Index

A

a_centered_orthorhombic() (in module pydefect.tests.conftest) abs_charge (pydefect.analyzer.concentration.concentration.CarrierConcentration property) (pydefect.analyzer.concentration.concentration.Concentration property) (pydefect.analyzer.concentration.concentration.DefectConcentration property) acceptor_phs (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) add_atom_to_structure() (in module pydefect.input_maker.defect_entries_maker) add_degeneracy() (pydefect.analyzer.concentration.degeneracy.MakeDegeneracy method) add_interstitials_from_local_extrema() (in module pydefect.cli.main_util_functions) add_sub_parser() (in module pydefect.cli.main) additional_charge (pydefect.corrections.gkfo_correction.GkfoCorrection attribute) after_refine() (in module pydefect.tests.conftest) alignment_1st_term (pydefect.corrections.gkfo_correction.GkfoCorrection property) alignment_2nd_term (pydefect.corrections.gkfo_correction.GkfoCorrection property) alignment_3rd_term (pydefect.corrections.gkfo_correction.GkfoCorrection property) alignment_correction (pydefect.corrections.efnv_correction.ExtendedFnvCorrection property) all_element_set (pydefect.chem_pot_diag.chem_pot_diag.RelativeEnergies property) all_sorted_points (pydefect.analyzer.defect_energy.CrossPoints property) anchor_atom_coords (pydefect.input_maker.defect_entry.DefectEntry property) anchor_atom_idx (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) anchor_atom_index (pydefect.input_maker.defect_entry.DefectEntry property) angle (pydefect.analyzer.defect_structure_info.Displacement attribute) annotated_charge_positions (pydefect.analyzer.defect_energy.CrossPoints property) another (pydefect.analyzer.defect_structure_info.SymmRelation attribute) append_interstitial() (in module pydefect.input_maker.append_interstitial)

append_interstitial_to_supercell_info() (in module pydefect.cli.main_functions) append_sites_to_supercell_info() (pydefect.input_maker.local_extrema.VolumetricDataLocalExtrema method) as_dict() (pydefect.analyzer.concentration.degeneracy.Degeneracies method) atom_idx_at_center() (pydefect.util.structure_tools.Distances method) atom_io (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) (pydefect.analyzer.defect_energy.DefectEnergies attribute) (pydefect.analyzer.defect_energy.DefectEnergyInfo attribute) atom_mapping (pydefect.analyzer.defect_structure_comparator.DefectStructureComparator property) atomic_fractions() (in module pydefect.chem_pot_diag.chem_pot_diag) (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag method) atomic_site_potential() (pydefect.corrections.ewald.Ewald method) ave_charge_density (pydefect.analyzer.defect_charge_info.DefectChargeInfo attribute) ave_charge_density_dist() (in module pydefect.tests.analyzer.test_defect_charge_info) ave_chg_dens_distribution() (pydefect.analyzer.defect_charge_info.DefectChargeInfo method) ave_diele (pydefect.analyzer.unitcell.Unitcell property) ave_dielectric_tensor (pydefect.corrections.gkfo_correction.GkfoCorrection attribute) ave_ele_diele (pydefect.analyzer.unitcell.Unitcell property) ave_ele_mass (pydefect.analyzer.unitcell.Unitcell property) ave_electronic_dielectric_tensor (pydefect.corrections.gkfo_correction.GkfoCorrection attribute) ave_energy (pydefect.analyzer.band_edge_states.LocalizedOrbital attribute) ave_hole_mass (pydefect.analyzer.unitcell.Unitcell property) AveChargeDensityDist (class in pydefect.analyzer.defect_charge_info) average_angle (pydefect.input_maker.supercell.Supercell property) average_potential_diff (pydefect.corrections.efnv_correction.ExtendedFnvCorrection property) average_potential_diff_by_addition (pydefect.corrections.gkfo_correction.GkfoCorrection property)

B

band_edge_eigenvalues() (in module pydefect.tests.analyzer.test_band_edge_states) band_edge_orbital_infos() (in module pydefect.tests.analyzer.test_band_edge_states) band_edge_states() (in module pydefect.tests.analyzer.test_band_edge_states) (in module pydefect.tests.analyzer.test_make_band_edge_states) band_idx (pydefect.analyzer.band_edge_states.EdgeInfo attribute) (pydefect.analyzer.band_edge_states.LocalizedOrbital attribute) band_idxs (pydefect.analyzer.defect_charge_info.DefectChargeInfo attribute) band_index (pydefect.analyzer.band_edge_states.LocalizedOrbital property) band_indices_from_vbm_to_cbm (pydefect.analyzer.band_edge_states.BandEdgeStates property)

BandEdgeEigenvalues (class in pydefect.analyzer.band_edge_states) BandEdgeOrbitalInfos (class in pydefect.analyzer.band_edge_states) BandEdgeState (class in pydefect.analyzer.band_edge_states) BandEdgeStates (class in pydefect.analyzer.band_edge_states) bcc() (in module pydefect.tests.conftest) before_refine() (in module pydefect.tests.conftest) bins_middle_points (pydefect.analyzer.defect_charge_info.DefectChargeInfo property) boltzmann_dist() (in module pydefect.analyzer.concentration.distribution_function) boundary_points (pydefect.analyzer.defect_energy.CrossPoints attribute)

