Index

A

a (Kpoint attribute) (Lattice attribute) (PeriodicSite attribute) (Plane 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) 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) AbstractMolAtomMapper (class in pymatgen.analysis.molecule_matcher) 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_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_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_flow() (PyFlowScheduler method) add_gg_gap() (in module pymatgen.io.abinit.helpers) 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() (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() (in module pymatgen.analysis.adsorption) AdsorbateSiteFinder (class in pymatgen.analysis.adsorption) affine_matrix (SymmOp 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_utils) all_docs_with_tag() (YamlTokenizer method) all_done (Work attribute) all_energies (Oszicar attribute) all_entries (ComputedReaction attribute) (PourbaixDiagram attribute) all_entries_hulldata (PhaseDiagram attribute) all_families() (LibxcFunc static method) all_input (VaspInputSet attribute) all_input() (AbstractFeffInputSet method) all_kinds() (LibxcFunc static method) all_molecules (XYZ attribute) all_ok (Flow attribute) ALL_STATUS (Node attribute) all_status_strings() (pymatgen.io.abinit.nodes.Status class method) 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 (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) alpha (Lattice attribute) (WulffShape attribute) alphabetical_formula (Composition attribute) (Ion attribute) 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) ang() (NormalizedAngleDistanceNbSetWeight method) anginvdist() (NormalizedAngleDistanceNbSetWeight method) anginvndist() (NormalizedAngleDistanceNbSetWeight method) angle_cutoff (SimplestChemenvStrategy attribute) 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) 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) AntisiteDefectTransformation (class in pymatgen.transformations.defect_transformations) any2mb() (in module pymatgen.io.abinit.qutils) append() (Molecule method) (Structure method) append_defectsite() (Interstitial 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_strategy() (AbstractChemenvStrategy method) (SimplestChemenvStrategy method) apply_tags() (MultiStructuresVis method) apply_to_structure() (Deformation method) apply_transformation() (AbstractTransformation method) (AddSitePropertyTransformation method) (AntisiteDefectTransformation method) (AutoOxiStateDecorationTransformation method) (ChargeBalanceTransformation method) (DeformStructureTransformation method) (DopingTransformation method) (EnumerateStructureTransformation method) (InsertSitesTransformation method) (InterstitialTransformation method) (MagOrderingTransformation method) (MultipleSubstitutionTransformation method) (OrderDisorderedStructureTransformation method) (OxidationStateDecorationTransformation method) (OxidationStateRemovalTransformation method) (PartialRemoveSitesTransformation method) (PartialRemoveSpecieTransformation method) (PerturbStructureTransformation method) (PrimitiveCellTransformation method) (RemoveSitesTransformation method) (RemoveSpeciesTransformation method) (ReplaceSiteSpeciesTransformation method) (RotationTransformation method) (SlabTransformation method) (SubstitutionDefectTransformation method) (SubstitutionPredictorTransformation method) (SubstitutionTransformation method) (SuperTransformation method) (SupercellTransformation method) (TranslateSitesTransformation method) (VacancyTransformation method)

AqueousCorrection (class in pymatgen.entries.compatibility) Ar (Element attribute) are_collinear() (Magmom static method) are_equal() (AbstractComparator method) (ElementComparator method) (FrameworkComparator method) (MoleculeStructureComparator method) (OrderDisorderElementComparator method) (SpeciesComparator method) (SpinComparator method) are_symmetrically_equivalent() (SpacegroupOperations method) are_symmetrically_related() (SymmOp method) area_frac_vs_chempot_plot() (SurfaceEnergyAnalyzer 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) (Author method) (BSVasprun method) (BalancedReaction method) (BandStructure method) (BandStructureSymmLine method) (BoltztrapAnalyzer method) (BoltztrapRunner method) (CNBiasNbSetWeight method) (CSMFloat method) (ChemicalEnvironments method) (CifParser 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) (DeltaCSMNbSetWeight method) (DetailedVoronoiContainer method) (DiffusionAnalyzer method) (DistanceAngleAreaNbSetWeight method) (DistanceCutoffFloat method) (Dos method) (DummySpecie method) (Eels method) (Electrons method) (ElectronsAlgorithm method) (Element method) (EwaldElectrostaticModel method) (ExpEntry method) (FiestaInput method) (Fiesta_run method) (Flow method) (ForceField method) (GaussianInput method) (GaussianOutput method) (GaussianToComputedEntryDrone method) (GrandPotPDEntry method) (GrandPotentialPhaseDiagram method) (HistoryNode method) (HistoryRecord method) (IMolecule method) (IStructure method) (Incar method) (InchiMolAtomMapper method) (InsertionElectrode method) (Ion method) (IonEntry method) (IsingModel method) (IsomorphismMolAtomMapper method) (KSampling method) (Kpoint method) (Kpoints method) (LammpsData method) (LammpsInputSet method) (LammpsLog method) (LammpsRun method) (Lattice method) (LibxcFunc method) (LightStructureEnvironments method) (LightStructureEnvironments.NeighborsSet method) (MagSymmOp method) (MoleculeMatcher method) (MoleculeStructureComparator method) (MultiWeightsChemenvStrategy method) (NEBAnalysis method) (NMRChemicalShiftNotation method) (NbSetWeight method) (NodeResults method) (NormalizedAngleDistanceNbSetWeight method) (NsitesModel method) (NwInput method) (NwTask method) (Nwchem2Fiesta method) (Oszicar method) (Outcar method) (PDEntry method) (PPModel method) (ParalHints method) (PeriodicSite method) (PhaseDiagram method) (PhononBandStructure method) (PhononBandStructureSymmLine method) (PhononDos method) (Poscar method) (Potcar method) (PourbaixEntry 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) (Smearing method) (Specie method) (SpecieProximityFilter method) (SpinMode method) (StrategyOption method) (StructureEnvironments method) (StructureEnvironments.NeighborsSet method) (StructureMatcher method) (StructureNL method) (Substitutor method) (SymmOp method) (SymmetryModel method) (Tags method) (TargettedPenaltiedAbundanceChemenvStrategy method) (TaskManager method) (ThermoData method) (TransformedPDEntry method) (TransformedStructure method) (TranslateSitesTransformation method) (VaspInput method) (VaspInputSet method) (VaspToComputedEntryDrone method) (Vasprun 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_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) 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_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) 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) AVAILABLE_RADIATION (XRDCalculator attribute) average_coordination_number() (in module pymatgen.analysis.structure_analyzer) average_electroneg (Composition attribute) average_ionic_radius (Element attribute), [1] aweight() (NormalizedAngleDistanceNbSetWeight method) axis_off (WulffShape attribute)

B

B (Element attribute) b (Kpoint attribute) (Lattice attribute) (PeriodicSite attribute) (Plane attribute) b0 (EOSBase attribute) b0_GPa (EOSBase attribute) b1 (EOSBase attribute) Ba (Element attribute) BabelMolAdaptor (class in pymatgen.io.babel) bad_sections() (ParallelEfficiency method) bader_analysis_from_objects() (in module pymatgen.command_line.bader_caller) bader_analysis_from_path() (in module pymatgen.command_line.bader_caller) BaderAnalysis (class in pymatgen.command_line.bader_caller) BalancedReaction (class in pymatgen.analysis.reaction_calculator) 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_utils) basename (Directory attribute) (File 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) 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) bohr_to_ang (in module pymatgen.core.units) 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) BorgQueen (class in pymatgen.apps.borg.queen) box_lengths (LammpsRun attribute) Br (Element attribute) break_bond() (IMolecule method) brinell_hardness (Element attribute) broken_bond_vs_gamma() (SurfaceEnergyAnalyzer method) 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) bulk_modulus (Element 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) cache (Specie 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_gamma() (SurfaceEnergyAnalyzer method) calculate_stress() (ElasticTensorExpansion method) (NthOrderElasticTensor method) calculated_reaction_energy (ComputedReaction attribute) callback() (PyFlowScheduler method) cancel() (Flow method) (TaskManager method) cart_coords (Kpoint attribute) (SiteCollection attribute) cart_forces (GaussianOutput attribute) cart_to_frac() (in module pymatgen.analysis.adsorption) 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) Cf (Element attribute) changebasis() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) charge (GaussianOutput attribute) (IMolecule attribute) Charge (in module pymatgen.core.units) charge (Ion attribute) (Outcar attribute) (SiteCollection 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) ChargeBalanceTransformation (class in pymatgen.transformations.advanced_transformations) check() (SchedulerErrorHandler method) check_acc_bzt_bands() (BoltztrapAnalyzer static method) check_box_size() (LammpsData 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) ChemEnvConfig (class in pymatgen.analysis.chemenv.utils.chemenv_config) ChemenvError ChemenvStrategyError chemical_shifts (Outcar attribute) chemical_symbols (ETSF_Reader attribute) ChemicalEnvironments (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) ChemicalPotential (class in pymatgen.core.composition) chempot_range (SurfaceEnergyAnalyzer attribute) chempot_vs_gamma_plot() (SurfaceEnergyAnalyzer 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) cleanup() (PyFlowScheduler method) close() (AtomicFile method) (NetcdfReader method) (YamlTokenizer method) cluster (Atoms attribute) cluster_from_file() (Atoms static method) cluster_sites() (in module pymatgen.symmetry.analyzer) Cm (Element 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) collinear() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) color_area (WulffShape attribute) color_opts (Status attribute) color_rgb (AnaddbTask attribute) (DdkTask 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) 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) CompleteDos (class in pymatgen.electronic_structure.dos) 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) (PourbaixEntry 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() (OrderParameters method) ComputedEntry (class in pymatgen.entries.computed_entries) ComputedReaction (class in pymatgen.analysis.reaction_calculator) ComputedStructureEntry (class in pymatgen.entries.computed_entries) conc_term (MultiEntry attribute) (PourbaixEntry attribute) 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) 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) 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_obatoms_to_molecule() (PackmolRunner method) convert_strain_to_deformation() (in module pymatgen.analysis.elasticity.strain) convert_to_ieee() (Tensor method) (TensorCollection method) coord_list_mapping() (in module pymatgen.util.coord_utils) coord_list_mapping_pbc() (in module pymatgen.util.coord_utils) (in module pymatgen.util.coord_utils_cython) coordination_geometry_symmetry_measures() (LocalGeometryFinder method) coordination_geometry_symmetry_measures_fallback_random() (LocalGeometryFinder method) coordination_geometry_symmetry_measures_safe_override() (LocalGeometryFinder method) coordination_geometry_symmetry_measures_separation_plane() (LocalGeometryFinder method) coordination_geometry_symmetry_measures_standard() (LocalGeometryFinder method) coordination_number (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) (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) corrected_compound_formulas (EntryPostProcessor attribute) Correction (class in pymatgen.entries.compatibility) 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) CovalentBond (class in pymatgen.core.bonds) CovalentRadius (class in pymatgen.analysis.molecule_structure_comparator) cpuwall_histogram() (AbinitTimer method) Cr (Element attribute) create_tasks() (QptdmWork method) created (HistoryRecord attribute) critical() (NodeHistory method) CRITICAL_EVENTS (NscfTask attribute) (PhononTask attribute) (RelaxTask attribute) (ScfTask attribute) (SigmaTask attribute) critical_temperature (Element attribute) crosses_origin (Plane attribute) Cs (Element attribute) cs_core_contribution (Outcar 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)

