (Element attribute) icohp (IcohpValue attribute) icohp() (IcohpValue property) IcohpCollection (class in pymatgen.electronic_structure.cohp) icohpcollection() (Icohplist property) Icohplist (class in pymatgen.io.lobster) icohplist() (Icohplist property) IcohpValue (class in pymatgen.electronic_structure.cohp) icohpvalue() (IcohpValue method) icsd_oxidation_states() (Element property) id_generator() (in module pymatgen.util.convergence) idos (Vasprun attribute) iflat_nodes() (Flow method) iflat_tasks() (Flow method) iflat_tasks_wti() (Flow method) image() (Neighbor property) 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) in_spectator_mode() (Node property) Incar (class in pymatgen.io.vasp.inputs) incar (Vasprun attribute) incar() (DictSet property) (MPNMRSet property) (MPNonSCFSet property) (MPSOCSet property) (MPStaticSet property) (MVLGBSet property) (MVLGWSet property) (VaspInputSet property) InchiMolAtomMapper (class in pymatgen.analysis.molecule_matcher) inclvkb() (ExcHamiltonian property) increase_cpus() (CorrectorProtocolScheduler method) increase_mem() (CorrectorProtocolScheduler method) (TaskManager method) increase_ncpus() (TaskManager method) increase_resources() (TaskManager method) increase_time() (CorrectorProtocolScheduler method) (TaskManager method) ind_zero_freq (PhononDos attribute) indent() (ExcitingInput static method) index() (ConnectedSite property) (Neighbor property) indices_from_symbol() (SiteCollection method) indices_separate() (Plane method) info (AbinitBuild attribute) info() (Dependency property) (NodeHistory method) (StructureEnvironments.NeighborsSet property) info_dict() (LibxcFunc property) infos_on_basis_set() (Basis_set_reader method) infos_on_system() (FiestaInput property) init_3points() (Plane method) init_counter() (in module pymatgen.io.abinit.nodes) init_neighbors_sets() (StructureEnvironments method) InitializationChemenvError insert() (Molecule method) (Structure method) insert_node() (MoleculeGraph method) (StructureGraph method) InsertionElectrode (class in pymatgen.apps.battery.insertion_battery) InsertionVoltagePair (class in pymatgen.apps.battery.insertion_battery) InsertSitesTransformation (class in pymatgen.transformations.site_transformations) inspect() (Flow method) (PhononTask method) (RelaxTask method) (ScfTask method) install_event_handlers() (Node method) 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) inv_ordered_indices() (SeparationPlane property) invdist() (NormalizedAngleDistanceNbSetWeight method) inverse() (AbstractTransformation property) (AddAdsorbateTransformation property) (AddSitePropertyTransformation property) (AutoOxiStateDecorationTransformation property) (ChargeBalanceTransformation property) (ChargedCellTransformation property) (ConventionalCellTransformation property) (CubicSupercellTransformation property) (DefectTransformation property) (DeformStructureTransformation property) (DiscretizeOccupanciesTransformation property) (DisorderOrderedTransformation property) (DopingTransformation property) (EnumerateStructureTransformation property) (GrainBoundaryTransformation property) (InsertSitesTransformation property) (JonesFaithfulTransformation property) (MagOrderingTransformation property) (MultipleSubstitutionTransformation property) (OrderDisorderedStructureTransformation property) (OxidationStateDecorationTransformation property) (OxidationStateRemovalTransformation property) (PartialRemoveSitesTransformation property) (PartialRemoveSpecieTransformation property) (PerturbStructureTransformation property) (PrimitiveCellTransformation property) (RemoveSitesTransformation property) (RemoveSpeciesTransformation property) (ReplaceSiteSpeciesTransformation property) (RotationTransformation property) (SQSTransformation property) (ScaleToRelaxedTransformation property) (SlabTransformation property) (SubstituteSurfaceSiteTransformation property) (SubstitutionPredictorTransformation property) (SubstitutionTransformation property) (SuperTransformation property) (SupercellTransformation 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_or_solid_comp_object() (in module pymatgen.analysis.pourbaix_diagram) IonEntry (class in pymatgen.analysis.pourbaix_diagram) ionic_element_list (MoleculeStructureComparator attribute) ionic_radii (Element attribute) ionic_radii() (Element property) ionic_radius (Specie attribute) ionic_radius() (Specie property) ionic_steps (Vasprun attribute) IONMOV_DEFAULT (RelaxationMethod attribute) Ir (Element attribute) irdvars_for_ext() (in module pymatgen.io.abinit.utils) is_a_valid_coordination_geometry() (AllCoordinationGeometries method) is_actinoid (Element attribute) is_actinoid() (Element property) is_alkali (Element attribute) is_alkali() (Element property) is_alkaline (Element attribute) is_alkaline() (Element property) is_already_analyzed() (in module pymatgen.core.surface) is_anion_cation_bond() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) is_block_key() (AdfKey method) is_bonded() (CovalentBond static method) is_c_kind() (LibxcFunc property)

is_chalcogen() (Element property) is_close_to() (ChemicalEnvironments method) (DetailedVoronoiContainer method) is_complete() (PseudoTable method) is_completed() (QueueJob property) is_converged() (in module pymatgen.io.abinit.helpers) (WorkFunctionAnalyzer method) is_coord_subset() (in module pymatgen.util.coord) is_coord_subset_pbc() (in module pymatgen.util.coord) (in module pymatgen.util.coord_cython) is_critical() (Status property) is_dfpt_task() (AbinitTask property) is_element() (Composition property) (ComputedEntry property) (GrandPotPDEntry property) (PDEntry property) is_failed (AdfOutput attribute) is_failed() (QueueJob property) is_file() (Node property) is_fit_to_structure() (Tensor method) (TensorCollection method) is_flow() (Node property) is_gga_family() (LibxcFunc property) is_gs_task() (AbinitTask property) is_halogen (Element attribute) is_halogen() (Element property) is_hexagonal() (Lattice method) is_homogeneous() (KSampling property) is_hubbard() (Vasprun property) is_hyb_gga_family() (LibxcFunc property) is_hyb_mgga_family() (LibxcFunc property) is_image() (VoronoiPolyhedron method) is_implemented() (CoordinationGeometry method) is_in_list() (Plane method) is_in_plane() (Plane method) is_independent() (Deformation method) is_internal_crash (AdfOutput attribute) is_jahn_teller_active() (JahnTellerAnalyzer method) is_k_kind() (LibxcFunc property) is_lanthanoid (Element attribute) is_lanthanoid() (Element property) is_laue() (SpacegroupAnalyzer method) is_lda_family() (LibxcFunc property) is_magnetic() (CollinearMagneticStructureAnalyzer property) is_metal() (BandStructure method) (Element property) is_metalloid (Element attribute) is_metalloid() (Element property) is_mgga_family() (LibxcFunc property) is_noble_gas (Element attribute) is_noble_gas() (Element property) is_numeric() (in module pymatgen.io.adf) is_one_to_many() (AbstractTransformation property) (AddAdsorbateTransformation property) (AddSitePropertyTransformation property) (AutoOxiStateDecorationTransformation property) (ChargeBalanceTransformation property) (ChargedCellTransformation property) (ConventionalCellTransformation property) (CubicSupercellTransformation property) (DefectTransformation property) (DeformStructureTransformation property) (DiscretizeOccupanciesTransformation property) (DisorderOrderedTransformation property) (DopingTransformation property) (EnumerateStructureTransformation property) (GrainBoundaryTransformation property) (InsertSitesTransformation property) (MagOrderingTransformation property) (MultipleSubstitutionTransformation property) (OrderDisorderedStructureTransformation property) (OxidationStateDecorationTransformation property) (OxidationStateRemovalTransformation property) (PartialRemoveSitesTransformation property) (PartialRemoveSpecieTransformation property) (PerturbStructureTransformation property) (PrimitiveCellTransformation property) (RemoveSitesTransformation property) (RemoveSpeciesTransformation property) (ReplaceSiteSpeciesTransformation property) (RotationTransformation property) (SQSTransformation property) (ScaleToRelaxedTransformation property) (SlabTransformation property) (SubstituteSurfaceSiteTransformation property) (SubstitutionPredictorTransformation property) (SubstitutionTransformation property) (SuperTransformation property) (SupercellTransformation property) (TranslateSitesTransformation property) is_ordered() (Site property) (SiteCollection property) is_orthogonal() (Lattice property) is_ox() (in module pymatgen.analysis.structure_prediction.volume_predictor) is_pcm (GaussianOutput attribute) is_periodic_image() (PeriodicSite method) is_polar() (Slab method) is_post_transition_metal (Element attribute) is_post_transition_metal() (Element property) is_quadrupolar() (Element property) is_rare_earth_metal (Element attribute) is_rare_earth_metal() (Element property) is_redox_active_intercalation() (in module pymatgen.apps.battery.analyzer) is_rotation() (SquareTensor method) is_running() (QueueJob property) 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_task() (Node property) is_transition_metal (Element attribute) is_transition_metal() (Element property) is_valid() (SiteCollection method) is_valid_bibtex() (in module pymatgen.util.provenance) is_valid_op() (PointGroupAnalyzer method) is_valid_symbol (Element attribute) is_voigt_symmetric() (Tensor method) (TensorCollection method) is_work() (Node property) is_x_kind() (LibxcFunc property) is_xc_kind() (LibxcFunc property) IsingModel (class in pymatgen.analysis.energy_models) isinstance() (Node method) isnc() (AbinitTask property) (Pseudo property) (Work property) isncfile() (File property) isomorphic_to() (MoleculeGraph method) IsomorphismMolAtomMapper (class in pymatgen.analysis.molecule_matcher) ispaw() (AbinitTask property) (Pseudo property) (Work property) IStructure (class in pymatgen.core.structure) items() (CyclesPlotter method) (TensorMapping method) iterative_symmetrize() (in module pymatgen.symmetry.analyzer) iterlines() (in module pymatgen.io.adf) IUCr_symbol() (CoordinationGeometry property) IUCr_symbol_str() (CoordinationGeometry property) iupac_formula() (Composition property) iupac_ordering (Element attribute) iupac_ordering() (Element property) IUPAC_symbol() (CoordinationGeometry property) IUPAC_symbol_str() (CoordinationGeometry property)

J

j() (Orbital property) JahnTellerAnalyzer (class in pymatgen.analysis.magnetism.jahnteller) jimage() (ConnectedSite property) JmolNN (class in pymatgen.analysis.local_env) JobStatus (class in pymatgen.io.abinit.qjobs)

JonesFaithfulTransformation (class in pymatgen.symmetry.settings) json_dump() (NodeResults method) json_load() (NodeResults class method) json_pretty_dump() (in module pymatgen.util.serialization) JSON_SCHEMA (NodeResults attribute)

K

K (Element attribute) k_reuss() (ElasticTensor property) k_voigt() (ElasticTensor property) k_vrh() (ElasticTensor property) kappa() (ChemicalShielding.MarylandNotation property) key() (AdfKey property) keyPressEvent() (MultiStructuresInteractorStyle method) (StructureInteractorStyle method) keyword_line() (GulpIO method) keywords (PotcarSingle attribute) kpath() (HighSymmKpath property) Kpoint (class in pymatgen.electronic_structure.bandstructure) Kpoints (class in pymatgen.io.vasp.inputs) kpoints (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) Kr (Element attribute) KSampling (class in pymatgen.io.abinit.abiobjects) KSamplingModes (class in pymatgen.io.abinit.abiobjects) KumagaiCorrection (class in pymatgen.analysis.defects.corrections)

L

l() (Orbital property) (OrbitalDescription property) l_local() (Pseudo property) l_max() (Pseudo property) La (Element attribute) label (SlabEntry attribute) label() (FreqUnits property) (Kpoint property) labels() (InterfacialReactivity method) LammpsBox (class in pymatgen.io.lammps.data) LammpsData (class in pymatgen.io.lammps.data) LammpsDump (class in pymatgen.io.lammps.outputs) LammpsRun (class in pymatgen.io.lammps.inputs) LammpsRunner (class in pymatgen.io.lammps.utils) laplacian() (CriticalPoint property) last_etotal() (D2DEScfCycle property) (GroundStateScfCycle property) last_iteration() (ScfCycle property) last_nneigh() (LocalStructOrderParams property) last_resort_solution() (AbstractError method) latexify() (in module pymatgen.util.string) latexify_ion() (in module pymatgen.analysis.pourbaix_diagram) latexify_spacegroup() (in module pymatgen.util.string) Lattice (class in pymatgen.core.lattice) lattice (WulffShape attribute) lattice() (IStructure property) (Kpoint property) (PeriodicSite property) (Structure property) (Vasprun 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_rec() (Vasprun property) lattice_type() (PWOutput property) launch() (TaskManager method) 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_X (LibxcFunc attribute) LDA_X_1D (LibxcFunc attribute)