C

c_centered_monoclinic() (in module pydefect.tests.conftest) calc_carrier_concentrations() (in module pydefect.cli.main_util_functions) calc_charge_state() (in module pydefect.cli.vasp.main_vasp_util_functions) calc_cross_points() (pydefect.analyzer.defect_energy.ChargeEnergies method) calc_defect_concentrations() (in module pydefect.cli.main_util_functions) calc_defect_structure_info() (in module pydefect.cli.main_functions) calc_disp_angle() (pydefect.analyzer.make_defect_structure_info.MakeDefectStructureInfo static method) calc_displacements() (pydefect.analyzer.make_defect_structure_info.MakeDefectStructureInfo method) calc_grids() (in module pydefect.cli.vasp.main_vasp_util_functions) calc_max_sphere_radius() (in module pydefect.cli.vasp.make_efnv_correction) calc_orbital_character() (in module pydefect.cli.vasp.make_band_edge_orbital_infos) calc_participation_ratio() (in module pydefect.cli.vasp.make_band_edge_orbital_infos) calc_results() (in module pydefect.tests.analyzer.test_calc_results) calc_summary() (in module pydefect.tests.analyzer.test_calc_summary) calc_u_values() (in module pydefect.analyzer.defect_energy_util) CalcResults (class in pydefect.analyzer.calc_results) CalcSummary (class in pydefect.analyzer.calc_summary) carrier (pydefect.analyzer.concentration.concentration.Concentration attribute) carrier_concentration() (in module pydefect.tests.analyzer.concentration.test_concentration) (pydefect.analyzer.concentration.make_concentration.Dos method) (pydefect.analyzer.concentration.make_concentration.MakeCarrierConcentrations method) carrier_type (pydefect.analyzer.concentration.make_concentration.CBDos attribute) (pydefect.analyzer.concentration.make_concentration.VBDos attribute) CarrierConcentration (class in pydefect.analyzer.concentration.concentration) CBDos (class in pydefect.analyzer.concentration.make_concentration) cbm (pydefect.analyzer.concentration.make_concentration.TotalDos attribute) (pydefect.analyzer.defect_energy.DefectEnergySummary attribute) (pydefect.analyzer.transition_levels.TransitionLevels attribute) (pydefect.analyzer.unitcell.Unitcell attribute) cbm_electron_occupation (pydefect.analyzer.band_edge_states.BandEdgeState attribute) cbm_info (pydefect.analyzer.band_edge_states.BandEdgeState attribute) (pydefect.analyzer.band_edge_states.PerfectBandEdgeState attribute) cbm_orbital_diff (pydefect.analyzer.band_edge_states.BandEdgeState attribute) center (pydefect.analyzer.band_edge_states.LocalizedOrbital attribute) (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) center_1d_periodic_quantity() (in module pydefect.cli.vasp.make_defect_charge_info) change_element_sequence() (in module pydefect.chem_pot_diag.chem_pot_diag) charge (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) (pydefect.analyzer.defect_energy.DefectEnergyInfo attribute) (pydefect.corrections.efnv_correction.ExtendedFnvCorrection attribute) (pydefect.corrections.gkfo_correction.GkfoCorrection property) (pydefect.input_maker.defect_entry.DefectEntry attribute) charge_center (pydefect.analyzer.defect_charge_info.AveChargeDensityDist attribute) charge_dist_list() (in module pydefect.tests.cli.vasp.test_make_defect_charge_info) charge_distribution_df (pydefect.cli.vasp.make_local_extrema.ChargeDensityAnalyzer property) charge_dists (pydefect.analyzer.defect_charge_info.DefectChargeInfo attribute) charge_energies (pydefect.analyzer.defect_energy.SingleChargeEnergies attribute) charge_energies() (in module pydefect.tests.analyzer.test_defect_energy) (pydefect.analyzer.defect_energy.DefectEnergySummary method) charge_energies_at_ef() (pydefect.analyzer.defect_energy.SingleChargeEnergies method) charge_energies_dict (pydefect.analyzer.defect_energy.ChargeEnergies attribute) charge_list (pydefect.analyzer.defect_energy.CrossPoints property) (pydefect.input_maker.complex_defect_set.ComplexDefect property) (pydefect.input_maker.defect.Defect property) charge_set() (in module pydefect.input_maker.defect_set_maker) ChargeDensityAnalyzer (class in pydefect.cli.vasp.make_local_extrema) ChargeEnergies (class in pydefect.analyzer.defect_energy) charges (pydefect.analyzer.concentration.concentration.DefectConcentration attribute) (pydefect.analyzer.defect_energy.CrossPoints property) (pydefect.analyzer.defect_energy.DefectEnergies attribute) (pydefect.analyzer.transition_levels.TransitionLevel attribute) (pydefect.analyzer.transition_levels_plotter.MplTLData attribute) (pydefect.input_maker.complex_defect_set.ComplexDefect attribute) (pydefect.input_maker.defect.Defect attribute)