D

d (OrbitalType attribute) (Plane attribute) D2DEScfCycle (class in pymatgen.io.abinit.abiinspect) 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) debye_temperature_gibbs() (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) 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_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.point_defects) defect_count() (RelaxedInterstitial method) defectsite_count() (Defect method) 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_defectsite() (Interstitial method) delete_snl() (MPRester 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) 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) determine_min_cell() (pymatgen.transformations.advanced_transformations.MagOrderingTransformation class method) 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) dieze_tag (GaussianOutput attribute) diff() (Incar method) (Tags method) diff_fit() (in module pymatgen.analysis.elasticity.elastic) diff_incar() (in module pymatgen.cli.pmg) differences_wrt() (StructureEnvironments method) DiffusionAnalyzer (class in pymatgen.analysis.diffusion_analyzer) dilute_solution_model() (in module pymatgen.analysis.defects.dilute_solution_model) dipole (Slab attribute) directional_elastic_mod() (ElasticTensor method) directional_poisson_ratio() (ElasticTensor method) Directory (class in pymatgen.io.abinit.utils) dirname (File attribute) disable_symmetry() (QcTask method) discard() (AtomicFile method) disconnect_signals() (Flow method) DiskError (class in pymatgen.io.abinit.scheduler_error_parsers) display_help() (MultiStructuresVis method) (StructureVis method) display_info() (MultiStructuresVis method) display_warning() (MultiStructuresVis method) 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_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) distances (StructureEnvironments.NeighborsSet attribute) distfactor_max (CoordinationGeometry attribute) divisors() (in module pymatgen.analysis.chemenv.utils.math_utils) djrepo_path (Pseudo attribute) do_query() (in module pymatgen.cli.pmg_query) domain_vertices() (PourbaixPlotter method) DopingTransformation (class in pymatgen.transformations.advanced_transformations) DOS (class in pymatgen.electronic_structure.dos) Dos (class in pymatgen.electronic_structure.dos) 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) 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_of_element (SurfaceEnergyAnalyzer attribute) e_surf_list (WulffShape attribute) edge (Xmu 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) efg (Outcar attribute) eigenvalue_band_properties (Vasprun attribute) eigenvalues (GaussianOutput attribute) (Vasprun attribute) eigenvectors (GaussianOutput attribute) eigvec_to_eigdispl() (in module pymatgen.io.phonopy) einsum_sequence() (Tensor method) elastic_tensor (Outcar attribute) ElasticTensor (class in pymatgen.analysis.elasticity.elastic) ElasticTensorExpansion (class in pymatgen.analysis.elasticity.elastic) electrical_resistivity (Element attribute) 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) email (Author attribute) END_TAG (AbinitTimerParser attribute) endpoints_minima() (EnergyTrend method) energies (AdfOutput attribute) (Eels attribute) (GaussianOutput attribute) (Xmu attribute) energy (ComputedEntry attribute) Energy (in module pymatgen.core.units) energy (PourbaixEntry attribute) energy_density() (ElasticTensorExpansion method) (NthOrderElasticTensor method) energy_per_atom (ComputedEntry attribute) (IonEntry 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) EntryPostProcessor (class in pymatgen.entries.post_processors_abc) enumerate_defectsites() (Defect method) (Interstitial method) (StructureMotifInterstitial method) (Vacancy method) enumerate_ordering() (PartialRemoveSitesTransformation method) EnumerateStructureTransformation (class in pymatgen.transformations.advanced_transformations) EnumlibAdaptor() (in module pymatgen.command_line.enumlib_caller) EOS (class in pymatgen.analysis.eos) EOSBase (class in pymatgen.analysis.eos)

EOSError epsilon_ionic (Vasprun attribute), [1] epsilon_static (Vasprun attribute), [1] epsilon_static_wolfe (Vasprun attribute), [1] equivalent_site_index() (AbstractChemenvStrategy method) 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) 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) evaluate() (RatioFunction method) evaluate_rpn() (in module pymatgen.io.abinit.utils) 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) 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_metadata() (AbstractErrorParser static method) extrapolate_reciprocal() (in module pymatgen.util.convergence) extrapolate_simple_reciprocal() (in module pymatgen.util.convergence)

F

F (Element attribute) f (OrbitalType attribute) f0 (Orbital attribute) 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 (PourbaixDiagram attribute) (WulffShape 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 fetch_tasks_to_run() (PyLauncher 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) filename (HistoryRecord 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) 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_deadlocks() (Flow method) find_eq_stress() (in module pymatgen.analysis.elasticity.elastic) find_equivalent_sites() (SymmetrizedStructure method) find_in_coord_list() (in module pymatgen.util.coord_utils) find_in_coord_list_pbc() (in module pymatgen.util.coord_utils) find_last_timden_file() (Directory method) find_mapping() (Lattice method) find_optconf() (AbinitTask method) find_primitive() (SpacegroupAnalyzer 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_structure() (MPRester method) find_surface_sites_by_height() (AdsorbateSiteFinder method) fine_structure (Eels attribute) fit() (DeltaFactor method) (EOS method) (EOSBase method) (MoleculeMatcher method) (NumericalEOS method) (PolynomialEOS method) (StructureMatcher method) fit_anonymous() (StructureMatcher method) fit_arrhenius() (in module pymatgen.analysis.diffusion_analyzer) fit_error() (Plane method) fit_least_square_distance_error() (Plane method) fit_maximum_distance_error() (Plane method) fit_to_structure() (Tensor method) (TensorCollection method) fix_abicritical() (AbinitTask method) (Flow method) (OpticTask method) fix_ofiles() (RelaxTask method) fix_paths() (FilepathFixer method) fix_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) fn (PymatgenTest attribute) fold_point() (in module pymatgen.electronic_structure.plotter) force_constants (Vasprun attribute) ForceField (class in pymatgen.io.lammps.force_field) forces (EwaldSummation attribute) formation_energy() (RelaxedInterstitial 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) frac_to_cart() (in module pymatgen.analysis.adsorption) 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) frequencies (AdfOutput attribute) (GaussianOutput attribute) 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_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_csv() (PDEntry static method) (PDEntryIO static method) (PourbaixEntryIO 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() (Author static method) (BoltztrapAnalyzer static method) (Element static method) (HistoryNode static method) (LibxcFunc 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.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.DistanceAngleAreaNbSetWeight class method) (pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceCutoffFloat 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.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.CSMFiniteRatioFunction class method) (pymatgen.analysis.chemenv.utils.func_utils.CSMInfiniteRatioFunction class method) (pymatgen.analysis.chemenv.utils.func_utils.DeltaCSMRatioFunction class method) (pymatgen.analysis.diffusion_analyzer.DiffusionAnalyzer class method) (pymatgen.analysis.energy_models.EnergyModel class method) (pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper class method) (pymatgen.analysis.molecule_matcher.InchiMolAtomMapper class method) (pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper class method) (pymatgen.analysis.molecule_matcher.MoleculeMatcher class method) (pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator class method) (pymatgen.analysis.nmr.NMRChemicalShiftNotation 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.pourbaix.entry.IonEntry class method) (pymatgen.analysis.pourbaix.entry.PourbaixEntry 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.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.xcfunc.XcFunc class method) (pymatgen.electronic_structure.bandstructure.BandStructure class method) (pymatgen.electronic_structure.bandstructure.BandStructureSymmLine class method) (pymatgen.electronic_structure.dos.CompleteDos class method) (pymatgen.electronic_structure.dos.Dos 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.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.LammpsData class method) (pymatgen.io.lammps.force_field.ForceField class method) (pymatgen.io.lammps.output.LammpsLog class method) (pymatgen.io.lammps.output.LammpsRun class method) (pymatgen.io.lammps.sets.LammpsInputSet class method) (pymatgen.io.nwchem.NwInput class method) (pymatgen.io.nwchem.NwTask class method) (pymatgen.io.qchem.QcInput class method) (pymatgen.io.qchem.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() (VaspInput static method) from_file() (BabelMolAdaptor static method) (Chgcar static method) (Cssr static method) (Eels static method) (ExcitingInput static method) (ForceField 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) (Tags static method) (XYZ static method) (Xmu static method) (Xr static method) (ZeoCssr static method) (ZeoVoronoiXYZ static method) (pymatgen.core.structure.IMolecule class method) (pymatgen.core.structure.IStructure class method) (pymatgen.core.structure.SiteCollection 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.LammpsData class method) (pymatgen.io.lammps.data.LammpsForceFieldData class method) (pymatgen.io.lammps.input.LammpsInput class method) (pymatgen.io.lammps.output.LammpsDump class method) (pymatgen.io.lammps.sets.LammpsInputSet class method) (pymatgen.io.nwchem.NwInput class method) (pymatgen.io.qchem.QcInput class method) (pymatgen.io.qchem.QcTask class method) from_filenames() (CifTransmuter static method) (PoscarTransmuter static method) from_files() (BoltztrapAnalyzer static method) (pymatgen.analysis.diffusion_analyzer.DiffusionAnalyzer class method) from_forcefield_and_topology() (LammpsForceFieldData static method) from_formula() (Ion static method) from_global_moment_and_saxis() (pymatgen.electronic_structure.core.Magmom 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.NMRChemicalShiftNotation class method) from_molecule() (pymatgen.io.nwchem.NwTask class method) (Topology static 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_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) 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 static method) from_scaling_factors() (SupercellTransformation static method) from_scf_input() (pymatgen.io.abinit.works.PhononWork class method) from_scf_task() (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() (AdfKey static method) (BabelMolAdaptor 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) (Kpoints_supported_modes 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.input.LammpsInput class method) (pymatgen.io.nwchem.NwInput class method) (pymatgen.io.qchem.QcInput class method) (pymatgen.io.qchem.QcTask class method) (pymatgen.io.xcrysden.XSF class method) from_structure() (pymatgen.io.lammps.data.LammpsData class method) (pymatgen.io.lammps.sets.LammpsInputSet 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.analysis.elasticity.tensors.Tensor class method) from_vaspruns() (pymatgen.analysis.diffusion_analyzer.DiffusionAnalyzer class method) from_voigt() (pymatgen.analysis.elasticity.tensors.Tensor class method) (pymatgen.analysis.elasticity.tensors.TensorCollection class method) from_xyz_string() (SymmOp static method) from_xyzt_string() (MagSymmOp static method) from_Z() (Element static method) 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

