Index

A

a (Kpoint attribute) (Lattice attribute) (PeriodicSite attribute) (Plane attribute) (Wavecar attribute) abc (Lattice attribute) abcd (Plane attribute) 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) 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) 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_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_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() (Molecule method) (Structure method) add_oxidation_state_by_guess() (Structure method) add_oxidation_state_by_site() (Structure 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() (Molecule method) (Structure method) add_source() (StructureEnvironments.NeighborsSet method) add_spectra() (SpectrumPlotter method) add_spectrum() (SpectrumPlotter method) add_spin_by_element() (Structure method) add_spin_by_site() (Structure method) add_strategy_visualization_to_subplot() (SimplestChemenvStrategy method) add_subkey() (AdfKey method) add_tags() (StandardTransmuter method) add_text() (StructureVis method) add_triangle() (StructureVis method) additional_condition (SimplestChemenvStrategy attribute) 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 attribute) algorithms (CoordinationGeometry attribute) aliases() (pymatgen.core.xcfunc.XcFunc class method) ALL (AdditionalConditions attribute) all_combinations_for_elements() (PseudoTable method) all_comp (BalancedReaction attribute) all_distances() (in module pymatgen.util.coord) all_docs_with_tag() (YamlTokenizer method) all_done (Work attribute) all_energies (Oszicar attribute) all_entries (ComputedReaction attribute) all_entries_hulldata (PhaseDiagram attribute) all_families (LibxcFunc attribute) all_input (VaspInputSet attribute) all_input() (AbstractFeffInputSet method) all_kinds (LibxcFunc attribute) all_molecules (XYZ attribute) all_ok (Flow attribute) all_slab_entries (SurfaceEnergyPlotter attribute) all_stable_entries (DefectPhaseDiagram attribute) ALL_STATUS (Node attribute) all_status_strings() (pymatgen.io.abinit.nodes.Status class method) all_unstable_entries (DefectPhaseDiagram attribute) all_yaml_docs() (YamlTokenizer method) AllCoordinationGeometries (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) allnc (PseudoTable attribute) allocate() (Flow method) (Work method) allocated (Flow 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 attribute) almost_equals() (Composition method) along_c (WorkFunctionAnalyzer attribute) alpha (Lattice attribute) (WulffShape attribute) alphabetical_formula (Composition attribute) (Ion attribute) alter_edge() (MoleculeGraph method) (StructureGraph method) alternate() (in module pymatgen.io.abinit.abitimer) alternative_keys (QcTask attribute) alternative_values (QcTask attribute) 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 attribute) 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 attribute) (StructureEnvironments.NeighborsSet attribute) angn() (NormalizedAngleDistanceNbSetWeight method) angninvdist() (NormalizedAngleDistanceNbSetWeight method) angninvndist() (NormalizedAngleDistanceNbSetWeight method) AnionCorrection (class in pymatgen.entries.compatibility) anisotropy (WulffShape attribute) anonymized_formula (Composition attribute) (Ion attribute) 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 attribute) (MemoryCancelError attribute) (TimeCancelError attribute) 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) apply_strain() (Structure method) apply_tags() (MultiStructuresVis method) apply_to_structure() (Deformation method) apply_transformation() (AbstractTransformation method) (AddSitePropertyTransformation method) (AutoOxiStateDecorationTransformation method) (ChargedCellTransformation method) (DefectTransformation method) (DeformStructureTransformation method) (DiscretizeOccupanciesTransformation method) (InsertSitesTransformation method) (OrderDisorderedStructureTransformation method) (OxidationStateDecorationTransformation method) (OxidationStateRemovalTransformation method) (PartialRemoveSitesTransformation method) (PartialRemoveSpecieTransformation method) (PerturbStructureTransformation method) (PrimitiveCellTransformation method) (RemoveSitesTransformation method) (RemoveSpeciesTransformation method) (ReplaceSiteSpeciesTransformation method) (RotationTransformation method) (SubstitutionTransformation method) (SupercellTransformation method) (TranslateSitesTransformation method)

AqueousCorrection (class in pymatgen.entries.compatibility) Ar (Element attribute) are_collinear() (Magmom static method) are_coops (IcohpCollection attribute), [1] (IcohpValue attribute), [1] are_equal() (AbstractComparator method) (ElementComparator method) (FrameworkComparator method) (MoleculeStructureComparator method) (OccupancyComparator method) (OrderDisorderElementComparator 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 attribute) argsorted_ref_separation_perm (SeparationPlane attribute) ArrayWithUnit (class in pymatgen.core.units) As (Element attribute) as_base_units (ArrayWithUnit attribute) (FloatWithUnit attribute) (Unit attribute) as_bool() (in module pymatgen.io.abinit.utils) as_condition() (pymatgen.io.abinit.utils.Condition class method) as_dict (ExplicitPermutationsAlgorithm attribute) (SeparationPlane attribute) 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) (ConversionElectrode method) (ConversionVoltagePair method) (CoordinationGeometry method) (CoordinationGeometry.NeighborsSetsHints method) (Correction 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) (EwaldElectrostaticModel method) (ExpEntry method) (FiestaInput method) (Fiesta_run method) (Flow method) (GaussianInput method) (GaussianOutput method) (GaussianToComputedEntryDrone method) (GrandPotPDEntry method) (GrandPotentialPhaseDiagram method) (HistoryNode method) (HistoryRecord method) (IMolecule method) (IStructure method) (Incar method) (InsertionElectrode method) (Ion method) (IsingModel method) (KSampling method) (Kpoint method) (Kpoints method) (LMTOCtrl method) (LammpsData method) (LammpsDump method) (Lattice method) (LibxcFunc method) (LightStructureEnvironments method) (LightStructureEnvironments.NeighborsSet method) (MVLSlabSet method) (MagSymmOp method) (MoleculeGraph method) (MoleculeStructureComparator 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) (Pseudo method) (PseudoTable method) (QcInput method) (QcTask method) (Reaction method) (RelaxationMethod method) (RemoveExistingFilter method) (SelfCSMNbSetWeight method) (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) (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() (pymatgen.io.abinit.flows.Flow class method) as_manager() (pymatgen.io.abinit.tasks.TaskManager class method) as_ncreader() (in module pymatgen.io.abinit.netcdf) as_node() (pymatgen.io.abinit.nodes.Node class method) as_phononwebsite() (PhononBandStructureSymmLine method) as_ppmodel() (pymatgen.io.abinit.abiobjects.PPModel class method) as_pseudo() (pymatgen.io.abinit.pseudos.Pseudo class method) as_smearing() (pymatgen.io.abinit.abiobjects.Smearing class method) as_spinmode() (pymatgen.io.abinit.abiobjects.SpinMode class method) as_status() (pymatgen.io.abinit.nodes.Status class method) as_table() (pymatgen.io.abinit.pseudos.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() (pymatgen.core.xcfunc.XcFunc class method) asymmetry (ElectricFieldGradient attribute) At (Element attribute) atom_basis_labels (GaussianOutput attribute) atomic_background (Eels attribute) atomic_mass (Element attribute) atomic_no (PotcarSingle attribute) atomic_numbers (SiteCollection attribute) atomic_orbitals (Element attribute) atomic_radius (Element attribute) atomic_radius_calculated (Element attribute) atomic_symbols (Vasprun attribute) AtomicFile (class in pymatgen.util.io_utils) atoms (AbstractFeffInputSet attribute) Atoms (class in pymatgen.io.feff.inputs) atoms (FEFFDictSet attribute) atoms_and_cell() (pymatgen.io.abinit.abiobjects.RelaxationMethod class method) atoms_only() (pymatgen.io.abinit.abiobjects.RelaxationMethod class method) atoms_string_from_file() (Atoms static method) attribute (PDEntry attribute) Au (Element attribute) Author (class in pymatgen.util.provenance) auto_load() (pymatgen.analysis.chemenv.utils.chemenv_config.ChemEnvConfig class method) autodoc() (pymatgen.io.abinit.db.DBConnector class method) (pymatgen.io.abinit.launcher.PyFlowScheduler class method) (pymatgen.io.abinit.tasks.TaskManager class method) Automatic (Kpoints_supported_modes attribute) automatic (KSamplingModes attribute) automatic() (Kpoints static method) automatic_density() (Kpoints static method) (pymatgen.io.abinit.abiobjects.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) ave_bulk_p (WorkFunctionAnalyzer attribute) ave_locpot (WorkFunctionAnalyzer attribute) average_coordination_number() (in module pymatgen.analysis.structure_analyzer) average_electroneg (Composition attribute) average_ionic_radius (Element attribute), [1] average_over_unit_sphere() (Tensor method) aweight() (NormalizedAngleDistanceNbSetWeight method) axis_off (WulffShape attribute)

B

B (Element attribute) b (Kpoint attribute) (Lattice attribute) (PeriodicSite attribute) (Plane attribute) (Wavecar attribute) b0 (EOSBase attribute) b0_GPa (EOSBase attribute) b1 (EOSBase attribute) Ba (Element attribute) 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) 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) 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 (Directory attribute) (File attribute) (FileNode attribute) (Pseudo attribute) 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 attribute) beta (Lattice attribute) Bi (Element attribute)

Birch (class in pymatgen.analysis.eos) BirchMurnaghan (class in pymatgen.analysis.eos) Bk (Element attribute) block (Element attribute), [1] 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) BorgQueen (class in pymatgen.apps.borg.queen) 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 attribute) 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_slabs() (ReconstructionGenerator method) build_unique_fragments() (MoleculeGraph method) bulk_gform() (NanoscaleStability method) bulk_modulus (Element attribute) bulk_structure (Defect attribute) (DefectEntry attribute) BVA_DISTANCE_SCALE_FACTORS (LocalGeometryFinder attribute) BVAnalyzer (class in pymatgen.analysis.bond_valence) BVAValencesNotFoundChemenvError

C

C (Element attribute) c (Kpoint attribute) (Lattice attribute) (PeriodicSite attribute) (Plane attribute) Ca (Element attribute) cage (CriticalPointType attribute) cahill_thermalcond() (ElasticTensor method) calc (Xmu attribute) 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_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 attribute) callback() (PyFlowScheduler method) can_change_physics (DilatmxErrorHandler attribute) cancel() (Flow method) (TaskManager method) cart_coords (Kpoint attribute) (SiteCollection attribute) cart_forces (GaussianOutput attribute) Cartesian (Kpoints_supported_modes attribute) cbk_qptdm_workflow() (G0W0WithQptdmFlow method) Cd (Element attribute) Ce (Element attribute) ce_symbol (CoordinationGeometry attribute) center_of_mass (IMolecule attribute) (Slab attribute) center_slab (SlabGenerator attribute) center_slab() (in module pymatgen.core.surface) Cf (Element attribute) changebasis() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) Charge (class in pymatgen.io.lobster) charge (Defect attribute) (DefectEntry attribute) (GaussianOutput attribute) (IMolecule attribute) Charge (in module pymatgen.core.units) charge (Ion attribute) (IStructure attribute) (Outcar attribute) (SiteCollection attribute) charge_distribution_df (ChargeDensityAnalyzer attribute) CHARGE_NEUTRALITY_TOLERANCE (BVAnalyzer attribute) charge_transfer_from_file() (LDos static method) charge_transfer_to_string() (LDos method) ChargeBalanceFilter (class in pymatgen.alchemy.filters) 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_input() (in module pymatgen.analysis.defects.dilute_solution_model) check_mappings() (in module pymatgen.core.units) 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) 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) Chgcar (class in pymatgen.io.vasp.outputs) ChgcarPotential (class in pymatgen.analysis.path_finder) chi (Xmu attribute) 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 attribute) cleanup() (PyFlowScheduler method) clear_environments() (LightStructureEnvironments method) close() (AtomicFile method) (NetcdfReader method) (YamlTokenizer method) closestsites() (in module pymatgen.analysis.defects.utils) cluster (Atoms attribute) cluster_from_file() (Atoms static method) cluster_nodes() (ChargeDensityAnalyzer method) (TopographyAnalyzer method) cluster_sites() (in module pymatgen.symmetry.analyzer) Cm (Element attribute) cn (AbstractGeometry attribute) CNBiasNbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) Co (Element attribute) COD (class in pymatgen.ext.cod) coefficient_of_linear_thermal_expansion (Element attribute) coefficients (Plane attribute) coeffs (BalancedReaction attribute) (Wavecar attribute) Cohp (class in pymatgen.electronic_structure.cohp) Cohpcar (class in pymatgen.io.lobster) CohpPlotter (class in pymatgen.electronic_structure.plotter) 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 attribute) 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 attribute) colours (StringColorizer attribute) combine_neb_plots() (in module pymatgen.analysis.transition_state) combiplot() (CyclesPlotter method) comment (Poscar attribute) (Xdatcar attribute) common_oxidation_states (Element attribute), [1]