check_site_structure_consistency() (in module pydefect.input_maker.manual_supercell_maker) chem_pot (pydefect.chem_pot_diag.chem_pot_diag.TargetVertex attribute) chem_pot_diag (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiagMaker property) chem_pots (pydefect.chem_pot_diag.chem_pot_diag.TargetVertices property) chemical_system (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag property) ChemPotDiag (class in pydefect.chem_pot_diag.chem_pot_diag) ChemPotDiag2DMplPlotter (class in pydefect.chem_pot_diag.cpd_plotter) ChemPotDiag3DMplPlotter (class in pydefect.chem_pot_diag.cpd_plotter) ChemPotDiagMaker (class in pydefect.chem_pot_diag.chem_pot_diag) ChemPotDiagMplPlotter (class in pydefect.chem_pot_diag.cpd_plotter) chemsys() (in module pydefect.util.mp_tools) chgcar() (in module pydefect.tests.analyzer.test_grids) cluster_nodes() (pydefect.cli.vasp.make_local_extrema.ChargeDensityAnalyzer method) comp_centers (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag property) comp_energies() (in module pydefect.tests.cli.vasp.test_make_composition_energies_from_mp) comp_energies_corr() (in module pydefect.tests.cli.vasp.test_make_composition_energies_from_mp) comp_energies_with_element() (pydefect.chem_pot_diag.chem_pot_diag.RelativeEnergies method) comp_to_element_set() (in module pydefect.chem_pot_diag.chem_pot_diag) competing_phases (pydefect.chem_pot_diag.chem_pot_diag.TargetVertex attribute) complex_defect() (in module pydefect.tests.input_maker.test_complex_defect_set) complex_defect_set() (in module pydefect.tests.input_maker.test_complex_defect_set) complex_monoclinic() (in module pydefect.tests.conftest) ComplexDefect (class in pydefect.input_maker.complex_defect_set) ComplexDefectEntriesMaker (class in pydefect.input_maker.complex_defect_entries_make) ComplexDefectSet (class in pydefect.input_maker.complex_defect_set) composition_energies_from_mp() (in module pydefect.cli.main_util_functions) CompositionEnergies (class in pydefect.chem_pot_diag.chem_pot_diag) CompositionEnergy (class in pydefect.chem_pot_diag.chem_pot_diag) con_by_Ef() (in module pydefect.tests.analyzer.concentration.test_concentration) Concentration (class in pydefect.analyzer.concentration.concentration) concentration() (in module pydefect.tests.analyzer.concentration.test_concentration) ConcentrationByFermiLevel (class in pydefect.analyzer.concentration.concentration) concentrations (pydefect.analyzer.concentration.concentration.ConcentrationByFermiLevel attribute) (pydefect.analyzer.concentration.concentration.DefectConcentration attribute) config_list (pydefect.analyzer.calc_summary.SingleCalcSummary property) construct_plot() (pydefect.analyzer.concentration.plot_concentration.DefectConcentrationMplPlotter method) (pydefect.analyzer.defect_energy_plotter.DefectEnergyMplPlotter method) (pydefect.analyzer.eigenvalue_plotter.EigenvalueMplPlotter method) (pydefect.corrections.site_potential_plotter.SitePotentialMplPlotter method) Coordination (class in pydefect.util.structure_tools) coordination (pydefect.input_maker.local_extrema.CoordInfo attribute) coordination() (pydefect.util.structure_tools.Distances method) CoordInfo (class in pydefect.input_maker.local_extrema) coords() (pydefect.input_maker.supercell_info.SupercellInfo method) copy_to_structure() (in module pydefect.input_maker.defect_entries_maker) Correction (class in pydefect.corrections.abstract_correction) correction_dict (pydefect.corrections.efnv_correction.ExtendedFnvCorrection property) (pydefect.corrections.no_correction.NoCorrection property) correction_energy (pydefect.corrections.efnv_correction.ExtendedFnvCorrection property) (pydefect.corrections.gkfo_correction.GkfoCorrection property) (pydefect.corrections.no_correction.NoCorrection property) CpdAbstractEnergies (class in pydefect.chem_pot_diag.chem_pot_diag) CpdMplSettings (class in pydefect.chem_pot_diag.cpd_plotter) CpdNotSupportedError cross_point_dicts (pydefect.analyzer.defect_energy.ChargeEnergies property) cross_points() (in module pydefect.tests.analyzer.test_defect_energy) (in module pydefect.tests.analyzer.test_transition_levels) CrossPoints (class in pydefect.analyzer.defect_energy) cubic_supercell() (in module pydefect.tests.conftest) cubic_supercell_info() (in module pydefect.tests.input_maker.test_defect_entries_maker) cubic_supercell_info_wo_int() (in module pydefect.tests.conftest) cubic_supercell_w_vacancy() (in module pydefect.tests.conftest) cubic_supercell_w_vacancy_w_perturb() (in module pydefect.tests.conftest) cutoff (pydefect.util.structure_tools.Coordination attribute)