g() (PourbaixAnalyzer method) g0 (PourbaixEntry attribute) g0_add() (PourbaixEntry method) g0_replace() (PourbaixEntry method) 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) gbulk (SurfaceEnergyAnalyzer attribute) 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_full_symmops() (in module pymatgen.symmetry.analyzer) generate_potcar() (in module pymatgen.cli.pmg_potcar) generate_pseudo() (in module pymatgen.analysis.elasticity.elastic) generate_sl_transformation_sets() (ZSLGenerator method) generate_surface_vectors() (SubstrateAnalyzer method) generators (PointGroup attribute) (SpaceGroup attribute) 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_distance_and_image() (Lattice method) get_all_distances() (Lattice method) get_all_entries() (InsertionElectrode method) get_all_neighbors() (IStructure method) get_all_status() (Work method) get_all_substrates() (MPRester method) get_allowed_species() (Substitutor method) get_angle() (in module pymatgen.util.coord_utils) (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_atoms_data() (LammpsData static method) (LammpsForceFieldData 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_basic_system_info() (LammpsData static method) (LammpsForceFieldData static method) get_best_electronegativity_anonymous_mapping() (StructureMatcher method) get_bibtex_strings() (CifParser method) get_bond_length() (in module pymatgen.core.bonds) get_boxed_structure() (IMolecule method) get_branch() (BandStructureSymmLine method) (PhononBandStructureSymmLine method) get_brillouin_zone() (Lattice method) get_bulk_structure() (RelaxedInterstitial 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() (PourbaixPlotter 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_coordination_number() (RelaxedInterstitial method) get_charge_transfer() (BaderAnalysis method) get_chempot_range_map() (PhaseDiagram method) (PourbaixAnalyzer method) get_chempot_range_map_plot() (PDPlotter method) get_chempot_range_stability_phase() (PhaseDiagram method) get_chgint_plot() (in module pymatgen.cli.pmg_plot) get_children() (Node method) get_cn() (NearNeighbors method) get_cod_ids() (COD method) get_coeff() (BalancedReaction 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_computed_entry() (Vasprun method) get_conductivity() (BoltztrapAnalyzer 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_coordinated_bulk_sites() (RelaxedInterstitial method) get_coordinated_elements() (Defect method) get_coordinated_site_displacement() (RelaxedInterstitial method) get_coordinated_sites() (Defect method) (JMolCoordFinder method) (RelaxedInterstitial method) (VoronoiCoordFinder method) get_coordinating_elements_cns() (StructureMotifInterstitial method) get_coordination_environments() (StructureEnvironments method) get_coordination_number() (CoordinationGeometry method) (JMolCoordFinder method) (RelaxedInterstitial method) (VoronoiCoordFinder method) get_coordination_symmetry_measures() (LocalGeometryFinder method) get_coordsites_charge_sum() (Interstitial method) get_coordsites_min_max_charge() (Interstitial method) (Vacancy method) get_correction() (Correction 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_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_data() (BorgQueen method) (MPRester method) get_dataframe() (AbinitTimer method) get_decomp_and_e_above_hull() (PhaseDiagram method) (PourbaixAnalyzer method) get_decomposition() (PhaseDiagram method) (PourbaixAnalyzer method) get_def_profile() (in module pymatgen.cli.pydii) 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() (Defect method) (RelaxedInterstitial method) get_defectsite_coordination_number() (Defect method) get_defectsite_effective_charge() (Vacancy method) get_defectsite_multiplicity() (Defect method) get_defectsite_structure_index() (Vacancy method) get_defectsite_structure_indices() (Vacancy 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_diffusion_analyzer() (LammpsRun method) get_dihedral() (SiteCollection method) get_dimensionality() (in module pymatgen.analysis.structure_analyzer) get_direct_band_gap() (BandStructure method) get_displacements() (LammpsRun method) get_distance() (IMolecule method) (IStructure method) (SiteCollection method) get_distance_and_image() (Lattice method) get_distribution_corrected_center() (PourbaixPlotter method) get_dos_by_material_id() (MPRester method) get_dos_dict() (DosPlotter method) (PhononDosPlotter method) get_dos_plot() (in module pymatgen.cli.pmg_plot) get_drift_corrected_structures() (DiffusionAnalyzer method) get_e_above_hull() (PhaseDiagram method) (PourbaixAnalyzer 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) 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) (InterstitialAnalyzer method) (IsingModel method) (NsitesModel method) (SymmetryModel method) (VacancyFormationEnergy 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_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_facet_chempots() (PhaseDiagram method) (PourbaixAnalyzer method) get_facets() (in module pymatgen.analysis.phase_diagram) get_factors() (in module pymatgen.analysis.substrate_analyzer) 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_gruneisen_parameter() (ElasticTensorExpansion method) get_hall() (SpacegroupAnalyzer method) get_hall_carrier_concentration() (BoltztrapAnalyzer method) get_hash() (AbstractComparator method) (ElementComparator method) (FrameworkComparator 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_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_integrated_diff() (VolumetricData method) get_interpolated_gap() (DOS method) (Dos method) get_interpolated_value() (Dos method) (PhononDos method) (Spectrum method) get_intersections() (SurfaceEnergyAnalyzer method) get_interstitial_structure() (RelaxedInterstitial method) get_ir_reciprocal_mesh() (SpacegroupAnalyzer method) get_kinks() (InterfacialReactivity method) get_kpoint_weights() (SpacegroupAnalyzer method) get_kpoints() (HighSymmKpath method) (in module pymatgen.ext.jhu) get_lattice() (CifParser method) get_lattice_quanta() (Polarization method) get_lattice_type() (SpacegroupAnalyzer method) get_linear_interpolated_value() (in module pymatgen.util.coord_utils) 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_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_magsymops() (CifParser method) get_mapping() (StructureMatcher method) get_materials_id_from_task_id() (MPRester method) get_materials_id_references() (MPRester method) get_max_bond_distance() (JMolCoordFinder method) (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_molecule_hash() (AbstractMolAtomMapper method) (InchiMolAtomMapper method) (IsomorphismMolAtomMapper method) get_moment() (Magmom method) get_moment_relative_to_crystal_axes() (Magmom method) get_mongo_info() (Flow method) get_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_nn() (NearNeighbors method) get_nn_images() (NearNeighbors method) get_nn_info() (JMolNN method) (MinimumDistanceNN method) (MinimumOKeeffeNN method) (MinimumVIRENN method) (NearNeighbors method) (VoronoiNN method) get_no_mixing_energy() (InterfacialReactivity method) get_nodes() (QueueJob 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_order_parameters() (OrderParameters 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_param_coeff() (LammpsForceFieldData static method) get_param_data() (LammpsForceFieldData static method) get_parameters() (OrderParameters 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_bond_distance_change() (InterstitialAnalyzer method) (RelaxedInterstitial method) get_percentage_lattice_parameter_change() (InterstitialAnalyzer method) (RelaxedInterstitial method) get_percentage_lattice_parameter_changes() (RelaxationAnalyzer method) get_percentage_volume_change() (InterstitialAnalyzer method) (RelaxationAnalyzer method) (RelaxedInterstitial 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_frequencies() (Dynmat method) get_plot() (BSDOSPlotter method) (BSPlotter 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_pmeshes_test() (CoordinationGeometry method) get_point_group() (SpacegroupAnalyzer method) 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_pourbaix_mark_passive() (PourbaixPlotter method) get_pourbaix_plot() (PourbaixPlotter method) get_pourbaix_plot_colorfill_by_domain_name() (PourbaixPlotter method) get_pourbaix_plot_colorfill_by_element() (PourbaixPlotter method) get_power_factor() (BoltztrapAnalyzer 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_pseudos_for_structure() (PseudoTable method) get_q2() (OrderParameters method) get_q4() (OrderParameters method) get_q6() (OrderParameters method) get_radii() (Interstitial method) get_radius() (Interstitial method) get_reaction() (MPRester method) 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_energy() (InterstitialStructureRelaxer method) get_relaxed_interstitial() (InterstitialStructureRelaxer method) get_relaxed_structure() (GulpIO method) (InterstitialAnalyzer method) (InterstitialStructureRelaxer method) (StructureRelaxer method) get_removals_int_oxid() (BatteryAnalyzer method) get_results() (AnaddbTask method) (DdkTask method) (FileNode method) (Flow method) (NscfTask method) (OpticTask method) (PhononTask method) (RelaxTask method) (ScfTask method) (SigmaTask method) get_rms_anonymous() (StructureMatcher method) get_rms_dist() (StructureMatcher method) get_rmsd() (MoleculeMatcher method) get_rot() (in module pymatgen.analysis.adsorption) get_s2_like_s1() (StructureMatcher method) get_same_branch_polarization_data() (Polarization method) get_sc_scale() (in module pymatgen.cli.pydii) 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_site_ce_fractions_and_neighbors() (AbstractChemenvStrategy method) get_site_coordination_environment() (AbstractChemenvStrategy method) (MultiWeightsChemenvStrategy method) (SimpleAbundanceChemenvStrategy method) (SimplestChemenvStrategy method) (TargettedPenaltiedAbundanceChemenvStrategy method) get_site_coordination_environments() (AbstractChemenvStrategy method) (MultiWeightsChemenvStrategy method) (SimpleAbundanceChemenvStrategy method) (SimplestChemenvStrategy method) get_site_coordination_environments_fractions() (AbstractChemenvStrategy method) (MultiWeightsChemenvStrategy method) (SimplestChemenvStrategy method) get_site_dos() (CompleteDos method) (CompletePhononDos method) get_site_info_for_specie_allces() (LightStructureEnvironments method) get_site_info_for_specie_ce() (LightStructureEnvironments method) get_site_neighbors() (AbstractChemenvStrategy method) (MultiWeightsChemenvStrategy method) (SimpleAbundanceChemenvStrategy method) (SimplestChemenvStrategy method) get_site_orbital_dos() (CompleteDos method) get_site_spd_dos() (CompleteDos method) get_site_t2g_eg_resolved_dos() (CompleteDos method) get_sitej() (VoronoiConnectivity method) get_sites_in_sphere() (IMolecule method) (IStructure method) get_slab() (SlabGenerator method) get_slabs() (SlabGenerator method) get_slope_and_intercept() (SurfaceEnergyAnalyzer method) get_smeared_densities() (Dos method) (PhononDos method) get_solute_def_profile() (in module pymatgen.cli.pydii) get_sorted_structure() (IStructure method) (Slab method) get_space_group() (SpacegroupAnalyzer 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) 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_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) (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_structures() (CifParser method) (MPRester method) get_structures_from_trajectory() (LammpsRun method) get_sub_electrodes() (ConversionElectrode method) (InsertionElectrode method) get_substrates() (MPRester method) get_suggested_saxis() (Magmom static method) get_summary_dict() (ConversionElectrode method) (DiffusionAnalyzer method) (QuasiharmonicDebyeApprox method) get_supercell_matrix() (StructureMatcher method) get_surface_area() (Vacancy method) get_surface_sites() (Slab method) get_symbol_cn_mapping() (AllCoordinationGeometries 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_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() (SpacegroupAnalyzer method) get_symops() (CifParser method) get_task_data() (MPRester method) get_tasker2_slabs() (Slab method) get_template() (LammpsInput static method) get_tgt() (ElasticTensorExpansion method) get_thermal_conductivity() (BoltztrapAnalyzer method) get_ticks() (BSPlotter method) (PhononBSPlotter method) get_tkd_value() (in module pymatgen.analysis.elasticity.tensors) 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() (OrderParameters method) get_unique_families() (in module pymatgen.analysis.diffraction.xrd) get_unstable_entries() (InsertionElectrode method) get_uvec() (in module pymatgen.analysis.elasticity.tensors) get_v() (StaticPotential method) get_valences() (BVAnalyzer method) get_valid_paths() (AbstractDrone method) (GaussianToComputedEntryDrone method) (VaspToComputedEntryDrone method) get_values() (AbinitTimer 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_volume() (Vacancy method) get_voronoi_nodes() (in module pymatgen.io.zeopp) get_voronoi_polyhedra() (VoronoiCoordFinder method) (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_xrd_pattern() (XRDCalculator method) get_xrd_plot() (in module pymatgen.cli.pmg_plot) (XRDCalculator 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) gkk_filepath (AnaddbTask attribute) global_moment (Magmom attribute) godby (PPModelModes attribute) good_sections() (ParallelEfficiency method) GPa_to_eV_A3 (NthOrderElasticTensor attribute) gramschmidt() (in module pymatgen.analysis.structure_analyzer) GrandPotentialPhaseDiagram (class in pymatgen.analysis.phase_diagram) GrandPotPDEntry (class in pymatgen.analysis.phase_diagram) green_kristoffel() (ElasticTensor method) green_lagrange_strain (Deformation attribute) grid_off (WulffShape attribute) gridfs_files (NodeResults attribute) GridFsFile (class in pymatgen.io.abinit.nodes) 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_molecules() (MoleculeMatcher method) group_structures() (StructureMatcher method) groupby_status() (Flow method) groupby_task_class() (Flow method) gruneisen_parameter() (QuasiharmonicDebyeApprox method) GulpCaller (class in pymatgen.command_line.gulp_caller) GulpConvergenceError GulpError GulpIO (class in pymatgen.command_line.gulp_caller) gw_run() (Fiesta_run method) gwcalctyp (SelfEnergy attribute) gweight() (NormalizedAngleDistanceNbSetWeight method)