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 attribute) complete_ordering() (PartialRemoveSitesTransformation method) CompleteCohp (class in pymatgen.electronic_structure.cohp) CompleteDos (class in pymatgen.electronic_structure.dos) completedos (Doscar attribute), [1] CompletePhononDos (class in pymatgen.phonon.dos) compliance_tensor (ElasticTensor attribute) ComplianceTensor (class in pymatgen.analysis.elasticity.elastic) Composition (class in pymatgen.core.composition) composition (ConversionElectrode attribute) (Ion attribute) (MolecularOrbitals attribute) (PDEntry attribute) (SiteCollection attribute) 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) concatenate() (Xdatcar method) Condition (class in pymatgen.io.abinit.utils) CONDITION_DESCRIPTION (AdditionalConditions attribute) CONFIG (MITRelaxSet attribute) (MPELNESSet attribute) (MPEXAFSSet attribute) (MPEXELFSSet attribute) (MPHSERelaxSet attribute) (MPRelaxSet attribute) (MPXANESSet attribute) (MVLGWSet 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 attribute) Constraints (class in pymatgen.io.abinit.abiobjects) 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 attribute) contract() (in module pymatgen.io.abinit.abiobjects) CONV_FACT (EwaldSummation attribute) conventional (HighSymmKpath attribute) converge() (in module pymatgen.analysis.defects.utils) converged (Vasprun attribute) converged_electronic (Vasprun attribute) converged_ionic (Vasprun attribute) 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_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 attribute) 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 attribute) (CoordinationGeometry attribute) CoordinationGeometry (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) CoordinationGeometry.NeighborsSetsHints (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometries) coords (Simplex attribute) (Site attribute) (StructureEnvironments.NeighborsSet attribute) copy() (Composition method) (Defect method) (DefectEntry method) (IStructure method) (Lattice method) (Molecule method) (ParalHints method) (Reaction method) (Slab method) (Spectrum method) copy_abiext() (Directory method) copy_r() (Directory method) correct() (SchedulerErrorHandler method) correct_entry() (Correction method) (DefectCorrection method) corrected_compound_formulas (EntryPostProcessor attribute) Correction (class in pymatgen.entries.compatibility) (class in pymatgen.io.abinit.events) corrections (GaussianOutput attribute) (Node attribute) 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) 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_slab_label (SlabEntry attribute) 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_temperature (Element attribute) CriticalPoint (class in pymatgen.command_line.critic2_caller) CriticalPointType (class in pymatgen.command_line.critic2_caller) crosses_origin (Plane attribute) CrystalNN (class in pymatgen.analysis.local_env) Cs (Element attribute) cs_core_contribution (Outcar attribute) csm_skip_algo (CoordinationGeometry attribute) CSM_SKIP_SEPARATION_PLANE_ALGO (CoordinationGeometry attribute) CSMFiniteRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) CSMFloat (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) CSMInfiniteRatioFunction (class in pymatgen.analysis.chemenv.utils.func_utils) Cssr (class in pymatgen.io.cssr) Cu (Element attribute) cubic() (HighSymmKpath method) (Lattice static method) 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) (Plane attribute) D2DEScfCycle (class in pymatgen.io.abinit.abiinspect) d_hkl() (Lattice method) data (Dynmat attribute) (Element attribute) (PotcarSingle attribute) (Procar attribute) (Wavederf attribute) db_insert() (Flow method) DBConnector (class in pymatgen.io.abinit.db) ddb_filepath (AnaddbTask attribute) ddk_filepath (AnaddbTask attribute) ddk_filepaths (OpticTask attribute) 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 attribute) (Interstitial attribute) (Substitution attribute) (Vacancy attribute) defect_concentration() (DefectEntry method) defect_concentrations() (DefectPhaseDiagram method) defect_types (DefectPhaseDiagram attribute) 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 attribute) DeformedStructureSet (class in pymatgen.analysis.elasticity.strain) DeformStructureTransformation (class in pymatgen.transformations.standard_transformations) delete_snl() (MPRester method) delocalization_analysis() (DefectCompatibility method) delta_cn_specifics() (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.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 attribute) density_of_solid (Element attribute) Dependency (class in pymatgen.io.abinit.nodes) depends_on() (Node method) deps (Node attribute) deps_status (Node attribute)

description (AdditionalConditionInt attribute) (HistoryNode attribute) det (SquareTensor attribute) DetailedVoronoiContainer (class in pymatgen.analysis.chemenv.coordination_environments.voronoi) determine_convergence() (in module pymatgen.util.convergence) dev_principal_invariants (Stress attribute) deviator_stress (Stress attribute) dft_task() (pymatgen.io.nwchem.NwTask class method) diamond_functions() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) DictSet (class in pymatgen.io.vasp.sets) dielectric (Vasprun attribute), [1] dieze_tag (GaussianOutput attribute) diff() (Incar method) (MoleculeGraph method) (StructureGraph method) (Tags method) diff_fit() (in module pymatgen.analysis.elasticity.elastic) differences_wrt() (StructureEnvironments method) DiffusionAnalyzer (class in pymatgen.analysis.diffusion_analyzer) DilatmxError (class in pymatgen.io.abinit.events) DilatmxErrorHandler (class in pymatgen.io.abinit.events) dipole (Slab attribute) directional_elastic_mod() (ElasticTensor method) directional_poisson_ratio() (ElasticTensor method) Directory (class in pymatgen.io.abinit.utils) dirname (File attribute) Dirviz (class in pymatgen.io.abinit.utils) disable_symmetry() (QcTask method) disassemble() (LammpsData method) discard() (AtomicFile 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) display_help() (MultiStructuresVis method) (StructureVis method) display_info() (MultiStructuresVis method) display_warning() (MultiStructuresVis method) dist (ConnectedSite attribute) distance() (PeriodicSite method) (Site method) distance_and_image() (PeriodicSite method) distance_and_image_from_frac_coords() (PeriodicSite method) distance_cutoff (SimplestChemenvStrategy attribute) distance_from_point() (Site method) distance_matrix (IStructure attribute) (SiteCollection attribute) distance_plateau() (StructureEnvironments.NeighborsSet method) distance_to_origin (Plane attribute) 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 (StructureEnvironments.NeighborsSet attribute) distances() (Plane method) distances_indices_groups() (Plane method) distances_indices_sorted() (Plane method) distfactor_max (CoordinationGeometry attribute) divisors() (in module pymatgen.analysis.chemenv.utils.math_utils) djrepo_path (Pseudo attribute) DLSVolumePredictor (class in pymatgen.analysis.structure_prediction.volume_predictor) do_query() (in module pymatgen.cli.pmg_query) 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 attribute) (OrbitalDescription attribute) e0 (EOSBase attribute) e_fermi (Xmu attribute) e_surf_list (WulffShape attribute) EconNN (class in pymatgen.analysis.local_env) edge (Xmu attribute) edge_weight_name (MoleculeGraph attribute) (StructureGraph attribute) edge_weight_unit (MoleculeGraph attribute) (StructureGraph attribute) 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 attribute) efg (Outcar attribute) eigenvalue_band_properties (Vasprun attribute) 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 attribute) 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 attribute) (Pseudo attribute) (Specie attribute) element_composition (Composition attribute) ElementComparator (class in pymatgen.analysis.structure_matcher) elements (BalancedReaction attribute) (Composition attribute) (MolecularOrbitals attribute) ellipticity (CriticalPoint attribute) email (Author attribute) encut (Wavecar attribute) END_TAG (AbinitTimerParser attribute) endpoints_minima() (EnergyTrend method) energies (AdfOutput attribute) (Doscar attribute), [1] (Eels attribute) (GaussianOutput attribute) (Xmu attribute) energy (ComputedEntry attribute) (DefectEntry attribute) Energy (in module pymatgen.core.units) energy (PDEntry attribute) energy_density() (ElasticTensorExpansion method) (NthOrderElasticTensor method) energy_per_atom (ComputedEntry attribute) (PDEntry attribute) EnergyModel (class in pymatgen.analysis.energy_models) EnergyTrend (class in pymatgen.analysis.ferroelectricity.polarization) ensemble_center() (AdsorbateSiteFinder method) ENTRIES (TaskManager attribute) entries_charge (ConversionVoltagePair attribute) entries_discharge (ConversionVoltagePair attribute) entropy() (PhononDos method) entry_dict_from_list() (in module pymatgen.analysis.surface_analysis) EntryPostProcessor (class in pymatgen.entries.post_processors_abc) enumerate_defectsites() (StructureMotifInterstitial method) enumerate_ordering() (PartialRemoveSitesTransformation method) 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), [1] epsilon_static (Vasprun attribute), [1] epsilon_static_wolfe (Vasprun attribute), [1] 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 attribute) (PBSErrorParser attribute) (SlurmErrorParser attribute) errored_tasks (Flow attribute) errors (GaussianOutput attribute) Es (Element attribute) esp_task() (pymatgen.io.nwchem.NwTask class method) estimate_band_connection() (in module pymatgen.phonon.bandstructure) estimated_start_time() (PbsProJob method) (QueueJob method) (SlurmJob method) eta (EwaldSummation attribute) 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 attribute) 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 attribute) 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 attribute) (AnaddbTask attribute) (OpticTask attribute) exists (Directory attribute) (File attribute) expand() (in module pymatgen.io.abinit.helpers) ExpEntry (class in pymatgen.entries.exp_entries) explain() (Compatibility method) explicit() (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight class method) explicit_path() (pymatgen.io.abinit.abiobjects.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_transformations() (StandardTransmuter method) (TransformedStructure method) extract_cluster() (IMolecule method) extract_metadata() (AbstractErrorParser static method) extrapolate_reciprocal() (in module pymatgen.util.convergence) extrapolate_simple_reciprocal() (in module pymatgen.util.convergence) extrema_df (ChargeDensityAnalyzer attribute) extremum_icohpvalue() (IcohpCollection method)