D

d (pydefect.analyzer.concentration.degeneracy.Degeneracies attribute) def_str_info() (in module pydefect.tests.conftest) Defect (class in pydefect.input_maker.defect) defect_center (pydefect.input_maker.defect_entry.DefectEntry attribute) defect_center_coord (pydefect.analyzer.defect_structure_comparator.DefectStructureComparator property) defect_charge_info() (in module pydefect.tests.analyzer.test_defect_charge_info) defect_concentration() (in module pydefect.tests.analyzer.concentration.test_concentration) defect_coords (pydefect.corrections.efnv_correction.ExtendedFnvCorrection attribute) defect_energies (pydefect.analyzer.defect_energy.DefectEnergies attribute) (pydefect.analyzer.defect_energy.DefectEnergySummary attribute) defect_energies() (in module pydefect.tests.conftest) defect_energy (pydefect.analyzer.defect_energy.DefectEnergyInfo attribute) defect_energy() (in module pydefect.tests.analyzer.test_defect_energy) defect_energy_info() (in module pydefect.tests.analyzer.test_defect_energy) defect_energy_info2() (in module pydefect.tests.analyzer.test_defect_energy) defect_energy_summary() (in module pydefect.tests.analyzer.test_defect_energy_plotter) (in module pydefect.tests.conftest) defect_entry() (in module pydefect.tests.input_maker.test_defect_entry) defect_mpl_name() (in module pydefect.util.prepare_names) defect_region_radius (pydefect.corrections.efnv_correction.ExtendedFnvCorrection attribute) (pydefect.corrections.gkfo_correction.GkfoCorrection property) defect_set() (in module pydefect.tests.input_maker.test_defect_set) defect_type (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) (pydefect.analyzer.defect_structure_info.DefectStructureInfo property) DefectChargeInfo (class in pydefect.analyzer.defect_charge_info) DefectConcentration (class in pydefect.analyzer.concentration.concentration) DefectConcentrationMplPlotter (class in pydefect.analyzer.concentration.plot_concentration) DefectEnergies (class in pydefect.analyzer.defect_energy) DefectEnergiesMplSettings (class in pydefect.analyzer.defect_energy_plotter) DefectEnergy (class in pydefect.analyzer.defect_energy) DefectEnergyInfo (class in pydefect.analyzer.defect_energy) DefectEnergyMplPlotter (class in pydefect.analyzer.defect_energy_plotter) DefectEnergyPlotter (class in pydefect.analyzer.defect_energy_plotter) DefectEnergySummary (class in pydefect.analyzer.defect_energy) DefectEntriesMaker (class in pydefect.input_maker.defect_entries_maker) DefectEntry (class in pydefect.input_maker.defect_entry) defects (pydefect.analyzer.concentration.concentration.Concentration attribute) DefectSet (class in pydefect.input_maker.defect_set)

DefectSetMaker (class in pydefect.input_maker.defect_set_maker) DefectStructureComparator (class in pydefect.analyzer.defect_structure_comparator) DefectStructureInfo (class in pydefect.analyzer.defect_structure_info) DefectType (class in pydefect.analyzer.defect_structure_info) Degeneracies (class in pydefect.analyzer.concentration.degeneracy) degeneracies (pydefect.analyzer.concentration.degeneracy.MakeDegeneracy property) Degeneracy (class in pydefect.analyzer.concentration.degeneracy) degeneracy (pydefect.analyzer.concentration.degeneracy.Degeneracy property) dielectric_constant (pydefect.analyzer.unitcell.Unitcell property) diff_pot (pydefect.corrections.efnv_correction.PotentialSite property) dim (pydefect.analyzer.grids.Grids attribute) (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag property) disp_vector (pydefect.analyzer.defect_structure_info.Displacement attribute) displace_distance (pydefect.analyzer.defect_structure_info.Displacement attribute) Displacement (class in pydefect.analyzer.defect_structure_info) displacement (pydefect.input_maker.defect_entry.PerturbedSite attribute) displacements (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) displacements() (in module pydefect.tests.conftest) dist_tol (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) distance (pydefect.corrections.efnv_correction.PotentialSite attribute) (pydefect.input_maker.defect_entry.PerturbedSite attribute) distance_bins (pydefect.analyzer.defect_charge_info.DefectChargeInfo attribute) distance_data (pydefect.analyzer.grids.Grids attribute) distance_dict (pydefect.util.structure_tools.Coordination attribute) distance_from_defect (pydefect.analyzer.defect_structure_info.Displacement attribute) Distances (class in pydefect.util.structure_tools) distances() (pydefect.util.structure_tools.Distances method) donor_phs (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) Dos (class in pydefect.analyzer.concentration.make_concentration) dos (pydefect.analyzer.concentration.make_concentration.TotalDos attribute) doses (pydefect.analyzer.concentration.make_concentration.Dos attribute) draw_diagram() (pydefect.chem_pot_diag.cpd_plotter.ChemPotDiagMplPlotter method) draw_simplex() (pydefect.chem_pot_diag.cpd_plotter.ChemPotDiag2DMplPlotter method) (pydefect.chem_pot_diag.cpd_plotter.ChemPotDiag3DMplPlotter method) (pydefect.chem_pot_diag.cpd_plotter.ChemPotDiagMplPlotter method) drift_dist (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) drift_vector (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) dump() (pydefect.analyzer.grids.Grids method)

E

e_max (pydefect.analyzer.defect_energy.ChargeEnergies attribute) e_min (pydefect.analyzer.defect_energy.ChargeEnergies attribute) e_min_max_energies_dict (pydefect.analyzer.defect_energy.ChargeEnergies property) EdgeInfo (class in pydefect.analyzer.band_edge_states) Ef (pydefect.analyzer.concentration.concentration.Concentration attribute) effective_ionic_diele_const (pydefect.analyzer.unitcell.Unitcell property) efnv_cor() (in module pydefect.tests.corrections.test_site_potential_plotter) efnv_correction() (in module pydefect.tests.conftest) eigenvalue (pydefect.analyzer.band_edge_states.LocalizedOrbital property) eigenvalue_mpl_plotter() (in module pydefect.tests.analyzer.test_eigenvalue_plotter) EigenvalueMplPlotter (class in pydefect.analyzer.eigenvalue_plotter) EigenvalueMplSettings (class in pydefect.analyzer.eigenvalue_plotter) EigenvaluePlotter (class in pydefect.analyzer.eigenvalue_plotter) eigval_shift (pydefect.analyzer.band_edge_states.BandEdgeOrbitalInfos attribute) ele_dielectric_const (pydefect.analyzer.unitcell.Unitcell attribute) electron_mass (pydefect.analyzer.unitcell.Unitcell attribute) electronegativity() (in module pydefect.database.database) electronic_conv (pydefect.analyzer.calc_results.CalcResults attribute) (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) element (pydefect.input_maker.defect_entry.PerturbedSite attribute) (pydefect.input_maker.supercell_info.SimpleSite attribute) elements (pydefect.chem_pot_diag.chem_pot_diag.CompositionEnergies property) elongated_tetragonal() (in module pydefect.tests.conftest)

