Index

A

a (Kpoint attribute) (Lattice attribute) (PeriodicSite attribute) abc (Lattice attribute) abinit_output_iscomplete() (in module pymatgen.io.abinitio.utils) abiobjects (InputWriter attribute) AbiStructure (class in pymatgen.io.abinitio.abiobjects) AbivarAble (class in pymatgen.io.abinitio.abiobjects) absorbing_atom (Xmu attribute) AbstractComparator (class in pymatgen.analysis.structure_matcher) AbstractDrone (class in pymatgen.apps.borg.hive) AbstractElectrode (class in pymatgen.apps.battery.battery_abc) AbstractFeffInputSet (class in pymatgen.io.feffio_set) AbstractStructureFilter (class in pymatgen.alchemy.filters) AbstractTransformation (class in pymatgen.transformations.transformation_abc) AbstractVaspInputSet (class in pymatgen.io.vaspio_set) AbstractVoltagePair (class in pymatgen.apps.battery.battery_abc) accept_pseudo() (DojoMaster method) accuracy (Strategy attribute) AconvaspError acquire() (FileLock method) across_section (Xmu attribute) action() (Event method) actual_kpoints (Vasprun attribute) actual_kpoints_weights (Vasprun attribute) add_abiobj() (InputWriter method) add_bonds() (StructureVis method) add_comment() (ScriptEditor method) add_densities() (in module pymatgen.electronic_structure.dos) add_dos() (DosPlotter method) add_dos_dict() (DosPlotter method) add_electrode() (VoltageProfilePlotter method) add_emptyline() (ScriptEditor method) add_extra_abivars() (InputWriter method) (Strategy method) add_line() (ScriptEditor method) (StructureVis method) add_lines() (ScriptEditor method) add_m_list() (EwaldMinimizer method) add_oxidation_state_by_element() (Structure method) add_oxidation_state_by_site() (Structure 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_tags() (StandardTransmuter method) add_text() (StructureVis method) affine_matrix (SymmOp 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) all_comp (Reaction attribute) all_energies (Oszicar attribute) all_orbitals (Orbital attribute) all_pseudos (PseudoDatabase attribute)

all_spins (Spin attribute) alldone (Workflow attribute) almost_equals() (Composition method) alpha (Lattice attribute) alphabetical_formula (Composition attribute) amount_tol (CompoundPhaseDiagram attribute) amount_tolerance (Composition attribute) AMU_TO_KG (in module pymatgen.core.physical_constants) Anaddb (class in pymatgen.io.abinitio.wrappers) Anaddb.AnaddbError Ang2Bohr() (in module pymatgen.core.physical_constants) angles (Lattice attribute) anonymized_formula (Composition attribute) any2eV() (in module pymatgen.core.units) any2Ha() (in module pymatgen.core.units) append() (EventList method) (Molecule method) (Structure method) append_filter() (TransformedStructure method) append_transformation() (StandardTransmuter method) (TransformedStructure method) append_transformed_structures() (StandardTransmuter method) apply_filter() (StandardTransmuter method) apply_operation() (Molecule method) (Structure method) apply_rotation_only() (SymmOp method) apply_scissor() (BandStructureSymmLine method) apply_strain() (Structure method) apply_transformation() (AbstractTransformation method) (AutoOxiStateDecorationTransformation method) (ChargeBalanceTransformation method) (EnumerateStructureTransformation method) (IdentityTransformation method) (InsertSitesTransformation 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) (SubstitutionPredictorTransformation method) (SubstitutionTransformation method) (SuperTransformation method) (SupercellTransformation method) (TranslateSitesTransformation method) are_equal() (AbstractComparator method) (ElementComparator method) (FrameworkComparator method) (SpeciesComparator method) are_symmetrically_equivalent() (Spacegroup method) are_symmetrically_related() (SymmOp method) asabistructure() (AbiStructure static method) (in module pymatgen.io.abinitio.abiobjects) AseAtomsAdaptor (class in pymatgen.io.aseio) asppmodel() (pymatgen.io.abinitio.abiobjects.PPModel class method) aspseudo() (pymatgen.io.abinitio.pseudos.Pseudo class method) assert_almost_equal() (PymatgenTest static method) assert_equal() (PymatgenTest static method) assert_valid() (WorkFlowResults method) assimilate() (AbstractDrone method) (DeltaDrone method) (GaussianToComputedEntryDrone method) (SimpleVaspToComputedEntryDrone method) (VaspToComputedEntryDrone method) assmearing() (pymatgen.io.abinitio.abiobjects.Smearing class method) asspinmode() (pymatgen.io.abinitio.abiobjects.SpinMode class method) atomic_mass (Element attribute) atomic_numbers (SiteCollection attribute) atomic_radius (Element attribute) atomic_radius_calculated (Element attribute) atomic_symbols (Vasprun attribute) atoms_and_cell() (pymatgen.io.abinitio.abiobjects.RelaxationMethod class method) atoms_only() (pymatgen.io.abinitio.abiobjects.RelaxationMethod class method) atoms_string_from_file() (FeffAtoms static method) AttrDict (class in pymatgen.core.design_patterns) Author (class in pymatgen.matproj.snl) automatic() (Kpoints static method) automatic_density() (Kpoints static method) (pymatgen.io.abinitio.abiobjects.KSampling class method) AutoOxiStateDecorationTransformation (class in pymatgen.transformations.standard_transformations) average_electroneg (Composition attribute) average_ionic_radius (Element attribute) AVOGADROS_CONST (in module pymatgen.core.physical_constants)

B

b (Kpoint attribute) (Lattice attribute) (PeriodicSite attribute) BabelMolAdaptor (class in pymatgen.io.babelio) BaderAnalysis() (in module pymatgen.command_line.bader_caller) BalancedReaction (class in pymatgen.analysis.reaction_calculator) bands (BandStructure attribute) BandStructure (class in pymatgen.electronic_structure.bandstructure) (class in pymatgen.io.abinitio.workflow) bandstructure() (in module pymatgen.io.abinitio.calculations) BandStructureSymmLine (class in pymatgen.electronic_structure.bandstructure) barycentric_coords() (in module pymatgen.util.coord_utils) baseclass (Event attribute) basename (File attribute) BaseWorkflow (class in pymatgen.io.abinitio.workflow) basis_set (GaussianOutput attribute) batch_write_vasp_input() (in module pymatgen.alchemy.transmuters) (in module pymatgen.io.vaspio_set) bcc() (HighSymmKpath method) bctet1() (HighSymmKpath method) bctet2() (HighSymmKpath method) best_case() (EwaldMinimizer method) best_first_ordering() (PartialRemoveSitesTransformation method) best_m_list (EwaldMinimizer attribute) beta (Lattice attribute) BetheSalpeter (class in pymatgen.io.abinitio.abiobjects)

Birch() (EOS static method) Birch_Murnaghan() (EOS static method) block (Element attribute) BM() (in module pymatgen.io.abinitio.deltafactor.eosfit) Bohr2Ang() (in module pymatgen.core.physical_constants) Bohr_Ang (in module pymatgen.core.physical_constants) boiling_point (Element attribute) BOLTZMANN_CONST (in module pymatgen.core.physical_constants) BorgQueen (class in pymatgen.apps.borg.queen) boxed_atom() (pymatgen.io.abinitio.abiobjects.AbiStructure class method) boxed_molecule() (pymatgen.io.abinitio.abiobjects.AbiStructure class method) break_bond() (IMolecule method) brinell_hardness (Element attribute) bs_plot_data() (BSPlotter method) BSPlotter (class in pymatgen.electronic_structure.plotter) BSPlotterProjected (class in pymatgen.electronic_structure.plotter) Bug (class in pymatgen.io.abinitio.events) bugs (EventList attribute) build() (Workflow method) bulk_modulus (Element attribute) BVAnalyzer (class in pymatgen.analysis.bond_valence)