F

F (Element attribute) f (OrbitalType attribute) f0 (Orbital attribute) f0() (in module pymatgen.electronic_structure.dos) f1 (Orbital attribute) f2 (Orbital attribute) f3 (Orbital attribute) f_1 (Orbital attribute) f_2 (Orbital attribute) f_3 (Orbital attribute) faces() (CoordinationGeometry method) facets (WulffShape attribute) factor (FreqUnits attribute) fake() (pymatgen.io.abinit.abitimer.AbinitTimerSection class method) farid (PPModelModes attribute) fast_norm() (in module pymatgen.analysis.substrate_analyzer) fast_ordering() (PartialRemoveSitesTransformation method) 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 attribute) filename (HistoryRecord attribute) (Wavecar attribute) filenames (AbinitTimerParser attribute) FileNode (class in pymatgen.io.abinit.nodes) filepath (Product attribute) (Pseudo attribute) FilepathFixer (class in pymatgen.io.abinit.utils) filesfile_string (AbinitTask attribute) (AnaddbTask attribute) (OpticTask attribute) FiM (Ordering attribute) final_energy (AdfOutput attribute) (GaussianOutput attribute) (Oszicar attribute) (PWOutput attribute) (QcOutput attribute) (Vasprun attribute) final_structure (AdfOutput attribute) (GaussianOutput attribute) (QcOutput attribute) finalize() (Flow method) finalized (Node attribute) 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.find_dimension) find_connected_atoms() (in module pymatgen.analysis.find_dimension) find_deadlocks() (Flow method) find_dimension() (in module pymatgen.analysis.find_dimension) 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_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_structure() (MPRester method) find_surface_sites_by_height() (AdsorbateSiteFinder method) fine_structure (Eels attribute) fit() (DeltaFactor method) (EOS method) (EOSBase 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_queue_critical() (AbinitTask method) (Flow method) (OpticTask method) FloatWithUnit (class in pymatgen.core.units) Flow (class in pymatgen.io.abinit.flows) flow (PyFlowScheduler attribute) (Work attribute) 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) ForceField (class in pymatgen.io.lammps.data) forces (EwaldSummation attribute) formation_energy() (DefectEntry method) formation_energy_tol (PhaseDiagram attribute) formula (Composition attribute) (Header attribute) (Ion attribute) (SiteCollection attribute) formula_double_format() (in module pymatgen.util.string) Fr (Element attribute) frac_charge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) frac_coords (IStructure attribute) (Kpoint attribute) (PeriodicSite attribute) frac_discharge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) fractional_composition (Composition attribute) fractions() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) 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) FreqUnits (class in pymatgen.phonon.plotter) FreysoldtCorrection (class in pymatgen.analysis.defects.corrections) from_2points_and_origin() (pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane class method) from_3points() (pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane class method) from_abinit_ixc() (pymatgen.core.xcfunc.XcFunc class method) from_axis_angle_and_translation() (SymmOp static method) from_bonding() (pymatgen.io.lammps.data.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() (pymatgen.analysis.adsorption.AdsorbateSiteFinder class method) from_cg() (pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry class method) from_cif_file() (Header static method) from_cif_string() (TransformedStructure static method) from_coefficients() (pymatgen.analysis.chemenv.utils.coordination_geometry_utils.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() (PDEntry static method) from_deformation() (pymatgen.analysis.elasticity.strain.Strain class method) from_description() (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight class method) from_dict (Element attribute) (LibxcFunc attribute) from_dict() (Author static method) (BoltztrapAnalyzer static method) (HistoryNode static method) (PPModel static method) (Smearing static method) (Tags static method) (pymatgen.alchemy.filters.ContainsSpecieFilter class method) (pymatgen.alchemy.filters.SpecieProximityFilter class method) (pymatgen.alchemy.materials.TransformedStructure class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AnglePlateauNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaCSMNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaDistanceNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceAngleAreaNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceCutoffFloat class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistancePlateauNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SelfCSMNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargettedPenaltiedAbundanceChemenvStrategy class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy class method) (pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry class method) (pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.NeighborsSetsHints class method) (pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.ExplicitPermutationsAlgorithm class method) (pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.SeparationPlane class method) (pymatgen.analysis.chemenv.coordination_environments.structure_environments.ChemicalEnvironments class method) (pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments class method) (pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.NeighborsSet class method) (pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments class method) (pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet class method) (pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer class method) (pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction class method) (pymatgen.analysis.diffusion_analyzer.DiffusionAnalyzer class method) (pymatgen.analysis.energy_models.EnergyModel class method) (pymatgen.analysis.graphs.MoleculeGraph class method) (pymatgen.analysis.graphs.StructureGraph class method) (pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator class method) (pymatgen.analysis.phase_diagram.CompoundPhaseDiagram class method) (pymatgen.analysis.phase_diagram.GrandPotPDEntry class method) (pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram class method) (pymatgen.analysis.phase_diagram.PDEntry class method) (pymatgen.analysis.phase_diagram.PhaseDiagram class method) (pymatgen.analysis.phase_diagram.TransformedPDEntry class method) (pymatgen.analysis.reaction_calculator.BalancedReaction class method) (pymatgen.analysis.reaction_calculator.ComputedReaction class method) (pymatgen.analysis.reaction_calculator.Reaction class method) (pymatgen.analysis.structure_matcher.AbstractComparator class method) (pymatgen.analysis.structure_matcher.StructureMatcher class method) (pymatgen.analysis.structure_prediction.substitutor.Substitutor class method) (pymatgen.analysis.surface_analysis.SlabEntry class method) (pymatgen.analysis.thermochemistry.ThermoData class method) (pymatgen.apps.battery.conversion_battery.ConversionElectrode class method) (pymatgen.apps.battery.conversion_battery.ConversionVoltagePair class method) (pymatgen.apps.battery.insertion_battery.InsertionElectrode class method) (pymatgen.apps.borg.hive.GaussianToComputedEntryDrone class method) (pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone class method) (pymatgen.apps.borg.hive.VaspToComputedEntryDrone class method) (pymatgen.core.composition.Composition class method) (pymatgen.core.ion.Ion class method) (pymatgen.core.lattice.Lattice class method) (pymatgen.core.operations.MagSymmOp class method) (pymatgen.core.operations.SymmOp class method) (pymatgen.core.periodic_table.DummySpecie class method) (pymatgen.core.periodic_table.Specie class method) (pymatgen.core.sites.PeriodicSite class method) (pymatgen.core.sites.Site class method) (pymatgen.core.structure.IMolecule class method) (pymatgen.core.structure.IStructure class method) (pymatgen.core.surface.Slab class method) (pymatgen.core.tensors.Tensor class method) (pymatgen.core.tensors.TensorCollection class method) (pymatgen.core.xcfunc.XcFunc class method) (pymatgen.electronic_structure.bandstructure.BandStructure class method) (pymatgen.electronic_structure.bandstructure.BandStructureSymmLine class method) (pymatgen.electronic_structure.cohp.Cohp class method) (pymatgen.electronic_structure.cohp.CompleteCohp class method) (pymatgen.electronic_structure.dos.CompleteDos class method) (pymatgen.electronic_structure.dos.Dos class method) (pymatgen.electronic_structure.dos.LobsterCompleteDos class method) (pymatgen.entries.computed_entries.ComputedEntry class method) (pymatgen.entries.computed_entries.ComputedStructureEntry class method) (pymatgen.entries.exp_entries.ExpEntry class method) (pymatgen.io.abinit.abiobjects.Electrons class method) (pymatgen.io.abinit.abiobjects.ElectronsAlgorithm class method) (pymatgen.io.abinit.abiobjects.KSampling class method) (pymatgen.io.abinit.abiobjects.RelaxationMethod class method) (pymatgen.io.abinit.abiobjects.SpinMode class method) (pymatgen.io.abinit.events.Correction class method) (pymatgen.io.abinit.events.DilatmxErrorHandler class method) (pymatgen.io.abinit.flows.Flow class method) (pymatgen.io.abinit.nodes.HistoryRecord class method) (pymatgen.io.abinit.nodes.NodeResults class method) (pymatgen.io.abinit.pseudos.Pseudo class method) (pymatgen.io.abinit.pseudos.PseudoTable class method) (pymatgen.io.abinit.tasks.ParalHints class method) (pymatgen.io.abinit.tasks.TaskManager class method) (pymatgen.io.adf.AdfKey class method) (pymatgen.io.adf.AdfTask class method) (pymatgen.io.fiesta.FiestaInput class method) (pymatgen.io.fiesta.Fiesta_run class method) (pymatgen.io.fiesta.Nwchem2Fiesta class method) (pymatgen.io.gaussian.GaussianInput class method) (pymatgen.io.lammps.data.ForceField class method) (pymatgen.io.lammps.data.LammpsData class method) (pymatgen.io.lammps.outputs.LammpsDump class method) (pymatgen.io.lmto.LMTOCtrl class method) (pymatgen.io.nwchem.NwInput class method) (pymatgen.io.nwchem.NwTask class method) (pymatgen.io.pwscf.PWInput class method) (pymatgen.io.qchem_deprecated.QcInput class method) (pymatgen.io.qchem_deprecated.QcTask class method) (pymatgen.io.vasp.inputs.Incar class method) (pymatgen.io.vasp.inputs.Kpoints class method) (pymatgen.io.vasp.inputs.Poscar class method) (pymatgen.io.vasp.inputs.Potcar class method) (pymatgen.io.vasp.inputs.VaspInput class method) (pymatgen.phonon.bandstructure.PhononBandStructure class method) (pymatgen.phonon.bandstructure.PhononBandStructureSymmLine class method) (pymatgen.phonon.dos.CompletePhononDos class method) (pymatgen.phonon.dos.PhononDos class method) (pymatgen.util.provenance.StructureNL class method)