H

H (Element attribute) haeberlen_values (NMRChemicalShiftNotation attribute) HaeberlenNotation (NMRChemicalShiftNotation attribute) halogen_list (MoleculeStructureComparator attribute) has_abiext() (Directory method) has_chrooted (Flow attribute) has_db (Flow attribute) (TaskManager attribute) has_dojo_report (Pseudo attribute) has_eigendisplacements (PhononBandStructure 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_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) 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) 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) 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_utils) in_coord_list_pbc() (in module pymatgen.util.coord_utils) in_simplex() (Simplex method) in_spectator_mode (Node attribute) Incar (class in pymatgen.io.vasp.inputs) incar (DictSet attribute) (MPNonSCFSet attribute) (MPSOCSet attribute) (MPStaticSet attribute) (MVLGBSet attribute) (MVLGWSet attribute) (VaspInputSet attribute) (Vasprun attribute) InchiMolAtomMapper (class in pymatgen.analysis.molecule_matcher) 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) indent() (ExcitingInput static method) 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) 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) interpolate() (IStructure method) (NEBPathfinder method) Interstitial (class in pymatgen.analysis.defects.point_defects) InterstitialAnalyzer (class in pymatgen.analysis.defects.point_defects) InterstitialStructureRelaxer (class in pymatgen.analysis.defects.point_defects) InterstitialTransformation (class in pymatgen.transformations.defect_transformations) inv (SquareTensor attribute) inv_matrix (Lattice attribute) inv_ordered_indices (SeparationPlane attribute) invdist() (NormalizedAngleDistanceNbSetWeight method) inverse (AbstractTransformation attribute) (AddSitePropertyTransformation attribute) (AntisiteDefectTransformation attribute) (AutoOxiStateDecorationTransformation attribute) (ChargeBalanceTransformation attribute) (DeformStructureTransformation attribute) (DopingTransformation attribute) (EnumerateStructureTransformation attribute) (InsertSitesTransformation attribute) (InterstitialTransformation attribute) (JonesFaithfulTransformation attribute) (MagOrderingTransformation attribute) (MultipleSubstitutionTransformation attribute) (OrderDisorderedStructureTransformation attribute) (OxidationStateDecorationTransformation attribute) (OxidationStateRemovalTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) (PerturbStructureTransformation attribute) (PrimitiveCellTransformation attribute) (RemoveSitesTransformation attribute) (RemoveSpeciesTransformation attribute) (ReplaceSiteSpeciesTransformation attribute) (RotationTransformation attribute) (SlabTransformation attribute) (SubstitutionDefectTransformation attribute) (SubstitutionPredictorTransformation attribute) (SubstitutionTransformation attribute) (SuperTransformation attribute) (SupercellTransformation attribute) (SymmOp attribute) (TranslateSitesTransformation attribute) (VacancyTransformation attribute) inversion() (SymmOp static method) inversion_op (PointGroupAnalyzer attribute) invndist() (NormalizedAngleDistanceNbSetWeight method) Ion (class in pymatgen.core.ion) ion_or_solid_comp_object() (in module pymatgen.analysis.pourbaix.entry) IonEntry (class in pymatgen.analysis.pourbaix.entry) 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) is_coord_subset() (in module pymatgen.util.coord_utils) is_coord_subset_pbc() (in module pymatgen.util.coord_utils) (in module pymatgen.util.coord_utils_cython) is_critical (Status attribute) is_element (Composition attribute) (ComputedEntry attribute) (GrandPotPDEntry attribute) (PDEntry attribute) is_failed (AdfOutput attribute) (QueueJob attribute) is_file (Node attribute) is_fit_to_structure() (Tensor method) (TensorCollection method) is_flow (Node attribute) is_gga_family (LibxcFunc 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_implemented() (CoordinationGeometry method) is_in_list() (Plane method) is_in_plane() (Plane method) is_independent() (Deformation method) is_internal_crash (AdfOutput attribute) is_k_kind (LibxcFunc attribute) is_lanthanoid (Element attribute), [1] is_laue() (SpacegroupAnalyzer method) is_lda_family (LibxcFunc 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) (AntisiteDefectTransformation attribute) (AutoOxiStateDecorationTransformation attribute) (ChargeBalanceTransformation attribute) (DeformStructureTransformation attribute) (DopingTransformation attribute) (EnumerateStructureTransformation attribute) (InsertSitesTransformation attribute) (InterstitialTransformation attribute) (MagOrderingTransformation attribute) (MultipleSubstitutionTransformation attribute) (OrderDisorderedStructureTransformation attribute) (OxidationStateDecorationTransformation attribute) (OxidationStateRemovalTransformation attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) (PerturbStructureTransformation attribute) (PrimitiveCellTransformation attribute) (RemoveSitesTransformation attribute) (RemoveSpeciesTransformation attribute) (ReplaceSiteSpeciesTransformation attribute) (RotationTransformation attribute) (SlabTransformation attribute) (SubstitutionDefectTransformation attribute) (SubstitutionPredictorTransformation attribute) (SubstitutionTransformation attribute) (SuperTransformation attribute) (SupercellTransformation attribute) (TranslateSitesTransformation attribute) (VacancyTransformation attribute) is_ordered (Site attribute) (SiteCollection attribute) is_pcm (GaussianOutput attribute) is_periodic_image() (PeriodicSite method) is_polar() (Slab method) 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) 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 static method) 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) isnc (AbinitTask attribute) (Pseudo attribute) (Work attribute) isncfile (File attribute) IsomorphismMolAtomMapper (class in pymatgen.analysis.molecule_matcher) ispaw (AbinitTask attribute) (Pseudo attribute) (Work attribute) IStructure (class in pymatgen.core.structure) 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) JMolCoordFinder (class in pymatgen.analysis.structure_analyzer) 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 (NMRChemicalShiftNotation.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) 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 (Kpoint attribute) labels() (InterfacialReactivity method) LammpsData (class in pymatgen.io.lammps.data) LammpsDump (class in pymatgen.io.lammps.output) LammpsForceFieldData (class in pymatgen.io.lammps.data) LammpsInput (class in pymatgen.io.lammps.input) LammpsInputSet (class in pymatgen.io.lammps.sets) LammpsLog (class in pymatgen.io.lammps.output) LammpsRun (class in pymatgen.io.lammps.output) LammpsRunner (class in pymatgen.io.lammps.utils) last_etotal (D2DEScfCycle attribute) (GroundStateScfCycle attribute) last_iteration (ScfCycle attribute) last_nneigh (OrderParameters attribute) last_resort_solution() (AbstractError method) latexify() (in module pymatgen.util.string) latexify_ion() (in module pymatgen.analysis.pourbaix.plotter) 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_from_abivars() (in module pymatgen.io.abinit.abiobjects) lattice_points_in_supercell() (in module pymatgen.util.coord_utils) 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) legend() (PourbaixPlotter 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) load_data() (BorgQueen method) load_module() (ScriptEditor method) load_modules() (ScriptEditor method) LocalGeometryFinder (class in pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder) localopt() (BabelMolAdaptor method) lockxyz (ExcitingInput attribute), [1] Locpot (class in pymatgen.io.vasp.outputs) log_correction() (Node method) long_v() (ElasticTensor method) look_before_you_leap() (Flow method) lowest_energy_structure (OrderDisorderedStructureTransformation attribute) Lr (Element attribute) Lu (Element attribute)