energies (pydefect.analyzer.concentration.make_concentration.Dos attribute) (pydefect.analyzer.concentration.make_concentration.TotalDos attribute) (pydefect.analyzer.transition_levels.TransitionLevel attribute) energies_and_occupations (pydefect.analyzer.band_edge_states.BandEdgeEigenvalues attribute) (pydefect.analyzer.band_edge_states.BandEdgeOrbitalInfos property) energy (pydefect.analyzer.band_edge_states.EdgeInfo property) (pydefect.analyzer.band_edge_states.OrbitalInfo attribute) (pydefect.analyzer.calc_results.CalcResults attribute) (pydefect.chem_pot_diag.chem_pot_diag.CompositionEnergy attribute) energy() (pydefect.analyzer.defect_energy.DefectEnergy method) energy_at_ef() (pydefect.analyzer.defect_energy.SingleChargeEnergies method) energy_corrections (pydefect.analyzer.defect_energy.DefectEnergy attribute) energy_range() (pydefect.analyzer.defect_energy.ChargeEnergies method) equilibrium_concentration (pydefect.analyzer.concentration.concentration.ConcentrationByFermiLevel attribute) equilibrium_concentration() (in module pydefect.analyzer.concentration.make_concentration) equivalent_atoms (pydefect.input_maker.supercell_info.SimpleSite property) Ewald (class in pydefect.corrections.ewald) ewald() (in module pydefect.tests.corrections.test_ewald) ewald_real() (pydefect.corrections.ewald.Ewald method) ewald_rec() (pydefect.corrections.ewald.Ewald method) ExtendedFnvCorrection (class in pydefect.corrections.efnv_correction) extrema_coords() (in module pydefect.cli.vasp.make_local_extrema) extrema_df (pydefect.cli.vasp.make_local_extrema.ChargeDensityAnalyzer property) extrema_points (pydefect.input_maker.local_extrema.VolumetricDataLocalExtrema attribute)

F

fcc() (in module pydefect.tests.conftest) fermi_dirac() (in module pydefect.analyzer.concentration.distribution_function) fermi_level (pydefect.analyzer.band_edge_states.BandEdgeOrbitalInfos attribute) (pydefect.analyzer.concentration.make_concentration.TotalDos property) fermi_levels (pydefect.analyzer.transition_levels.TransitionLevel attribute) final_pos (pydefect.analyzer.defect_structure_info.Displacement attribute) final_site_sym (pydefect.analyzer.concentration.degeneracy.Degeneracy attribute) (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) (pydefect.analyzer.make_defect_structure_info.MakeDefectStructureInfo property) find_inequivalent_coords() (in module pydefect.cli.vasp.make_local_extrema) fold_coords_in_structure() (in module pydefect.cli.make_defect_vesta_file) folded_coords() (in module pydefect.analyzer.make_defect_structure_info) formation_energy (pydefect.analyzer.defect_energy.DefectEnergy attribute) frac_coords (pydefect.input_maker.local_extrema.CoordInfo attribute) (pydefect.input_maker.supercell_info.Interstitial attribute) from_chgcar() (pydefect.analyzer.grids.Grids class method) from_dict() (pydefect.analyzer.concentration.degeneracy.Degeneracies class method) (pydefect.analyzer.defect_structure_comparator.SiteDiff class method) (pydefect.chem_pot_diag.chem_pot_diag.CompositionEnergies class method) (pydefect.input_maker.defect.Defect class method) (pydefect.input_maker.defect.SimpleDefect class method) (pydefect.input_maker.defect_entry.DefectEntry class method) (pydefect.input_maker.defect_entry.PerturbedSite class method) (pydefect.input_maker.supercell_info.SupercellInfo class method)

from_efnv_corr() (pydefect.corrections.site_potential_plotter.SitePotentialPlotter class method) from_file() (pydefect.analyzer.grids.Grids class method) (pydefect.cli.vasp.make_local_extrema.ChargeDensityAnalyzer class method) from_gkfo_corr() (pydefect.corrections.site_potential_plotter.SitePotentialPlotter class method) from_json_file() (pydefect.corrections.abstract_correction.Correction class method) from_yaml() (pydefect.analyzer.defect_energy.DefectEnergyInfo class method) (pydefect.analyzer.unitcell.Unitcell class method) (pydefect.chem_pot_diag.chem_pot_diag.CompositionEnergies class method) (pydefect.chem_pot_diag.chem_pot_diag.CpdAbstractEnergies class method) (pydefect.chem_pot_diag.chem_pot_diag.TargetVertices class method) (pydefect.input_maker.complex_defect_set.ComplexDefectSet class method) (pydefect.input_maker.defect_set.DefectSet class method) full_name (pydefect.input_maker.defect_entry.DefectEntry property)