from_diff_fit() (pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion class method) (pymatgen.analysis.elasticity.elastic.NthOrderElasticTensor class method) from_dir() (pymatgen.analysis.transition_state.NEBAnalysis class method) (pymatgen.io.abinit.pseudos.PseudoTable class method) from_directory() (FEFFDictSet static method) (VaspInput static method) from_ff_and_topologies() (pymatgen.io.lammps.data.LammpsData class method) from_file() (Chgcar static method) (Cssr static method) (Eels static method) (ExcitingInput static method) (GaussianInput static method) (Header static method) (Incar static method) (Kpoints static method) (LDos static method) (Locpot static method) (PWInput static method) (Poscar static method) (Potcar static method) (PotcarSingle static method) (Pseudo static method) (QCInput static method) (Tags static method) (XYZ static method) (Xmu static method) (Xr static method) (ZeoCssr static method) (ZeoVoronoiXYZ static method) (pymatgen.analysis.defects.utils.ChargeDensityAnalyzer class method) (pymatgen.core.structure.IMolecule class method) (pymatgen.core.structure.IStructure class method) (pymatgen.core.structure.SiteCollection class method) (pymatgen.electronic_structure.cohp.CompleteCohp class method) (pymatgen.io.abinit.abiinspect.Relaxation class method) (pymatgen.io.abinit.abiinspect.ScfCycle class method) (pymatgen.io.abinit.launcher.PyFlowScheduler class method) (pymatgen.io.abinit.nodes.Product class method) (pymatgen.io.abinit.tasks.TaskManager class method) (pymatgen.io.cif.CifFile class method) (pymatgen.io.fiesta.FiestaInput class method) (pymatgen.io.lammps.data.ForceField class method) (pymatgen.io.lammps.data.LammpsData class method) (pymatgen.io.lmto.LMTOCtrl class method) (pymatgen.io.nwchem.NwInput class method) (pymatgen.io.qchem_deprecated.QcInput class method) (pymatgen.io.qchem_deprecated.QcTask class method) from_filenames() (CifTransmuter static method) (PoscarTransmuter static method) from_files() (BoltztrapAnalyzer static method) (WorkFunctionAnalyzer static method) (pymatgen.analysis.diffusion_analyzer.DiffusionAnalyzer class method) from_formula() (pymatgen.core.ion.Ion class method) from_global_moment_and_saxis() (pymatgen.electronic_structure.core.Magmom class method) from_hdf5() (pymatgen.io.vasp.outputs.VolumetricData class method) from_independent_strains() (pymatgen.analysis.elasticity.elastic.ElasticTensor class method) from_index_amount() (pymatgen.analysis.elasticity.strain.Deformation class method) (pymatgen.analysis.elasticity.strain.Strain class method) from_input() (pymatgen.io.abinit.tasks.AbinitTask class method) from_inputs() (pymatgen.io.abinit.flows.Flow class method) from_lengths_and_angles() (Lattice static method) from_magnetic_spacegroup() (pymatgen.core.structure.IStructure class method) from_maryland_notation() (pymatgen.analysis.nmr.ChemicalShielding class method) from_molecule() (pymatgen.io.nwchem.NwTask class method) from_moment_relative_to_crystal_axes() (pymatgen.electronic_structure.core.Magmom class method) from_mpi_omp_lists() (pymatgen.io.abinit.tasks.ParalHints class method) from_multi_jobs_file() (pymatgen.io.qchem.inputs.QCInput class method) from_name() (pymatgen.core.xcfunc.XcFunc class method) from_node() (pymatgen.io.abinit.nodes.NodeResults class method) from_npoints() (pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane class method) from_npoints_least_square_distance() (pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane class method) from_npoints_maximum_distance() (pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane class method) from_old_dict() (pymatgen.electronic_structure.bandstructure.BandStructure class method) (pymatgen.electronic_structure.bandstructure.BandStructureSymmLine class method) from_origin_axis_angle() (SymmOp static method) from_origin_shift() (pymatgen.symmetry.settings.JonesFaithfulTransformation class method) from_outcars() (pymatgen.analysis.transition_state.NEBAnalysis class method) from_outcars_and_structures() (pymatgen.analysis.ferroelectricity.polarization.Polarization class method) from_parameters() (Lattice static method) from_path() (pymatgen.command_line.bader_caller.BaderAnalysis class method) (pymatgen.command_line.critic2_caller.Critic2Caller class method) from_poscar_string() (TransformedStructure static method) from_prev_calc() (pymatgen.io.vasp.sets.MPHSEBSSet class method) (pymatgen.io.vasp.sets.MPNonSCFSet class method) (pymatgen.io.vasp.sets.MPSOCSet class method) (pymatgen.io.vasp.sets.MPStaticSet class method) (pymatgen.io.vasp.sets.MVLGWSet class method) from_pseudoinverse() (pymatgen.analysis.elasticity.elastic.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() (pymatgen.io.abinit.works.PhononWork class method) from_scf_task() (pymatgen.io.abinit.works.BecWork class method) (pymatgen.io.abinit.works.DteWork class method) (pymatgen.io.abinit.works.PhononWork class method) from_sites() (pymatgen.core.structure.IMolecule class method) (pymatgen.core.structure.IStructure class method) from_snl() (pymatgen.alchemy.materials.TransformedStructure class method) from_spacegroup() (pymatgen.core.structure.IStructure class method) from_steps() (ConversionVoltagePair static method) from_str() (pymatgen.core.structure.IMolecule class method) (pymatgen.core.structure.IStructure class method) (pymatgen.core.structure.SiteCollection class method) from_stream() (pymatgen.io.abinit.abiinspect.Relaxation class method) (pymatgen.io.abinit.abiinspect.ScfCycle class method) from_string (Kpoints_supported_modes attribute) from_string() (AdfKey static method) (BalancedReaction static method) (CifParser static method) (Cssr static method) (DummySpecie static method) (ExcitingInput static method) (GaussianInput static method) (Header static method) (Incar static method) (Kpoints static method) (PWInput static method) (Poscar static method) (Specie static method) (XYZ static method) (Xr static method) (ZeoCssr static method) (ZeoVoronoiXYZ static method) (pymatgen.core.units.FloatWithUnit class method) (pymatgen.io.abinit.launcher.PyFlowScheduler class method) (pymatgen.io.abinit.nodes.Status class method) (pymatgen.io.abinit.qjobs.JobStatus class method) (pymatgen.io.abinit.tasks.TaskManager class method) (pymatgen.io.cif.CifBlock class method) (pymatgen.io.cif.CifFile class method) (pymatgen.io.fiesta.FiestaInput class method) (pymatgen.io.lammps.outputs.LammpsDump class method) (pymatgen.io.lmto.LMTOCtrl class method) (pymatgen.io.nwchem.NwInput class method) (pymatgen.io.qchem.inputs.QCInput class method) (pymatgen.io.qchem_deprecated.QcInput class method) (pymatgen.io.qchem_deprecated.QcTask class method) (pymatgen.io.xcrysden.XSF class method) from_structure() (pymatgen.io.lammps.data.LammpsData class method) from_structure_environments() (pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments class method) from_structures() (pymatgen.analysis.diffusion_analyzer.DiffusionAnalyzer class method) (StandardTransmuter static method) (pymatgen.util.provenance.StructureNL class method) from_symbol_and_functional() (PotcarSingle static method) from_symmop() (pymatgen.core.operations.MagSymmOp class method) from_transformation_string() (pymatgen.symmetry.settings.JonesFaithfulTransformation class method) from_type_name() (pymatgen.core.xcfunc.XcFunc class method) from_user_config() (pymatgen.io.abinit.launcher.PyFlowScheduler class method) (pymatgen.io.abinit.tasks.TaskManager class method) from_values_indices() (pymatgen.core.tensors.Tensor class method) from_vaspruns() (pymatgen.analysis.diffusion_analyzer.DiffusionAnalyzer class method) from_voigt() (pymatgen.core.tensors.Tensor class method) (pymatgen.core.tensors.TensorCollection class method) from_xyz_string() (SymmOp static method) from_xyzt_string() (MagSymmOp static method) from_Z (Element attribute) full_electronic_structure (Element attribute), [1] FullQueueError (class in pymatgen.io.abinit.scheduler_error_parsers) fully_charged_entry (InsertionElectrode attribute) fully_discharged_entry (InsertionElectrode attribute) func() (EOSBase method) func_name (HistoryRecord attribute) function_comparison() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) functional (GaussianOutput attribute) (PotcarSingle attribute) FUNCTIONAL_CHOICES (Potcar attribute) functional_class (PotcarSingle attribute) functional_dir (PotcarSingle attribute) functional_tags (PotcarSingle attribute)

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 attribute) g_voigt (ElasticTensor attribute) g_vrh (ElasticTensor attribute) Ga (Element attribute) Gamma (Kpoints_supported_modes attribute) gamma (Lattice attribute) gamma_automatic() (Kpoints static method) gamma_centered() (pymatgen.io.abinit.abiobjects.KSampling class method) gamma_only() (pymatgen.io.abinit.abiobjects.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) gc (Node attribute) Gd (Element attribute) Ge (Element attribute) 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_full_symmops() (in module pymatgen.symmetry.analyzer) generate_potcar() (in module pymatgen.cli.pmg_potcar) generate_pseudo() (in module pymatgen.analysis.elasticity.elastic) 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() (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.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_neighbors() (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_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_atom_map() (in module pymatgen.io.feff.inputs) get_atomic_fraction() (Composition method) get_atoms() (AseAtomsAdaptor static 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_by_material_id() (MPRester 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_range_map() (PhaseDiagram method) get_chempot_range_map_plot() (PDPlotter method) get_chempot_range_stability_phase() (PhaseDiagram method) get_children() (Node method) 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) (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_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) (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_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() (in module pymatgen.analysis.structure_analyzer) 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() (MPRester method) get_doping() (FermiDos method) get_dos_by_material_id() (MPRester method) get_dos_dict() (DosPlotter method) (PhononDosPlotter method) get_drift_corrected_structures() (DiffusionAnalyzer method) get_e_above_hull() (PhaseDiagram method) get_effective_csm() (in module pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) get_effective_ecs() (ElasticTensorExpansion method) get_el_amount() (BalancedReaction method) get_el_amt_dict() (Composition method) get_el_sp() (in module pymatgen.core.periodic_table) get_element_dos() (CompleteDos method) (CompletePhononDos method) get_element_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_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_fermi() (FermiDos method) get_fermi_interextrapolated() (FermiDos method) get_ferromagnetic_structure() (CollinearMagneticStructureAnalyzer method) get_filepaths_and_exts() (Dependency 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_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_high_accuracy_voronoi_nodes() (in module pymatgen.io.zeopp) get_hull_energy() (PhaseDiagram method) get_icohp() (Cohp method) (CompleteCohp method) get_icohp_by_label() (IcohpCollection method) get_icohp_dict_by_bondlengths() (IcohpCollection method) get_icohp_dict_of_certain_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.surface) get_integrated_diff() (VolumetricData 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_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_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_mi_vec() (in module pymatgen.analysis.adsorption) get_min_instability() (InsertionElectrode method) get_min_muO2() (InsertionElectrode method) get_minkowski_red() (in module pymatgen.command_line.aconvasp_caller) get_moment() (Magmom method) get_moment_relative_to_crystal_axes() (Magmom method) get_mongo_info() (Flow method) get_monolayer (SlabEntry attribute) get_motif_type() (StructureMotifInterstitial method) get_mp_structure() (pymatgen.util.testing.PymatgenTest class method) get_msd_plot() (DiffusionAnalyzer method) get_mu_bounds() (BoltztrapAnalyzer 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_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() (pymatgen.io.abinit.abiobjects.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_resolved_cohp() (CompleteCohp method) get_order_parameters() (LocalStructOrderParams method) get_ordered_with_policy() (ParalHints method) 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_parents() (Node method) get_parser() (in module pymatgen.io.abinit.scheduler_error_parsers) 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_plot() (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_pourbaix_entries() (MPRester 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) (Procar method) get_projections_on_elements_and_orbitals() (BandStructure method) get_prototypes() (AflowPrototypeMatcher method) get_pseudos_for_structure() (PseudoTable method) get_q2() (LocalStructOrderParams method) get_q4() (LocalStructOrderParams method) get_q6() (LocalStructOrderParams method) get_rdf_figure() (DetailedVoronoiContainer method) get_reaction() (MPRester method) get_reasonable_repetitions() (in module pymatgen.phonon.bandstructure) get_reconstructed_band_structure() (in module pymatgen.electronic_structure.bandstructure) get_recp_symmetry_operation() (in module pymatgen.core.surface) 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_rot() (in module pymatgen.analysis.adsorption) 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_shannon_radius() (Specie method) 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_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_slabs() (SlabGenerator method) get_smeared_densities() (Dos method) (PhononDos method) get_sorted_structure() (IStructure method) (Slab method) get_space_group_info() (IStructure method) get_space_group_number() (SpacegroupAnalyzer method) get_space_group_operations() (SpacegroupAnalyzer method) get_space_group_symbol() (SpacegroupAnalyzer method) get_spd_dos() (CompleteDos method) (LobsterCompleteDos method) get_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_at_u() (SurfaceEnergyPlotter 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() (Incar method) (LMTOCtrl method) (LammpsBox method) (LammpsData method) (Poscar method) (Tags method) (Xdatcar method) get_structure() (AseAtomsAdaptor static method) (LocalGeometryFinder method) (pymatgen.util.testing.PymatgenTest class method) get_structure_by_formula() (COD method) get_structure_by_id() (COD method) get_structure_by_material_id() (MPRester method) get_structure_from_dict() (in module pymatgen.io.phonopy) get_structure_from_mp() (in module pymatgen) get_structure_from_prev_run() (in module pymatgen.io.vasp.sets) get_structure_property_dict() (ElasticTensor method) get_structure_with_charges() (Charge method) get_structure_with_nodes() (ChargeDensityAnalyzer method) (TopographyAnalyzer method) get_structure_with_only_magnetic_atoms() (CollinearMagneticStructureAnalyzer method) get_structure_with_spin() (CollinearMagneticStructureAnalyzer method) get_structures() (CifParser method) (MPRester method) get_sub_electrodes() (ConversionElectrode method) (InsertionElectrode method) get_subgraphs_as_molecules() (StructureGraph method) get_substrates() (MPRester method) get_suggested_saxis() (Magmom static method) get_summary_dict() (ConversionElectrode method) (DiffusionAnalyzer method) (QuasiharmonicDebyeApprox method) get_summed_icohp_by_labellist() (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_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_transformation() (StructureMatcher method) get_transition_chempots() (PhaseDiagram method) get_tri_area() (in module pymatgen.analysis.wulff) get_type() (LocalStructOrderParams method) get_unit_primitive_area (SlabEntry attribute) get_unreconstructed_slabs() (ReconstructionGenerator method) get_unstable_entries() (InsertionElectrode 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) 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_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_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 attribute) global_moment (Magmom attribute) godby (PPModelModes attribute) good_sections() (ParallelEfficiency method) GPa_to_eV_A3 (NthOrderElasticTensor attribute) Gpoints (Wavecar attribute) 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 attribute) grid_off (WulffShape attribute) gridfs_files (NodeResults attribute) GridFsFile (class in pymatgen.io.abinit.nodes) ground_state_term_symbol (Element attribute) GroundStateScfCycle (class in pymatgen.io.abinit.abiinspect) group (Element attribute), [1] group_by_types() (SiteCollection method) group_entries_by_structure() (in module pymatgen.entries.entry_tools) 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 attribute) gweight() (NormalizedAngleDistanceNbSetWeight method)