C

c (Kpoint attribute) (Lattice attribute) (PeriodicSite attribute) cached_class() (in module pymatgen.util.decorators) calc (Xmu attribute) calculate_bv_sum() (in module pymatgen.analysis.bond_valence) calculate_energy() (Reaction method) calculated_reaction_energy (ComputedReaction attribute) cart_coords (Kpoint attribute) (SiteCollection attribute) CDFrequencyMesh (class in pymatgen.io.abinitio.abiobjects) center_of_mass (IMolecule attribute) central_atom (FeffAtoms attribute) (FeffPot attribute) challenge() (DeltaFactorMaster method) (DojoMaster method) (HintsMaster method) challenge_pseudo() (Dojo method) characters() (VasprunHandler method) charge (GaussianOutput attribute) (IMolecule attribute) (Outcar attribute) (SiteCollection attribute) charge_transfer (FeffLdos attribute) charge_transfer_from_file() (FeffLdos static method) charge_transfer_to_string() (FeffLdos method) ChargeBalanceFilter (class in pymatgen.alchemy.filters) ChargeBalanceTransformation (class in pymatgen.transformations.advanced_transformations) check_conv() (in module pymatgen.io.abinitio.workflow) check_etotal_convergence() (PseudoIterativeConvergence method) checksum() (Pseudo method) Chgcar (class in pymatgen.io.vaspio.vasp_output) chunks() (in module pymatgen.util.num_utils) (Workflow method) CIFNotFoundError CifParser (class in pymatgen.io.cifio) CifTransmuter (class in pymatgen.alchemy.transmuters) CifWriter (class in pymatgen.io.cifio) clean_json() (in module pymatgen.util.io_utils) clean_lines() (in module pymatgen.util.io_utils) close() (NetcdfReader method) cls (in module pymatgen.io.abinitio.pseudo_dojo) cluster_sites() (in module pymatgen.symmetry.pointgroup) coefficient_of_linear_thermal_expansion (Element attribute) coeffs (Reaction attribute) colours (StringColorizer attribute) Comment (class in pymatgen.io.abinitio.events)

comment (Poscar attribute) comments (EventList attribute) common_oxidation_states (Element attribute) communicate() (BaseWorkflow method) Compatibility (class in pymatgen.entries.compatibility) complete_dos (FeffLdos attribute) (Vasprun attribute) complete_ordering() (PartialRemoveSitesTransformation method) CompleteDos (class in pymatgen.electronic_structure.dos) Composition (class in pymatgen.core.composition) composition (ConversionElectrode attribute) (PDEntry attribute) (SiteCollection attribute) CompoundPhaseDiagram (class in pymatgen.phasediagram.pdmaker) compute_average_oxidation_state() (in module pymatgen.analysis.ewald) compute_hints() (in module pymatgen.io.abinitio.workflow) compute_partial_energy() (EwaldSummation method) compute_sub_structure() (EwaldSummation method) ComputedEntry (class in pymatgen.entries.computed_entries) ComputedReaction (class in pymatgen.analysis.reaction_calculator) ComputedStructureEntry (class in pymatgen.entries.computed_entries) connectivity_array (VoronoiConnectivity attribute) Constraints (class in pymatgen.io.abinitio.abiobjects) contains_peroxide() (in module pymatgen.analysis.structure_analyzer) ContainsSpecieFilter (class in pymatgen.alchemy.filters) CONV_FACT (EwaldSummation attribute) converged (Vasprun attribute) ConversionElectrode (class in pymatgen.apps.battery.conversion_battery) ConversionVoltagePair (class in pymatgen.apps.battery.conversion_battery) coords (Site attribute) copy() (Composition method) (IStructure method) (Molecule method) (Reaction method) corrected_compound_formulas (Compatibility attribute) (EntryPostProcessor attribute) corrections (GaussianOutput attribute) CovalentBond (class in pymatgen.core.bonds) critical_events (EventList attribute) critical_temperature (Element attribute) Cssr (class in pymatgen.io.cssrio) cubic() (HighSymmKpath method) (Lattice static method) cutoff (VoronoiConnectivity attribute)

D

data (PotcarSingle attribute) (Procar attribute) (Strategy attribute) (Xmu attribute) declare_var() (ScriptEditor method) declare_vars() (ScriptEditor method) decode() (PMGJSONDecoder method) default() (PMGJSONEncoder method) default_cutoff (VoronoiCoordFinder attribute) DEFAULT_FUNCTIONAL (Potcar attribute) DeltaDrone (class in pymatgen.io.abinitio.deltaworks) DeltaFactorDataset() (in module pymatgen.io.abinitio.deltafactor.dataset) DeltaFactorMaster (class in pymatgen.io.abinitio.pseudo_dojo) DeltaFactory (class in pymatgen.io.abinitio.deltaworks) DeltaFactoryError DeltaTest (class in pymatgen.io.abinitio.workflow) density (IStructure attribute) density_of_solid (Element attribute) deprecated() (in module pymatgen.util.decorators) description (HistoryNode attribute) diagonalize_1q() (Anaddb method) DictVaspInputSet (class in pymatgen.io.vaspio_set) dielectric (Vasprun attribute) diff() (FeffTags method) (Incar method) DiffusionAnalyzer (class in pymatgen.analysis.diffusion_analyzer) dirname (File attribute) (PseudoDatabase attribute)

display_help() (StructureVis method) distance() (PeriodicSite method) (Site method) distance_and_image() (PeriodicSite method) distance_and_image_from_frac_coords() (PeriodicSite method) distance_from_point() (Site method) distance_matrix (SiteCollection attribute) DISTANCE_TOLERANCE (SiteCollection attribute) Dojo (class in pymatgen.io.abinitio.pseudo_dojo) dojo_key (DeltaFactorMaster attribute) (HintsMaster attribute) dojo_key2level() (in module pymatgen.io.abinitio.pseudo_dojo) dojo_level (DeltaFactorMaster attribute) (HintsMaster attribute) (Pseudo attribute) DojoError DojoMaster (class in pymatgen.io.abinitio.pseudo_dojo) Dos (class in pymatgen.electronic_structure.dos) DosPlotter (class in pymatgen.electronic_structure.plotter) down (Spin attribute) DummySpecie (class in pymatgen.core.periodic_table) dump_results() (DeltaDrone method) dx2 (Orbital attribute) dxy (Orbital attribute) dxz (Orbital attribute) dyz (Orbital attribute) dz2 (Orbital attribute)

E

ecut (Strategy attribute) ecut_list (PseudoIterativeConvergence attribute) edge (Xmu attribute) efermi (BandStructure attribute) (Vasprun attribute) eigenvalue_band_properties (Vasprun attribute) eigenvalues (Vasprun attribute) electrical_resistivity (Element attribute) ELECTRON_CHARGE (in module pymatgen.core.physical_constants) ELECTRON_TO_AMPERE_HOURS (in module pymatgen.core.physical_constants) ELECTRON_VOLT (in module pymatgen.core.physical_constants) electronic_steps (Oszicar attribute) electronic_structure (Element attribute) Electrons (class in pymatgen.io.abinitio.abiobjects) ElectronsAlgorithm (class in pymatgen.io.abinitio.abiobjects) Element (class in pymatgen.core.periodic_table) element (Pseudo attribute) element_composition (Composition attribute) ElementComparator (class in pymatgen.analysis.structure_matcher) elements (Composition attribute) (Reaction attribute) email (Author attribute) endElement() (VasprunHandler method) energies (GaussianOutput attribute) (Xmu attribute) energy (ComputedEntry attribute) (PDEntry attribute) energy_per_atom (PDEntry attribute) entries_charge (ConversionVoltagePair attribute) entries_discharge (ConversionVoltagePair attribute) EntryPostProcessor (class in pymatgen.entries.post_processors_abc) Enum (class in pymatgen.core.design_patterns)

enumerate_ordering() (PartialRemoveSitesTransformation method) EnumerateStructureTransformation (class in pymatgen.transformations.advanced_transformations) EnumlibAdaptor() (in module pymatgen.command_line.enumlib_caller) EOS (class in pymatgen.io.abinitio.eos) EPSILON_0 (in module pymatgen.core.physical_constants) equivalent_sites (SymmetrizedStructure attribute) Error (Anaddb attribute) (BaseWorkflow attribute) (DeltaFactory attribute) (Dojo attribute) (DojoMaster attribute) (EOS attribute) (EventParser attribute) (Mrggkk attribute) (Mrgscr attribute) (Workflow attribute) (class in pymatgen.io.abinitio.events) errors (EventList attribute) eta (EwaldSummation attribute) eV2Ha() (in module pymatgen.core.physical_constants) EV_PER_ATOM_TO_J_PER_MOL (in module pymatgen.core.physical_constants) EV_PER_ATOM_TO_KJ_PER_MOL (in module pymatgen.core.physical_constants) Event (class in pymatgen.io.abinitio.events) EventList (class in pymatgen.io.abinitio.events) EventParser (class in pymatgen.io.abinitio.events) EventParserError EwaldMinimizer (class in pymatgen.analysis.ewald) EwaldSummation (class in pymatgen.analysis.ewald) EXC_KEY (WorkFlowResults attribute) exceptions (WorkFlowResults attribute) exists (File attribute) exit_iteration() (IterativeWork method) (PseudoIterativeConvergence method) ExpEntry (class in pymatgen.entries.exp_entries) explicit_path() (pymatgen.io.abinitio.abiobjects.KSampling class method) export_envar() (ScriptEditor method) export_envars() (ScriptEditor method) extend_transformations() (StandardTransmuter method) (TransformedStructure method)