LDA_X_2D (LibxcFunc attribute) LDA_XC_KSDT (LibxcFunc attribute) LDA_XC_TETER93 (LibxcFunc attribute) LDA_XC_ZLP (LibxcFunc attribute) LDos (class in pymatgen.io.feff.outputs) leftButtonPressEvent() (StructureInteractorStyle method) leftButtonReleaseEvent() (StructureInteractorStyle method) Length (in module pymatgen.core.units) length() (CovalentBond property) lengths() (Lattice property) lengths_and_angles() (Lattice property) levelname (HistoryRecord attribute) levelno (HistoryRecord attribute) Li (Element attribute) library_line() (GulpIO method) LibxcFunc (class in pymatgen.core.libxcfunc) LightStructureEnvironments (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) LightStructureEnvironments.NeighborsSet (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) likely_code_error() (QueueJob method) limit() (MemoryCancelError property) (TimeCancelError property) linden (PPModelModes attribute) line_intersection() (Simplex method) Line_mode (Kpoints_supported_modes attribute) linear_add() (VolumetricData method) LinearAssignment (class in pymatgen.optimization.linear_assignment) (class in pymatgen.optimization.linear_assignment_numpy) linearly_equidistant() (CNBiasNbSetWeight class method) lineno (HistoryRecord attribute) (YamlDoc attribute) link0 (GaussianOutput attribute) link_marked_atoms() (FunctionalGroupExtractor method) liquid_range (Element attribute) list_filepaths() (Directory method) list_prediction() (SubstitutionPredictor method) listext() (Flow 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) load_module() (ScriptEditor method) load_modules() (ScriptEditor method) loadfn() (in module pymatgen) LobsterBandStructureSymmLine (class in pymatgen.electronic_structure.bandstructure) LobsterCompleteDos (class in pymatgen.electronic_structure.dos) Lobsterin (class in pymatgen.io.lobster) Lobsterout (class in pymatgen.io.lobster) LobsterSet (class in pymatgen.io.vasp.sets) LocalGeometryFinder (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) localopt() (BabelMolAdaptor method) LocalStructOrderParams (class in pymatgen.analysis.local_env) lockxyz (ExcitingInput attribute) lockxyz() (ExcitingInput property) Locpot (class in pymatgen.io.vasp.outputs) locpot_along_c (WorkFunctionAnalyzer attribute) log_correction() (Node method) logger (in module pymatgen.command_line.critic2_caller) long_name (Element attribute) long_v() (ElasticTensor method) look_before_you_leap() (Flow method) lower_and_check_unique() (in module pymatgen.io.qchem.utils) lowest_energy_structure() (OrderDisorderedStructureTransformation property) Lr (Element attribute) Lu (Element attribute)

M

MAGIC (D2DEScfCycle attribute) (GroundStateScfCycle attribute) Magmom (class in pymatgen.electronic_structure.core) magmoms() (CollinearMagneticStructureAnalyzer property) magnetic_deformation() (in module pymatgen.analysis.magnetism.analyzer) magnetic_species_and_magmoms() (CollinearMagneticStructureAnalyzer property) MagneticSpaceGroup (class in pymatgen.symmetry.maggroups) MagneticStructureEnumerator (class in pymatgen.analysis.magnetism.analyzer) magnetization (Outcar attribute) MagOrderingTransformation (class in pymatgen.transformations.advanced_transformations) MagOrderParameterConstraint (class in pymatgen.transformations.advanced_transformations) MagSymmOp (class in pymatgen.core.operations) mAh() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) main() (in module pymatgen.cli.feff_input_generation) (in module pymatgen.cli.feff_plot_cross_section) (in module pymatgen.cli.feff_plot_dos) (in module pymatgen.cli.gaussian_analyzer) (in module pymatgen.cli.get_environment) (in module pymatgen.cli.pmg) make3d() (BabelMolAdaptor method) make_dir() (File method) make_FULL_BSE_Densities_folder() (FiestaInput method) make_input() (OpticTask method) make_interface() (InterfaceBuilder method) make_light_tarfile() (Flow method) make_links() (AnaddbTask method) (OpticTask method) make_movie() (in module pymatgen.vis.structure_vtk) make_qadapter() (in module pymatgen.io.abinit.qadapters) make_scheduler() (Flow method) make_supercell() (Structure method) make_supercells_with_defects() (StructureMotifInterstitial method) make_symmetric_matrix_from_upper_tri() (in module pymatgen.util.num) make_tarfile() (Flow method) makedirs() (Directory method) map2rpn() (in module pymatgen.io.abinit.utils) maps (ForceField attribute) maps_and_surfaces() (DetailedVoronoiContainer method) maps_and_surfaces_bounded() (DetailedVoronoiContainer method) maryland_values() (ChemicalShielding property) Mass (in module pymatgen.core.units) mass_charge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) mass_discharge() (AbstractVoltagePair property) (ConversionVoltagePair property) (InsertionVoltagePair property) masses (ForceField attribute) masses() (Dynmat property) MasterProcessMemoryCancelError (class in pymatgen.io.abinit.scheduler_error_parsers) match_as_dict() (ZSLGenerator method) matches() (IStructure method) matches_ordering() (CollinearMagneticStructureAnalyzer method) material_formula() (Xmu property) MaterialsProjectAqueousCompatibility (class in pymatgen.entries.compatibility) MaterialsProjectCompatibility (class in pymatgen.entries.compatibility) matrix() (Lattice property) matrixTimesVector() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) max_cation_insertion() (BatteryAnalyzer property) max_cation_removal() (BatteryAnalyzer property) max_connectivity() (VoronoiConnectivity property) max_cores (ParalHints attribute) max_cores() (TaskManager property) max_delta_volume() (AbstractElectrode property) max_efficiency (ParalHints attribute) max_electronegativity() (MolecularOrbitals method) max_mem_per_proc (ParalHints attribute) max_oxidation_state (Element attribute) max_oxidation_state() (Element property) max_speedup (ParalHints attribute) max_spline_jump() (EnergyTrend method) max_spline_jumps() (Polarization method) max_voltage() (AbstractElectrode property) max_voltage_step() (AbstractElectrode property) maxlen (CifBlock attribute) maxloc() (in module pymatgen.util.num) mcl() (HighSymmKpath method) mclc1() (HighSymmKpath method) mclc2() (HighSymmKpath method) mclc3() (HighSymmKpath method) mclc4() (HighSymmKpath method) mclc5() (HighSymmKpath method) Mcsqs (class in pymatgen.io.atat) Md (Element attribute) md() (LammpsRun class method) md5 (Pseudo attribute) md_filepath() (AnaddbTask property) mean_estimator() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) mean_stress() (Stress property) measure() (in module pymatgen.util.convergence) mehring_values() (ChemicalShielding property) melting_point (Element attribute) mem_per_proc() (TaskManager property) Memory (in module pymatgen.core.units) MemoryCancelError (class in pymatgen.io.abinit.scheduler_error_parsers) mendeleev_no (Element attribute) merge() (Mrgddb method) (Mrgdvdb method) (Mrggkk method) merge_qpoints() (Mrgscr method) merge_scrfiles() (QptdmWork method) merge_sites() (Structure method) merge_slabs() (in module pymatgen.analysis.interface) message (HistoryRecord attribute) metal_edge_extender() (in module pymatgen.analysis.fragmenter) metallic_radius() (Element property) metric_tensor() (Lattice property) Mg (Element attribute) MGGA_C_BC95 (LibxcFunc attribute) MGGA_C_CC06 (LibxcFunc attribute) MGGA_C_CS (LibxcFunc attribute) MGGA_C_DLDF (LibxcFunc attribute) MGGA_C_M05 (LibxcFunc attribute) MGGA_C_M05_2X (LibxcFunc attribute) MGGA_C_M06 (LibxcFunc attribute) MGGA_C_M06_2X (LibxcFunc attribute) MGGA_C_M06_HF (LibxcFunc attribute) MGGA_C_M06_L (LibxcFunc attribute) MGGA_C_M08_HX (LibxcFunc attribute) MGGA_C_M08_SO (LibxcFunc attribute) MGGA_C_M11 (LibxcFunc attribute) MGGA_C_M11_L (LibxcFunc attribute) MGGA_C_MN12_L (LibxcFunc attribute) MGGA_C_MN12_SX (LibxcFunc attribute) MGGA_C_MN15 (LibxcFunc attribute) MGGA_C_MN15_L (LibxcFunc attribute) MGGA_C_PKZB (LibxcFunc attribute) MGGA_C_REVTPSS (LibxcFunc attribute) MGGA_C_SCAN (LibxcFunc attribute) MGGA_C_TPSS (LibxcFunc attribute) MGGA_C_TPSSLOC (LibxcFunc attribute) MGGA_C_VSXC (LibxcFunc attribute) MGGA_X_2D_PRHG07 (LibxcFunc attribute) MGGA_X_2D_PRHG07_PRP10 (LibxcFunc attribute) MGGA_X_BJ06 (LibxcFunc attribute) MGGA_X_BLOC (LibxcFunc attribute) MGGA_X_BR89 (LibxcFunc attribute) MGGA_X_GVT4 (LibxcFunc attribute) MGGA_X_LTA (LibxcFunc attribute) MGGA_X_M05 (LibxcFunc attribute) MGGA_X_M05_2X (LibxcFunc attribute) MGGA_X_M06 (LibxcFunc attribute) MGGA_X_M06_2X (LibxcFunc attribute) MGGA_X_M06_HF (LibxcFunc attribute)