H

H (Element attribute) haeberlen_values (ChemicalShielding attribute) HaeberlenNotation (ChemicalShielding attribute) halogen_list (MoleculeStructureComparator attribute) handle_input_event() (DilatmxErrorHandler method) handle_task_event() (DilatmxErrorHandler method) has_abiext() (Directory method) has_chrooted (Flow attribute) has_db (Flow attribute) (TaskManager attribute) has_dojo_report (Pseudo attribute) has_eigendisplacements (PhononBandStructure attribute) has_errors (CifParser attribute) has_hints (Pseudo attribute) has_imaginary_freq() (PhononBandStructure method) has_materials_project_access (ChemEnvConfig attribute) has_mpi (AbinitBuild attribute) has_mpiio (AbinitBuild attribute) has_nac (PhononBandStructure attribute) has_netcdf (AbinitBuild attribute) has_node_failures (QueueJob attribute) has_omp (AbinitBuild attribute) (TaskManager attribute) has_option() (AdfKey method) has_queue (TaskManager attribute) has_scheduler (Flow attribute) 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) 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 attribute) 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_tuple_to_str() (in module pymatgen.analysis.wulff) Ho (Element attribute) homogeneous_poisson (ElasticTensor attribute) htmlify() (in module pymatgen.util.string) hubbards (Vasprun attribute) 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), [1] IcohpCollection (class in pymatgen.electronic_structure.cohp) icohpcollection (Icohplist attribute) Icohplist (class in pymatgen.io.lobster) icohplist (Icohplist attribute) IcohpValue (class in pymatgen.electronic_structure.cohp) icohpvalue() (IcohpValue method) icsd_oxidation_states (Element attribute) id_generator() (in module pymatgen.util.convergence) idos (Vasprun attribute) iflat_nodes() (Flow method) iflat_tasks() (Flow method) iflat_tasks_wti() (Flow method) images (NEBPathfinder attribute) 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 attribute) Incar (class in pymatgen.io.vasp.inputs) incar (DictSet attribute) (MPNMRSet attribute) (MPNonSCFSet attribute) (MPSOCSet attribute) (MPStaticSet attribute) (MVLGBSet attribute) (MVLGWSet attribute) (VaspInputSet attribute) (Vasprun attribute) inclvkb (ExcHamiltonian attribute) 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 attribute) indices_from_symbol() (SiteCollection method) indices_separate() (Plane method) info (AbinitBuild attribute) (Dependency attribute) (StructureEnvironments.NeighborsSet attribute) info() (NodeHistory method) info_dict (LibxcFunc attribute) infos_on_basis_set() (Basis_set_reader method) infos_on_system (FiestaInput attribute) 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) InterfacialReactivity (class in pymatgen.analysis.interface_reactions) internal_energy() (PhononDos method) interpolate() (IStructure method) (NEBPathfinder method) Interstitial (class in pymatgen.analysis.defects.core) InterstitialGenerator (class in pymatgen.analysis.defects.generators) inv (SquareTensor attribute) inv_matrix (Lattice attribute) inv_ordered_indices (SeparationPlane attribute) invdist() (NormalizedAngleDistanceNbSetWeight method) inverse (AbstractTransformation attribute) (AddSitePropertyTransformation attribute) (AutoOxiStateDecorationTransformation attribute) (ChargedCellTransformation attribute) (DefectTransformation attribute) (DeformStructureTransformation attribute) (DiscretizeOccupanciesTransformation attribute) (InsertSitesTransformation attribute) (JonesFaithfulTransformation attribute) (OrderDisorderedStructureTransformation attribute) (OxidationStateDecorationTransformation attribute) (OxidationStateRemovalTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) (PerturbStructureTransformation attribute) (PrimitiveCellTransformation attribute) (RemoveSitesTransformation attribute) (RemoveSpeciesTransformation attribute) (ReplaceSiteSpeciesTransformation attribute) (RotationTransformation attribute) (SubstitutionTransformation attribute) (SupercellTransformation attribute) (SymmOp attribute) (TranslateSitesTransformation attribute) 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) ionic_element_list (MoleculeStructureComparator attribute) ionic_radii (Element attribute), [1] ionic_radius (Specie attribute), [1] 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), [1] is_alkali (Element attribute), [1] is_alkaline (Element attribute), [1] 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 attribute) is_chalcogen (Element attribute)

is_close_to() (ChemicalEnvironments method) (DetailedVoronoiContainer method) is_complete() (PseudoTable method) is_completed (QueueJob attribute) 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 attribute) is_dfpt_task (AbinitTask attribute) is_element (Composition attribute) (ComputedEntry attribute) (GrandPotPDEntry attribute) (PDEntry attribute) is_failed (AdfOutput attribute) (QueueJob attribute) is_file (Node attribute) is_final_relaxed_structure_delocalized() (DefectCompatibility method) is_fit_to_structure() (Tensor method) (TensorCollection method) is_flow (Node attribute) is_freysoldt_delocalized() (DefectCompatibility method) is_gga_family (LibxcFunc attribute) is_gs_task (AbinitTask attribute) is_halogen (Element attribute), [1] is_hexagonal() (Lattice method) is_homogeneous (KSampling attribute) is_hubbard (Vasprun attribute) is_hyb_gga_family (LibxcFunc attribute) is_hyb_mgga_family (LibxcFunc attribute) 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 attribute) is_kumagai_delocalized() (DefectCompatibility method) is_lanthanoid (Element attribute), [1] is_laue() (SpacegroupAnalyzer method) is_lda_family (LibxcFunc attribute) is_magnetic (CollinearMagneticStructureAnalyzer attribute) is_metal() (BandStructure method) is_metalloid (Element attribute), [1] is_mgga_family (LibxcFunc attribute) is_noble_gas (Element attribute), [1] is_numeric() (in module pymatgen.io.adf) is_one_to_many (AbstractTransformation attribute) (AddSitePropertyTransformation attribute) (AutoOxiStateDecorationTransformation attribute) (ChargedCellTransformation attribute) (DefectTransformation attribute) (DeformStructureTransformation attribute) (DiscretizeOccupanciesTransformation attribute) (InsertSitesTransformation attribute) (OrderDisorderedStructureTransformation attribute) (OxidationStateDecorationTransformation attribute) (OxidationStateRemovalTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) (PerturbStructureTransformation attribute) (PrimitiveCellTransformation attribute) (RemoveSitesTransformation attribute) (RemoveSpeciesTransformation attribute) (ReplaceSiteSpeciesTransformation attribute) (RotationTransformation attribute) (SubstitutionTransformation attribute) (SupercellTransformation attribute) (TranslateSitesTransformation attribute) is_ordered (Site attribute) (SiteCollection attribute) 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), [1] is_quadrupolar (Element attribute) is_rare_earth_metal (Element attribute), [1] is_redox_active_intercalation() (in module pymatgen.apps.battery.analyzer) is_rotation() (SquareTensor method) is_running (QueueJob attribute) is_same_plane_as() (Plane method) is_same_vectors() (ZSLGenerator method) is_spin (GaussianOutput attribute) (Vasprun attribute) is_spin_polarized (BandStructure attribute) (Doscar attribute), [1] (IcohpCollection attribute), [1] (IcohpValue attribute) 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 attribute) is_transition_metal (Element attribute), [1] 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 attribute) is_x_kind (LibxcFunc attribute) is_xc_kind (LibxcFunc attribute) IsingModel (class in pymatgen.analysis.energy_models) isinstance() (Node method) isnc (AbinitTask attribute) (Pseudo attribute) (Work attribute) isncfile (File attribute) isomorphic_to() (MoleculeGraph method) ispaw (AbinitTask attribute) (Pseudo attribute) (Work attribute) 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 attribute) IUCr_symbol_str (CoordinationGeometry attribute) IUPAC_symbol (CoordinationGeometry attribute) IUPAC_symbol_str (CoordinationGeometry attribute)

J

j (Orbital attribute) JahnTellerAnalyzer (class in pymatgen.analysis.magnetism.jahnteller) jimage (ConnectedSite attribute) 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() (pymatgen.io.abinit.nodes.NodeResults class method) json_pretty_dump() (in module pymatgen.util.serialization) JSON_SCHEMA (NodeResults attribute)

K

K (Element attribute) k_reuss (ElasticTensor attribute) k_voigt (ElasticTensor attribute) k_vrh (ElasticTensor attribute) kappa (ChemicalShielding.MarylandNotation attribute) kcal_per_mol_2_eV (QcOutput attribute) key (AdfKey attribute) keyPressEvent() (MultiStructuresInteractorStyle method) (StructureInteractorStyle method) keyword_line() (GulpIO method) keywords (PotcarSingle attribute) kpath (HighSymmKpath attribute) Kpoint (class in pymatgen.electronic_structure.bandstructure) Kpoints (class in pymatgen.io.vasp.inputs)

kpoints (DictSet attribute) (MITMDSet attribute) (MPHSEBSSet attribute) (MPNonSCFSet attribute) (MPStaticSet attribute) (MVLGBSet attribute) (MVLGWSet attribute) (MVLSlabSet attribute) (VaspInputSet attribute) (Vasprun attribute) (Wavecar attribute) 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)

L

l (Orbital attribute) (OrbitalDescription attribute) l_local (Pseudo attribute) l_max (Pseudo attribute) La (Element attribute) label (FreqUnits attribute) (Kpoint attribute) (SlabEntry attribute) 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) laplacian (CriticalPoint attribute) last_etotal (D2DEScfCycle attribute) (GroundStateScfCycle attribute) last_iteration (ScfCycle attribute) last_nneigh (LocalStructOrderParams attribute) last_resort_solution() (AbstractError method) latexify() (in module pymatgen.util.string) latexify_spacegroup() (in module pymatgen.util.string) Lattice (class in pymatgen.core.lattice) lattice (IStructure attribute) (Kpoint attribute) (PeriodicSite attribute) (Vasprun attribute) (WulffShape attribute) 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) (Vasprun attribute) lattice_type (PWOutput attribute) 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 (CovalentBond attribute) Length (in module pymatgen.core.units) lengths_and_angles (Lattice attribute) 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 attribute) (TimeCancelError attribute) 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() (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight class method) lineno (HistoryRecord attribute) (YamlDoc attribute) link0 (GaussianOutput attribute) liquid_range (Element attribute) list_filepaths() (Directory method) list_prediction() (SubstitutionPredictor method) listext() (Flow method) lll_inverse (Lattice attribute) lll_mapping (Lattice attribute) lll_matrix (Lattice attribute) 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) LobsterCompleteDos (class in pymatgen.electronic_structure.dos) LocalGeometryFinder (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) LocalStructOrderParams (class in pymatgen.analysis.local_env) lockxyz (ExcitingInput attribute), [1] 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 attribute) Lr (Element attribute) Lu (Element attribute)