F

f0 (Orbital attribute) f1 (Orbital attribute) f2 (Orbital attribute) f3 (Orbital attribute) f_1 (Orbital attribute) f_2 (Orbital attribute) f_3 (Orbital attribute) fast_ordering() (PartialRemoveSitesTransformation method) fcc() (HighSymmKpath method) FeffAtoms (class in pymatgen.io.feffio) FeffInputSet (class in pymatgen.io.feffio_set) FeffLdos (class in pymatgen.io.feffio) FeffParserError FeffPot (class in pymatgen.io.feffio) FeffTags (class in pymatgen.io.feffio) fetch_task_to_run() (BaseWorkflow method) File (class in pymatgen.io.abinitio.utils) FileLock (class in pymatgen.util.io_utils) FileLockException filepath (Pseudo attribute) final_energy (GaussianOutput attribute) (Oszicar attribute) (Vasprun attribute) final_structure (GaussianOutput attribute) (TransformedStructure attribute) (Vasprun attribute) find_equivalent_sites() (SymmetrizedStructure method) find_file() (in module pymatgen.io.abinitio.utils) find_in_coord_list() (in module pymatgen.util.coord_utils) find_in_coord_list_pbc() (in module pymatgen.util.coord_utils) find_indexes() (StructureMatcher method) find_mapping() (Lattice method) find_primitive() (SymmetryFinder method) fit() (EOS method) (StructureMatcher method) fit_anonymous() (StructureMatcher method) float_from_str() (in module pymatgen.io.cifio) forces (EwaldSummation attribute) formation_energy_tol (PhaseDiagram attribute) formula (Composition attribute) (Header attribute) (SiteCollection attribute) formula_double_format() (in module pymatgen.util.string_utils)

frac_charge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) frac_coords (IStructure attribute) (Kpoint attribute) (PeriodicSite attribute) frac_discharge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) FrameworkComparator (class in pymatgen.analysis.structure_matcher) from_axis_angle_and_translation() (SymmOp static method) from_cif_file() (Header static method) from_cif_string() (TransformedStructure static method) from_composition_and_entries() (ConversionElectrode static method) from_composition_and_pd() (ConversionElectrode static method) from_csv() (PDEntryIO static method) from_dict() (AbstractComparator static method) (AbstractFeffInputSet static method) (Author static method) (DictVaspInputSet static method) (FeffAtoms static method) (FeffLdos static method) (FeffPot static method) (FeffTags static method) (Header static method) (HistoryNode static method) (Incar static method) (Kpoints static method) (MITGGAVaspInputSet static method) (MITHSEVaspInputSet static method) (MITMDVaspInputSet static method) (MITVaspInputSet static method) (MPGGAVaspInputSet static method) (MPVaspInputSet static method) (PPModel static method) (Poscar static method) (Potcar static method) (Smearing static method) (StructureMatcher static method) (VaspInput static method) (VaspInputSet static method) (Workflow static method) (Xmu static method) (pymatgen.alchemy.filters.AbstractStructureFilter class method) (pymatgen.alchemy.materials.TransformedStructure class method) (pymatgen.analysis.diffusion_analyzer.DiffusionAnalyzer 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.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.lattice.Lattice class method) (pymatgen.core.operations.SymmOp 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.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.abinitio.events.Event class method) (pymatgen.io.abinitio.events.EventList class method) (pymatgen.io.abinitio.workflow.WorkFlowResults class method) (pymatgen.matproj.snl.StructureNL class method) (pymatgen.phasediagram.entries.GrandPotPDEntry class method) (pymatgen.phasediagram.entries.PDEntry class method) (pymatgen.phasediagram.entries.TransformedPDEntry class method) (pymatgen.serializers.json_coders.MSONable class method) (pymatgen.structure_prediction.substitutor.Substitutor class method) (pymatgen.transformations.transformation_abc.AbstractTransformation class method) from_directory() (VaspInput static method) from_file() (BabelMolAdaptor static method) (Chgcar static method) (Cssr static method) (FeffLdos static method) (FeffTags static method) (GaussianInput static method) (Header static method) (Incar static method) (Kpoints static method) (Locpot static method) (Poscar static method) (Potcar static method) (XYZ static method) (Xmu static method) from_filename() (Pseudo static method) from_filenames() (CifTransmuter static method) (PoscarTransmuter static method) from_formula() (Composition static method) from_int() (Spin static method) from_lengths_and_angles() (Lattice static method) from_origin_axis_angle() (SymmOp static method) from_parameters() (Lattice static method) from_poscar_string() (TransformedStructure static method) from_previous_vasp_run() (MPNonSCFVaspInputSet static method) (MPStaticVaspInputSet static method) from_rotation_and_translation() (SymmOp static method) from_rotation_matrix_and_translation_vector() (SymmOp static method) from_scaling_factors() (SupercellTransformation static method) from_sites() (pymatgen.core.structure.IMolecule class method) (pymatgen.core.structure.IStructure class method) from_steps() (ConversionVoltagePair static method) from_string() (BabelMolAdaptor static method) (BalancedReaction static method) (CifParser static method) (Cssr static method) (Event static method) (FeffAtoms static method) (GaussianInput static method) (Header static method) (Orbital static method) (Poscar static method) (XYZ static method) from_structures() (StandardTransmuter static method) from_vasp_index() (Orbital static method) from_vaspruns() (DiffusionAnalyzer static method) full_electronic_structure (Element attribute) fully_charged_entry (InsertionElectrode attribute) fully_discharged_entry (InsertionElectrode attribute) functional (GaussianOutput attribute) functions (EOS attribute)

G

g0w0_with_ppmodel() (in module pymatgen.io.abinitio.calculations) gamma (Lattice attribute) gamma_automatic() (Kpoints static method) gamma_centered() (pymatgen.io.abinitio.abiobjects.KSampling class method) gamma_only() (pymatgen.io.abinitio.abiobjects.KSampling class method) GaussianInput (class in pymatgen.io.gaussianio) GaussianOutput (class in pymatgen.io.gaussianio) GaussianToComputedEntryDrone (class in pymatgen.apps.borg.hive) generate_full_symmops() (in module pymatgen.symmetry.pointgroup) generate_latex_table() (in module pymatgen.util.string_utils) get_abivars() (Product method) (WorkLink method) get_adjusted_fermi_level() (in module pymatgen.io.vaspio.vasp_output) get_all_entries() (InsertionElectrode method) get_all_feff_input() (AbstractFeffInputSet method) get_all_neighbors() (IStructure method) get_all_vasp_input() (AbstractVaspInputSet method) get_allowed_species() (Substitutor method) get_angle() (in module pymatgen.util.coord_utils) (SiteCollection method) get_atomic_fraction() (Composition method) get_atoms() (AseAtomsAdaptor static method) get_average_along_axis() (VolumetricData method) get_average_voltage() (AbstractElectrode method) get_axis_grid() (VolumetricData method) get_band_gap() (BandStructureSymmLine method) get_band_structure() (GSR_Reader method) (Vasprun method) get_band_structure_from_vasp_multiple_branches() (in module pymatgen.io.vaspio.vasp_output) get_bond_length() (in module pymatgen.core.bonds) get_boxed_structure() (IMolecule method) get_branch() (BandStructureSymmLine method) get_brillouin_zone() (Lattice method) get_capacity_grav() (AbstractElectrode method) get_capacity_vol() (AbstractElectrode method) get_cartesian_coords() (Lattice method) get_cbm() (BandStructureSymmLine method) get_cbm_vbm() (Dos method) get_centered_molecule() (IMolecule method) get_chempot_range_map() (PDAnalyzer method) get_chempot_range_map_plot() (PDPlotter method) get_coeff() (Reaction method) get_contour_pd_plot() (PDPlotter method) get_conv_struct() (in module pymatgen.command_line.aconvasp_caller) get_conventional_standard_structure() (SymmetryFinder method) get_conversion_factor() (in module pymatgen.analysis.diffusion_analyzer) get_coordinated_sites() (VoronoiCoordFinder method) get_coordination_number() (VoronoiCoordFinder method) get_covalent_bonds() (IMolecule method) get_crystal_system() (SymmetryFinder method) get_d_occupation() (Procar method) get_data() (BorgQueen method) get_decomp_and_e_above_hull() (PDAnalyzer method) get_decomposition() (PDAnalyzer method) get_densities() (Dos method) get_dihedral() (SiteCollection method) get_direct_band_gap() (BandStructureSymmLine method) get_distance() (IMolecule method) (IStructure method) (SiteCollection method) get_dos_dict() (DosPlotter method) get_e_above_hull() (PDAnalyzer method) get_el_amount() (Reaction method) get_el_amt_dict() (Composition method) get_element_dos() (CompleteDos method) get_element_profile() (PDAnalyzer method) get_elt_projected_plots() (BSPlotterProjected method) get_elt_projected_plots_color() (BSPlotterProjected method) get_energy_density() (AbstractElectrode method) get_equilibrium_reaction_energy() (PDAnalyzer method) get_equivalent_kpoints() (BandStructureSymmLine method) get_facet_chempots() (PDAnalyzer method) get_feff_atoms() (AbstractFeffInputSet method) (FeffInputSet method) get_feff_pot() (AbstractFeffInputSet method) (FeffInputSet method) get_feff_tags() (AbstractFeffInputSet method) (FeffInputSet method) get_filepath() (Product method) get_filepaths_and_exts() (WorkLink method) get_form_energy() (PhaseDiagram method) get_form_energy_per_atom() (PhaseDiagram method) get_fractional_composition() (Composition method) get_fractional_coords() (Lattice method) get_gap() (Dos method) get_hall() (SymmetryFinder method) get_header() (AbstractFeffInputSet method) (FeffInputSet method) get_incar() (AbstractVaspInputSet method) (DictVaspInputSet method) get_incar_settings() (MPNonSCFVaspInputSet static method) get_integrated_diff() (VolumetricData method) get_interpolated_gap() (Dos method) get_interpolated_value() (Dos method) get_ir_kpoints() (SymmetryFinder method) get_ir_kpoints_mapping() (SymmetryFinder method) get_ir_reciprocal_mesh() (SymmetryFinder method) get_kpath_plot() (HighSymmKpath method) get_kpoints() (AbstractVaspInputSet method) (DictVaspInputSet method) (HighSymmKpath method) (MITMDVaspInputSet method) (MPNonSCFVaspInputSet method) (MPStaticVaspInputSet method) get_lattice_type() (SymmetryFinder method) get_linear_interpolated_value() (in module pymatgen.util.coord_utils) get_lines_voronoi() (in module pymatgen.electronic_structure.plotter) get_lll_reduced_lattice() (Lattice method)