MGGA_X_M06_L (LibxcFunc attribute) MGGA_X_M08_HX (LibxcFunc attribute) MGGA_X_M08_SO (LibxcFunc attribute) MGGA_X_M11 (LibxcFunc attribute) MGGA_X_M11_L (LibxcFunc attribute) MGGA_X_MBEEF (LibxcFunc attribute) MGGA_X_MBEEFVDW (LibxcFunc attribute) MGGA_X_MK00 (LibxcFunc attribute) MGGA_X_MK00B (LibxcFunc attribute) MGGA_X_MN12_L (LibxcFunc attribute) MGGA_X_MN15_L (LibxcFunc attribute) MGGA_X_MODTPSS (LibxcFunc attribute) MGGA_X_MS0 (LibxcFunc attribute) MGGA_X_MS1 (LibxcFunc attribute) MGGA_X_MS2 (LibxcFunc attribute) MGGA_X_MVS (LibxcFunc attribute) MGGA_X_PKZB (LibxcFunc attribute) MGGA_X_REVTPSS (LibxcFunc attribute) MGGA_X_RPP09 (LibxcFunc attribute) MGGA_X_SCAN (LibxcFunc attribute) MGGA_X_TAU_HCTH (LibxcFunc attribute) MGGA_X_TB09 (LibxcFunc attribute) MGGA_X_TPSS (LibxcFunc attribute) MGGA_XC_B97M_V (LibxcFunc attribute) MGGA_XC_OTPSS_D (LibxcFunc attribute) MGGA_XC_TPSSLYP1W (LibxcFunc attribute) MGGA_XC_ZLP (LibxcFunc attribute) micro_pyawk() (in module pymatgen.util.io_utils) miller_area (WulffShape attribute) miller_area_dict() (WulffShape property) miller_energy_dict() (WulffShape property) miller_index (Slab attribute) (SlabEntry attribute) (SlabGenerator attribute) miller_index_from_sites() (in module pymatgen.core.surface) miller_list (WulffShape attribute) min_cost() (LinearAssignment property) min_freq() (PhononBandStructure method) min_max_indexes() (in module pymatgen.util.num) min_oxidation_state (Element attribute) min_oxidation_state() (Element property) min_slab_size (SlabGenerator attribute) min_vac_size (SlabGenerator attribute) min_voltage() (AbstractElectrode property) mineral_hardness (Element attribute) minimize_matrix() (EwaldMinimizer method) minimized_sum() (EwaldMinimizer property) minimum() (InterfacialReactivity method) minimum_geometries() (ChemicalEnvironments method) minimum_geometry() (ChemicalEnvironments method) MinimumDistanceNN (class in pymatgen.analysis.local_env) MinimumOKeeffeNN (class in pymatgen.analysis.local_env) MinimumVIRENN (class in pymatgen.analysis.local_env) minloc() (in module pymatgen.util.num) MITAqueousCompatibility (class in pymatgen.entries.compatibility) MITCompatibility (class in pymatgen.entries.compatibility) MITMDSet (class in pymatgen.io.vasp.sets) MITNEBSet (class in pymatgen.io.vasp.sets) MITRelaxSet (class in pymatgen.io.vasp.sets) MixedPotential (class in pymatgen.analysis.path_finder) Mn (Element attribute) Mo (Element attribute) MO_coefficients (GaussianOutput attribute) MoabJob (class in pymatgen.io.abinit.qjobs) mode() (Smearing property) ModelDielectricFunction (class in pymatgen.io.abinit.abiobjects) MODELS (EOS attribute) modify_lattice() (Structure method) module (HistoryRecord attribute) MODULE_DIR (PymatgenTest attribute) molar_volume (Element attribute) molecular_orbital (GaussianOutput attribute) MolecularOrbitals (class in pymatgen.core.molecular_orbitals) Molecule (class in pymatgen.core.structure) molecule() (FiestaInput property) (GaussianInput property) (NwInput property) (XYZ property) molecule_template() (QCInput static method) MoleculeGraph (class in pymatgen.analysis.graphs) MoleculeMatcher (class in pymatgen.analysis.molecule_matcher) MoleculeStructureComparator (class in pymatgen.analysis.molecule_structure_comparator) MolGraphSplitError mongo_assimilate() (Flow method) mongo_getattr() (in module pymatgen.io.abinit.db) mongo_id() (Flow property) mongodb_upload() (Flow method) Monkhorst (Kpoints_supported_modes attribute) monkhorst (KSamplingModes attribute) monkhorst() (KSampling class method) monkhorst_automatic() (Kpoints static method) (KSampling class method) monoclinic() (Lattice static method) monolayer_vs_BE() (SurfaceEnergyPlotter method) monotonic() (in module pymatgen.util.num) mouseMoveEvent() (StructureInteractorStyle method) move() (File method) (Work method) move_atoms() (RelaxationMethod property) move_cell() (RelaxationMethod property) move_to_other_side() (SlabGenerator method) mp_symbol() (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) mpi_procs() (TaskManager property) 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 MPSOCSet (class in pymatgen.io.vasp.sets) MPStaticSet (class in pymatgen.io.vasp.sets) MPXANESSet (class in pymatgen.io.feff.sets) Mrgddb (class in pymatgen.io.abinit.wrappers) Mrgdvdb (class in pymatgen.io.abinit.wrappers) Mrggkk (class in pymatgen.io.abinit.wrappers) Mrgscr (class in pymatgen.io.abinit.wrappers) 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) multidimensional_optimization() (ParalHints method) MultiEntry (class in pymatgen.analysis.pourbaix_diagram) multiple_outputs_from_file() (QCOutput static method) MultipleSubstitutionTransformation (class in pymatgen.transformations.advanced_transformations) multiplicity() (Defect property) (DefectEntry property) MultiStructuresInteractorStyle (class in pymatgen.vis.structure_vtk) MultiStructuresVis (class in pymatgen.vis.structure_vtk) MultiWeightsChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) Murnaghan (class in pymatgen.analysis.eos) MVLElasticSet (class in pymatgen.io.vasp.sets) MVLGBSet (class in pymatgen.io.vasp.sets) MVLGWSet (class in pymatgen.io.vasp.sets) MVLNPTMDSet (class in pymatgen.io.vasp.sets) MVLRelax52Set (class in pymatgen.io.vasp.sets) MVLScanRelaxSet (class in pymatgen.io.vasp.sets) MVLSlabSet (class in pymatgen.io.vasp.sets) my_solid_angle() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils)

N

N (Element attribute) n() (Orbital property) Na (Element attribute) Nads_in_slab() (SlabEntry property) name (Author attribute) (HistoryNode attribute) (IonEntry attribute) (PDEntry attribute) (XcFunc attribute) name() (AbstractError property) (CorrectorProtocolApplication property) (CorrectorProtocolScheduler property) (Defect property) (DefectEntry property) (Interstitial property) (MoleculeGraph property) (MultiEntry property) (Node property) (PourbaixEntry property) (StructureGraph property) (Substitution property) (Vacancy property) names_and_values() (AbinitTimer method) NanoscaleStability (class in pymatgen.analysis.surface_analysis) natoms() (Dynmat property) (Poscar property) (Xdatcar property) Nb (Element attribute) nb (Wavecar attribute) nb_bands (BandStructure attribute) nb_bands() (Wavederf property) nb_kpoints() (Wavederf property) nbands() (Waveder property) NbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) ncores_allocated() (Flow property) ncores_reserved() (Flow property) ncores_used() (Flow property) ncpus() (AbinitTimer property) Nd (Element attribute) NDCalculator (class in pymatgen.analysis.diffraction.neutron) ndisps() (Dynmat 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) neighbors() (DetailedVoronoiContainer method) neighbors_map() (DetailedVoronoiContainer method) neighbors_surfaces() (DetailedVoronoiContainer method) neighbors_surfaces_bounded() (DetailedVoronoiContainer method) NeighborsNotComputedChemenvError nelec() (BoltztrapRunner property) nelect() (DictSet property) (Waveder property) nelectrons() (IMolecule property) (PotcarSingle property) net_magnetization() (Chgcar property) NetcdfReader (class in pymatgen.io.abinit.netcdf) new_with_fixed_mpi_omp() (TaskManager method) next() (YamlTokenizer method) next_doc_with_tag() (YamlTokenizer method) ngf (Outcar attribute) ngridpts (VolumetricData attribute) nH2O() (PourbaixEntry property) Ni (Element attribute) nionic_steps (Vasprun attribute) nk (Wavecar attribute) nkpoints() (Waveder property) NM (Ordering attribute) nmr_quadrupole_moment() (Element property) NNData (CrystalNN attribute) No (Element attribute) NO_AC (AdditionalConditions attribute) NO_ADDITIONAL_CONDITION (AdditionalConditions attribute)

NO_DEFAULT (class in pymatgen.io.abinit.netcdf) NO_E2SEB (AdditionalConditions attribute) NO_ELEMENT_TO_SAME_ELEMENT_BONDS (AdditionalConditions attribute) Node (class in pymatgen.io.abinit.nodes) node() (Dependency property) node_from_nid() (Flow method) node_id() (Node property) NodeCorrections (class in pymatgen.io.abinit.nodes) NodeError NodeFailureError (class in pymatgen.io.abinit.scheduler_error_parsers) NodeHistory (class in pymatgen.io.abinit.nodes) NodeResults (class in pymatgen.io.abinit.nodes) nodes() (NodeFailureError property) non_decreasing() (in module pymatgen.util.num) non_increasing() (in module pymatgen.util.num) NONE (AdditionalConditions attribute) none (OverwriteMagmomMode attribute) nonstoichiometric_symmetrized_slab() (SlabGenerator method) noppmodel (PPModelModes attribute) norm() (Lattice method) normal() (Slab property) normal_cdf_step() (in module pymatgen.analysis.chemenv.utils.math_utils) normal_modes (AdfOutput attribute) normalization_factor() (PourbaixEntry property) normalization_mass() (AbstractElectrode property) normalization_volume() (AbstractElectrode property) normalize (OverwriteMagmomMode attribute) normalize() (ComputedEntry method) (Spectrum method) (StaticPotential method) normalize_to() (BalancedReaction method) normalize_to_element() (BalancedReaction method) normalized_angles() (StructureEnvironments.NeighborsSet property) normalized_distances() (StructureEnvironments.NeighborsSet property) normalized_energy() (PourbaixEntry property) normalized_energy_at_conditions() (PourbaixEntry method) normalized_repr() (BalancedReaction property) normalized_repr_and_factor() (BalancedReaction method) NormalizedAngleDistanceNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) normalmode_eigenvals (Vasprun attribute) normalmode_eigenvecs (Vasprun attribute) nosmearing() (Smearing static method) now() (in module pymatgen.io.abinit.helpers) Np (Element attribute) npH() (PourbaixEntry property) nPhi() (PourbaixEntry property) NscfConvergenceWarning (class in pymatgen.io.abinit.events) NscfTask (class in pymatgen.io.abinit.tasks) 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_cores() (TaskManager property) num_corrections() (Node property) num_errored_tasks() (Flow property) num_excs() (PyFlowScheduler property) num_ops() (LocalStructOrderParams property) num_sites() (SiteCollection property) num_steps() (AbstractElectrode property) num_tasks() (Flow property) num_unconverged_tasks() (Flow property) number (Element attribute) number() (Element property) number_of_magnetic_sites() (CollinearMagneticStructureAnalyzer property) number_of_permutations() (CoordinationGeometry property) number_of_unique_magnetic_sites() (CollinearMagneticStructureAnalyzer method) NUMERIC_FIELDS (AbinitTimerSection attribute) numerical_tol (PhaseDiagram attribute) NumericalEOS (class in pymatgen.analysis.eos) Nwchem2Fiesta (class in pymatgen.io.fiesta) NwInput (class in pymatgen.io.nwchem) NwInputError NwOutput (class in pymatgen.io.nwchem) NwTask (class in pymatgen.io.nwchem)

O

O (Element attribute) obj_with_unit() (in module pymatgen.core.units) obtain_all_bond_lengths() (in module pymatgen.core.bonds) obtain_band_edges() (MolecularOrbitals method) occ() (Orbital property) OccupancyComparator (class in pymatgen.analysis.structure_matcher) off_color (WulffShape attribute) offset_vector() (Interface property) omega() (ChemicalShielding.MarylandNotation property) (ElasticTensorExpansion method) omp_threads() (TaskManager property) on_all_ok() (BecWork method) (DteWork method) (PhononWfkqWork method) (PhononWork method) (QptdmWork method) on_dep_ok() (Flow method) on_ok() (GKKPWork method) (PhononWfkqWork method) (RelaxWork method) on_wulff (WulffShape 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) opath_from_ext() (FileNode method) (Work method) open_files() (Flow method) open_gsr() (FileNode method) open_phbst() (AnaddbTask method) open_phdos() (AnaddbTask method) open_pspsfile() (Pseudo method) open_ring() (in module pymatgen.analysis.fragmenter) open_sigres() (SigmaTask method) openbabel_mol() (BabelMolAdaptor property) OpenBabelNN (class in pymatgen.analysis.local_env) operate() (SymmOp method) operate_magmom() (MagSymmOp method) operate_multi() (SymmOp method) operations (AdfTask attribute) (NwTask attribute) opt_template() (QCInput static method) OPTCELL_DEFAULT (RelaxationMethod attribute) optical_absorption_coeff() (Vasprun property) OpticTask (class in pymatgen.io.abinit.tasks) optimize_gibbs_free_energy() (QuasiharmonicDebyeApprox method) optimizer() (QuasiharmonicDebyeApprox method) OptSet (class in pymatgen.io.qchem.sets)