M

MAGIC (D2DEScfCycle attribute) (GroundStateScfCycle attribute) Magmom (class in pymatgen.electronic_structure.core) MagneticSpaceGroup (class in pymatgen.symmetry.maggroups) magnetization (Outcar attribute) MagOrderingTransformation (class in pymatgen.transformations.advanced_transformations) 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) (in module pymatgen.cli.pmg) (in module pymatgen.cli.pydii) 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) (PhononTask 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() (Defect method) (Interstitial method) (StructureMotifInterstitial method) (Vacancy method) make_tarfile() (Flow method) makedirs() (Directory method) map2rpn() (in module pymatgen.io.abinit.utils) maps_and_surfaces() (DetailedVoronoiContainer method) maps_and_surfaces_bounded() (DetailedVoronoiContainer method) maryland_values (NMRChemicalShiftNotation 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) MasterProcessMemoryCancelError (class in pymatgen.io.abinit.scheduler_error_parsers) match_as_dict() (ZSLGenerator method) matches() (IStructure method) material_formula (Xmu attribute) MaterialsProjectAqueousCompatibility (class in pymatgen.entries.compatibility) MaterialsProjectCompatibility (class in pymatgen.entries.compatibility) matrix (Lattice attribute) matrixMultiplication() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) 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_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) Md (Element attribute) 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 (NMRChemicalShiftNotation 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) 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) (SlabGenerator attribute) 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) mol_trajectory (LammpsRun attribute) mol_velocity (LammpsRun attribute) molar_volume (Element attribute) molecular_orbital (GaussianOutput attribute) Molecule (class in pymatgen.core.structure) molecule (FiestaInput attribute) (GaussianInput attribute) (NwInput attribute) (QcTask attribute) (XYZ attribute) MoleculeMatcher (class in pymatgen.analysis.molecule_matcher) MoleculeStructureComparator (class in pymatgen.analysis.molecule_structure_comparator) 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) monotonic() (in module pymatgen.util.num) mouseMoveEvent() (StructureInteractorStyle method) move() (File method) (Work method) move_atoms (RelaxationMethod attribute) move_cell (RelaxationMethod attribute) 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) MPNonSCFSet (class in pymatgen.io.vasp.sets) MPRelaxSet (class in pymatgen.io.vasp.sets) MPRester (class in pymatgen.ext.matproj) mprester (SurfaceEnergyAnalyzer attribute) 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) Mulliken_charges (GaussianOutput attribute) multi_curve_fit() (in module pymatgen.util.convergence) multi_reciprocal_extra() (in module pymatgen.util.convergence) multidimensional_optimization() (ParalHints method) MultiEntry (class in pymatgen.analysis.pourbaix.entry) MultipleSubstitutionTransformation (class in pymatgen.transformations.advanced_transformations) 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) 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) name (AbstractError attribute) (Author attribute) (CorrectorProtocolApplication attribute) (CorrectorProtocolScheduler attribute) (Element attribute) (HistoryNode attribute) (IonEntry attribute) (Node attribute) (PDEntry attribute) (XcFunc attribute) names_and_values() (AbinitTimer method) natoms (Dynmat attribute) (LammpsRun attribute) (Poscar attribute) (Xdatcar attribute) Nb (Element 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_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) ngridpts (VolumetricData attribute) Ni (Element attribute) nionic_steps (Vasprun attribute) NMRChemicalShiftNotation (class in pymatgen.analysis.nmr) NMRChemicalShiftNotation.MarylandNotation (class in pymatgen.analysis.nmr) NMRChemicalShiftNotation.MehringNotation (class in pymatgen.analysis.nmr) 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_modes (AdfOutput attribute) normalization_factor (MultiEntry attribute) (PourbaixEntry attribute) normalization_mass (AbstractElectrode attribute) normalization_volume (AbstractElectrode attribute) normalize() (PourbaixEntry method) (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) 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) NthOrderElasticTensor (class in pymatgen.analysis.elasticity.elastic) ntypesp (SiteCollection attribute) num_atoms (Composition attribute) (PourbaixEntry attribute) num_basis_func (GaussianOutput attribute) num_cores (TaskManager attribute) num_corrections (Node attribute) num_errored_tasks (Flow attribute) num_excs (PyFlowScheduler attribute) num_ops (OrderParameters attribute) num_sites (SiteCollection attribute) num_steps (AbstractElectrode attribute) num_tasks (Flow attribute) num_unconverged_tasks (Flow attribute) number (Element attribute), [1] number_of_permutations (CoordinationGeometry attribute) NUMERIC_FIELDS (AbinitTimerSection attribute) numerical_tol (PhaseDiagram attribute) (PourbaixAnalyzer 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) occ (Orbital attribute) off_color (WulffShape attribute) omega (NMRChemicalShiftNotation.MarylandNotation attribute) omega() (ElasticTensorExpansion method) omp_threads (TaskManager attribute) on_all_ok() (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_phbst() (AnaddbTask method) open_phdos() (AnaddbTask method) open_pspsfile() (Pseudo method) open_sigres() (SigmaTask method) openbabel_mol (BabelMolAdaptor attribute) operate() (SymmOp method) operate_magmom() (MagSymmOp method) operate_multi() (SymmOp method) operations (AdfTask attribute) (NwTask attribute) OPTCELL_DEFAULT (RelaxationMethod attribute) OpticTask (class in pymatgen.io.abinit.tasks) optimize_gibbs_free_energy() (QuasiharmonicDebyeApprox method) optimizer() (QuasiharmonicDebyeApprox method) optional_keywords_list (QcTask attribute) 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) OrderParameters (class in pymatgen.analysis.structure_analyzer) oriented_unit_cell (SlabGenerator attribute) orthongonalize_structure() (StructureVis method) orthonormal_vectors() (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) PackmolRunner (class in pymatgen.io.lammps.utils) ParalHints (class in pymatgen.io.abinit.tasks) ParalHintsParser (class in pymatgen.io.abinit.tasks) parallel_assimilate() (BorgQueen method) ParallelEfficiency (class in pymatgen.io.abinit.abitimer) parameters (Vasprun attribute) 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_coords() (GaussianInput static method) parse_criteria() (MPRester static method) parse_data_file() (in module pymatgen.io.lammps.data) 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_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_timers() (Work method) parse_timing() (AbinitTask method) (Flow method) parse_transdos() (BoltztrapAnalyzer static method) parse_transformation_string() (JonesFaithfulTransformation static method) parse_view() (in module pymatgen.cli.pmg) 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) Pb (Element attribute) pbc_diff() (in module pymatgen.util.coord_utils) pbc_shortest_vectors() (in module pymatgen.util.coord_utils) (in module pymatgen.util.coord_utils_cython) pbc_wrap() (in module pymatgen.io.lammps.output) PBSErrorParser (class in pymatgen.io.abinit.scheduler_error_parsers) PbsProJob (class in pymatgen.io.abinit.qjobs) PBSSTAT_TO_SLURM (PbsProJob attribute) pcm (GaussianOutput attribute) pconfs (AbinitTask attribute) Pd (Element attribute) pd_coords() (PhaseDiagram method) pd_plot_data (PDPlotter attribute) PDAnalyzer (class in pymatgen.analysis.phase_diagram) PDEntry (class in pymatgen.analysis.phase_diagram) PDEntryIO (class in pymatgen.analysis.phase_diagram) pdos (CompleteDos attribute) (CompletePhononDos attribute) (Vasprun attribute) PDPlotter (class in pymatgen.analysis.phase_diagram) pefficiency() (AbinitTimerParser method) PenaltyFunctionError 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) (InterfacialReactivity method) (Relaxation method) (ScfCycle method) (SparseHistogram method) (in module pymatgen.cli.pmg_plot) plot_all() (AbinitTimerParser 