get_max_instability() (InsertionElectrode method) get_max_muO2() (InsertionElectrode method) get_min_instability() (InsertionElectrode method) get_min_muO2() (InsertionElectrode method) get_minimax_rms_anonymous() (StructureMatcher method) get_minkowski_red() (in module pymatgen.command_line.aconvasp_caller) get_most_compact_basis_on_lattice() (Lattice method) get_neighbors() (IMolecule method) (IStructure method) get_neighbors_in_shell() (IMolecule method) (IStructure method) get_next_index() (EwaldMinimizer method) get_niggli_reduced_lattice() (Lattice method) get_num_division_kpoints() (in module pymatgen.command_line.aconvasp_caller) get_occupation() (Procar method) get_oxi_state_decorated_structure() (BVAnalyzer method) get_percentage_bond_dist_changes() (RelaxationAnalyzer method) get_percentage_lattice_parameter_changes() (RelaxationAnalyzer method) get_percentage_volume_change() (RelaxationAnalyzer method) get_plot() (BSPlotter method) (DosPlotter method) (VoltageProfilePlotter method) get_plot_data() (VoltageProfilePlotter method) get_point_group() (in module pymatgen.symmetry.finder) (SymmetryFinder method) get_points_in_sphere_pbc() (in module pymatgen.util.coord_utils) get_poscar() (AbstractVaspInputSet method) get_potcar() (AbstractVaspInputSet method) (DictVaspInputSet method) get_potcar_dir() (in module pymatgen.io.vaspio.vasp_input) get_potcar_symbols() (AbstractVaspInputSet method) (DictVaspInputSet method) get_prim_struct() (in module pymatgen.command_line.aconvasp_caller) get_primitive_standard_structure() (SymmetryFinder method) get_primitive_structure() (IStructure method) get_projected_plots_dots() (BSPlotterProjected method) get_projection_on_elements() (BandStructure method) get_projections_on_elts_and_orbitals() (BandStructure method) get_publication_quality_plot() (in module pymatgen.util.plotting_utils) get_reconstructed_band_structure() (in module pymatgen.electronic_structure.bandstructure) get_reduced_composition_and_factor() (Composition method) get_reduced_formula_and_factor() (Composition method) get_reduced_structure() (IStructure method) get_refined_structure() (SymmetryFinder method) get_results() (BaseWorkflow method) (DeltaTest method) (PseudoConvergence method) (PseudoIterativeConvergence method) get_rms_dist() (StructureMatcher method) get_script_str() (ScriptEditor method) get_site_dos() (CompleteDos method) get_site_orbital_dos() (CompleteDos method) get_site_t2g_eg_resolved_dos() (CompleteDos method) get_sitej() (VoronoiConnectivity method) get_sites_in_sphere() (IMolecule method) (IStructure method) get_smeared_densities() (Dos method) get_sorted_structure() (IStructure method) get_spacegroup() (SymmetryFinder method) get_spacegroup_number() (SymmetryFinder method) get_spacegroup_symbol() (SymmetryFinder method) get_spd_dos() (CompleteDos method) get_specific_energy() (AbstractElectrode method) get_stable_entries() (InsertionElectrode method) get_status() (Workflow method) get_string() (FeffAtoms method) (FeffTags method) (Incar method) (InputWriter method) (Poscar method) get_structure() (AseAtomsAdaptor static method) (GSR_Reader method) (MPStaticVaspInputSet static method) get_structure_hash() (AbstractComparator method) (ElementComparator method) (FrameworkComparator method) (SpeciesComparator method) get_structures() (CifParser method) get_sub_electrodes() (ConversionElectrode method) (InsertionElectrode method) get_summary_dict() (ConversionElectrode method) get_symmetrized_structure() (SymmetryFinder method) get_symmetry_dataset() (SymmetryFinder method) get_symmetry_operations() (SymmetryFinder method) get_ticks() (BSPlotter method) get_transformed_structures() (StandardTransmuter method) get_transition_chempots() (PDAnalyzer method) get_unstable_entries() (InsertionElectrode method) get_valences() (BVAnalyzer method) get_valid_paths() (AbstractDrone method) (GaussianToComputedEntryDrone method) (VaspToComputedEntryDrone method) get_value() (NetcdfReader method) get_values() (NetcdfReader method) get_variable() (NetcdfReader method) get_variables() (NetcdfReader method) get_varnames() (NetcdfReader method) get_vasp_input() (TransformedStructure method) get_vasp_kpoint_file_sym() (in module pymatgen.command_line.aconvasp_caller) get_vbm() (BandStructureSymmLine method) get_voronoi_polyhedra() (VoronoiCoordFinder method) get_wigner_seitz_cell() (Lattice method) get_wt_fraction() (Composition method) get_zmatrix() (GaussianInput method) GGA_FHI_PPTABLE (PseudoDatabase attribute) GGA_HGHK_PPTABLE (PseudoDatabase attribute) GrandPotentialPhaseDiagram (class in pymatgen.phasediagram.pdmaker) GrandPotPDEntry (class in pymatgen.phasediagram.entries) group (Element attribute) group_by_types() (SiteCollection method) group_entries_by_structure() (in module pymatgen.entries.entry_tools) group_structures() (StructureMatcher method) GSR_Reader (class in pymatgen.io.abinitio.netcdf) GW_Workflow (class in pymatgen.io.abinitio.workflow) gwcalctyp (SelfEnergy attribute)

H

Ha2eV() (in module pymatgen.core.physical_constants) Ha2meV() (in module pymatgen.core.physical_constants) Ha_eV (in module pymatgen.core.physical_constants) has_dojo_report (Pseudo attribute) has_hilbert_transform (Screening attribute) has_hints (Pseudo attribute) has_ppmodel (SelfEnergy attribute) has_wmesh (Screening attribute) Header (class in pymatgen.io.feffio) header_string_from_file() (Header static method)

hex() (HighSymmKpath method) hexagonal() (Lattice static method) HighSymmKpath (class in pymatgen.symmetry.bandstructure) HilbertTransform (class in pymatgen.io.abinitio.abiobjects) hint_for_accuracy() (Pseudo method) HintsMaster (class in pymatgen.io.abinitio.pseudo_dojo) history (TransformedStructure attribute) HistoryNode (class in pymatgen.matproj.snl) hubbards (Vasprun attribute)

I

IdentityTransformation (class in pymatgen.transformations.standard_transformations) idos (Vasprun attribute) IMolecule (class in pymatgen.core.structure) in_coord_list() (in module pymatgen.util.coord_utils) in_coord_list_pbc() (in module pymatgen.util.coord_utils) Incar (class in pymatgen.io.vaspio.vasp_input) incar (Vasprun attribute) initial_structure (Vasprun attribute) InputWriter (class in pymatgen.io.abinitio.strategies) 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) interpolate() (IStructure method) inv_matrix (Lattice attribute) inverse (AbstractTransformation attribute) (AutoOxiStateDecorationTransformation attribute) (ChargeBalanceTransformation attribute) (EnumerateStructureTransformation attribute) (IdentityTransformation attribute) (InsertSitesTransformation 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) (SubstitutionPredictorTransformation attribute) (SubstitutionTransformation attribute) (SuperTransformation attribute) (SupercellTransformation attribute) (SymmOp attribute) (TranslateSitesTransformation attribute) inversion() (SymmOp static method) ionic_radii (Element attribute) ionic_radius (Specie attribute) ionic_steps (Vasprun attribute) IONMOV_DEFAULT (RelaxationMethod attribute) is_actinoid (Element attribute) is_alkali (Element attribute) is_alkaline (Element attribute) is_bonded() (CovalentBond static method) is_element (Composition attribute) (GrandPotPDEntry attribute) (PDEntry attribute) is_halogen (Element attribute)