Orbital (class in pymatgen.electronic_structure.core) (class in pymatgen.io.vasp.inputs) orbital_type() (Orbital property) OrbitalDescription (class in pymatgen.io.vasp.inputs) OrbitalType (class in pymatgen.electronic_structure.core) orc() (HighSymmKpath method) orcc() (HighSymmKpath method) orcf1() (HighSymmKpath method) orcf2() (HighSymmKpath method) orcf3() (HighSymmKpath method) orci() (HighSymmKpath method) order (SpaceGroup attribute) order() (ElasticTensorExpansion property) (NthOrderElasticTensor property) 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) ordered_indices() (SeparationPlane property) Ordering (class in pymatgen.analysis.magnetism.analyzer) ordering() (CollinearMagneticStructureAnalyzer property) oriented_unit_cell (SlabGenerator attribute) orthongonalize_structure() (StructureVis method) orthonormal_vectors() (Plane method) orthonormal_vectors_old() (Plane method) orthorhombic() (Lattice static method) Os (Element attribute) Oszicar (class in pymatgen.io.vasp.outputs) other_dielectric (Vasprun attribute) Outcar (class in pymatgen.io.vasp.outputs) output_lists() (EwaldMinimizer property) override_from_prev_calc() (MPHSEBSSet method) (MPNonSCFSet method) (MPSOCSet method) (MPStaticSet method) (MVLGWSet method) OverwriteMagmomMode (class in pymatgen.analysis.magnetism.analyzer) oxi_prob (Composition attribute) oxi_state (DummySpecie attribute) (Specie attribute) oxi_state() (DummySpecie property) (Specie property) oxi_state_guesses() (Composition method) oxidation_states (Element attribute) oxidation_states() (Element property) OxidationStateDecorationTransformation (class in pymatgen.transformations.standard_transformations) OxidationStateRemovalTransformation (class in pymatgen.transformations.standard_transformations) oxide_type() (in module pymatgen.analysis.structure_analyzer) OxideType (class in pymatgen.analysis.structure_analyzer)

P

P (Element attribute) p (OrbitalType attribute) P() (JonesFaithfulTransformation property) p() (JonesFaithfulTransformation property) p0_exponential() (in module pymatgen.util.convergence) p0_reciprocal() (in module pymatgen.util.convergence) p0_simple_2reciprocal() (in module pymatgen.util.convergence) p0_simple_4reciprocal() (in module pymatgen.util.convergence) p0_simple_5reciprocal() (in module pymatgen.util.convergence) p0_simple_reciprocal() (in module pymatgen.util.convergence) p0_single_reciprocal() (in module pymatgen.util.convergence) Pa (Element attribute) package_options_description() (ChemEnvConfig method) PackmolRunner (class in pymatgen.io.lammps.utils) ParalHints (class in pymatgen.io.abinit.tasks) ParalHintsParser (class in pymatgen.io.abinit.tasks) parallel_assimilate() (BorgQueen method) ParallelEfficiency (class in pymatgen.io.abinit.abitimer) parameters (Vasprun attribute) params_keys (Control attribute) parent (SlabGenerator attribute) parse() (AbinitTimerParser method) (AbstractErrorParser method) (EventsParser method) (ParalHintsParser method) parse_author() (Author static method) parse_bool() (in module pymatgen.io.vasp.inputs) parse_cond_and_hall() (BoltztrapAnalyzer static method) parse_criteria() (MPRester static method) parse_file() (VolumetricData static method) parse_float() (in module pymatgen.io.vasp.inputs) parse_functions (PotcarSingle attribute) parse_history_node() (HistoryNode static method) parse_int() (in module pymatgen.io.vasp.inputs) parse_intrans() (BoltztrapAnalyzer static method) parse_lammps_dumps() (in module pymatgen.io.lammps.outputs) parse_lammps_log() (in module pymatgen.io.lammps.outputs) parse_list() (in module pymatgen.io.vasp.inputs) parse_magmoms() (CifParser method) parse_outputtrans() (BoltztrapAnalyzer static method) parse_oxi_states() (CifParser method) parse_oxide() (OxideType method) parse_single() (AbstractErrorParser method) parse_string() (in module pymatgen.io.vasp.inputs) parse_struct() (BoltztrapAnalyzer static method) parse_tddft() (NwOutput method) parse_timers() (Work method) parse_timing() (AbinitTask method) (Flow 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() (Directory property) (File property) path_from_structure() (KSampling class method) path_in() (Directory method) path_in_workdir() (Work method) path_join() (Directory method) pathname (HistoryRecord attribute) 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) PBSErrorParser (class in pymatgen.io.abinit.scheduler_error_parsers) PbsProJob (class in pymatgen.io.abinit.qjobs) PBSSTAT_TO_SLURM (PbsProJob attribute) pcm (GaussianOutput attribute) pcm_template() (QCInput static method) pconfs() (AbinitTask property) Pd (Element attribute) pd_coords() (PhaseDiagram method) pd_plot_data() (PDPlotter property) PDEntry (class in pymatgen.analysis.phase_diagram) pdos (CompleteDos attribute) (CompletePhononDos attribute) (Doscar attribute) (Vasprun attribute) pdos() (Doscar property) PDPlotter (class in pymatgen.analysis.phase_diagram) pefficiency() (AbinitTimerParser method) PenaltyFunctionError perform_all_corrections() (DefectCompatibility method) perform_band_edge_shifting() (DefectCompatibility method) perform_bandfill_corr() (BandFillingCorrection method) perform_bandfilling() (DefectCompatibility method) perform_es_corr() (FreysoldtCorrection method) (KumagaiCorrection method) perform_freysoldt() (DefectCompatibility method) perform_kumagai() (DefectCompatibility method) perform_pot_corr() (FreysoldtCorrection method) (KumagaiCorrection method) periodic_table_heatmap() (in module pymatgen.util.plotting) PeriodicSite (class in pymatgen.core.sites) permutations() (ExplicitPermutationsAlgorithm property) (SeparationPlane property) perpendicular_bisector() (Plane class method) persistent_id() (PmgPickler method) persistent_load() (PmgUnpickler method) perturb() (Molecule method) (Structure method) PerturbStructureTransformation (class in pymatgen.transformations.standard_transformations) PhaseDiagram (class in pymatgen.analysis.phase_diagram) PhaseDiagramError phonon_flow() (in module pymatgen.io.abinit.flows) 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) PhononTask (class in pymatgen.io.abinit.tasks) PhononWfkqWork (class in pymatgen.io.abinit.works) PhononWork (class in pymatgen.io.abinit.works) pickle_dump() (Flow method) pickle_dumps() (Flow method) pickle_file() (Flow property) PICKLE_FNAME (Flow attribute) pickle_load() (Flow class method) pickle_loads() (Flow class method) pid() (PyFlowScheduler property) pid_file() (Flow property) (PyFlowScheduler property) 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) (InterfacialReactivity method) (KumagaiCorrection method) (Relaxation method) (ScfCycle method) (SparseHistogram method) (in module pymatgen.cli.pmg_plot) plot_all() (AbinitTimerParser method) plot_all_stability_map() (NanoscaleStability method) plot_ax() (EOSBase method) plot_brillouin() (BSPlotter method) (PhononBSPlotter method) plot_brillouin_zone() (in module pymatgen.electronic_structure.plotter) plot_brillouin_zone_from_kpath() (in module pymatgen.electronic_structure.plotter) plot_carriers() (BoltztrapPlotter method) plot_chempot_range_map() (PDPlotter method) plot_compare() (BSPlotter method) (PhononBSPlotter method) plot_complexity_factor_mu() (BoltztrapPlotter method) plot_conductivity_dop() (BoltztrapPlotter method) plot_conductivity_mu() (BoltztrapPlotter method) plot_conductivity_temp() (BoltztrapPlotter method) plot_csm_and_maps() (StructureEnvironments method) plot_cv() (ThermoPlotter method) plot_dos() (BoltztrapPlotter method) plot_ebands() (BandStructureWork method) plot_ebands_with_edos() (BandStructureWork method) plot_edoses() (BandStructureWork 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_ion_relaxation() (RelaxWork method) plot_ioncell_relaxation() (RelaxWork method) plot_labels() (in module pymatgen.electronic_structure.plotter) plot_lattice_vectors() (in module pymatgen.electronic_structure.plotter) plot_msd() (DiffusionAnalyzer method) plot_networkx() (Flow method) plot_one_stability_map() (NanoscaleStability method) plot_path() (in module pymatgen.electronic_structure.plotter) plot_pie() (AbinitTimerParser method) plot_points() (in module pymatgen.electronic_structure.plotter) plot_power_factor_dop() (BoltztrapPlotter method) plot_power_factor_mu() (BoltztrapPlotter method) plot_power_factor_temp() (BoltztrapPlotter method) plot_seebeck_dop() (BoltztrapPlotter method) plot_seebeck_eff_mass_mu() (BoltztrapPlotter method) plot_seebeck_mu() (BoltztrapPlotter method) plot_seebeck_temp() (BoltztrapPlotter method) plot_slab() (in module pymatgen.analysis.adsorption) plot_stacked_hist() (AbinitTimerParser method) plot_structures() (AbstractDiffractionPatternCalculator method) plot_thermodynamic_properties() (ThermoPlotter method) plot_vor_analysis() (VoronoiAnalyzer static method) plot_wigner_seitz() (in module pymatgen.electronic_structure.plotter) plot_zt_dop() (BoltztrapPlotter method) plot_zt_mu() (BoltztrapPlotter method) plot_zt_temp() (BoltztrapPlotter method) plottable_from_outfile() (in module pymatgen.io.abinit.abiinspect) Pm (Element attribute) pmg_pickle_dump() (in module pymatgen.util.serialization) pmg_pickle_load() (in module pymatgen.util.serialization) pmg_serialize() (in module pymatgen.util.serialization) PmgPickler (class in pymatgen.util.serialization) PmgUnpickler (class in pymatgen.util.serialization) Po (Element attribute) point_energy() (EwaldSummation property) point_energy_matrix() (EwaldSummation property) point_from_bary_coords() (Simplex method) PointDefectComparator (class in pymatgen.analysis.structure_matcher) PointGroup (class in pymatgen.symmetry.groups) PointGroupAnalyzer (class in pymatgen.symmetry.analyzer) PointGroupOperations (class in pymatgen.symmetry.analyzer) points_wcs_csc() (AbstractGeometry method) points_wcs_ctwcc() (AbstractGeometry method) points_wcs_ctwocc() (AbstractGeometry method) points_wocs_csc() (AbstractGeometry method) points_wocs_ctwcc() (AbstractGeometry method) points_wocs_ctwocc() (AbstractGeometry method) poissons_ratio (Element attribute) polar_decomposition() (SquareTensor method) Polarization (class in pymatgen.analysis.ferroelectricity.polarization) PolarizationLattice (class in pymatgen.analysis.ferroelectricity.polarization) Polymer (class in pymatgen.io.lammps.utils) PolynomialEOS (class in pymatgen.analysis.eos) populate() (Tensor method) pos (Work attribute) pos_str() (Work property) 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) (RatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) power2_inverse_decreasing() (CSMInfiniteRatioFunction method) (RatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) power2_inverse_power2_decreasing() (CSMInfiniteRatioFunction method) (RatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) power2_inverse_powern_decreasing() (in module pymatgen.analysis.chemenv.utils.math_utils) power2_tangent_decreasing() (in module pymatgen.analysis.chemenv.utils.math_utils) power3_step() (in module pymatgen.analysis.chemenv.utils.math_utils) powern_decreasing() (in module pymatgen.analysis.chemenv.utils.math_utils) powern_parts_step() (in module pymatgen.analysis.chemenv.utils.math_utils) PPModel (class in pymatgen.io.abinit.abiobjects) PPModelModes (class in pymatgen.io.abinit.abiobjects) Pr (Element attribute) pred_from_comp() (Substitutor method) pred_from_list() (Substitutor method) pred_from_structures() (Substitutor method) predict() (DLSVolumePredictor method) (RLSVolumePredictor method) predict_mp() (CrystalAIRester method) predict_structure() (CrystalAIRester method) predictor_corrector (Poscar attribute) predictor_corrector() (Poscar property) predictor_corrector_preamble (Poscar attribute) prepare_symmetries() (AbstractChemenvStrategy method) PRESETS (LocalGeometryFinder attribute) pretty_plot() (in module pymatgen.util.plotting) pretty_plot_two_axis() (in module pymatgen.util.plotting) pretty_polyfit_plot() (in module pymatgen.util.plotting) pretty_print() (AllCoordinationGeometries method) prim() (HighSymmKpath property) prim_rec() (HighSymmKpath property) prime_factors() (in module pymatgen.analysis.chemenv.utils.math_utils) PrimitiveCellTransformation (class in pymatgen.transformations.standard_transformations) principal_axis_system() (ChemicalShielding property) (ElectricFieldGradient property) principal_invariants() (SquareTensor property) print_and_raise_error() (in module pymatgen.util.convergence) print_gnuplot_header() (in module pymatgen.io.abinit.helpers) print_periodic_table (Element attribute) print_plot_line() (in module pymatgen.util.convergence) print_stats() (TopographyAnalyzer method) print_table() (PseudoTable method) print_tree() (NetcdfReader method) Prismatic (class in pymatgen.io.prismatic) proc_dir() (in module pymatgen.cli.pmg_potcar)