M

MAGIC (D2DEScfCycle attribute) (GroundStateScfCycle attribute) Magmom (class in pymatgen.electronic_structure.core) magmoms (CollinearMagneticStructureAnalyzer attribute) magnetic_deformation() (in module pymatgen.analysis.magnetism.analyzer) magnetic_species_and_magmoms (CollinearMagneticStructureAnalyzer attribute) MagneticSpaceGroup (class in pymatgen.symmetry.maggroups) magnetization (Outcar attribute) MagSymmOp (class in pymatgen.core.operations) mAh (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) 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) make_dir() (File method) make_FULL_BSE_Densities_folder() (FiestaInput method) make_input() (OpticTask 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 attribute) Mass (in module pymatgen.core.units) mass_charge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) mass_discharge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) masses (Dynmat attribute) (ForceField attribute) MasterProcessMemoryCancelError (class in pymatgen.io.abinit.scheduler_error_parsers) match_as_dict() (ZSLGenerator method) matches() (IStructure method) matches_ordering() (CollinearMagneticStructureAnalyzer method) material_formula (Xmu attribute) MaterialsProjectAqueousCompatibility (class in pymatgen.entries.compatibility) MaterialsProjectCompatibility (class in pymatgen.entries.compatibility) matrix (Lattice attribute) matrixTimesVector() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) max_cation_insertion (BatteryAnalyzer attribute) max_cation_removal (BatteryAnalyzer attribute) max_connectivity (VoronoiConnectivity attribute) max_cores (ParalHints attribute) (TaskManager attribute) max_delta_volume (AbstractElectrode attribute) max_efficiency (ParalHints attribute) max_electronegativity() (MolecularOrbitals method) max_mem_per_proc (ParalHints attribute) max_oxidation_state (Element attribute), [1] max_speedup (ParalHints attribute) max_spline_jump() (EnergyTrend method) max_spline_jumps() (Polarization method) max_voltage (AbstractElectrode attribute) max_voltage_step (AbstractElectrode attribute) 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() (pymatgen.io.lammps.inputs.LammpsRun class method) md5 (Pseudo attribute) md_filepath (AnaddbTask attribute) mean_estimator() (CSMFiniteRatioFunction method) (CSMInfiniteRatioFunction method) mean_stress (Stress attribute) measure() (in module pymatgen.util.convergence) mehring_values (ChemicalShielding attribute) melting_point (Element attribute) mem_per_proc (TaskManager attribute) 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_pot1_files() (PhononWork method) merge_qpoints() (Mrgscr method) merge_scrfiles() (QptdmWork method) merge_sites() (Structure method) message (HistoryRecord attribute) metallic_radius (Element attribute) metric_tensor (Lattice attribute) 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 attribute) miller_energy_dict (WulffShape attribute) miller_index (Slab attribute) (SlabEntry attribute) (SlabGenerator attribute) miller_index_from_sites() (in module pymatgen.core.surface) miller_list (WulffShape attribute) min_cost (LinearAssignment attribute) min_freq() (PhononBandStructure method) min_max_indexes() (in module pymatgen.util.num) min_oxidation_state (Element attribute), [1] min_slab_size (SlabGenerator attribute) min_vac_size (SlabGenerator attribute) min_voltage (AbstractElectrode attribute) mineral_hardness (Element attribute) minimize_matrix() (EwaldMinimizer method) minimized_sum (EwaldMinimizer attribute) 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 attribute) 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 attribute) (GaussianInput attribute) (NwInput attribute) (QcTask attribute) (XYZ attribute) molecule_template() (QCInput static method) MoleculeGraph (class in pymatgen.analysis.graphs) MoleculeStructureComparator (class in pymatgen.analysis.molecule_structure_comparator) MolGraphSplitError mongo_assimilate() (Flow method) mongo_getattr() (in module pymatgen.io.abinit.db) mongo_id (Flow attribute) mongodb_upload() (Flow method) Monkhorst (Kpoints_supported_modes attribute) monkhorst (KSamplingModes attribute) monkhorst() (pymatgen.io.abinit.abiobjects.KSampling class method) monkhorst_automatic() (Kpoints static method) (pymatgen.io.abinit.abiobjects.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 attribute) move_cell (RelaxationMethod attribute) move_to_other_side() (SlabGenerator method) mp_symbol (CoordinationGeometry attribute) 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 attribute) 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 attribute) mu0 (Xmu attribute) 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) multiplicity (Defect attribute) (DefectEntry attribute) (Interstitial attribute) (Substitution attribute) (Vacancy attribute) 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) MVLScanRelaxSet (class in pymatgen.io.vasp.sets) MVLSlabSet (class in pymatgen.io.vasp.sets) my_solid_angle() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils)

N

N (Element attribute) n (Orbital attribute) Na (Element attribute) Nads_in_slab (SlabEntry attribute) name (AbstractError attribute) (Author attribute) (CorrectorProtocolApplication attribute) (CorrectorProtocolScheduler attribute) (Defect attribute) (DefectEntry attribute) (HistoryNode attribute) (Interstitial attribute) (MoleculeGraph attribute) (Node attribute) (PDEntry attribute) (StructureGraph attribute) (Substitution attribute) (Vacancy attribute) (XcFunc attribute) names_and_values() (AbinitTimer method) NanoscaleStability (class in pymatgen.analysis.surface_analysis) natoms (Dynmat attribute) (Poscar attribute) (Xdatcar attribute) Nb (Element attribute) nb (Wavecar attribute) nb_bands (BandStructure attribute) (Wavederf attribute) nb_kpoints (Wavederf attribute) NbSetWeight (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) ncores_allocated (Flow attribute) ncores_reserved (Flow attribute) ncores_used (Flow attribute) ncpus (AbinitTimer attribute) Nd (Element attribute) ndisps (Dynmat attribute) 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 attribute) (StructureEnvironments.NeighborsSet attribute) neighb_coordsOpt (StructureEnvironments.NeighborsSet attribute) neighb_indices_and_images (LightStructureEnvironments.NeighborsSet attribute) neighb_sites (LightStructureEnvironments.NeighborsSet attribute) (StructureEnvironments.NeighborsSet attribute) neighb_sites_and_indices (LightStructureEnvironments.NeighborsSet attribute) (StructureEnvironments.NeighborsSet attribute) neighbors() (DetailedVoronoiContainer method) neighbors_map() (DetailedVoronoiContainer method) neighbors_surfaces() (DetailedVoronoiContainer method) neighbors_surfaces_bounded() (DetailedVoronoiContainer method) NeighborsNotComputedChemenvError nelec (BoltztrapRunner attribute) nelect (DictSet attribute) nelectrons (IMolecule attribute) (PotcarSingle attribute) net_magnetization (Chgcar attribute) 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) Ni (Element attribute) nionic_steps (Vasprun attribute) nk (Wavecar attribute) NM (Ordering attribute) nmr_quadrupole_moment (Element attribute) 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 attribute) node_from_nid() (Flow method) node_id (Node attribute) 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 attribute) non_decreasing() (in module pymatgen.util.num) non_increasing() (in module pymatgen.util.num) NONE (AdditionalConditions attribute) nonstoichiometric_symmetrized_slab() (SlabGenerator method) noppmodel (PPModelModes attribute) norm() (Lattice method) normal (Slab attribute) normal_cdf_step() (in module pymatgen.analysis.chemenv.utils.math_utils) normal_modes (AdfOutput attribute) normalization_mass (AbstractElectrode attribute) normalization_volume (AbstractElectrode attribute) normalize() (Spectrum method) (StaticPotential method) normalize_to() (BalancedReaction method) normalize_to_element() (BalancedReaction method) normalized_angles (StructureEnvironments.NeighborsSet attribute) normalized_distances (StructureEnvironments.NeighborsSet attribute) normalized_repr (BalancedReaction attribute) 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) NscfConvergenceWarning (class in pymatgen.io.abinit.events) NscfTask (class in pymatgen.io.abinit.tasks) NsitesModel (class in pymatgen.analysis.energy_models) nspden (Electrons attribute) nspecs (Dynmat attribute) nspinor (Electrons attribute) nsppol (Electrons attribute) Nsurfs_ads_in_slab (SlabEntry attribute) NthOrderElasticTensor (class in pymatgen.analysis.elasticity.elastic) ntypesp (SiteCollection attribute) nucleus (CriticalPointType attribute) num_atoms (Composition attribute) num_basis_func (GaussianOutput attribute) num_bonds (IcohpValue attribute), [1] num_cores (TaskManager attribute) num_corrections (Node attribute) num_errored_tasks (Flow attribute) num_excs (PyFlowScheduler attribute) num_ops (LocalStructOrderParams attribute) num_sites (SiteCollection attribute) num_steps (AbstractElectrode attribute) num_tasks (Flow attribute) num_unconverged_tasks (Flow attribute) number (Element attribute), [1] number_of_magnetic_sites (CollinearMagneticStructureAnalyzer attribute) number_of_permutations (CoordinationGeometry attribute) 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 attribute) OccupancyComparator (class in pymatgen.analysis.structure_matcher) off_color (WulffShape attribute) omega (ChemicalShielding.MarylandNotation attribute) omega() (ElasticTensorExpansion method) omp_threads (TaskManager attribute) on_all_ok() (BecWork method) (DteWork method) (PhononWork method) (QptdmWork method) on_dep_ok() (Flow method) on_ok() (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_sigres() (SigmaTask method) 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 attribute) OpticTask (class in pymatgen.io.abinit.tasks) optimize_gibbs_free_energy() (QuasiharmonicDebyeApprox method) optimizer() (QuasiharmonicDebyeApprox method)