is_homogeneous (KSampling attribute) is_hubbard (Vasprun attribute) is_lanthanoid (Element attribute) is_metal() (BandStructureSymmLine method) is_metalloid (Element attribute) is_noble_gas (Element attribute) is_one_to_many (AbstractTransformation attribute) (AutoOxiStateDecorationTransformation attribute) (ChargeBalanceTransformation attribute) (EnumerateStructureTransformation attribute) (IdentityTransformation attribute) (InsertSitesTransformation 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) (SubstitutionPredictorTransformation attribute) (SubstitutionTransformation attribute) (SuperTransformation attribute) (SupercellTransformation attribute) (TranslateSitesTransformation attribute) is_ordered (Site attribute) (SiteCollection attribute) is_pcm (GaussianOutput attribute) is_periodic_image() (PeriodicSite method) is_rare_earth_metal (Element attribute) is_spin (Vasprun attribute) is_spin_polarized (BandStructure attribute) is_stopped (Outcar attribute) is_super_electrode() (ConversionElectrode method) is_transition_metal (Element attribute) is_valid() (SiteCollection method) is_valid_bibtex() (in module pymatgen.matproj.snl) iscritical (Bug attribute) (Error attribute) (Warning attribute) iscritical() (Event method) isnc (Pseudo attribute) (Strategy attribute) (Workflow attribute) isncfile (File attribute) ispaw (Pseudo attribute) (Strategy attribute) (Workflow attribute) IStructure (class in pymatgen.core.structure) IterativeWork (class in pymatgen.io.abinitio.workflow) iterator_from_slice() (in module pymatgen.util.num_utils)

J

json_dump() (WorkFlowResults method) json_load() (in module pymatgen.serializers.json_coders) (pymatgen.io.abinitio.workflow.WorkFlowResults class method)

json_pretty_dump() (in module pymatgen.serializers.json_coders)

K

keyPressEvent() (StructureInteractorStyle static method) keywords (PotcarSingle attribute) kpath (HighSymmKpath attribute) Kpoint (class in pymatgen.electronic_structure.bandstructure)

kpoints (BandStructure attribute) Kpoints (class in pymatgen.io.vaspio.vasp_input) kpoints (Vasprun attribute) KSampling (class in pymatgen.io.abinitio.abiobjects)

L

l_local (Pseudo attribute) l_max (Pseudo attribute) label (Kpoint attribute) latexify() (in module pymatgen.util.string_utils) latexify_spacegroup() (in module pymatgen.util.string_utils) lattice (BandStructure attribute) Lattice (class in pymatgen.core.lattice) lattice (IStructure attribute) (Kpoint attribute) (PeriodicSite attribute) lattice_vectors() (IStructure method) launch() (ShellLauncher method) LDA_HGH_PPTABLE (PseudoDatabase attribute) learn() (Strategy method) leftButtonPressEvent() (StructureInteractorStyle static method) leftButtonReleaseEvent() (StructureInteractorStyle static method)

length (CovalentBond attribute) lengths_and_angles (Lattice attribute) linear_add() (VolumetricData method) LinearAssignment (class in pymatgen.optimization.linear_assignment) liquid_range (Element attribute) list_strings() (in module pymatgen.util.string_utils) load_data() (BorgQueen method) load_module() (ScriptEditor method) load_modules() (ScriptEditor method) localopt() (BabelMolAdaptor method) Locpot (class in pymatgen.io.vaspio.vasp_output) logged() (in module pymatgen.util.decorators) lowest_energy_structure (OrderDisorderedStructureTransformation attribute)

M

magnetization (Outcar attribute) mAh (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) main() (in module pymatgen.io.abinitio.ppdojo) make_dir() (File method) make_input() (NscfStrategy method) (RelaxStrategy method) (ScfStrategy method) (ScreeningStrategy method) (SelfEnergyStrategy method) (Strategy method) make_movie() (in module pymatgen.vis.structure_vtk) make_report() (DeltaFactorMaster method) (DojoMaster method) (HintsMaster method) make_rsmheader() (ShellLauncher method) make_supercell() (Structure method) map_method() (in module pymatgen.io.abinitio.workflow) mass_charge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) mass_discharge (AbstractVoltagePair attribute) (ConversionVoltagePair attribute) (InsertionVoltagePair attribute) material_formula (Xmu attribute) MaterialsProjectCompatibility (class in pymatgen.entries.compatibility) MaterialsProjectFeffInputSet (class in pymatgen.io.feffio_set) matrix (Lattice attribute) max_connectivity (VoronoiConnectivity attribute) max_delta_volume (AbstractElectrode attribute) max_oxidation_state (Element attribute) max_voltage (AbstractElectrode attribute) max_voltage_step (AbstractElectrode attribute) mcl() (HighSymmKpath method) mclc1() (HighSymmKpath method) mclc2() (HighSymmKpath method) mclc3() (HighSymmKpath method) mclc4() (HighSymmKpath method) mclc5() (HighSymmKpath method) melting_point (Element attribute) mendeleev_no (Element attribute) merge() (Mrggkk method) merge_qpoints() (Mrgscr method) micro_pyawk() (in module pymatgen.util.io_utils) min_cost (LinearAssignment attribute) min_max_indexes() (in module pymatgen.util.num_utils) min_oxidation_state (Element attribute) min_voltage (AbstractElectrode attribute) mineral_hardness (Element attribute)

minimize_matrix() (EwaldMinimizer method) minimized_sum (EwaldMinimizer attribute) MITCompatibility (class in pymatgen.entries.compatibility) MITGGAVaspInputSet (class in pymatgen.io.vaspio_set) MITHSEVaspInputSet (class in pymatgen.io.vaspio_set) MITMDVaspInputSet (class in pymatgen.io.vaspio_set) MITVaspInputSet (class in pymatgen.io.vaspio_set) mode (Smearing attribute) ModelDielectricFunction (class in pymatgen.io.abinitio.abiobjects) modes (KSampling attribute) (PPModel attribute) modified_structure (StructureModifier attribute) modify_lattice() (Structure method) molar_volume (Element attribute) Molecule (class in pymatgen.core.structure) molecule (GaussianInput attribute) (XYZ attribute) monkhorst() (pymatgen.io.abinitio.abiobjects.KSampling class method) monkhorst_automatic() (Kpoints static method) (pymatgen.io.abinitio.abiobjects.KSampling class method) monoclinic() (Lattice static method) monotonic() (in module pymatgen.io.abinitio.workflow) mouseMoveEvent() (StructureInteractorStyle static method) move() (Workflow method) move_atoms (RelaxationMethod attribute) move_cell (RelaxationMethod attribute) MPGGAVaspInputSet (class in pymatgen.io.vaspio_set) MPNonSCFVaspInputSet (class in pymatgen.io.vaspio_set) MPRester (class in pymatgen.matproj.rest) MPRestError MPStaticVaspInputSet (class in pymatgen.io.vaspio_set) MPVaspInputSet (class in pymatgen.io.vaspio_set) Mrggkk (class in pymatgen.io.abinitio.wrappers) Mrggkk.MrggkkError Mrgscr (class in pymatgen.io.abinitio.wrappers) Mrgscr.MrgscrError MSONable (class in pymatgen.serializers.json_coders) MultipleSubstitutionTransformation (class in pymatgen.transformations.advanced_transformations) Murnaghan() (EOS static method)

N

name (Author attribute) (Element attribute) (Event attribute) (HistoryNode attribute) (PDEntry attribute) (Pseudo attribute) natoms (Poscar attribute) nb_bands (BandStructure attribute) nc_pseudos() (PseudoDatabase method) nc_tables() (PseudoDatabase method) ncpus_reserved (BaseWorkflow attribute) need_forces (Strategy attribute) need_stress (Strategy attribute) nelectrons (IMolecule attribute) NetcdfReader (class in pymatgen.io.abinitio.netcdf) new_event_parser() (EventParser static method) next_task() (IterativeWork method) ngridpts (VolumetricData attribute) non_decreasing() (in module pymatgen.io.abinitio.workflow) non_increasing() (in module pymatgen.io.abinitio.workflow) noppmodel() (pymatgen.io.abinitio.abiobjects.PPModel class method) normalization_mass (AbstractElectrode attribute) normalization_volume (AbstractElectrode attribute)

normalize_to() (Reaction method) normalize_to_element() (Reaction method) normalized_repr (Reaction attribute) normalized_repr_and_factor() (Reaction method) nosmearing() (Smearing static method) NscfStrategy (class in pymatgen.io.abinitio.strategies) nspden (Electrons attribute) nspinor (Electrons attribute) nsppol (Electrons attribute) ntypesp (SiteCollection attribute) NullFile (class in pymatgen.io.abinitio.utils) NullStream (class in pymatgen.io.abinitio.utils) num_atoms (Composition attribute) num_basis_func (GaussianOutput attribute) num_sites (SiteCollection attribute) num_steps (AbstractElectrode attribute) number (Element attribute) numerical_tol (PDAnalyzer attribute)