proc_val() (Incar static method) (PWInput method) (Tags static method) Procar (class in pymatgen.io.vasp.outputs) process_entries() (Compatibility method) (EntryPostProcessor method) process_entry() (Compatibility method) (DefectCompatibility method) (EntryPostProcessor method) process_multientry() (PourbaixDiagram static method) process_parsed_coords() (in module pymatgen.io.qchem.utils) processes() (Work property) Product (class in pymatgen.io.abinit.nodes) products (Dependency attribute) products() (BalancedReaction property) (FileNode property) project() (Tensor method) project_and_to2dim() (Plane method) project_and_to2dim_ordered_indices() (Plane method) projected_eigenvalues (Vasprun attribute) projection() (Magmom property) projectionpoints() (Plane method) projections (BandStructure attribute) properly_terminated (GaussianOutput attribute) property_dict() (ElasticTensor property) Pseudo (class in pymatgen.io.abinit.pseudos) pseudo_with_symbol() (PseudoTable method) pseudos() (AbinitTask property) pseudos_with_symbols() (PseudoTable method) PseudoTable (class in pymatgen.io.abinit.pseudos) Pt (Element attribute) Pu (Element attribute) push_exceptions() (NodeResults method) 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) pyfile() (Flow property) PyFlowScheduler (class in pymatgen.io.abinit.launcher) PyLauncher (class in pymatgen.io.abinit.launcher) pymatgen (module) pymatgen.alchemy (module) pymatgen.alchemy.filters (module) pymatgen.alchemy.materials (module) pymatgen.alchemy.transmuters (module) pymatgen.analysis (module) pymatgen.analysis.adsorption (module) pymatgen.analysis.aflow_prototypes (module) pymatgen.analysis.bond_dissociation (module) pymatgen.analysis.bond_valence (module) pymatgen.analysis.chemenv (module) pymatgen.analysis.chemenv.coordination_environments (module) pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies (module) pymatgen.analysis.chemenv.coordination_environments.coordination_geometries (module) pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files (module) pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder (module) pymatgen.analysis.chemenv.coordination_environments.strategy_files (module) pymatgen.analysis.chemenv.coordination_environments.structure_environments (module) pymatgen.analysis.chemenv.coordination_environments.voronoi (module) pymatgen.analysis.chemenv.utils (module) pymatgen.analysis.chemenv.utils.chemenv_config (module) pymatgen.analysis.chemenv.utils.chemenv_errors (module) pymatgen.analysis.chemenv.utils.coordination_geometry_utils (module) pymatgen.analysis.chemenv.utils.defs_utils (module) pymatgen.analysis.chemenv.utils.func_utils (module) pymatgen.analysis.chemenv.utils.math_utils (module) pymatgen.analysis.chemenv.utils.scripts_utils (module) pymatgen.analysis.cost (module) pymatgen.analysis.cost.cost (module) pymatgen.analysis.defects (module) pymatgen.analysis.defects.core (module) pymatgen.analysis.defects.corrections (module) pymatgen.analysis.defects.defect_compatibility (module) pymatgen.analysis.defects.dilute_solution_model (module) pymatgen.analysis.defects.generators (module) pymatgen.analysis.defects.thermodynamics (module) pymatgen.analysis.defects.utils (module) pymatgen.analysis.diffraction (module) pymatgen.analysis.diffraction.core (module) pymatgen.analysis.diffraction.neutron (module) pymatgen.analysis.diffraction.xrd (module) pymatgen.analysis.diffusion_analyzer (module) pymatgen.analysis.dimensionality (module) pymatgen.analysis.elasticity (module) pymatgen.analysis.elasticity.elastic (module) pymatgen.analysis.elasticity.strain (module) pymatgen.analysis.elasticity.stress (module) pymatgen.analysis.elasticity.tensors (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.hhi.hhi (module) pymatgen.analysis.interface (module) pymatgen.analysis.interface_reactions (module) pymatgen.analysis.local_env (module) pymatgen.analysis.magnetism (module) pymatgen.analysis.magnetism.analyzer (module) pymatgen.analysis.magnetism.heisenberg (module) pymatgen.analysis.magnetism.jahnteller (module) pymatgen.analysis.molecule_matcher (module) pymatgen.analysis.molecule_structure_comparator (module) pymatgen.analysis.nmr (module) pymatgen.analysis.path_finder (module) pymatgen.analysis.phase_diagram (module) pymatgen.analysis.piezo (module) pymatgen.analysis.piezo_sensitivity (module) pymatgen.analysis.pourbaix_diagram (module) pymatgen.analysis.quasiharmonic (module) pymatgen.analysis.reaction_calculator (module) pymatgen.analysis.structure_analyzer (module) pymatgen.analysis.structure_matcher (module) pymatgen.analysis.structure_prediction (module) pymatgen.analysis.structure_prediction.dopant_predictor (module) pymatgen.analysis.structure_prediction.substitution_probability (module) pymatgen.analysis.structure_prediction.substitutor (module) pymatgen.analysis.structure_prediction.volume_predictor (module) pymatgen.analysis.substrate_analyzer (module) pymatgen.analysis.surface_analysis (module) pymatgen.analysis.thermochemistry (module) pymatgen.analysis.transition_state (module) pymatgen.analysis.wulff (module) pymatgen.analysis.xas (module) pymatgen.analysis.xas.spectrum (module) pymatgen.apps (module) pymatgen.apps.battery (module) pymatgen.apps.battery.analyzer (module) pymatgen.apps.battery.battery_abc (module) pymatgen.apps.battery.conversion_battery (module) pymatgen.apps.battery.insertion_battery (module) pymatgen.apps.battery.plotter (module) pymatgen.apps.borg (module) pymatgen.apps.borg.hive (module) pymatgen.apps.borg.queen (module) pymatgen.cli (module) pymatgen.cli.feff_input_generation (module) pymatgen.cli.feff_plot_cross_section (module) pymatgen.cli.feff_plot_dos (module) pymatgen.cli.gaussian_analyzer (module) pymatgen.cli.get_environment (module) pymatgen.cli.pmg (module) pymatgen.cli.pmg_analyze (module) pymatgen.cli.pmg_config (module) pymatgen.cli.pmg_plot (module) pymatgen.cli.pmg_potcar (module) pymatgen.cli.pmg_query (module) pymatgen.cli.pmg_structure (module) pymatgen.command_line (module) pymatgen.command_line.aconvasp_caller (module) pymatgen.command_line.bader_caller (module) pymatgen.command_line.critic2_caller (module) pymatgen.command_line.enumlib_caller (module) pymatgen.command_line.gulp_caller (module) pymatgen.command_line.mcsqs_caller (module) pymatgen.command_line.vampire_caller (module) pymatgen.core (module) pymatgen.core.bonds (module) pymatgen.core.composition (module) pymatgen.core.ion (module) pymatgen.core.lattice (module) pymatgen.core.libxcfunc (module) pymatgen.core.molecular_orbitals (module) pymatgen.core.operations (module) pymatgen.core.periodic_table (module) pymatgen.core.sites (module) pymatgen.core.spectrum (module) pymatgen.core.structure (module) pymatgen.core.surface (module) pymatgen.core.tensors (module) pymatgen.core.trajectory (module) pymatgen.core.units (module) pymatgen.core.xcfunc (module) pymatgen.dao (module) pymatgen.electronic_structure (module) pymatgen.electronic_structure.bandstructure (module) pymatgen.electronic_structure.boltztrap (module) pymatgen.electronic_structure.cohp (module) pymatgen.electronic_structure.core (module) pymatgen.electronic_structure.dos (module) pymatgen.electronic_structure.plotter (module) pymatgen.entries (module) pymatgen.entries.compatibility (module) pymatgen.entries.computed_entries (module) pymatgen.entries.entry_tools (module) pymatgen.entries.exp_entries (module) pymatgen.entries.post_processors_abc (module) pymatgen.ext (module) pymatgen.ext.cod (module) pymatgen.ext.crystalsai (module) pymatgen.ext.jhu (module) pymatgen.ext.matproj (module) pymatgen.io (module) pymatgen.io.abinit (module) pymatgen.io.abinit.abiinspect (module) pymatgen.io.abinit.abiobjects (module) pymatgen.io.abinit.abitimer (module) pymatgen.io.abinit.calculations (module) pymatgen.io.abinit.db (module) pymatgen.io.abinit.events (module) pymatgen.io.abinit.flows (module) pymatgen.io.abinit.helpers (module) pymatgen.io.abinit.launcher (module) pymatgen.io.abinit.netcdf (module) pymatgen.io.abinit.nodes (module) pymatgen.io.abinit.pseudos (module) pymatgen.io.abinit.qadapters (module) pymatgen.io.abinit.qjobs (module) pymatgen.io.abinit.qutils (module) pymatgen.io.abinit.scheduler_error_handlers (module) pymatgen.io.abinit.scheduler_error_parsers (module) pymatgen.io.abinit.tasks (module) pymatgen.io.abinit.utils (module) pymatgen.io.abinit.works (module) pymatgen.io.abinit.wrappers (module) pymatgen.io.adf (module) pymatgen.io.aiida (module) pymatgen.io.ase (module) pymatgen.io.atat (module) pymatgen.io.babel (module) pymatgen.io.cif (module) pymatgen.io.cssr (module) pymatgen.io.exciting (module) pymatgen.io.exciting.inputs (module) pymatgen.io.feff (module) pymatgen.io.feff.inputs (module) pymatgen.io.feff.outputs (module) pymatgen.io.feff.sets (module) pymatgen.io.fiesta (module) pymatgen.io.gaussian (module) pymatgen.io.lammps (module) pymatgen.io.lammps.data (module) pymatgen.io.lammps.inputs (module) pymatgen.io.lammps.outputs (module) pymatgen.io.lammps.utils (module) pymatgen.io.lmto (module) pymatgen.io.lobster (module) pymatgen.io.nwchem (module) pymatgen.io.phonopy (module) pymatgen.io.prismatic (module) pymatgen.io.pwscf (module) pymatgen.io.qchem (module) pymatgen.io.qchem.inputs (module) pymatgen.io.qchem.outputs (module) pymatgen.io.qchem.sets (module) pymatgen.io.qchem.utils (module) pymatgen.io.shengbte (module) pymatgen.io.vasp (module) pymatgen.io.vasp.inputs (module) pymatgen.io.vasp.outputs (module) pymatgen.io.vasp.sets (module) pymatgen.io.xcrysden (module) pymatgen.io.xr (module) pymatgen.io.xyz (module) pymatgen.io.zeopp (module) pymatgen.optimization (module) pymatgen.optimization.linear_assignment (module) pymatgen.optimization.linear_assignment_numpy (module) pymatgen.phonon (module) pymatgen.phonon.bandstructure (module) pymatgen.phonon.dos (module) pymatgen.phonon.plotter (module) pymatgen.symmetry (module) pymatgen.symmetry.analyzer (module) pymatgen.symmetry.bandstructure (module) pymatgen.symmetry.groups (module) pymatgen.symmetry.maggroups (module) pymatgen.symmetry.settings (module) pymatgen.symmetry.site_symmetries (module) pymatgen.symmetry.structure (module) pymatgen.transformations (module) pymatgen.transformations.advanced_transformations (module) pymatgen.transformations.defect_transformations (module) pymatgen.transformations.site_transformations (module) pymatgen.transformations.standard_transformations (module) pymatgen.transformations.transformation_abc (module) pymatgen.util (module) pymatgen.util.convergence (module) pymatgen.util.coord (module) pymatgen.util.coord_cython (module) pymatgen.util.io_utils (module) pymatgen.util.num (module) pymatgen.util.plotting (module) pymatgen.util.provenance (module) pymatgen.util.sequence (module) pymatgen.util.serialization (module) pymatgen.util.string (module) pymatgen.util.testing (module) pymatgen.util.typing (module) pymatgen.vis (module) pymatgen.vis.plotters (module) pymatgen.vis.structure_chemview (module) pymatgen.vis.structure_vtk (module) pymatgen_mol() (BabelMolAdaptor property) PymatgenTest (class in pymatgen.util.testing) pz (Orbital attribute)