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) (PourbaixPlotter 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_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_ellipsoid() (in module pymatgen.electronic_structure.plotter) plot_environments() (StructureEnvironments method) plot_fermi_surface() (in module pymatgen.electronic_structure.plotter) plot_hall_carriers() (BoltztrapPlotter method) plot_images() (NEBPathfinder 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_path() (in module pymatgen.electronic_structure.plotter) plot_pie() (AbinitTimerParser method) plot_planes() (PourbaixPlotter method) plot_points() (in module pymatgen.electronic_structure.plotter) plot_pourbaix() (PourbaixPlotter method) plot_power_factor_dop() (BoltztrapPlotter method) plot_power_factor_mu() (BoltztrapPlotter method) plot_power_factor_temp() (BoltztrapPlotter method) plot_seebeck_dop() (BoltztrapPlotter method) plot_seebeck_eff_mass_mu() (BoltztrapPlotter method) plot_seebeck_mu() (BoltztrapPlotter method) plot_seebeck_temp() (BoltztrapPlotter method) plot_slab() (in module pymatgen.analysis.adsorption) plot_stacked_hist() (AbinitTimerParser method) plot_structures() (XRDCalculator 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) Polymer (class in pymatgen.io.lammps.utils) 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) pourbaix_hull_plot_data (PourbaixPlotter attribute) pourbaix_plot_data() (PourbaixPlotter method) PourbaixAnalyzer (class in pymatgen.analysis.pourbaix.analyzer) PourbaixDiagram (class in pymatgen.analysis.pourbaix.maker) PourbaixEntry (class in pymatgen.analysis.pourbaix.entry) PourbaixEntryIO (class in pymatgen.analysis.pourbaix.entry) PourbaixPlotter (class in pymatgen.analysis.pourbaix.plotter) PourierTarantola (class in pymatgen.analysis.eos) power2_decreasing_exp() (CSMFiniteRatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) power2_inverse_decreasing() (CSMInfiniteRatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) power2_inverse_power2_decreasing() (CSMInfiniteRatioFunction 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) predictor_corrector (Poscar attribute), [1] predictor_corrector_preamble (Poscar attribute) prepare_symmetries() (AbstractChemenvStrategy method) 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_invariants (SquareTensor attribute) print_and_raise_error() (in module pymatgen.util.convergence) print_gnuplot_header() (in module pymatgen.io.abinit.helpers) print_name() (PourbaixPlotter method) print_periodic_table() (Element static method) print_plot_line() (in module pymatgen.util.convergence) 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) (EntryPostProcessor method)

processes (Work attribute) Product (class in pymatgen.io.abinit.nodes) products (BalancedReaction attribute) (Dependency attribute) (FileNode attribute) 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) properly_terminated (GaussianOutput attribute) properties (Site attribute) property_dict (ElasticTensor attribute) prune_close_defectsites() (Interstitial method) prune_defectsites() (Interstitial method) 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) pybel_mol (BabelMolAdaptor 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.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.dilute_solution_model (module) pymatgen.analysis.defects.point_defects (module) pymatgen.analysis.defects.surf_error (module) pymatgen.analysis.diffraction (module) pymatgen.analysis.diffraction.xrd (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.ferroelectricity (module) pymatgen.analysis.ferroelectricity.polarization (module) pymatgen.analysis.hhi (module) pymatgen.analysis.hhi.hhi (module) pymatgen.analysis.interface_reactions (module) pymatgen.analysis.local_env (module) pymatgen.analysis.molecule_matcher (module) pymatgen.analysis.molecule_structure_comparator (module) pymatgen.analysis.nmr (module) pymatgen.analysis.path_finder (module) pymatgen.analysis.phase_diagram (module) pymatgen.analysis.piezo (module) pymatgen.analysis.pourbaix (module) pymatgen.analysis.pourbaix.analyzer (module) pymatgen.analysis.pourbaix.entry (module) pymatgen.analysis.pourbaix.maker (module) pymatgen.analysis.pourbaix.plotter (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.substrate_analyzer (module) pymatgen.analysis.surface_analysis (module) pymatgen.analysis.thermochemistry (module) pymatgen.analysis.transition_state (module) pymatgen.analysis.wulff (module) pymatgen.analysis.xas (module) pymatgen.analysis.xas.spectrum (module) pymatgen.apps (module) pymatgen.apps.battery (module) pymatgen.apps.battery.analyzer (module) pymatgen.apps.battery.battery_abc (module) pymatgen.apps.battery.conversion_battery (module) pymatgen.apps.battery.insertion_battery (module) pymatgen.apps.battery.plotter (module) pymatgen.apps.borg (module) pymatgen.apps.borg.hive (module) pymatgen.apps.borg.queen (module) pymatgen.cli (module) pymatgen.cli.feff_input_generation (module) pymatgen.cli.feff_plot_cross_section (module) pymatgen.cli.feff_plot_dos (module) pymatgen.cli.gaussian_analyzer (module) pymatgen.cli.get_environment (module) pymatgen.cli.pmg (module) pymatgen.cli.pmg_analyze (module) pymatgen.cli.pmg_config (module) pymatgen.cli.pmg_plot (module) pymatgen.cli.pmg_potcar (module) pymatgen.cli.pmg_query (module) pymatgen.cli.pmg_structure (module) pymatgen.cli.pydii (module) pymatgen.command_line (module) pymatgen.command_line.aconvasp_caller (module) pymatgen.command_line.bader_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.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.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.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.babel (module) pymatgen.io.cif (module) pymatgen.io.cssr (module) pymatgen.io.exciting (module) pymatgen.io.exciting.inputs (module) pymatgen.io.feff (module) pymatgen.io.feff.inputs (module) pymatgen.io.feff.outputs (module) pymatgen.io.feff.sets (module) pymatgen.io.fiesta (module) pymatgen.io.gaussian (module) pymatgen.io.lammps (module) pymatgen.io.lammps.data (module) pymatgen.io.lammps.force_field (module) pymatgen.io.lammps.input (module) pymatgen.io.lammps.output (module) pymatgen.io.lammps.sets (module) pymatgen.io.lammps.topology (module) pymatgen.io.lammps.utils (module) pymatgen.io.nwchem (module) pymatgen.io.phonopy (module) pymatgen.io.pwscf (module) pymatgen.io.qchem (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.matproj (module) pymatgen.matproj.rest (module) pymatgen.matproj.snl (module) pymatgen.optimization (module) pymatgen.optimization.linear_assignment (module) pymatgen.optimization.linear_assignment_numpy (module) pymatgen.phasediagram (module) pymatgen.phasediagram.analyzer (module) pymatgen.phasediagram.entries (module) pymatgen.phasediagram.maker (module) pymatgen.phasediagram.plotter (module) pymatgen.phonon (module) pymatgen.phonon.bandstructure (module) pymatgen.phonon.dos (module) pymatgen.phonon.plotter (module) pymatgen.serializers (module) pymatgen.serializers.json_coders (module) pymatgen.serializers.pickle_coders (module) pymatgen.structure_prediction (module) pymatgen.structure_prediction.substitution_probability (module) pymatgen.structure_prediction.substitutor (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.advanced_transformations (module) pymatgen.transformations.defect_transformations (module) pymatgen.transformations.site_transformations (module) pymatgen.transformations.standard_transformations (module) pymatgen.transformations.transformation_abc (module) pymatgen.util (module) pymatgen.util.convergence (module) pymatgen.util.coord_utils (module) pymatgen.util.coord_utils_cython (module) pymatgen.util.io_utils (module) pymatgen.util.num (module) pymatgen.util.num_utils (module) pymatgen.util.plotting (module) pymatgen.util.plotting_utils (module) pymatgen.util.provenance (module) pymatgen.util.serialization (module) pymatgen.util.string (module) pymatgen.util.string_utils (module) pymatgen.util.testing (module) pymatgen.vis (module) pymatgen.vis.plotters (module) pymatgen.vis.structure_chemview (module) pymatgen.vis.structure_vtk (module) pymatgen_mol (BabelMolAdaptor attribute) PymatgenTest (class in pymatgen.util.testing) pz (Orbital attribute)