O

openbabel_mol (BabelMolAdaptor attribute) operate() (SymmOp method) OPTCELL_DEFAULT (RelaxationMethod attribute) optdriver (Strategy attribute) Orbital (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_assimilation() (in module pymatgen.apps.borg.queen) OrderDisorderedStructureTransformation (class in pymatgen.transformations.standard_transformations)

original_entry (GrandPotPDEntry attribute) (TransformedPDEntry attribute) original_structure (StructureModifier attribute) orthongonalize_structure() (StructureVis method) orthorhombic() (Lattice static method) Oszicar (class in pymatgen.io.vaspio.vasp_output) other_parameters (TransformedStructure attribute) Outcar (class in pymatgen.io.vaspio.vasp_output) output_lists (EwaldMinimizer attribute) oxi_state (DummySpecie attribute) (Specie attribute) oxidation_states (Element attribute) OxidationStateDecorationTransformation (class in pymatgen.transformations.standard_transformations) OxidationStateRemovalTransformation (class in pymatgen.transformations.standard_transformations)

P

parallel_assimilate() (BorgQueen method) parameters (Vasprun attribute) parse() (EventParser static method) parse_author() (Author static method) parse_coords() (GaussianInput static method) parse_file() (VolumetricData static method) parse_from_incar() (in module pymatgen.io.vaspio.vasp_output) parse_history_node() (HistoryNode static method) parse_parameters() (in module pymatgen.io.vaspio.vasp_output) parse_symmetry_operations() (in module pymatgen.io.cifio) parse_v_parameters() (in module pymatgen.io.vaspio.vasp_output) PartialRemoveSitesTransformation (class in pymatgen.transformations.site_transformations) PartialRemoveSpecieTransformation (class in pymatgen.transformations.standard_transformations) path (PseudoDatabase attribute) path_from_structure() (pymatgen.io.abinitio.abiobjects.KSampling class method) path_in_workdir() (Workflow method) paw_tables() (PseudoDatabase method) pawecutdg (Strategy attribute) pbc_all_distances() (in module pymatgen.util.coord_utils) pbc_diff() (in module pymatgen.util.coord_utils) pbc_shortest_vectors() (in module pymatgen.util.coord_utils) pcm (GaussianOutput attribute) pd_plot_data (PDPlotter attribute) PDAnalyzer (class in pymatgen.phasediagram.pdanalyzer) PDEntry (class in pymatgen.phasediagram.entries) PDEntryIO (class in pymatgen.phasediagram.entries) pdos (CompleteDos attribute) (Vasprun attribute) PDPlotter (class in pymatgen.phasediagram.plotter) PeriodicSite (class in pymatgen.core.sites) perturb() (Molecule method) (Structure method) PerturbStructureTransformation (class in pymatgen.transformations.standard_transformations) PhaseDiagram (class in pymatgen.phasediagram.pdmaker) PhaseDiagramError plot_brillouin() (BSPlotter method) plot_chempot_range_map() (PDPlotter method) plot_compare() (BSPlotter method) plot_etotal() (in module pymatgen.io.abinitio.workflow) PMGJSONDecoder (class in pymatgen.serializers.json_coders) PMGJSONEncoder (class in pymatgen.serializers.json_coders) point_energy (EwaldSummation attribute) point_energy_matrix (EwaldSummation attribute) PointGroup (class in pymatgen.symmetry.pointgroup) PointGroupAnalyzer() (in module pymatgen.symmetry.pointgroup) poissons_ratio (Element attribute) poll() (BaseWorkflow method) Poscar (class in pymatgen.io.vaspio.vasp_input) PoscarTransmuter (class in pymatgen.alchemy.transmuters) position_atol (Site attribute) pot_dict (FeffAtoms attribute) (FeffPot attribute) pot_dict_from_string() (FeffPot static method) pot_string_from_file() (FeffPot static method) Potcar (class in pymatgen.io.vaspio.vasp_input) potcar_symbols (Vasprun attribute) PotcarSingle (class in pymatgen.io.vaspio.vasp_input) Pourier_Tarantola() (EOS static method) PPConvergenceFactory (class in pymatgen.io.abinitio.calculations) PPModel (class in pymatgen.io.abinitio.abiobjects) pprint_table() (in module pymatgen.util.string_utils) pred_from_comp() (Substitutor method) pred_from_list() (Substitutor method) pred_from_structures() (Substitutor method) predictor_corrector (Poscar attribute) PrimitiveCellTransformation (class in pymatgen.transformations.standard_transformations) print_tree() (NetcdfReader method) proc_val() (FeffTags static method) (Incar static method) Procar (class in pymatgen.io.vaspio.vasp_output) process_decoded() (PMGJSONDecoder method) process_entries() (Compatibility method) (EntryPostProcessor method) process_entry() (Compatibility method) (EntryPostProcessor method) processes (BaseWorkflow attribute) (Workflow attribute) produces_exts() (WorkLink method) Product (class in pymatgen.io.abinitio.workflow) products (Reaction attribute) (WorkLink attribute) projected_eigenvalues (Vasprun attribute) properly_terminated (GaussianOutput attribute) properties (Site attribute) Pseudo (class in pymatgen.io.abinitio.pseudos) PseudoConvergence (class in pymatgen.io.abinitio.workflow) PseudoDatabase (class in pymatgen.io.abinitio.pseudos) PseudoIterativeConvergence (class in pymatgen.io.abinitio.workflow) PSP_TYPES (PseudoDatabase attribute) push_exceptions() (WorkFlowResults method) px (Orbital attribute) py (Orbital attribute) pybel_mol (BabelMolAdaptor attribute) pymatgen.__init__ (module) pymatgen.alchemy (module) pymatgen.alchemy.filters (module) pymatgen.alchemy.materials (module) pymatgen.alchemy.transmuters (module) pymatgen.analysis (module) pymatgen.analysis.bond_valence (module) pymatgen.analysis.diffusion_analyzer (module) pymatgen.analysis.ewald (module) pymatgen.analysis.reaction_calculator (module) pymatgen.analysis.structure_analyzer (module) pymatgen.analysis.structure_matcher (module) pymatgen.analysis.thermochemistry (module) pymatgen.apps (module) pymatgen.apps.battery (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.command_line (module) pymatgen.command_line.aconvasp_caller (module) pymatgen.command_line.bader_caller (module) pymatgen.command_line.enumlib_caller (module) pymatgen.core (module) pymatgen.core.bonds (module) pymatgen.core.composition (module) pymatgen.core.design_patterns (module) pymatgen.core.lattice (module) pymatgen.core.operations (module) pymatgen.core.periodic_table (module) pymatgen.core.physical_constants (module) pymatgen.core.sites (module) pymatgen.core.structure (module) pymatgen.core.structure_modifier (module) pymatgen.core.units (module) pymatgen.electronic_structure (module) pymatgen.electronic_structure.bandstructure (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.io (module) pymatgen.io.abinitio (module) pymatgen.io.abinitio.abiobjects (module) pymatgen.io.abinitio.calculations (module) pymatgen.io.abinitio.deltafactor.calcDelta (module) pymatgen.io.abinitio.deltafactor.dataset (module) pymatgen.io.abinitio.deltafactor.eosfit (module) pymatgen.io.abinitio.deltaworks (module) pymatgen.io.abinitio.eos (module) pymatgen.io.abinitio.events (module) pymatgen.io.abinitio.launcher (module) pymatgen.io.abinitio.netcdf (module) pymatgen.io.abinitio.ppdojo (module) pymatgen.io.abinitio.pseudo_dojo (module) pymatgen.io.abinitio.pseudos (module) pymatgen.io.abinitio.strategies (module) pymatgen.io.abinitio.task (module) pymatgen.io.abinitio.utils (module) pymatgen.io.abinitio.workflow (module) pymatgen.io.abinitio.wrappers (module) pymatgen.io.aseio (module) pymatgen.io.babelio (module) pymatgen.io.cifio (module) pymatgen.io.cssrio (module) pymatgen.io.feffio (module) pymatgen.io.feffio_set (module) pymatgen.io.gaussianio (module) pymatgen.io.smartio (module) pymatgen.io.vaspio (module) pymatgen.io.vaspio.vasp_input (module) pymatgen.io.vaspio.vasp_output (module) pymatgen.io.vaspio_set (module) pymatgen.io.xyzio (module) pymatgen.matproj (module) pymatgen.matproj.rest (module) pymatgen.matproj.snl (module) pymatgen.optimization.linear_assignment (module) pymatgen.phasediagram (module) pymatgen.phasediagram.entries (module) pymatgen.phasediagram.pdanalyzer (module) pymatgen.phasediagram.pdmaker (module) pymatgen.phasediagram.plotter (module) pymatgen.serializers (module) pymatgen.serializers.json_coders (module) pymatgen.structure_prediction.substitution_probability (module) pymatgen.structure_prediction.substitutor (module) pymatgen.symmetry (module) pymatgen.symmetry.bandstructure (module) pymatgen.symmetry.finder (module) pymatgen.symmetry.pointgroup (module) pymatgen.symmetry.spacegroup (module) pymatgen.symmetry.structure (module) pymatgen.transformations (module) pymatgen.transformations.advanced_transformations (module) pymatgen.transformations.site_transformations (module) pymatgen.transformations.standard_transformations (module) pymatgen.transformations.transformation_abc (module) pymatgen.util (module) pymatgen.util.coord_utils (module) pymatgen.util.decorators (module) pymatgen.util.io_utils (module) pymatgen.util.num_utils (module) pymatgen.util.plotting_utils (module) pymatgen.util.string_utils (module) pymatgen.util.testing (module) pymatgen.vis (module) pymatgen.vis.structure_vtk (module) pymatgen_mol (BabelMolAdaptor attribute) PymatgenTest (class in pymatgen.util.testing) pz (Orbital attribute)