optional_keywords_list (QcTask attribute) OptSet (class in pymatgen.io.qchem.sets) Orbital (class in pymatgen.electronic_structure.core) (class in pymatgen.io.vasp.inputs) orbital_type (Orbital attribute) 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 (ElasticTensorExpansion attribute) (NthOrderElasticTensor attribute) (SpaceGroup attribute) 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 attribute) Ordering (class in pymatgen.analysis.magnetism.analyzer) ordering (CollinearMagneticStructureAnalyzer attribute) 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 attribute) oxi_prob (Composition attribute) oxi_state (DummySpecie attribute), [1] (Specie attribute), [1] oxi_state_guesses() (Composition method) oxidation_states (Element attribute), [1] 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) (JonesFaithfulTransformation attribute) p (JonesFaithfulTransformation attribute) (OrbitalType attribute) 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) 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) 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) PartialRemoveSitesTransformation (class in pymatgen.transformations.site_transformations) PartialRemoveSpecieTransformation (class in pymatgen.transformations.standard_transformations) path (Directory attribute) (File attribute) (KSamplingModes attribute) path_from_structure() (pymatgen.io.abinit.abiobjects.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 attribute) Pb (Element attribute) 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 attribute) Pd (Element attribute) pd_coords() (PhaseDiagram method) pd_plot_data (PDPlotter attribute) PDEntry (class in pymatgen.analysis.phase_diagram) pdos (CompleteDos attribute) (CompletePhononDos attribute) (Doscar attribute), [1] (Vasprun attribute) 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) perform_freysoldt() (DefectCompatibility method) perform_pot_corr() (FreysoldtCorrection method) periodic_table_heatmap() (in module pymatgen.util.plotting) PeriodicSite (class in pymatgen.core.sites) permutations (ExplicitPermutationsAlgorithm attribute) (SeparationPlane attribute) perpendicular_bisector() (pymatgen.analysis.chemenv.utils.coordination_geometry_utils.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) PhononWork (class in pymatgen.io.abinit.works) pickle_dump() (Flow method) pickle_dumps() (Flow method) pickle_file (Flow attribute) PICKLE_FNAME (Flow attribute) pickle_load() (pymatgen.io.abinit.flows.Flow class method) pickle_loads() (pymatgen.io.abinit.flows.Flow class method) pid (PyFlowScheduler attribute) pid_file (Flow attribute) (PyFlowScheduler attribute) 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() (EOSBase method) (FreysoldtCorrection method) (InterfacialReactivity method) (Relaxation method) (ScfCycle method) (SparseHistogram method) plot_all() (AbinitTimerParser method) plot_all_stability_map() (NanoscaleStability method) plot_ax() (EOSBase method) plot_brillouin() (BSPlotter method) (PhononBSPlotter method) plot_brillouin_zone() (in module pymatgen.electronic_structure.plotter) plot_brillouin_zone_from_kpath() (in module pymatgen.electronic_structure.plotter) plot_carriers() (BoltztrapPlotter method) plot_chempot_range_map() (PDPlotter method) plot_compare() (BSPlotter method) (PhononBSPlotter method) plot_complexity_factor_mu() (BoltztrapPlotter method) plot_conductivity_dop() (BoltztrapPlotter method) plot_conductivity_mu() (BoltztrapPlotter method) plot_conductivity_temp() (BoltztrapPlotter method) plot_csm_and_maps() (StructureEnvironments method) plot_cv() (ThermoPlotter method) plot_dos() (BoltztrapPlotter method) plot_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_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_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 attribute) point_energy_matrix (EwaldSummation attribute) point_from_bary_coords() (Simplex method) 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) PolynomialEOS (class in pymatgen.analysis.eos) populate() (Tensor method) pos (Work attribute) pos_str (Work attribute) Poscar (class in pymatgen.io.vasp.inputs) poscar (DictSet attribute) (MITNEBSet attribute) (VaspInputSet attribute) poscars (MITNEBSet attribute) 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 attribute) potcar_symbols (VaspInputSet attribute) (Vasprun attribute) PotcarCorrection (class in pymatgen.entries.compatibility) PotcarSingle (class in pymatgen.io.vasp.inputs) potential (AbstractFeffInputSet attribute) Potential (class in pymatgen.io.feff.inputs) potential (FEFFDictSet attribute) potential_type (PotcarSingle attribute) 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) predictor_corrector (Poscar attribute), [1] 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 attribute) prim_rec (HighSymmKpath attribute) prime_factors() (in module pymatgen.analysis.chemenv.utils.math_utils) PrimitiveCellTransformation (class in pymatgen.transformations.standard_transformations) principal_axis_system (ChemicalShielding attribute) (ElectricFieldGradient attribute) principal_invariants (SquareTensor attribute) 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) 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_parsed_coords() (in module pymatgen.io.qchem.utils) processes (Work attribute) Product (class in pymatgen.io.abinit.nodes) products (BalancedReaction attribute) (Dependency attribute) (FileNode attribute) project() (Tensor method) project_and_to2dim() (Plane method) project_and_to2dim_ordered_indices() (Plane method) projected_eigenvalues (Vasprun attribute) projection (Magmom attribute) projectionpoints() (Plane method) projections (BandStructure attribute) propagation_vector (CollinearMagneticStructureAnalyzer attribute) properly_terminated (GaussianOutput attribute) properties (Site attribute) property_dict (ElasticTensor attribute) Pseudo (class in pymatgen.io.abinit.pseudos) pseudo_with_symbol() (PseudoTable method) pseudos (AbinitTask attribute) 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) pyfile (Flow attribute) 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_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.diffusion_analyzer (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.gb (module) pymatgen.analysis.graphs (module) pymatgen.analysis.hhi (module) pymatgen.analysis.hhi.hhi (module) pymatgen.analysis.interface_reactions (module) pymatgen.analysis.local_env (module) pymatgen.analysis.magnetism (module) pymatgen.analysis.magnetism.analyzer (module) pymatgen.analysis.magnetism.jahnteller (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.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.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_analyze (module) pymatgen.cli.pmg_config (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.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.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.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.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.lmto (module) pymatgen.io.lobster (module) pymatgen.io.nwchem (module) pymatgen.io.phonopy (module) pymatgen.io.pwscf (module) pymatgen.io.qchem (module) pymatgen.io.qchem.inputs (module) pymatgen.io.qchem.sets (module) pymatgen.io.qchem.utils (module) pymatgen.io.qchem_deprecated (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.structure (module) pymatgen.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.serialization (module) pymatgen.util.string (module) pymatgen.util.testing (module) pymatgen.vis (module) pymatgen.vis.plotters (module) pymatgen.vis.structure_chemview (module) pymatgen.vis.structure_vtk (module) PymatgenTest (class in pymatgen.util.testing) pz (Orbital attribute)

Q

qadapter (TaskManager attribute) qads (TaskManager attribute) QChemDictSet (class in pymatgen.io.qchem.sets) QCInput (class in pymatgen.io.qchem.inputs) QcInput (class in pymatgen.io.qchem_deprecated) QcNucVeloc (class in pymatgen.io.qchem_deprecated) QcOutput (class in pymatgen.io.qchem_deprecated) QcTask (class in pymatgen.io.qchem_deprecated) 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 attribute) radius (CovalentRadius attribute) raise_error_if_unphysical() (in module pymatgen.analysis.elasticity.elastic) ranked_compositions_from_indeterminate_formula() (Composition static method) ranks (TensorCollection attribute) 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 attribute) Rcut2 (OrbitalDescription attribute) Re (Element attribute) reactants (BalancedReaction attribute) 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_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 attribute) real_space_energy_matrix (EwaldSummation attribute) rebuild_chgcar() (pymatgen.command_line.bader_caller.BaderAnalysis class method) received_signal() (QueueJob method) Reciprocal (Kpoints_supported_modes attribute) reciprocal() (in module pymatgen.util.convergence) reciprocal_lattice (Lattice attribute) reciprocal_lattice_crystallographic (Lattice attribute) reciprocal_space_energy (EwaldSummation attribute) reciprocal_space_energy_matrix (EwaldSummation attribute) 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_vector() (in module pymatgen.core.surface) reduce_vectors() (in module pymatgen.analysis.substrate_analyzer) reduced_composition (Composition attribute) reduced_formula (Composition attribute) (Ion attribute) ref_entries (SurfaceEnergyPlotter attribute) ref_permutation() (CoordinationGeometry method) ref_separation_perm (SeparationPlane attribute) 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 attribute) 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 attribute) (File attribute) relworkdir (Node attribute) rem_template() (QCInput static method) remove() (File method) remove_collisions() (ChargeDensityAnalyzer method) (TopographyAnalyzer method) remove_deps() (Node method) remove_exts() (Directory method) remove_nodes() (MoleculeGraph method) (StructureGraph method) remove_option() (AdfKey method) remove_oxidation_states() (Structure method) remove_site_property() (Molecule method) (Structure method) remove_sites() (Molecule method) (Structure method) remove_species() (Molecule method) (Structure method) remove_spin() (Structure 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_group() (MoleculeGraph method) replace_species() (Molecule method) (Structure method) ReplaceSiteSpeciesTransformation (class in pymatgen.transformations.site_transformations) report_exception() (EventsParser method) rescale_field() (StaticPotential method) reset() (ScriptEditor method) reset_from_scratch() (AbinitTask method) (OpticTask method) restart() (AbinitTask method) (NscfTask method) (PhononTask method) (RelaxTask method) (ScfTask method) (SigmaTask method) Results (AbinitTask attribute) results (EOSBase attribute) Results (Flow attribute) (Node attribute) resumes (GaussianOutput attribute) return_corrections() (SchedulerErrorHandler method) Rh (Element attribute) rhl1() (HighSymmKpath method) rhl2() (HighSymmKpath method) rho_rec() (QModel method) rho_rec_limit0 (QModel attribute) 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 attribute) RotationTransformation (class in pymatgen.transformations.standard_transformations) rotoreflection() (SymmOp static method) round() (Tensor method) (TensorCollection method) round_to_sigfigs() (in module pymatgen.util.num) route (GaussianOutput attribute) row (Element attribute), [1] Ru (Element attribute) run() (BoltztrapRunner method) (Fiesta_run method) (GulpCaller method) (Nwchem2Fiesta method) run_aconvasp_command() (in module pymatgen.command_line.aconvasp_caller) run_stats (Outcar attribute) run_type (AdfOutput attribute) (Vasprun attribute) rxn (ConversionVoltagePair attribute)

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_from_composition() (pymatgen.core.periodic_table.DummySpecie class method) safe_separation_permutations() (SeparationPlane method) same_branch_splines() (Polarization 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_geom_opt_threshold() (QcTask method) scale_lattice() (Structure method) scaled_wulff() (NanoscaleStability method) 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 attribute) (MemoryCancelError attribute) (NodeFailureError attribute) (TimeCancelError attribute) SchedulerErrorHandler (class in pymatgen.io.abinit.scheduler_error_handlers) Screening (class in pymatgen.io.abinit.abiobjects) ScriptEditor (class in pymatgen.io.abinit.launcher) Se (Element attribute) se_analyzers (NanoscaleStability attribute) 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), [1] 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) (QcTask method) set_basis2() (QcTask method) set_basis_set() (QcTask method) set_BSE_options() (FiestaInput method) set_charge() (Defect method) (Structure method) set_charge_and_spin() (Molecule method) set_collection_name() (DBConnector method) set_dft_grid() (QcTask method) set_ecp() (QcTask method) set_flow() (Work method) set_garbage_collector() (Flow method) set_gc() (Node method) set_geom_max_iterations() (QcTask method) set_geom_opt_coords_type() (QcTask method) set_geom_opt_use_gdiis() (QcTask method) set_GW_options() (FiestaInput method) set_info() (in module pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) set_integral_threshold() (QcTask method) set_manager() (Work method) set_max_num_of_scratch_files() (QcTask method) set_mem_per_proc() (TaskManager method) set_memory() (QcTask 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_partial_hessian_atoms() (QcTask method) set_pconfs() (AbinitTask method) set_permutations_safe_override() (CoordinationGeometry method) set_pyfile() (Flow method) set_scf_algorithm_and_iterations() (QcTask method) set_scf_convergence_threshold() (QcTask method) set_scf_initial_guess() (QcTask 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_velocities() (QcTask 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 attribute) shebang() (ScriptEditor method) shell (ScriptEditor attribute) ShellJob (class in pymatgen.io.abinit.qjobs) shift (Slab attribute) 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) (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_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_11 (ChemicalShielding.MehringNotation attribute) sigma_22 (ChemicalShielding.MehringNotation attribute) sigma_33 (ChemicalShielding.MehringNotation attribute) sigma_iso (ChemicalShielding.MarylandNotation attribute) (ChemicalShielding.MehringNotation attribute) SigmaConvWork (class in pymatgen.io.abinit.works) SigmaTask (class in pymatgen.io.abinit.tasks) sigres_path (SigmaTask attribute) 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 attribute) (Defect attribute) (DefectEntry attribute) 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 attribute) site_symbols (Poscar attribute) (Xdatcar attribute) SiteCollection (class in pymatgen.core.structure) sites (IMolecule attribute) (IStructure attribute) (SiteCollection attribute)