Q

qadapter() (TaskManager property) qads() (TaskManager property) 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) QptdmWork (class in pymatgen.io.abinit.works) QTYPE (BlueGeneJob attribute) (MoabJob attribute) (PbsProJob attribute) (QueueJob attribute) (SgeJob attribute) (ShellJob attribute) (SlurmJob attribute) (TorqueJob attribute)

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) QueueJob (class in pymatgen.io.abinit.qjobs) quick_view() (in module pymatgen.vis.structure_chemview)

R

Ra (Element attribute) radii() (ValenceIonicRadiusEvaluator property) radius (CovalentRadius attribute) raise_error_if_unphysical() (in module pymatgen.analysis.elasticity.elastic) rand_piezo() (in module pymatgen.analysis.piezo_sensitivity) ranked_compositions_from_indeterminate_formula() (Composition static method) ranks() (TensorCollection property) rapidfire() (Flow method) (PyLauncher method) RatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) RatioFunctionError ratios() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) Rb (Element attribute) Rcut() (OrbitalDescription property) Rcut2() (OrbitalDescription property) Re (Element attribute) reactants() (BalancedReaction property) Reaction (class in pymatgen.analysis.reaction_calculator) ReactionDiagram (class in pymatgen.analysis.phase_diagram) ReactionError read() (File method) 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_etotals() (Work method) read_excitation_energies() (GaussianOutput method) read_extra_abivars() (in module pymatgen.io.abinit.helpers) read_fermi_contact_shift() (Outcar method) read_freq_dielectric() (Outcar method) read_grid_from_file() (in module pymatgen.io.abinit.helpers) read_igpar() (Outcar method) read_internal_strain_tensor() (Outcar method) read_keys() (NetcdfReader method) read_lcalcpol() (Outcar method) read_lepsilon() (Outcar method) read_lepsilon_ionic() (Outcar method) read_molecule() (QCInput static method) read_neb() (Outcar method) read_nmr_efg() (Outcar method) read_nmr_efg_tensor() (Outcar method) read_onsite_density_matrices() (Outcar method) read_opt() (QCInput static method) read_pattern() (in module pymatgen.io.qchem.utils) (Outcar method) (PWOutput method) read_pcm() (QCInput static method) read_piezo_tensor() (Outcar method) read_pseudo_zval() (Outcar method) read_rem() (QCInput static method) read_route_line() (in module pymatgen.io.gaussian) read_scan() (GaussianOutput method), [1] read_smx() (QCInput static method) read_solvent() (QCInput static method) read_structure() (ETSF_Reader method) read_table_pattern() (in module pymatgen.io.qchem.utils) (Outcar method) read_value() (NetcdfReader method) read_variable() (NetcdfReader method) read_varnames() (NetcdfReader method) readlines() (File method) real_space_energy() (EwaldSummation property) real_space_energy_matrix() (EwaldSummation property) rebuild_chgcar() (BaderAnalysis class method) received_signal() (QueueJob method) 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_dilatmx() (RelaxTask method) reduce_formula() (in module pymatgen.core.composition) reduce_mat() (GrainBoundaryGenerator static method) reduce_vector() (in module pymatgen.core.surface) reduce_vectors() (in module pymatgen.analysis.substrate_analyzer) reduced_composition() (Composition property) reduced_formula() (Composition property) (Ion property) ref_entries (SurfaceEnergyPlotter attribute) ref_permutation() (CoordinationGeometry method) ref_separation_perm() (SeparationPlane property) refine_rotation() (SquareTensor method) refine_structure() (in module pymatgen.io.abinit.helpers) reflection() (SymmOp static method) reflectivity (Element attribute) refractive_index (Element attribute) register() (Work method) register_gridfs_files() (NodeResults method) register_task() (Flow method) (Work method) register_work() (Flow method) register_work_from_cbk() (Flow 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) RelaxConvergenceWarning (class in pymatgen.io.abinit.events) RelaxTask (class in pymatgen.io.abinit.tasks) RelaxWork (class in pymatgen.io.abinit.works) reload() (Flow method) relpath() (Directory property) (File property) relworkdir() (Node property) rem_template() (QCInput static method) remove() (File method) remove_bond() (BabelMolAdaptor method) remove_charges() (Composition method) remove_collisions() (ChargeDensityAnalyzer method) (TopographyAnalyzer method) remove_deps() (Node method) remove_exts() (Directory 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) 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) rename_abiext() (Directory method) 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) report() (PBarSafe method) report_exception() (EventsParser method) required_params (Control attribute) rescale_field() (StaticPotential method) reset() (ScriptEditor method) reset_from_scratch() (AbinitTask method) (OpticTask method) respect_sign (OverwriteMagmomMode attribute) respect_zero (OverwriteMagmomMode attribute) restart() (AbinitTask method) (NscfTask method) (RelaxTask method) (ScfTask method) (SigmaTask method) restore_site_properties() (PackmolRunner method) Results (AbinitTask attribute) (Flow attribute) (Node attribute) results() (EOSBase property) resumes (GaussianOutput attribute) return_corrections() (SchedulerErrorHandler method) Rh (Element attribute) rhl1() (HighSymmKpath method) rhl2() (HighSymmKpath method) rho_rec() (QModel method) rho_rec_limit0() (QModel property) rhombohedral() (Lattice static method) rigidity_modulus (Element attribute) ring (CriticalPointType attribute) RLSVolumePredictor (class in pymatgen.analysis.structure_prediction.volume_predictor) rm_and_build() (Flow method) rm_indatadir() (Work method) rm_outdatadir() (Work method) rm_tmpdatadir() (Work method) rmtree() (Directory method) (Flow method) (Work method) Rn (Element attribute) rotate() (Tensor method) (TensorCollection method) rotate_sites() (Molecule method) (Structure method) rotate_view() (StructureVis method) rotateCoords() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) rotateCoordsOpt() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) rotation_matrix() (SymmOp property) RotationTransformation (class in pymatgen.transformations.standard_transformations) rotor_conformer() (BabelMolAdaptor method) rotoreflection() (SymmOp static method) round() (Tensor method) (TensorCollection method) round_to_sigfigs() (in module pymatgen.util.num) route (GaussianOutput attribute) row (Element attribute) row() (Element property) Ru (Element attribute) run() (BoltztrapRunner method) (Fiesta_run method) (GulpCaller method) (LammpsRunner method) (Nwchem2Fiesta method) (PackmolRunner method) run_aconvasp_command() (in module pymatgen.command_line.aconvasp_caller) run_mcsqs() (in module pymatgen.command_line.mcsqs_caller) run_stats (Outcar attribute) run_type (AdfOutput attribute) run_type() (Vasprun property) run_vasp() (VaspInput method) rxn() (ConversionVoltagePair property)

S

S (Element attribute) s (Orbital attribute) (OrbitalType attribute) S_ABICRITICAL (Node attribute) S_CANCELLED (QueueJob attribute) S_COMPLETED (QueueJob attribute) S_DONE (Node attribute) S_ERROR (Node attribute) S_FAILED (QueueJob attribute) S_INIT (Node attribute) S_LOCKED (Node attribute) s_name() (in module pymatgen.io.abinit.helpers) S_NODEFAIL (QueueJob attribute) S_OK (Node attribute) S_PENDING (QueueJob attribute) S_PREEMPTED (QueueJob attribute) S_QCRITICAL (Node attribute) S_READY (Node attribute) S_RESIZING (QueueJob attribute) S_RUN (Node attribute) S_RUNNING (QueueJob attribute) S_SUB (Node attribute) S_SUSPENDED (QueueJob attribute) S_TIMEOUT (QueueJob attribute) S_UNCONVERGED (Node attribute) S_UNKNOWN (QueueJob 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_lastnode_id() (in module pymatgen.io.abinit.nodes) 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_nestdict() (in module pymatgen.io.abinit.db) scatter_hist() (AbinitTimer method) ScfConvergenceWarning (class in pymatgen.io.abinit.events) ScfCycle (class in pymatgen.io.abinit.abiinspect) ScfTask (class in pymatgen.io.abinit.tasks) sch_symbol (PointGroupAnalyzer attribute) (PointGroupOperations attribute) scheduler_adapter_solutions() (AbstractError property) (MemoryCancelError property) (NodeFailureError property) (TimeCancelError property) SchedulerErrorHandler (class in pymatgen.io.abinit.scheduler_error_handlers) screened_energies (HeisenbergScreener attribute) screened_structures (HeisenbergScreener attribute) Screening (class in pymatgen.io.abinit.abiobjects) ScriptEditor (class in pymatgen.io.abinit.launcher) Se (Element attribute) se_analyzers (NanoscaleStability attribute) search_fragment_entries() (BondDissociationEnergies method) section_names() (AbinitTimerParser method) seebeck_eff_mass_from_carr() (in module pymatgen.electronic_structure.boltztrap) seebeck_eff_mass_from_seebeck_carr() (in module pymatgen.electronic_structure.boltztrap) seebeck_spb() (in module pymatgen.electronic_structure.boltztrap) seek() (YamlTokenizer method) select() (PseudoTable method) select_family() (PseudoTable method) select_files() (AbinitTask method) select_qadapter() (TaskManager method) select_rows() (PseudoTable method) select_symbols() (PseudoTable method) select_tasks() (Flow method) select_with_condition() (ParalHints 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) send_email() (PyFlowScheduler method) send_signal() (Node method) separation_in_list() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) SeparationPlane (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) serial_assimilate() (BorgQueen method) serialize_with_pickle() (PymatgenTest method) set_all_variables() (SurfaceEnergyPlotter method) set_animated_movie_options() (MultiStructuresVis method) set_auxiliary_basis_set() (FiestaInput method) set_BSE_options() (FiestaInput method) set_charge() (Defect method) (Structure method) set_charge_and_spin() (Molecule method) set_collection_name() (DBConnector method) set_flow() (Work method) set_garbage_collector() (Flow method) set_gc() (Node method) set_GW_options() (FiestaInput method) set_info() (in module pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) set_manager() (Work method) set_mem_per_proc() (TaskManager method) set_mpi_procs() (TaskManager method) set_n_nlmo() (Basis_set_reader method) set_name() (Node method) set_node_attributes() (MoleculeGraph method) (StructureGraph method) set_node_id() (Node method) set_omp_threads() (TaskManager method) set_option() (AbstractChemenvStrategy method) set_parameter() (StandardTransmuter method) (TransformedStructure method) set_pconfs() (AbinitTask method) set_permutations_safe_override() (CoordinationGeometry method) set_pyfile() (Flow method) set_spectator_mode() (Flow method) set_status_exitcode_signal() (QueueJob method) set_structure() (LocalGeometryFinder method) (MultiStructuresVis method) (StructureVis method) set_structure_environments() (AbstractChemenvStrategy method) set_structures() (MultiStructuresVis method) set_symbols() (Potcar method) set_temperature() (Poscar method) set_user_config_taskmanager() (in module pymatgen.io.abinit.tasks) set_vars() (OpticTask method) set_workdir() (Flow method) (OpticTask method) (Work method) setup() (AbinitTask method) (AnaddbTask method) (ChemEnvConfig method) (NscfTask method) (OpticTask method) (Work 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) (LocalGeometryFinder method) setup_potcars() (in module pymatgen.cli.pmg_config) setup_random_indices_local_geometry() (LocalGeometryFinder method) setup_random_structure() (LocalGeometryFinder method) setup_spline() (NEBAnalysis method) setup_statistic_lists() (LightStructureEnvironments method) setup_structure() (LocalGeometryFinder method) setup_test_perfect_environment() (LocalGeometryFinder method) setup_voronoi_list() (DetailedVoronoiContainer method) sg_symbol_from_int_number() (in module pymatgen.symmetry.groups) SgeJob (class in pymatgen.io.abinit.qjobs) shape_factor() (WulffShape property) shebang() (ScriptEditor method) shell() (ScriptEditor property) ShellJob (class in pymatgen.io.abinit.qjobs) shift (Slab attribute) shift_film() (Interface method) shift_film_along_surface_lattice() (Interface method) 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_abierrors() (Flow method) show_area (WulffShape attribute) show_corrections() (Flow method) show_dependencies() (Flow method) show_event_handlers() (Node method) show_events() (Flow method) show_history() (Flow method) show_info() (Flow method) show_inputs() (Flow method) show_plot() (AbstractDiffractionPatternCalculator method) show_qouts() (Flow method) show_receivers() (Flow method) show_status() (Flow method) show_summary() (Flow method) show_tricky_tasks() (Flow method) shutdown() (PyFlowScheduler method) Si (Element attribute) sigma() (GrainBoundary property) sigma_11() (ChemicalShielding.MehringNotation property) sigma_22() (ChemicalShielding.MehringNotation property) sigma_33() (ChemicalShielding.MehringNotation property) sigma_from_site_prop() (GrainBoundary property) sigma_iso() (ChemicalShielding.MarylandNotation property) (ChemicalShielding.MehringNotation property) SigmaConvWork (class in pymatgen.io.abinit.works) SigmaTask (class in pymatgen.io.abinit.tasks) sigres_path() (SigmaTask property) simple_2reciprocal() (in module pymatgen.util.convergence) simple_4reciprocal() (in module pymatgen.util.convergence) simple_5reciprocal() (in module pymatgen.util.convergence) simple_reciprocal() (in module pymatgen.util.convergence) SimpleAbundanceChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) SimpleChargeGenerator (class in pymatgen.analysis.defects.generators) 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) single_shot() (Flow method) (PyLauncher method) SinglePointSet (class in pymatgen.io.qchem.sets) Site (class in pymatgen.core.sites) site() (ConnectedSite property) (Defect property) (DefectEntry property) (Neighbor property) site_contains_environment() (LightStructureEnvironments method) site_has_clear_environment() (LightStructureEnvironments method) site_is_of_motif_type() (in module pymatgen.analysis.local_env) site_properties() (SiteCollection property) site_symbols() (Poscar property) (Xdatcar property) SiteCollection (class in pymatgen.core.structure) sites() (IMolecule property) (IStructure property) (SiteCollection property) Slab (class in pymatgen.core.surface) slab (WorkFunctionAnalyzer attribute) slab_from_csl() (GrainBoundaryGenerator static method) slab_scale_factor (SlabGenerator attribute) SlabEntry (class in pymatgen.analysis.surface_analysis) slabgen_params (ReconstructionGenerator attribute) SlabGenerator (class in pymatgen.core.surface) SlabTransformation (class in pymatgen.transformations.advanced_transformations) SlaveProcessMemoryCancelError (class in pymatgen.io.abinit.scheduler_error_parsers) slideshow() (CyclesPlotter method) (Relaxation method)