G

g_lattice_set() (pydefect.corrections.ewald.Ewald method) g_vector_nums (pydefect.corrections.ewald.Ewald property) get_calc_results() (in module pydefect.cli.main_functions) get_defect_charge_state() (in module pydefect.cli.vasp.get_defect_charge_state) get_edge_info() (in module pydefect.cli.vasp.make_perfect_band_edge_state) get_local_extrema() (pydefect.cli.vasp.make_local_extrema.ChargeDensityAnalyzer method) get_localized_orbs() (in module pydefect.analyzer.make_band_edge_states)

get_similar_orb_idx() (in module pydefect.analyzer.make_band_edge_states) get_structure_with_nodes() (pydefect.cli.vasp.make_local_extrema.ChargeDensityAnalyzer method) gkfo_correction() (in module pydefect.tests.corrections.test_gkfo_correction) gkfo_sites (pydefect.corrections.gkfo_correction.GkfoCorrection attribute) GkfoCorrection (class in pydefect.corrections.gkfo_correction) grid_number() (in module pydefect.corrections.ewald) Grids (class in pydefect.analyzer.grids) grids() (in module pydefect.tests.analyzer.test_grids)

H

half_charge_radius() (pydefect.analyzer.defect_charge_info.DefectChargeInfo method) has_acceptor_phs (pydefect.analyzer.band_edge_states.BandEdgeState property) (pydefect.analyzer.band_edge_states.BandEdgeStates property) has_donor_phs (pydefect.analyzer.band_edge_states.BandEdgeState property) (pydefect.analyzer.band_edge_states.BandEdgeStates property)

has_occupied_localized_state (pydefect.analyzer.band_edge_states.BandEdgeState property) (pydefect.analyzer.band_edge_states.BandEdgeStates property) has_unoccupied_localized_state (pydefect.analyzer.band_edge_states.BandEdgeState property) (pydefect.analyzer.band_edge_states.BandEdgeStates property) hole_mass (pydefect.analyzer.unitcell.Unitcell attribute) host_composition_energies() (pydefect.chem_pot_diag.chem_pot_diag.RelativeEnergies method)

I

impurity_chem_pot() (pydefect.chem_pot_diag.chem_pot_diag.RelativeEnergies method) impurity_phases (pydefect.chem_pot_diag.chem_pot_diag.TargetVertex attribute) in_atom (pydefect.input_maker.defect.SimpleDefect property) IncorrectSiteYamlFileError incremented_matrix() (pydefect.input_maker.supercell.RhombohedralSupercells method) (pydefect.input_maker.supercell.Supercells method) (pydefect.input_maker.supercell.TetragonalSupercells method) info (pydefect.input_maker.local_extrema.VolumetricDataLocalExtrema attribute) (pydefect.input_maker.supercell_info.Interstitial attribute) init_efnv_correction (pydefect.corrections.gkfo_correction.GkfoCorrection attribute) initial_coords (pydefect.input_maker.defect_entry.PerturbedSite attribute) initial_site_sym (pydefect.analyzer.concentration.degeneracy.Degeneracy attribute) (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) (pydefect.analyzer.make_defect_structure_info.MakeDefectStructureInfo property) inner_cross_points (pydefect.analyzer.defect_energy.CrossPoints attribute) inserted (pydefect.analyzer.defect_structure_comparator.SiteDiff attribute) inserted_by_sub (pydefect.analyzer.defect_structure_comparator.SiteDiff attribute) inserted_indices (pydefect.analyzer.defect_structure_comparator.DefectStructureComparator property) Interstitial (class in pydefect.input_maker.supercell_info) interstitial (pydefect.analyzer.defect_structure_info.DefectType attribute) interstitial() (in module pydefect.tests.input_maker.test_supercell_info) interstitial_coords() (pydefect.input_maker.supercell_info.SupercellInfo method)

interstitial_split (pydefect.analyzer.defect_structure_info.DefectType attribute) interstitials (pydefect.input_maker.supercell_info.SupercellInfo attribute) interval (pydefect.analyzer.concentration.make_concentration.Dos property) ion_dielectric_const (pydefect.analyzer.unitcell.Unitcell attribute) ionic_conv (pydefect.analyzer.calc_results.CalcResults attribute) (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) is_complex_defect (pydefect.analyzer.defect_structure_comparator.SiteDiff property) is_converged (pydefect.analyzer.calc_summary.SingleCalcSummary property) is_energy_strange (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) is_file() (in module pydefect.cli.vasp.main_vasp_util_functions) is_interstitial (pydefect.analyzer.defect_structure_comparator.SiteDiff property) is_min (pydefect.input_maker.local_extrema.VolumetricDataLocalExtrema attribute) is_no_diff (pydefect.analyzer.defect_structure_comparator.SiteDiff property) is_proper_result (pydefect.analyzer.calc_summary.SingleCalcSummary property) is_shallow (pydefect.analyzer.band_edge_states.BandEdgeState property) (pydefect.analyzer.band_edge_states.BandEdgeStates property) (pydefect.analyzer.defect_energy.DefectEnergy attribute) is_spin_polarized (pydefect.analyzer.defect_charge_info.DefectChargeInfo property) is_substituted (pydefect.analyzer.defect_structure_comparator.SiteDiff property) is_unusual (pydefect.analyzer.calc_summary.SingleCalcSummary property) is_vacancy (pydefect.analyzer.defect_structure_comparator.SiteDiff property) isotropy (pydefect.input_maker.supercell.Supercell property)

J

judge_defect_type() (in module pydefect.analyzer.defect_structure_info)