Slab (class in pymatgen.core.surface) slab (WorkFunctionAnalyzer attribute) slab_scale_factor (SlabGenerator attribute) SlabEntry (class in pymatgen.analysis.surface_analysis) slabgen_params (ReconstructionGenerator attribute) SlabGenerator (class in pymatgen.core.surface) 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) 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) sorted() (PseudoTable method) sorted_sites (WorkFunctionAnalyzer attribute) source (StructureEnvironments.NeighborsSet attribute) (Xmu attribute) 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 attribute) special_formulas (Composition attribute) Specie (class in pymatgen.core.periodic_table) specie (Site attribute) specie_potential_lines() (GulpIO method) SpecieProximityFilter (class in pymatgen.alchemy.filters) species (SiteCollection attribute) species_and_occu (Site attribute) (SiteCollection attribute) species_string (Site attribute) 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 attribute) Spin (class in pymatgen.electronic_structure.core) spin_data (VolumetricData attribute) spin_multiplicity (GaussianOutput attribute) (IMolecule attribute) spin_polarization (CompleteDos attribute) 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) SquareTensor (class in pymatgen.core.tensors) Sr (Element attribute) stable_entries (PhaseDiagram attribute) stable_u_range_dict() (SurfaceEnergyPlotter method) standard_orientation (GaussianOutput attribute) 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() (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy class method) Status (class in pymatgen.io.abinit.nodes) status (Dependency attribute) (FileNode attribute) (Flow attribute) (Node attribute) (Work attribute) status_counter (Flow attribute) (Work attribute) 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) 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) structure (BandStructure attribute) Structure (class in pymatgen.core.structure) structure (CompleteDos attribute) (ExcitingInput attribute) (HighSymmKpath attribute) (LammpsData attribute) (Poscar attribute) (ValenceIonicRadiusEvaluator attribute) (VolumetricData attribute) (WulffShape attribute) 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 attribute) 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) (TransformedStructure attribute) (Vasprun attribute), [1] (Xdatcar attribute) (in module pymatgen.command_line.enumlib_caller) STRUCTURES_DIR (PymatgenTest attribute) structures_input_orientation (GaussianOutput attribute) StructureVis (class in pymatgen.vis.structure_vtk) style (Kpoints attribute) 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) Substitution (class in pymatgen.analysis.defects.core) SubstitutionGenerator (class in pymatgen.analysis.defects.generators) SubstitutionPredictor (class in pymatgen.analysis.structure_prediction.substitution_probability) SubstitutionProbability (class in pymatgen.analysis.structure_prediction.substitution_probability) SubstitutionTransformation (class in pymatgen.transformations.standard_transformations) Substitutor (class in pymatgen.analysis.structure_prediction.substitutor) SubstrateAnalyzer (class in pymatgen.analysis.substrate_analyzer) subsurface_sites() (AdsorbateSiteFinder method) suggest_charges() (DefectPhaseDiagram method) sulfide_type() (in module pymatgen.analysis.structure_analyzer) sum_sections() (AbinitTimer method) summarize() (AbinitTimerParser method) summary (BaderAnalysis attribute) (Pseudo attribute) summed_icohp (IcohpValue attribute) SupercellTransformation (class in pymatgen.transformations.standard_transformations) superconduction_temperature (Element attribute) supported_modes (Kpoints attribute) SUPPORTED_MODES (MVLGWSet attribute) supported_properties (MPRester attribute) (Specie attribute) supported_task_properties (MPRester attribute) supported_units (ArrayWithUnit attribute) (FloatWithUnit attribute) supports_soc (Pseudo attribute) surface_area (Slab attribute) (SlabEntry attribute) (WulffShape attribute) surface_chempot_range_map() (SurfaceEnergyPlotter method) surface_energy() (SlabEntry method) surface_sites (AdsorbateSiteFinder attribute) SurfaceEnergyPlotter (class in pymatgen.analysis.surface_analysis) symbol (Deformation attribute) (DummySpecie attribute), [1] (Element attribute) (NthOrderElasticTensor attribute) (PointGroup attribute) (PotcarSingle attribute) (Pseudo attribute) (SpaceGroup attribute) (Strain attribute) (Stress attribute) (Tensor attribute) symbol_set (SiteCollection attribute) symbols (Potcar attribute) symlink_abiext() (Directory method) symm_reduce() (AdsorbateSiteFinder method) symmetrically_add_atom() (Slab method) symmetrically_remove_atoms() (Slab method) symmetrize_molecule() (PointGroupAnalyzer method) symmetrized (Tensor attribute) (TensorCollection attribute) SymmetrizedStructure (class in pymatgen.symmetry.structure) symmetry_measure() (in module pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) symmetry_measure_type (AbstractChemenvStrategy attribute) symmetry_ops (PointGroup attribute) (SymmetryGroup attribute) 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 attribute)

T

t (Status attribute) Ta (Element attribute) tag (YamlDoc attribute) tag_structure() (JahnTellerAnalyzer method) tags (AbstractFeffInputSet attribute) Tags (class in pymatgen.io.feff.inputs) tags (FEFFDictSet attribute) 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), [1] tdos (Doscar attribute), [1] (Vasprun attribute) Te (Element attribute) Temp (in module pymatgen.core.units) temp_shell_task() (pymatgen.io.abinit.tasks.AbinitTask class method) (pymatgen.io.abinit.tasks.AnaddbTask class method) temperature (Poscar attribute) template_dir (LammpsRun attribute) temporary_flow() (pymatgen.io.abinit.flows.Flow class method) Tensor (class in pymatgen.core.tensors) TensorCollection (class in pymatgen.core.tensors) TensorMapping (class in pymatgen.core.tensors) term_symbols (Element attribute) 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_STRUCTURES (PymatgenTest attribute) tet() (HighSymmKpath method) tet_coord() (in module pymatgen.analysis.phase_diagram) tetragonal() (Lattice static method) text (YamlDoc attribute) text_notag (YamlDoc attribute) 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) 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) time_steps (QcNucVeloc attribute) TimeCancelError (class in pymatgen.io.abinit.scheduler_error_parsers) timelimit_parser() (in module pymatgen.io.abinit.qutils) timeout (QueueJob attribute) 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) (PDEntry static method) to_csvline() (AbinitTimerSection method) to_data_dict (Composition attribute) to_dict() (AbinitTimerSection method) (Flow method) to_file() (ForceField method) to_hdf5() (VolumetricData method) to_input() (GaussianOutput method), [1] to_json() (AdfKey method) (AdfTask method) (LibxcFunc method) to_lattice() (LammpsBox method) to_reduced_dict (Composition attribute) (Ion attribute) to_shell_manager() (TaskManager method) to_snl() (TransformedStructure method) to_string() (GaussianInput method) (Mcsqs method) (NodeHistory method) (Pseudo method) (Relaxation method) (ScfCycle method) (XSF method) to_table() (AbinitTimer method) (PseudoTable method) to_tuple() (AbinitTimerSection method) to_unit_cell (PeriodicSite attribute) TOLERANCE (BalancedReaction attribute) 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 attribute) tot_edges (WulffShape attribute) totable() (AbinitTimer method) (ParallelEfficiency method) total_electrons (Composition attribute) total_energy (EwaldSummation attribute) total_energy_matrix (EwaldSummation attribute) total_spectrum (Eels attribute) total_surface_energy (WulffShape attribute) trans (SquareTensor attribute) trans_v() (ElasticTensor method) 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 attribute) 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 attribute) 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) type (CriticalPoint attribute) Type (OrbitalDescription attribute) type (Pseudo attribute) (XcFunc attribute) Type2 (OrbitalDescription attribute) typeidx_from_symbol() (ETSF_Reader method) types_and_weights_of_connections (StructureGraph attribute) types_of_coordination_environments() (StructureGraph method) types_of_magnetic_specie (CollinearMagneticStructureAnalyzer attribute) types_of_specie (SiteCollection attribute)

U

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

Unknown (Ordering attribute) unknown_status (QueueJob attribute) unstable_entries (PhaseDiagram attribute) unsym_cs_tensor (Outcar attribute), [1] up (Spin attribute) 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 attribute) use_cosmo() (QcTask method) use_direct_diago (ExcHamiltonian attribute) use_haydock (ExcHamiltonian attribute) use_hilbert (Screening attribute) use_multiprocessing (AbstractTransformation attribute) use_pcm() (QcTask method) use_ppmodel (SelfEnergy attribute) 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 attribute) V_xx (ElectricFieldGradient attribute) V_yy (ElectricFieldGradient attribute) V_zz (ElectricFieldGradient attribute) Vacancy (class in pymatgen.analysis.defects.core) VacancyGenerator (class in pymatgen.analysis.defects.generators) vacuum_locpot (WorkFunctionAnalyzer attribute) valence (Element attribute) ValenceIonicRadiusEvaluator (class in pymatgen.analysis.local_env) valences (ValenceIonicRadiusEvaluator attribute) validate_json_schema() (Flow method) (NodeResults method) values() (TensorMapping method) 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) vectorsToMatrix() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) velocities (Poscar attribute), [1] (QcNucVeloc attribute) 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) voigt (Tensor attribute) (TensorCollection attribute)

voigt_symmetrized (Tensor attribute) (TensorCollection attribute) vol (Wavecar attribute) vol_charge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) vol_discharge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) vol_tetra() (in module pymatgen.analysis.local_env) voltage (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) voltage_pairs (AbstractElectrode attribute) (ConversionElectrode attribute) (InsertionElectrode attribute) VoltageProfilePlotter (class in pymatgen.apps.battery.plotter) volume (IStructure attribute) (LammpsBox attribute) (Lattice attribute) (Simplex attribute) (VoronoiPolyhedron attribute) (WulffShape attribute) VolumetricData (class in pymatgen.io.vasp.outputs) von_mises (Stress attribute) von_mises_strain (Strain attribute) 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() (pymatgen.io.abinit.abitimer.AbinitTimerParser class method) walk_tree() (NetcdfReader method) warning() (NodeHistory method) was_modified (TransformedStructure attribute) Wavecar (class in pymatgen.io.vasp.outputs) Wavederf (class in pymatgen.io.vasp.outputs) wavenumber (Xmu attribute) weight (Composition attribute) (ConnectedSite attribute) weight() (AngleNbSetWeight method) (AnglePlateauNbSetWeight method) (CNBiasNbSetWeight method) (DeltaCSMNbSetWeight method) (DeltaDistanceNbSetWeight method) (DistanceAngleAreaNbSetWeight method) (DistanceNbSetWeight method) (DistancePlateauNbSetWeight method) (NbSetWeight method) (NormalizedAngleDistanceNbSetWeight method) (SelfCSMNbSetWeight method) weight_statistics (StructureGraph attribute) weighted_surface_energy (WulffShape attribute) 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 attribute) with_dojo_report() (PseudoTable method) with_edges() (MoleculeGraph static method) (StructureGraph static method) with_empty_graph() (pymatgen.analysis.graphs.MoleculeGraph class method) (pymatgen.analysis.graphs.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 attribute) (ConversionElectrode attribute) (ConversionVoltagePair attribute) (InsertionElectrode attribute) working_ion_entry (AbstractElectrode attribute) (AbstractVoltagePair attribute) (ConversionElectrode attribute) (ConversionVoltagePair attribute) (InsertionElectrode attribute) (InsertionVoltagePair attribute) works (Flow attribute) write() (File method) write_def() (BoltztrapRunner method) write_energy() (BoltztrapRunner method) write_etree() (ExcitingInput method)

write_file() (AdfInput method) (Atoms 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) (QcInput method) (QcTask method) (Tags method) (VolumetricData method) (XYZ method) (Xdatcar method) (Xr method) write_image() (PDPlotter method) (StructureVis 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_lammps_inputs() (in module pymatgen.io.lammps.inputs) write_multi_job_file() (QCInput static method) write_phononwebsite() (PhononBandStructureSymmLine 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), [1] (Element attribute), [1] x (Site attribute) XANES (class in pymatgen.analysis.xas.spectrum) XcFunc (class in pymatgen.core.xcfunc) Xdatcar (class in pymatgen.io.vasp.outputs) Xe (Element attribute) XLABEL (DOS attribute) (ExcitationSpectrum attribute) (Spectrum attribute) (XANES attribute)

Xmu (class in pymatgen.io.feff.outputs) Xr (class in pymatgen.io.xr) XSF (class in pymatgen.io.xcrysden) XYZ (class in pymatgen.io.xyz) xyz_patt (QcTask attribute)

Y

Y (Element attribute) y (Site attribute) y_mod (ElasticTensor attribute) 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 (DOS attribute) (ExcitationSpectrum attribute) (Spectrum attribute) (XANES attribute) youngs_modulus (Element attribute)

Z

Z (DummySpecie attribute), [1] (Element attribute) (Pseudo attribute) z (Site attribute) Z_val (Pseudo attribute) ZeoCssr (class in pymatgen.io.zeopp) ZeoVoronoiXYZ (class in pymatgen.io.zeopp) zero_point_energy() (PhononDos method)

zeroed() (Tensor method) (TensorCollection method) zlist (PseudoTable attribute) zmat_patt (QcTask attribute) 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)