SlotPickleMixin (class in pymatgen.util.serialization) slurm_parse_timestr() (in module pymatgen.io.abinit.qutils) SlurmErrorParser (class in pymatgen.io.abinit.scheduler_error_parsers) SlurmJob (class in pymatgen.io.abinit.qjobs) Sm (Element attribute) smear() (Spectrum method) Smearing (class in pymatgen.io.abinit.abiobjects) smootherstep() (CSMFiniteRatioFunction method) (DeltaCSMRatioFunction method) (RatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) smoothness() (EnergyTrend method) (Polarization method) smoothstep() (CSMFiniteRatioFunction method) (RatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) smx_template() (QCInput static method) Sn (Element attribute) snyder_ac() (ElasticTensor method) snyder_opt() (ElasticTensor method) snyder_total() (ElasticTensor method) solid_angle() (in module pymatgen.analysis.local_env) (in module pymatgen.analysis.structure_analyzer) solid_angles() (CoordinationGeometry method) SolidAngleError solute_defect_density() (in module pymatgen.analysis.defects.dilute_solution_model) solute_site_preference_finder() (in module pymatgen.analysis.defects.dilute_solution_model) solve_equilibrium_point() (NanoscaleStability method) solve_for_fermi_energy() (DefectPhaseDiagram method) solve_for_non_equilibrium_fermi_energy() (DefectPhaseDiagram method) solvent_template() (QCInput static method) sort() (MoleculeGraph method) (Structure method) (StructureGraph method) sort_by_efficiency() (ParalHints method) sort_by_mem_per_proc() (ParalHints method) sort_by_speedup() (ParalHints 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) SparseHistogram (class in pymatgen.io.abinit.utils) spec() (Potcar property) special_formulas (Composition attribute) Specie (class in pymatgen.core.periodic_table) specie() (Site property) specie_potential_lines() (GulpIO method) SpecieProximityFilter (class in pymatgen.alchemy.filters) species() (Site property) (SiteCollection property) species_and_occu() (Site property) (SiteCollection property) species_string() (Site property) SpeciesComparator (class in pymatgen.analysis.structure_matcher) SpeciesMaxDistFilter (class in pymatgen.alchemy.filters) SpectatorError (Node attribute) SpectatorNodeError Spectrum (class in pymatgen.core.spectrum) SpectrumPlotter (class in pymatgen.vis.plotters) speed_up() (CorrectorProtocolApplication method) sphere_fraction_angles() (StructureEnvironments.NeighborsSet property) Spin (class in pymatgen.electronic_structure.core) spin_data() (VolumetricData property) spin_multiplicity (GaussianOutput attribute) spin_multiplicity() (IMolecule property) spin_polarization() (CompleteDos property) SpinComparator (class in pymatgen.analysis.structure_matcher) SpinMode (class in pymatgen.io.abinit.abiobjects) spline() (EnergyTrend method) spline_functions() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) SplineInputError split_molecule_subgraphs() (MoleculeGraph method) SQSTransformation (class in pymatgen.transformations.advanced_transformations) SquareTensor (class in pymatgen.core.tensors) Sr (Element attribute) stable_entries() (PhaseDiagram property) (PourbaixDiagram property) stable_u_range_dict() (SurfaceEnergyPlotter method) standard_calculations_from_vasp_files() (Lobsterin class method) standard_orientation (GaussianOutput attribute) standardize_structure() (in module pymatgen.io.vasp.sets) StandardTransmuter (class in pymatgen.alchemy.transmuters) start() (PyFlowScheduler method) (Work method) StaticPotential (class in pymatgen.analysis.path_finder) stationary_type (GaussianOutput attribute) stats_article_weights_parameters() (MultiWeightsChemenvStrategy class method) Status (class in pymatgen.io.abinit.nodes) status() (Dependency property) (FileNode property) (Flow property) (Node property) (Work property) status_counter() (Flow property) (Work property) store_conv_results() (in module pymatgen.io.abinit.helpers) str2float() (in module pymatgen.io.cif) str_delimited() (in module pymatgen.util.string) str_deps() (Node method) STR_FIELDS (AbinitTimerSection attribute) straceback() (in module pymatgen.io.abinit.abiinspect) Strain (class in pymatgen.analysis.elasticity.strain) strain_slabs() (in module pymatgen.analysis.interface) STRATEGY_DESCRIPTION (AbstractChemenvStrategy attribute) (MultiWeightsChemenvStrategy attribute) (SimpleAbundanceChemenvStrategy attribute) (SimplestChemenvStrategy attribute) (WeightedNbSetChemenvStrategy attribute) STRATEGY_INFO_FIELDS (AbstractChemenvStrategy attribute) STRATEGY_OPTIONS (AbstractChemenvStrategy attribute) (SimpleAbundanceChemenvStrategy attribute) (SimplestChemenvStrategy attribute) StrategyOption (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) stream_has_colours() (in module pymatgen.util.string) Stress (class in pymatgen.analysis.elasticity.stress) strictly_decreasing() (in module pymatgen.util.num) strictly_increasing() (in module pymatgen.util.num) string_relax() (NEBPathfinder static method) StringColorizer (class in pymatgen.util.string) STRINGKEYWORDS (Lobsterin attribute) structure (BandStructure attribute) Structure (class in pymatgen.core.structure) structure (CompleteDos attribute) (ExcitingInput attribute) (Poscar attribute) (VolumetricData attribute) (WulffShape attribute) structure() (DictSet property) (HighSymmKpath property) (LammpsData property) (ValenceIonicRadiusEvaluator property) structure_contains_atom_environment() (LightStructureEnvironments method) structure_from_abivars() (in module pymatgen.io.abinit.abiobjects) structure_from_ncdata() (in module pymatgen.io.abinit.netcdf) structure_from_string() (Mcsqs static method) structure_graph() (Critic2Output method) structure_has_clear_environments() (LightStructureEnvironments method) structure_lines() (GulpIO method) STRUCTURE_REFINEMENT_NONE (LocalGeometryFinder attribute) STRUCTURE_REFINEMENT_REFINED (LocalGeometryFinder attribute) STRUCTURE_REFINEMENT_SYMMETRIZED (LocalGeometryFinder attribute) structure_symmetry() (Header property) structure_to_abivars() (in module pymatgen.io.abinit.abiobjects) structure_transform() (Tensor method) 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) (Vasprun attribute) (Xdatcar attribute) (in module pymatgen.command_line.enumlib_caller) structures() (TransformedStructure property) (Vasprun property) STRUCTURES_DIR (PymatgenTest attribute) structures_input_orientation (GaussianOutput attribute) StructureVis (class in pymatgen.vis.structure_vtk) style() (Kpoints property) sub_chempots() (in module pymatgen.analysis.surface_analysis) sub_keys (AdfKey attribute) sub_spgrp() (in module pymatgen.io.cif) submit_snl() (MPRester method) submit_structures() (MPRester method) submit_tasks() (Work method) submit_vasp_directory() (MPRester method) SubmitError (class in pymatgen.io.abinit.scheduler_error_parsers) subs() (in module pymatgen.analysis.elasticity.elastic) substitute() (Molecule method) (Structure method) substitute_group() (MoleculeGraph method) (StructureGraph method) SubstituteSurfaceSiteTransformation (class in pymatgen.transformations.advanced_transformations) Substitution (class in pymatgen.analysis.defects.core) SubstitutionGenerator (class in pymatgen.analysis.defects.generators) SubstitutionPredictor (class in pymatgen.analysis.structure_prediction.substitution_probability) SubstitutionPredictorTransformation (class in pymatgen.transformations.advanced_transformations) SubstitutionProbability (class in pymatgen.analysis.structure_prediction.substitution_probability) SubstitutionTransformation (class in pymatgen.transformations.standard_transformations) Substitutor (class in pymatgen.analysis.structure_prediction.substitutor) substrate() (Interface property) substrate_sites() (Interface property) SubstrateAnalyzer (class in pymatgen.analysis.substrate_analyzer) subsurface_sites() (AdsorbateSiteFinder method) suggest_charges() (DefectPhaseDiagram method) suggest_larger_supercells() (DefectPhaseDiagram method) sulfide_type() (in module pymatgen.analysis.structure_analyzer) sum_sections() (AbinitTimer method) summarize() (AbinitTimerParser method) summary() (BaderAnalysis property) (Pseudo property) summed_icohp() (IcohpValue property) SupercellTransformation (class in pymatgen.transformations.standard_transformations) superconduction_temperature (Element attribute) SuperTransformation (class in pymatgen.transformations.advanced_transformations) supported_modes (Kpoints attribute) SUPPORTED_MODES (MVLGWSet attribute) supported_properties (MPRester attribute) (Specie attribute) supported_task_properties (MPRester attribute) supported_units() (ArrayWithUnit property) (FloatWithUnit property) supports_soc() (Pseudo property) surface_area() (Slab property) (SlabEntry property) (WulffShape property) surface_chempot_range_map() (SurfaceEnergyPlotter method) surface_energy() (SlabEntry method) surface_sites() (AdsorbateSiteFinder property) SurfaceEnergyPlotter (class in pymatgen.analysis.surface_analysis) symbol (Deformation attribute) (DummySpecie attribute) (Element attribute) (NthOrderElasticTensor attribute) (PointGroup attribute) (SpaceGroup attribute) (Strain attribute) (Stress attribute) (Tensor attribute) symbol() (DummySpecie property) (PotcarSingle property) (Pseudo property) symbol_set() (SiteCollection property) symbols() (Potcar property) symlink_abiext() (Directory method) symm_group_cubic() (in module pymatgen.analysis.gb.grain) symm_reduce() (AdsorbateSiteFinder method) 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) TaskManager (class in pymatgen.io.abinit.tasks) tasks_from_nids() (Flow method) Tb (Element attribute) Tc (Element attribute) tdensities (Doscar attribute) tdensities() (Doscar property) tdos (Doscar attribute) (Vasprun attribute) tdos() (Doscar property) Te (Element attribute) Temp (in module pymatgen.core.units) temp_shell_task() (AbinitTask class method) (AnaddbTask class method) temperature (Poscar attribute) template_dir (LammpsRun attribute) temporary_flow() (Flow class method) Tensor (class in pymatgen.core.tensors) TensorCollection (class in pymatgen.core.tensors) TensorMapping (class in pymatgen.core.tensors) term_symbols() (Element property) tersoff_input() (GulpIO method) tersoff_potential() (GulpIO method) TersoffPotential (class in pymatgen.command_line.gulp_caller) test() (AbstractStructureFilter method) (ChargeBalanceFilter method) (ContainsSpecieFilter method) (RemoveDuplicatesFilter method) (RemoveExistingFilter method) (SpecieProximityFilter method) (SpeciesMaxDistFilter method) TEST_2D_POINTS (Plane attribute) TEST_FILES_DIR (PymatgenTest attribute) TEST_STRUCTURES (PymatgenTest attribute) tet() (HighSymmKpath method) tet_coord() (in module pymatgen.analysis.phase_diagram) tetragonal() (Lattice static method) text (YamlDoc attribute) text_notag() (YamlDoc property) Th (Element attribute) thankyou() (in module pymatgen.analysis.chemenv.utils.scripts_utils) theories (NwTask attribute) thermal_conductivity (Element attribute) thermal_conductivity() (QuasiharmonicDebyeApprox method) thermal_expansion_coeff() (ElasticTensorExpansion method) ThermoData (class in pymatgen.analysis.thermochemistry) ThermoPlotter (class in pymatgen.phonon.plotter) third_vect() (in module pymatgen.analysis.interface) Ti (Element attribute) Time (in module pymatgen.core.units) time2loadlever() (in module pymatgen.io.abinit.qutils) time2pbspro() (in module pymatgen.io.abinit.qutils) time2slurm() (in module pymatgen.io.abinit.qutils) TimeCancelError (class in pymatgen.io.abinit.scheduler_error_parsers) timelimit_parser() (in module pymatgen.io.abinit.qutils) timeout() (QueueJob property) timers() (AbinitTimerParser method) title (ExcitingInput attribute) (GaussianOutput attribute) Tl (Element attribute) Tm (Element attribute) tmpfile_write() (PymatgenTest method) to() (ArrayWithUnit method) (FloatWithUnit method) (IMolecule method) (IStructure method) (SiteCollection method) to_abivars() (AbivarAble method) (Constraints method) (Electrons method) (ElectronsAlgorithm method) (ExcHamiltonian method) (HilbertTransform method) (KSampling method) (ModelDielectricFunction method) (PPModel method) (RelaxationMethod method) (Screening method) (SelfEnergy method) (Smearing method) (SpinMode method)