Q

qvertex_target() (in module pymatgen.electronic_structure.plotter)

R

ranked_compositions_from_indeterminate_formula() (Composition static method) reactants (Reaction attribute) Reaction (class in pymatgen.analysis.reaction_calculator) ReactionError read() (File method) read_data_from_filename() (in module pymatgen.io.abinitio.deltafactor.dataset) read_dojo_report() (Pseudo method) read_etotal() (Workflow method) read_igpar() (Outcar method) read_lcalcpol() (Outcar method) read_lepsilon() (Outcar method) read_mol() (in module pymatgen.io.smartio) read_structure() (in module pymatgen.io.smartio) readlines() (File method) real_space_energy (EwaldSummation attribute) real_space_energy_matrix (EwaldSummation attribute) reciprocal_lattice (Lattice attribute) reciprocal_space_energy (EwaldSummation attribute) reciprocal_space_energy_matrix (EwaldSummation attribute) Record (class in pymatgen.io.abinitio.deltafactor.dataset) redo_next_change() (StandardTransmuter method) (TransformedStructure method) redraw() (StructureVis method) reduce_formula() (in module pymatgen.core.composition) reduced_composition (Composition attribute) reduced_formula (Composition attribute) reflection() (SymmOp static method) reflectivity (Element attribute) refractive_index (Element attribute) register_task() (Workflow method) Relaxation (class in pymatgen.io.abinitio.workflow) RelaxationAnalyzer (class in pymatgen.analysis.structure_analyzer) RelaxationMethod (class in pymatgen.io.abinitio.abiobjects) RelaxStrategy (class in pymatgen.io.abinitio.strategies)

release() (FileLock method) remove() (Molecule method) (Structure method) remove_dojo_report() (Pseudo method) remove_oxidation_states() (Structure method) remove_sites() (Molecule method) (Structure method) remove_species() (Molecule method) (Structure method) RemoveDuplicatesFilter (class in pymatgen.alchemy.filters) RemoveSitesTransformation (class in pymatgen.transformations.site_transformations) RemoveSpeciesTransformation (class in pymatgen.transformations.standard_transformations) replace() (Molecule method) (Structure method) replace_species() (Molecule method) (Structure method) ReplaceSiteSpeciesTransformation (class in pymatgen.transformations.site_transformations) repr_dojo_levels() (in module pymatgen.io.abinitio.pseudo_dojo) requires (class in pymatgen.util.decorators) requires_hubbard() (Compatibility method) reset() (ScriptEditor method) returncodes (BaseWorkflow attribute) reverse_readline() (in module pymatgen.util.io_utils) rhl1() (HighSymmKpath method) rhl2() (HighSymmKpath method) rhombohedral() (Lattice static method) rigidity_modulus (Element attribute) rmtree() (Workflow method) rotate_view() (StructureVis method) rotation_matrix (SymmOp attribute) RotationTransformation (class in pymatgen.transformations.standard_transformations) rotoreflection() (SymmOp static method) row (Element attribute) run_aconvasp_command() (in module pymatgen.command_line.aconvasp_caller) run_stats (Outcar attribute) run_type (Vasprun attribute) runlevel (NscfStrategy attribute) (RelaxStrategy attribute) (ScfStrategy attribute) (ScreeningStrategy attribute) (SelfEnergyStrategy attribute) (Strategy attribute) rxn (ConversionVoltagePair attribute)

S

s (Orbital attribute) save() (PseudoDatabase method) (VoltageProfilePlotter method) save_data() (BorgQueen method) save_plot() (BSPlotter method) (DosPlotter method) scale() (Lattice method) ScfStrategy (class in pymatgen.io.abinitio.strategies) sch_symbol (in module pymatgen.symmetry.pointgroup) (PointGroup attribute) Screening (class in pymatgen.io.abinitio.abiobjects) ScreeningStrategy (class in pymatgen.io.abinitio.strategies) ScriptEditor (class in pymatgen.io.abinitio.launcher) scross_section (Xmu attribute) select() (EventList method) select_pseudos() (in module pymatgen.io.abinitio.strategies) selective_dynamics (Poscar attribute) SelfEnergy (class in pymatgen.io.abinitio.abiobjects) SelfEnergyStrategy (class in pymatgen.io.abinitio.strategies) serial_assimilate() (BorgQueen method) set_accuracy() (Strategy method) set_charge_and_spin() (Molecule method) set_parameter() (StandardTransmuter method) (TransformedStructure method) set_structure() (StructureVis method) set_symbols() (Potcar method) set_temperature() (Poscar method) setup() (BaseWorkflow method) (Workflow method) shebang() (ScriptEditor method) shell (ScriptEditor attribute) ShellLauncher (class in pymatgen.io.abinitio.launcher) show() (BSPlotter method) (DosPlotter method) (PDPlotter method) (StructureVis method) (VoltageProfilePlotter method) SimpleVaspToComputedEntryDrone (class in pymatgen.apps.borg.hive) singleton() (in module pymatgen.io.abinitio.deltafactor.dataset) (in module pymatgen.util.decorators) Site (class in pymatgen.core.sites) site_properties (SiteCollection attribute) site_symbols (FeffAtoms attribute) (FeffPot attribute) (Header attribute) (Poscar attribute) SiteCollection (class in pymatgen.core.structure) sites (IMolecule attribute) (IStructure attribute) (SiteCollection attribute) smart_element_or_specie() (in module pymatgen.core.periodic_table) smart_float_gcd() (in module pymatgen.analysis.reaction_calculator) Smearing (class in pymatgen.io.abinitio.abiobjects) solid_angle() (in module pymatgen.analysis.structure_analyzer) sort_dict() (in module pymatgen.util.num_utils) source (Header attribute) (Xmu attribute) space_group (Header attribute) space_number (Header attribute) Spacegroup (class in pymatgen.symmetry.spacegroup) special_formulas (Composition attribute) Specie (class in pymatgen.core.periodic_table) specie (Site attribute) 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)

Spin (class in pymatgen.electronic_structure.core) spin_data (VolumetricData attribute) spin_mult (GaussianOutput attribute) spin_multiplicity (IMolecule attribute) SpinMode (class in pymatgen.io.abinitio.abiobjects) stable_entries (PhaseDiagram attribute) StandardTransmuter (class in pymatgen.alchemy.transmuters) start() (Workflow method) start_training() (DojoMaster method) startElement() (VasprunHandler method) stationary_type (GaussianOutput attribute) status (WorkLink attribute) str_aligned() (in module pymatgen.util.string_utils) str_delimited() (in module pymatgen.util.string_utils) Strategy (class in pymatgen.io.abinitio.strategies) strategy_with_ecut() (PseudoIterativeConvergence method) stream_has_colours() (in module pymatgen.util.string_utils) strictly_decreasing() (in module pymatgen.io.abinitio.workflow) strictly_increasing() (in module pymatgen.io.abinitio.workflow) StringColorizer (class in pymatgen.util.string_utils) struct (FeffAtoms attribute) (FeffPot attribute) (Header attribute) Structure (class in pymatgen.core.structure) structure (CompleteDos attribute) (HighSymmKpath attribute) (Poscar attribute) (VolumetricData attribute) structure_from_etsf_file() (in module pymatgen.io.abinitio.netcdf) structure_symmetry (Header attribute) StructureError StructureInteractorStyle (class in pymatgen.vis.structure_vtk) StructureMatcher (class in pymatgen.analysis.structure_matcher) StructureModifier (class in pymatgen.core.structure_modifier) StructureNL (class in pymatgen.matproj.snl) structures (GaussianOutput attribute) (TransformedStructure attribute) (Vasprun attribute) (in module pymatgen.command_line.enumlib_caller) StructureVis (class in pymatgen.vis.structure_vtk) subclass_from_dojo_level() (DojoMaster static method) submit_tasks() (IterativeWork method) (Workflow method) substitute() (Molecule method) SubstitutionPredictorTransformation (class in pymatgen.transformations.advanced_transformations) SubstitutionProbability (class in pymatgen.structure_prediction.substitution_probability) SubstitutionTransformation (class in pymatgen.transformations.standard_transformations) Substitutor (class in pymatgen.structure_prediction.substitutor) summary (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_properties (Site attribute) (Vasprun attribute) symbol (DummySpecie attribute) (Element attribute) (Pseudo attribute) symbol_from_Z() (in module pymatgen.core.periodic_table) symbols (Potcar attribute) SymmetrizedStructure (class in pymatgen.symmetry.structure) SymmetryFinder (class in pymatgen.symmetry.finder) SymmOp (class in pymatgen.core.operations) symsigma (SelfEnergy attribute)