Q

qadapter (TaskManager attribute) qads (TaskManager attribute) QcInput (class in pymatgen.io.qchem) QcNucVeloc (class in pymatgen.io.qchem) QcOutput (class in pymatgen.io.qchem) QcTask (class in pymatgen.io.qchem) qhull_data (PourbaixDiagram attribute) qhull_entries (PourbaixDiagram attribute) 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), [1] radius (CovalentRadius attribute) radius_prune_defectsites() (Interstitial method) 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) ReactionError read() (File method) read_abinit_hdr() (ETSF_Reader method) read_abinit_xcfunc() (ETSF_Reader method) read_avg_core_poten() (Outcar method) read_chemical_shifts() (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_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_keys() (NetcdfReader method) read_lcalcpol() (Outcar method) read_lepsilon() (Outcar method) read_lepsilon_ionic() (Outcar method) read_neb() (Outcar method) read_nmr_efg() (Outcar method) read_pattern() (Outcar method) (PWOutput method) read_piezo_tensor() (Outcar method) read_pseudo_zval() (Outcar method) read_route_line() (in module pymatgen.io.gaussian) read_scan() (GaussianOutput method), [1] read_structure() (ETSF_Reader method) read_table_pattern() (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) 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_defectsites() (Interstitial 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_entry() (PourbaixEntry method) reduced_formula (Composition attribute) (Ion attribute) ref_element (SurfaceEnergyAnalyzer attribute) ref_permutation() (CoordinationGeometry method) ref_separation_perm (SeparationPlane attribute) 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) relax() (InterstitialStructureRelaxer method) (StructureRelaxer method) Relaxation (class in pymatgen.io.abinit.abiinspect) RelaxationAnalyzer (class in pymatgen.analysis.structure_analyzer) RelaxationMethod (class in pymatgen.io.abinit.abiobjects) relaxed_energy_match() (InterstitialStructureRelaxer method) relaxed_structure_match() (InterstitialAnalyzer method) (InterstitialStructureRelaxer method) RelaxedInterstitial (class in pymatgen.analysis.defects.point_defects) 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) remove() (File method) remove_deps() (Node method) remove_exts() (Directory 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) replace() (Structure 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) restore_site_properties() (PackmolRunner 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) rhombohedral() (Lattice static method) rigidity_modulus (Element attribute) 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) rotate_view() (StructureVis method) rotateCoords() (in module pymatgen.analysis.chemenv.utils.coordination_geometry_utils) rotation_matrix (SymmOp attribute) RotationTransformation (class in pymatgen.transformations.standard_transformations) rotoreflection() (SymmOp static method) route (GaussianOutput attribute) row (Element attribute), [1] Ru (Element attribute) run() (BoltztrapRunner method) (Fiesta_run method) (GulpCaller method) (LammpsRunner method) (Nwchem2Fiesta method) (PackmolRunner method) run_aconvasp_command() (in module pymatgen.command_line.aconvasp_caller) run_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_plane_permutations() (SeparationPlane 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) (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) (PourbaixEntry 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_INTENSITY_TOL (XRDCalculator attribute) scan_nestdict() (in module pymatgen.io.abinit.db) scatter_hist() (AbinitTimer method) 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) 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_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_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_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_vars() (OpticTask method) set_velocities() (QcTask method) set_workdir() (Flow method) (OpticTask method) (Work method) setup() (AbinitTask method) (AnaddbTask method) (ChemEnvConfig 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() (LocalGeometryFinder method) (RatioFunction 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) show() (BSPlotter method) (DosPlotter method) (PDPlotter method) (PhononBSPlotter method) (PhononDosPlotter method) (PourbaixPlotter method) (SpectrumPlotter method) (StructureVis method) (VoltageProfilePlotter method) (WulffShape method) show_abierrors() (Flow method) show_area (WulffShape attribute) show_corrections() (Flow method) show_dependencies() (Flow method) show_event_handlers() (Node method) show_events() (Flow method) show_history() (Flow method) show_info() (Flow method) show_inputs() (Flow method) show_qouts() (Flow method) show_receivers() (Flow method) show_status() (Flow method) show_summary() (Flow method) show_xrd_plot() (XRDCalculator method) shutdown() (PyFlowScheduler method) Si (Element attribute) sigma_11 (NMRChemicalShiftNotation.MehringNotation attribute) sigma_22 (NMRChemicalShiftNotation.MehringNotation attribute) sigma_33 (NMRChemicalShiftNotation.MehringNotation attribute) sigma_iso (NMRChemicalShiftNotation.MarylandNotation attribute) (NMRChemicalShiftNotation.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) SimplestChemenvStrategy (class in pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies) SimpleVaspToComputedEntryDrone (class in pymatgen.apps.borg.hive) Simplex (class in pymatgen.util.coord_utils) single_cap_hints() (CoordinationGeometry.NeighborsSetsHints method) single_reciprocal() (in module pymatgen.util.convergence) single_shot() (Flow method) (PyLauncher method) Site (class in pymatgen.core.sites) site_contains_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_scale_factor (SlabGenerator attribute) SlabGenerator (class in pymatgen.core.surface) SlabTransformation (class in pymatgen.transformations.advanced_transformations) SlaveProcessMemoryCancelError (class in pymatgen.io.abinit.scheduler_error_parsers) 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) (in module pymatgen.analysis.chemenv.utils.math_utils) smoothness() (EnergyTrend method) (Polarization method) smoothstep() (CSMFiniteRatioFunction method) (in module pymatgen.analysis.chemenv.utils.math_utils) 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_def_parse_energy() (in module pymatgen.cli.pydii) solute_defect_density() (in module pymatgen.analysis.defects.dilute_solution_model) solute_site_preference_finder() (in module pymatgen.analysis.defects.dilute_solution_model) sort() (Structure 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) sorted() (PseudoTable method) 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) Spin (class in pymatgen.electronic_structure.core) spin_data (VolumetricData attribute) spin_mult (GaussianOutput attribute) spin_multiplicity (IMolecule 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 SquareTensor (class in pymatgen.analysis.elasticity.tensors) Sr (Element attribute) stable_entries (PhaseDiagram attribute) (PourbaixDiagram 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) 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) struct_radii (Defect attribute) struct_valences (Defect attribute) structure (BandStructure attribute) Structure (class in pymatgen.core.structure) structure (CompleteDos attribute) (Defect attribute) (ExcitingInput attribute) (HighSymmKpath attribute) (LammpsData attribute) (Poscar attribute) (ValenceIonicRadiusEvaluator attribute), [1] (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_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) StructureEnvironments (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) StructureEnvironments.NeighborsSet (class in pymatgen.analysis.chemenv.coordination_environments.structure_environments) StructureError StructureInteractorStyle (class in pymatgen.vis.structure_vtk) StructureMatcher (class in pymatgen.analysis.structure_matcher) StructureMotifInterstitial (class in pymatgen.analysis.defects.point_defects) StructureNL (class in pymatgen.util.provenance) StructureRelaxer (class in pymatgen.analysis.defects.point_defects) structures (AdfOutput attribute) (GaussianOutput attribute) (TransformedStructure attribute) (Vasprun attribute), [1] (Xdatcar attribute) (in module pymatgen.command_line.enumlib_caller) STRUCTURES_DIR (PymatgenTest attribute) StructureVis (class in pymatgen.vis.structure_vtk) style (Kpoints attribute) sub_keys (AdfKey attribute) 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) substitute_def_struct_gen() (in module pymatgen.cli.pydii) SubstitutionDefectTransformation (class in pymatgen.transformations.defect_transformations) SubstitutionPredictor (class in pymatgen.analysis.structure_prediction.substitution_probability) SubstitutionPredictorTransformation (class in pymatgen.transformations.advanced_transformations) SubstitutionProbability (class in pymatgen.analysis.structure_prediction.substitution_probability) SubstitutionTransformation (class in pymatgen.transformations.standard_transformations) Substitutor (class in pymatgen.analysis.structure_prediction.substitutor) SubstrateAnalyzer (class in pymatgen.analysis.substrate_analyzer) subsurface_sites() (AdsorbateSiteFinder method) sulfide_type() (in module pymatgen.analysis.structure_analyzer) sum_sections() (AbinitTimer method) summarize() (AbinitTimerParser method) summary (BaderAnalysis attribute) (Pseudo attribute) SupercellTransformation (class in pymatgen.transformations.standard_transformations) superconduction_temperature (Element attribute) SuperTransformation (class in pymatgen.transformations.advanced_transformations) supported_modes (Kpoints attribute) SUPPORTED_MODES (MVLGWSet attribute) supported_properties (MPRester attribute) (Specie attribute) supported_task_properties (MPRester attribute) supported_units (ArrayWithUnit attribute) (FloatWithUnit attribute) supports_soc (Pseudo attribute) surf_energy_error() (in module pymatgen.analysis.defects.surf_error) surface_area (Slab attribute) (WulffShape attribute) surface_sites (AdsorbateSiteFinder attribute) SurfaceEnergyAnalyzer (class in pymatgen.analysis.surface_analysis) symbol (DummySpecie attribute), [1] (Element attribute) (PointGroup attribute) (PotcarSingle attribute) (Pseudo attribute) (SpaceGroup attribute) symbol_set (SiteCollection attribute) symbols (Potcar attribute) symlink_abiext() (Directory method) symm_reduce() (AdsorbateSiteFinder 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.analysis.elasticity.tensors) symmetry_reduced_voronoi_nodes() (in module pymatgen.analysis.defects.point_defects) SymmetryGroup (class in pymatgen.symmetry.groups) SymmetryModel (class in pymatgen.analysis.energy_models) SymmOp (class in pymatgen.core.operations) symsigma (SelfEnergy attribute)