to_bson_voronoi_list2() (DetailedVoronoiContainer method) to_csv() (AbinitTimer method) (EntrySet method) to_csvline() (AbinitTimerSection method) to_data_dict() (Composition property) to_dict() (AbinitTimerSection method) (Flow method) to_displacements() (Trajectory method) to_file() (Control method) (ForceField method) to_hdf5() (VolumetricData method) to_input() (GaussianOutput method), [1] to_json() (AdfKey method) (AdfTask method) (LibxcFunc method) to_lattice() (LammpsBox method) to_positions() (Trajectory method) to_reduced_dict() (Composition property) (Ion property) to_shell_manager() (TaskManager method) to_snl() (TransformedStructure method) to_string() (GaussianInput method) (Mcsqs method) (NodeHistory method) (Prismatic method) (Pseudo method) (Relaxation method) (ScfCycle method) (XSF method) to_table() (AbinitTimer method) (PseudoTable method) to_tuple() (AbinitTimerSection method) to_unit_cell() (PeriodicSite method) TOLERANCE (BalancedReaction attribute) top_grain() (GrainBoundary property) TopographyAnalyzer (class in pymatgen.analysis.defects.utils) Topology (class in pymatgen.io.lammps.data) TorqueJob (class in pymatgen.io.abinit.qjobs) tot_corner_sites() (WulffShape property) tot_edges() (WulffShape property) totable() (AbinitTimer method) (ParallelEfficiency method) total_electrons() (Composition property) total_energy() (EwaldSummation property) total_energy_matrix() (EwaldSummation property) total_spectrum() (Eels property) total_surface_energy() (WulffShape property) Trajectory (class in pymatgen.core.trajectory) trans() (SquareTensor property) trans_v() (ElasticTensor method) transf_mat() (in module pymatgen.analysis.interface) transform() (Tensor method) (TensorCollection method) transform_coords() (JonesFaithfulTransformation method) transform_entries() (CompoundPhaseDiagram method) transform_lattice() (JonesFaithfulTransformation method) transform_symmop() (JonesFaithfulTransformation method) transform_tensor() (SymmOp method) transform_to_length() (CrystalNN static method) transformation_string() (JonesFaithfulTransformation property) transformation_to_string() (in module pymatgen.util.string) TransformedPDEntry (class in pymatgen.analysis.phase_diagram) TransformedStructure (class in pymatgen.alchemy.materials) translate_sites() (Molecule method) (Structure method) TranslateSitesTransformation (class in pymatgen.transformations.site_transformations) translation_vector() (SymmOp property) transparency (WulffShape attribute) tria() (HighSymmKpath method) triangular_coord() (in module pymatgen.analysis.phase_diagram) trib() (HighSymmKpath method) triple_cap_hints() (CoordinationGeometry.NeighborsSetsHints method) true_names (Poscar attribute) tune_for_gamma() (in module pymatgen.analysis.defects.utils) TWO_THETA_TOL (AbstractDiffractionPatternCalculator attribute) type (XcFunc attribute) type() (CriticalPoint property) Type() (OrbitalDescription property) type() (Pseudo property) Type2() (OrbitalDescription property) typeidx_from_symbol() (ETSF_Reader method) types_and_weights_of_connections() (StructureGraph property) types_of_coordination_environments() (StructureGraph method) types_of_magnetic_specie() (CollinearMagneticStructureAnalyzer property) types_of_specie() (SiteCollection property)

U

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

unitized() (in module pymatgen.core.units) universal_anisotropy() (ElasticTensor property) Unknown (Ordering attribute) unknown_status() (QueueJob property) unprocessed_entries() (PourbaixDiagram property) unstable_entries() (PhaseDiagram property) (PourbaixDiagram property) unsym_cs_tensor (Outcar attribute) up (Spin attribute) update() (PBarSafe method) update_charge_from_potcar() (Vasprun method) update_collection() (NodeResults 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) use_smartio() (Flow method) USER_CONFIG_DIR (PyFlowScheduler attribute) (TaskManager attribute) user_wants_to_exit() (Editor static method) uses_paral_kgb() (AbinitTask method)

V

V (Element attribute) v0() (EOSBase property) V_xx() (ElectricFieldGradient property) V_yy() (ElectricFieldGradient property) V_zz() (ElectricFieldGradient property) Vacancy (class in pymatgen.analysis.defects.core) VacancyGenerator (class in pymatgen.analysis.defects.generators) vacuum_locpot (WorkFunctionAnalyzer attribute) vacuum_thickness() (Interface property) valence() (Element property) ValenceIonicRadiusEvaluator (class in pymatgen.analysis.local_env) valences() (ValenceIonicRadiusEvaluator property) valid() (Composition property) validate_json_schema() (Flow method) (NodeResults 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) 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) version (AbinitBuild attribute) VERSION (Flow attribute) version_ge() (AbinitBuild method) vibrational_free_energy() (QuasiharmonicDebyeApprox method) vibrational_internal_energy() (QuasiharmonicDebyeApprox method) vickers_hardness (Element attribute) Vinet (class in pymatgen.analysis.eos) visualize() (in module pymatgen.analysis.chemenv.utils.scripts_utils)

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

W

W (Element attribute) w_area_has_intersection() (DistanceAngleAreaNbSetWeight method) w_area_has_intersection_smoothstep() (DistanceAngleAreaNbSetWeight method) w_area_intersection_nbsfh_fbs_onb0() (DistanceAngleAreaNbSetWeight method) walk() (AbinitTimerParser class method) walk_tree() (NetcdfReader method) warning() (NodeHistory method) was_modified() (TransformedStructure property) Wavecar (class in pymatgen.io.vasp.outputs) Waveder (class in pymatgen.io.vasp.outputs) Wavederf (class in pymatgen.io.vasp.outputs) wavenumber() (Xmu property) weight() (AngleNbSetWeight method) (AnglePlateauNbSetWeight method) (CNBiasNbSetWeight method) (Composition property) (ConnectedSite property) (DeltaCSMNbSetWeight method) (DeltaDistanceNbSetWeight method) (DistanceAngleAreaNbSetWeight method) (DistanceNbSetWeight method) (DistancePlateauNbSetWeight method) (NbSetWeight method) (NormalizedAngleDistanceNbSetWeight method) (SelfCSMNbSetWeight method) weight_statistics() (StructureGraph property) weighted_surface_energy() (WulffShape property) WeightedNbSetChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) weights (Procar attribute) welcome() (in module pymatgen.analysis.chemenv.utils.scripts_utils) wfk_filepath() (OpticTask property) 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 (class in pymatgen.io.abinit.works) work_function (WorkFunctionAnalyzer attribute) WorkFunctionAnalyzer (class in pymatgen.analysis.surface_analysis) working_ion() (AbstractElectrode property) (ConversionElectrode property) (ConversionVoltagePair property) (InsertionElectrode property) working_ion_entry() (AbstractElectrode property) (AbstractVoltagePair property) (ConversionElectrode property) (ConversionVoltagePair property) (InsertionElectrode property) (InsertionVoltagePair property) works() (Flow property) write() (File method) (QChemDictSet method) write_all_structures() (InterfaceBuilder method) write_def() (BoltztrapRunner method) write_energy() (BoltztrapRunner method) write_etree() (ExcitingInput method)

write_file() (AdfInput method) (Atoms method) (BabelMolAdaptor method) (CifWriter method) (Cssr method) (ExcitingInput method) (FiestaInput method) (GaussianInput method) (Header method) (Incar method) (Kpoints method) (LMTOCtrl method) (LammpsData method) (NwInput method) (PWInput method) (Paths method) (Poscar method) (Potcar method) (PotcarSingle method) (Potential method) (QCInput method) (Tags method) (VolumetricData method) (XYZ method) (Xdatcar method) (Xr 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_jobfile() (TaskManager method) write_KPOINTS() (Lobsterin static method) write_lammps_inputs() (in module pymatgen.io.lammps.inputs) write_lobsterin() (Lobsterin method) write_multi_job_file() (QCInput static method) write_pdb() (PackmolRunner method) write_phononwebsite() (PhononBandStructureSymmLine method) write_POSCAR_with_standard_primitive() (Lobsterin static method) write_proj() (BoltztrapRunner method) write_string() (ExcitingInput method) write_struct() (BoltztrapRunner method) write_topology() (TopographyAnalyzer method) write_vasp_input() (StandardTransmuter method) (TransformedStructure method) writelines() (File method) wti_from_nids() (Flow method) wulff_cv_simp (WulffShape attribute) wulff_from_chempot() (SurfaceEnergyPlotter method) wulff_gform_and_r() (NanoscaleStability method) wulff_pt_list (WulffShape attribute) WulffFacet (class in pymatgen.analysis.wulff) WulffShape (class in pymatgen.analysis.wulff)

X

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

XLABEL (DiffractionPattern attribute) (DOS attribute) (ExcitationSpectrum attribute) (Spectrum attribute) (XANES 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_FILE (PyFlowScheduler attribute) (TaskManager attribute) yaml_read_irred_perts() (in module pymatgen.io.abinit.abiinspect) yaml_read_kpoints() (in module pymatgen.io.abinit.abiinspect) yaml_tag (DilatmxError attribute) (NscfConvergenceWarning attribute) (RelaxConvergenceWarning attribute) (ScfConvergenceWarning attribute)

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) (XANES attribute) youngs_modulus (Element attribute)

Z

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

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