T

table() (PseudoDatabase method) task_factory() (in module pymatgen.io.abinitio.task) tdos (Vasprun attribute) temperature (Poscar attribute) test() (AbstractStructureFilter method) (ChargeBalanceFilter method) (ContainsSpecieFilter method) (RemoveDuplicatesFilter method) (SpecieProximityFilter method) tet() (HighSymmKpath method) tet_coord() (in module pymatgen.phasediagram.plotter) tetragonal() (Lattice static method) thermal_conductivity (Element attribute) ThermoData (class in pymatgen.analysis.thermochemistry) to_abivars() (AbiStructure method) (AbivarAble method) (CDFrequencyMesh method) (Constraints method) (Electrons method) (ElectronsAlgorithm method) (HilbertTransform method) (InputWriter method) (KSampling method) (ModelDielectricFunction method) (PPModel method) (RelaxationMethod method) (Screening method) (SelfEnergy method) (Smearing method) (SpinMode method) to_csv() (PDEntryIO static method) to_data_dict (Composition attribute) to_dict (AbstractComparator attribute) (Author attribute) (AutoOxiStateDecorationTransformation attribute) (BalancedReaction attribute) (BandStructureSymmLine attribute) (ChargeBalanceFilter attribute) (ChargeBalanceTransformation attribute) (CifParser attribute) (CompleteDos attribute) (Composition attribute) (ComputedEntry attribute) (ComputedReaction attribute) (ComputedStructureEntry attribute) (ContainsSpecieFilter attribute) (ConversionElectrode attribute) (ConversionVoltagePair attribute) (DictVaspInputSet attribute) (DiffusionAnalyzer attribute) (Dos attribute) (EnumerateStructureTransformation attribute) (Event attribute) (EventList attribute) (ExpEntry attribute) (FeffAtoms attribute) (FeffLdos attribute) (FeffPot attribute) (FeffTags attribute) (GaussianOutput attribute) (GaussianToComputedEntryDrone attribute) (GrandPotPDEntry attribute) (Header attribute) (HistoryNode attribute) (IMolecule attribute) (IStructure attribute) (IdentityTransformation attribute) (Incar attribute) (InsertSitesTransformation attribute) (InsertionElectrode attribute) (Kpoint attribute) (Kpoints attribute) (Lattice attribute) (MITGGAVaspInputSet attribute) (MITHSEVaspInputSet attribute) (MITMDVaspInputSet attribute) (MITVaspInputSet attribute) (MPGGAVaspInputSet attribute) (MPVaspInputSet attribute) (MSONable attribute) (MultipleSubstitutionTransformation attribute) (OrderDisorderedStructureTransformation attribute) (Oszicar attribute) (Outcar attribute) (OxidationStateDecorationTransformation attribute) (OxidationStateRemovalTransformation attribute) (PDEntry attribute) (PPModel attribute) (PartialRemoveSitesTransformation attribute) (PartialRemoveSpecieTransformation attribute) (PeriodicSite attribute) (PerturbStructureTransformation attribute) (Poscar attribute) (Potcar attribute) (PrimitiveCellTransformation attribute) (Reaction attribute) (RemoveDuplicatesFilter attribute) (RemoveSitesTransformation attribute) (RemoveSpeciesTransformation attribute) (ReplaceSiteSpeciesTransformation attribute) (RotationTransformation attribute) (SimpleVaspToComputedEntryDrone attribute) (Site attribute) (Smearing attribute) (SpecieProximityFilter attribute) (StructureMatcher attribute) (StructureNL attribute) (SubstitutionPredictorTransformation attribute) (SubstitutionTransformation attribute) (Substitutor attribute) (SuperTransformation attribute) (SupercellTransformation attribute) (SymmOp attribute) (ThermoData attribute) (TransformedPDEntry attribute) (TransformedStructure attribute) (TranslateSitesTransformation attribute) (VaspInput attribute) (VaspInputSet attribute) (VaspToComputedEntryDrone attribute) (Vasprun attribute) (WorkFlowResults attribute) (Workflow attribute) (Xmu attribute) to_dict() (AbstractFeffInputSet method) to_dict_summary() (InsertionElectrode method) to_json (MSONable attribute) to_reduced_dict (Composition attribute)

to_unit_cell (PeriodicSite attribute) TOLERANCE (Reaction attribute) tolerance (Strategy attribute) total_energy (EwaldSummation attribute) total_energy_matrix (EwaldSummation attribute) transform_entries() (CompoundPhaseDiagram method) transformations (TransformedStructure attribute) TransformedPDEntry (class in pymatgen.phasediagram.entries) TransformedStructure (class in pymatgen.alchemy.materials) translate_sites() (Molecule method) (Structure method) TranslateSitesTransformation (class in pymatgen.transformations.site_transformations) translation_vector (SymmOp attribute) tria() (HighSymmKpath method) triangular_coord() (in module pymatgen.phasediagram.plotter) trib() (HighSymmKpath method) true_names (Poscar attribute) types_of_specie (SiteCollection attribute)

U

uncorrected_energy (ComputedEntry attribute) undo_last_change() (StandardTransmuter method) (TransformedStructure method) uniquelines() (in module pymatgen.phasediagram.plotter) unstable_entries (PhaseDiagram attribute)

up (Spin attribute) url (HistoryNode attribute) use_multiprocessing (AbstractTransformation attribute)

V

van_der_waals_radius (Element attribute) VaspInput (class in pymatgen.io.vaspio.vasp_input) VaspInputSet (class in pymatgen.io.vaspio_set) VaspParserError Vasprun (class in pymatgen.io.vaspio.vasp_output) VasprunHandler (class in pymatgen.io.vaspio.vasp_output) VaspToComputedEntryDrone (class in pymatgen.apps.borg.hive) velocities (Poscar attribute) velocity_of_sound (Element attribute) vickers_hardness (Element attribute)

Vinet() (EOS static method) 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) VolumetricData (class in pymatgen.io.vaspio.vasp_output) VoronoiConnectivity (class in pymatgen.analysis.structure_analyzer) VoronoiCoordFinder (class in pymatgen.analysis.structure_analyzer)

W

wait() (BaseWorkflow method) walk_tree() (NetcdfReader method) Warning (class in pymatgen.io.abinitio.events) warnings (EventList attribute) was_modified (TransformedStructure attribute) weight (Composition attribute) which() (in module pymatgen.util.io_utils) work_for_pseudo() (DeltaFactory method) (PPConvergenceFactory method) Workflow (class in pymatgen.io.abinitio.workflow) WorkflowError WorkFlowResults (class in pymatgen.io.abinitio.workflow) 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)

WorkLink (class in pymatgen.io.abinitio.workflow) write() (File method) (NullStream method) write_dojo_report() (DojoMaster method) (Pseudo method) write_file() (BabelMolAdaptor method) (CifWriter method) (Cssr method) (FeffAtoms method) (FeffPot method) (FeffTags method) (GaussianInput method) (Header method) (Incar method) (Kpoints method) (Poscar method) (Potcar method) (VolumetricData method) (XYZ method) write_hash_table() (PseudoDatabase method) write_image() (PDPlotter method) (StructureVis method) write_input() (AbstractFeffInputSet method) (AbstractVaspInputSet method) (VaspInput method) write_mol() (in module pymatgen.io.smartio) write_structure() (in module pymatgen.io.smartio) write_to_json_file() (MSONable method) write_vasp_input() (StandardTransmuter method) (TransformedStructure method) writelines() (File method)

X

X (DummySpecie attribute) (Element attribute) x (Site attribute) XC_FAMILIES (PseudoDatabase attribute) XC_FLAVOR (PseudoDatabase attribute) xc_type (Pseudo attribute)

XC_TYPES (PseudoDatabase attribute) Xmu (class in pymatgen.io.feffio) XYZ (class in pymatgen.io.xyzio) xyz_patt (GaussianInput attribute)

Y

y (Site attribute)

youngs_modulus (Element attribute)

Z

Z (DummySpecie attribute) (Element attribute) (Pseudo attribute) z (Site attribute) Z_val (Pseudo attribute) zmat_patt (GaussianInput attribute)

zoom() (StructureVis method) zopen() (in module pymatgen.util.io_utils) zpath() (in module pymatgen.util.io_utils)