T

Ta (Element attribute) tag (YamlDoc attribute) 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) tdos (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 (LammpsData attribute) (LammpsForceFieldData attribute) temporary_flow() (pymatgen.io.abinit.flows.Flow class method) Tensor (class in pymatgen.analysis.elasticity.tensors) TensorCollection (class in pymatgen.analysis.elasticity.tensors) 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) 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) 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_bv_dict() (StructureEnvironments method) to_csv() (AbinitTimer method) (PDEntry static method) (PDEntryIO static method) (PourbaixEntryIO static method) to_csvline() (AbinitTimerSection method) to_data_dict (Composition attribute) to_dict() (AbinitTimerSection method) (Flow method) to_input() (GaussianOutput method), [1] to_json() (AdfKey method) (AdfTask method) (LibxcFunc method) to_reduced_dict (Composition attribute) (Ion attribute) to_shell_manager() (TaskManager method) to_snl() (TransformedStructure method) to_string() (GaussianInput method) (NodeHistory method) (Pseudo method) (XSF method) to_table() (AbinitTimer method) (PseudoTable method) to_tuple() (AbinitTimerSection method) to_unit_cell (PeriodicSite attribute) TOLERANCE (BalancedReaction attribute) Topology (class in pymatgen.io.lammps.topology) TorqueJob (class in pymatgen.io.abinit.qjobs) totable() (AbinitTimer method) (ParallelEfficiency method) total_energy (EwaldSummation attribute) total_energy_matrix (EwaldSummation attribute) total_spectrum (Eels attribute) traj_timesteps (LammpsRun 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) 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) TWO_THETA_TOL (XRDCalculator attribute) Type (OrbitalDescription attribute) type (Pseudo attribute) (XcFunc attribute) Type2 (OrbitalDescription attribute) typeidx_from_symbol() (ETSF_Reader method) types_of_specie (SiteCollection attribute)

U

U (Element attribute) ucell_entry (SurfaceEnergyAnalyzer attribute) UCorrection (class in pymatgen.entries.compatibility) unconverged_tasks (Flow attribute) UnconvergedVASPWarning undo_last_change() (StandardTransmuter method) (TransformedStructure method) uniform_labels() (AbstractMolAtomMapper method) (InchiMolAtomMapper method) (IsomorphismMolAtomMapper method) uniquelines() (in module pymatgen.analysis.phase_diagram) uniquely_determined_coordination_environments (LightStructureEnvironments attribute) uniquely_determines_coordination_environments (AbstractChemenvStrategy attribute) (MultiWeightsChemenvStrategy attribute) (SimpleAbundanceChemenvStrategy attribute) (SimplestChemenvStrategy attribute) (TargettedPenaltiedAbundanceChemenvStrategy 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_status (QueueJob attribute) unprocessed_entries (PourbaixDiagram attribute) unstable_entries (PhaseDiagram attribute) (PourbaixDiagram attribute) unsym_cs_tensor (Outcar attribute), [1] up (Spin attribute) update_collection() (NodeResults method) update_coordination_environments() (StructureEnvironments method) update_nb_set_environments() (LocalGeometryFinder method) update_potcar_spec() (Vasprun 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) vac_antisite_def_parse_energy() (in module pymatgen.cli.pydii) vac_antisite_def_struct_gen() (in module pymatgen.cli.pydii) Vacancy (class in pymatgen.analysis.defects.point_defects) VacancyFormationEnergy (class in pymatgen.analysis.defects.point_defects) VacancyTransformation (class in pymatgen.transformations.defect_transformations) ValenceIonicRadiusEvaluator (class in pymatgen.analysis.defects.point_defects) (class in pymatgen.analysis.local_env) valences (ValenceIonicRadiusEvaluator attribute), [1] validate_json_schema() (Flow method) (NodeResults 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) vasprun_dict (SurfaceEnergyAnalyzer attribute) 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) vertices (PourbaixDiagram attribute) vibrational_free_energy() (QuasiharmonicDebyeApprox method) vibrational_internal_energy() (QuasiharmonicDebyeApprox method) vickers_hardness (Element attribute)

Vinet (class in pymatgen.analysis.eos) visualize() (in module pymatgen.analysis.chemenv.utils.scripts_utils) voigt (Tensor attribute) (TensorCollection attribute) voigt_symmetrized (Tensor attribute) vol_charge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) vol_discharge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) 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) (Lattice attribute) (Simplex 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) VoronoiCoordFinder (class in pymatgen.analysis.structure_analyzer) VoronoiNN (class in pymatgen.analysis.local_env) VoronoiParametersError

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) Wavederf (class in pymatgen.io.vasp.outputs) wavenumber (Xmu attribute) weight (Composition attribute) weight() (AngleNbSetWeight method) (CNBiasNbSetWeight method) (DeltaCSMNbSetWeight method) (DistanceAngleAreaNbSetWeight method) (NbSetWeight method) (NormalizedAngleDistanceNbSetWeight method) (SelfCSMNbSetWeight method) weighted_surface_energy (WulffShape attribute) weights (Procar attribute) welcome() (in module pymatgen.analysis.chemenv.utils.scripts_utils) wfk_filepath (OpticTask attribute) with_dojo_report() (PseudoTable method) Work (class in pymatgen.io.abinit.works) 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) (BabelMolAdaptor method) (CifWriter method) (Cssr method) (ExcitingInput method) (FiestaInput method) (GaussianInput method) (Header method) (Incar method) (Kpoints method) (LammpsData method) (LammpsInput method) (NwInput method) (PWInput method) (Paths method) (Poscar method) (Potcar method) (PotcarSingle method) (Potential method) (QcInput method) (QcTask method) (Tags method) (VolumetricData method) (XYZ method) (Xdatcar method) (Xr method)

write_image() (PDPlotter method) (PourbaixPlotter method) (StructureVis method) write_input() (AbstractFeffInputSet method) (BoltztrapRunner method) (DictSet method) (LammpsInputSet method) (MITNEBSet method) (VaspInput method) (VaspInputSet method) write_intrans() (BoltztrapRunner method) write_jobfile() (TaskManager method) write_pdb() (PackmolRunner method) write_proj() (BoltztrapRunner method) write_string() (ExcitingInput method) write_struct() (BoltztrapRunner method) write_vasp_input() (StandardTransmuter method) (TransformedStructure method) writelines() (File method) wti_from_nids() (Flow method) wulff_cv_simp (WulffShape attribute) wulff_pt_list (WulffShape attribute) wulff_shape_dict() (SurfaceEnergyAnalyzer method) wulff_shape_from_chempot() (SurfaceEnergyAnalyzer method) WulffFacet (class in pymatgen.analysis.wulff) WulffShape (class in pymatgen.analysis.wulff)

X

X (DummySpecie attribute), [1] (Element attribute), [1] x (Site attribute) (SurfaceEnergyAnalyzer 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) (Spectrum attribute) (XANES attribute) (XRDPattern attribute)

Xmu (class in pymatgen.io.feff.outputs) Xr (class in pymatgen.io.xr) XRDCalculator (class in pymatgen.analysis.diffraction.xrd) XRDPattern (class in pymatgen.analysis.diffraction.xrd) XSF (class in pymatgen.io.xcrysden) XYZ (class in pymatgen.io.xyz) xyz_patt (GaussianInput attribute) (QcTask attribute)

Y

Y (Element attribute) y (Site attribute) (SurfaceEnergyAnalyzer 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)

YamlDoc (class in pymatgen.io.abinit.abiinspect) YamlTokenizer (class in pymatgen.io.abinit.abiinspect) YamlTokenizerError Yb (Element attribute) YLABEL (DOS attribute) (Spectrum attribute) (XANES attribute) (XRDPattern 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) zeroed() (Tensor method) (TensorCollection method)

zlist (PseudoTable attribute) zmat_patt (GaussianInput attribute) (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)