K

kpt_coord (pydefect.analyzer.band_edge_states.EdgeInfo attribute) kpt_coords (pydefect.analyzer.band_edge_states.BandEdgeEigenvalues attribute) (pydefect.analyzer.band_edge_states.BandEdgeOrbitalInfos attribute)

kpt_idx() (pydefect.analyzer.band_edge_states.BandEdgeOrbitalInfos method) kpt_weights (pydefect.analyzer.band_edge_states.BandEdgeOrbitalInfos attribute)

L

labels (pydefect.analyzer.transition_levels_plotter.MplTLData attribute) latexified_title (pydefect.analyzer.defect_energy.DefectEnergySummary property) lattice (pydefect.analyzer.grids.Grids attribute) lattice_energy (pydefect.corrections.ewald.Ewald property) local_extrema() (in module pydefect.tests.input_maker.test_local_extrema)

localized_orbitals (pydefect.analyzer.band_edge_states.BandEdgeState attribute) localized_orbitals() (pydefect.analyzer.defect_charge_info.DefectChargeInfo method) LocalizedOrbital (class in pydefect.analyzer.band_edge_states) lowest_band_index (pydefect.analyzer.band_edge_states.BandEdgeEigenvalues attribute) (pydefect.analyzer.band_edge_states.BandEdgeOrbitalInfos attribute)

M

mag_to_spin_degeneracy() (pydefect.analyzer.concentration.degeneracy.MakeDegeneracy method) magnetization (pydefect.analyzer.calc_results.CalcResults attribute) main() (in module pydefect.cli.main) (in module pydefect.cli.main_print_json) (in module pydefect.cli.main_util) (in module pydefect.cli.vasp.main_vasp) (in module pydefect.cli.vasp.main_vasp_util) make_band_edge_orb_infos_and_eigval_plot() (in module pydefect.cli.vasp.main_vasp_functions) make_band_edge_orbital_infos() (in module pydefect.cli.vasp.make_band_edge_orbital_infos) make_band_edge_states() (in module pydefect.analyzer.make_band_edge_states) make_band_edge_states_main_func() (in module pydefect.cli.main_functions) make_calc_results() (in module pydefect.cli.vasp.main_vasp_functions) make_calc_results_from_vasp() (in module pydefect.cli.vasp.make_calc_results) make_calc_summary() (in module pydefect.analyzer.make_calc_summary) make_calc_summary_main_func() (in module pydefect.cli.main_functions) make_charge_dist() (in module pydefect.cli.vasp.make_defect_charge_info) make_competing_phase_dirs() (in module pydefect.cli.vasp.main_vasp_functions) make_composition_energies() (in module pydefect.cli.vasp.main_vasp_functions) make_composition_energies_from_mp() (in module pydefect.cli.vasp.make_composition_energies_from_mp) make_concentrations_by_fermi_level() (pydefect.analyzer.concentration.make_concentration.MakeCarrierConcentrations method) (pydefect.analyzer.concentration.make_concentration.MakeConcentrations method) make_cpd_and_vertices() (in module pydefect.cli.main_functions) make_d_to_p() (pydefect.analyzer.defect_structure_comparator.DefectStructureComparator method) make_defect_charge_info() (in module pydefect.cli.vasp.make_defect_charge_info) make_defect_charge_info_main() (in module pydefect.cli.vasp.main_vasp_util_functions) make_defect_energy_info() (in module pydefect.analyzer.make_defect_energy_info) make_defect_energy_infos_main_func() (in module pydefect.cli.main_functions) make_defect_energy_summary() (in module pydefect.analyzer.make_defect_energy_summary) make_defect_energy_summary_main() (in module pydefect.cli.main_functions) make_defect_energy_summary_main_func() (in module pydefect.cli.main_functions) make_defect_entries() (in module pydefect.cli.vasp.main_vasp_functions) make_defect_entry() (in module pydefect.input_maker.defect_entry) make_defect_entry_main() (in module pydefect.cli.vasp.main_vasp_util_functions) make_defect_set() (in module pydefect.cli.main_functions) make_defect_vesta_file() (in module pydefect.cli.main_util_functions) make_degeneracies() (in module pydefect.cli.main_util_functions) make_efnv_correction() (in module pydefect.cli.vasp.make_efnv_correction) make_efnv_correction_main_func() (in module pydefect.cli.main_functions) make_final_structure() (pydefect.cli.make_defect_vesta_file.MakeDefectVestaFile method) make_gkfo_correction() (in module pydefect.cli.vasp.make_gkfo_correction) make_gkfo_correction_from_vasp() (in module pydefect.cli.main_util_functions) make_initial_structure() (pydefect.cli.make_defect_vesta_file.MakeDefectVestaFile method) make_local_extrema() (in module pydefect.cli.vasp.main_vasp_functions) make_local_extrema_from_volumetric_data() (in module pydefect.cli.vasp.make_local_extrema) make_mpl_tl_data() (in module pydefect.analyzer.transition_levels_plotter) make_p_to_d() (pydefect.analyzer.defect_structure_comparator.DefectStructureComparator method) make_parchg_dir() (in module pydefect.cli.vasp.main_vasp_util_functions) make_perfect_band_edge_state() (in module pydefect.cli.vasp.main_vasp_functions) make_perfect_band_edge_state_from_vasp() (in module pydefect.cli.vasp.make_perfect_band_edge_state) make_poscars_from_query() (in module pydefect.cli.vasp.make_poscars_from_query) make_refine_defect_poscar() (in module pydefect.cli.vasp.main_vasp_util_functions) make_single_calc_summary() (in module pydefect.analyzer.make_calc_summary) make_site_diff() (pydefect.analyzer.defect_structure_comparator.DefectStructureComparator method) make_sites() (in module pydefect.cli.vasp.make_efnv_correction) make_sites_from_yaml_file() (in module pydefect.input_maker.manual_supercell_maker) make_standard_and_relative_energies() (in module pydefect.cli.main_functions) make_supercell() (in module pydefect.cli.main_functions) make_total_dos() (in module pydefect.cli.vasp.main_vasp_util_functions) make_transition_levels() (in module pydefect.analyzer.transition_levels) make_unitcell() (in module pydefect.cli.vasp.main_vasp_functions) make_unitcell_from_vasp() (in module pydefect.cli.vasp.make_unitcell) MakeCarrierConcentrations (class in pydefect.analyzer.concentration.make_concentration) MakeConcentrations (class in pydefect.analyzer.concentration.make_concentration) MakeDefectStructureInfo (class in pydefect.analyzer.make_defect_structure_info) MakeDefectVestaFile (class in pydefect.cli.make_defect_vesta_file) MakeDegeneracy (class in pydefect.analyzer.concentration.degeneracy) ManualSupercellMaker (class in pydefect.input_maker.manual_supercell_maker) matrix_from_x_y() (pydefect.input_maker.supercell.TetragonalSupercells static method) min_dist (pydefect.input_maker.local_extrema.VolumetricDataAnalyzeParams attribute) min_range (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag property) module pydefect pydefect.analyzer pydefect.analyzer.band_edge_states pydefect.analyzer.calc_results pydefect.analyzer.calc_summary pydefect.analyzer.concentration pydefect.analyzer.concentration.concentration pydefect.analyzer.concentration.degeneracy pydefect.analyzer.concentration.distribution_function pydefect.analyzer.concentration.make_concentration pydefect.analyzer.concentration.plot_concentration pydefect.analyzer.defect_charge_info pydefect.analyzer.defect_energy pydefect.analyzer.defect_energy_plotter pydefect.analyzer.defect_energy_util pydefect.analyzer.defect_structure_comparator pydefect.analyzer.defect_structure_info pydefect.analyzer.eigenvalue_plotter pydefect.analyzer.grids pydefect.analyzer.make_band_edge_states pydefect.analyzer.make_calc_summary pydefect.analyzer.make_defect_energy_info pydefect.analyzer.make_defect_energy_summary pydefect.analyzer.make_defect_structure_info pydefect.analyzer.pinning_levels pydefect.analyzer.refine_defect_structure pydefect.analyzer.transition_levels pydefect.analyzer.transition_levels_plotter pydefect.analyzer.unitcell pydefect.chem_pot_diag pydefect.chem_pot_diag.chem_pot_diag pydefect.chem_pot_diag.cpd_plotter pydefect.cli pydefect.cli.main pydefect.cli.main_functions pydefect.cli.main_print_json pydefect.cli.main_tools pydefect.cli.main_util pydefect.cli.main_util_functions pydefect.cli.make_defect_vesta_file pydefect.cli.vasp pydefect.cli.vasp.get_defect_charge_state pydefect.cli.vasp.main_vasp pydefect.cli.vasp.main_vasp_functions pydefect.cli.vasp.main_vasp_util pydefect.cli.vasp.main_vasp_util_functions pydefect.cli.vasp.make_band_edge_orbital_infos pydefect.cli.vasp.make_calc_results pydefect.cli.vasp.make_composition_energies_from_mp pydefect.cli.vasp.make_defect_charge_info pydefect.cli.vasp.make_efnv_correction pydefect.cli.vasp.make_gkfo_correction pydefect.cli.vasp.make_local_extrema pydefect.cli.vasp.make_perfect_band_edge_state pydefect.cli.vasp.make_poscars_from_query pydefect.cli.vasp.make_unitcell pydefect.cli.vasp.molecules pydefect.cli.vasp.molecules.molecules pydefect.corrections pydefect.corrections.abstract_correction pydefect.corrections.efnv_correction pydefect.corrections.ewald pydefect.corrections.gkfo_correction pydefect.corrections.no_correction pydefect.corrections.site_potential_plotter pydefect.database pydefect.database.database pydefect.defaults pydefect.error pydefect.input_maker pydefect.input_maker.append_interstitial pydefect.input_maker.complex_defect_entries_make pydefect.input_maker.complex_defect_set pydefect.input_maker.defect pydefect.input_maker.defect_entries_maker pydefect.input_maker.defect_entry pydefect.input_maker.defect_set pydefect.input_maker.defect_set_maker pydefect.input_maker.local_extrema pydefect.input_maker.manual_supercell_maker pydefect.input_maker.supercell pydefect.input_maker.supercell_info pydefect.input_maker.supercell_maker pydefect.tests pydefect.tests.analyzer pydefect.tests.analyzer.concentration pydefect.tests.analyzer.concentration.test_concentration pydefect.tests.analyzer.concentration.test_degeneracy pydefect.tests.analyzer.concentration.test_distribution_function pydefect.tests.analyzer.concentration.test_make_concentration pydefect.tests.analyzer.concentration.test_plot_concentration pydefect.tests.analyzer.test_band_edge_states pydefect.tests.analyzer.test_calc_results pydefect.tests.analyzer.test_calc_summary pydefect.tests.analyzer.test_defect_charge_info pydefect.tests.analyzer.test_defect_energy pydefect.tests.analyzer.test_defect_energy_plotter pydefect.tests.analyzer.test_defect_energy_util pydefect.tests.analyzer.test_defect_structure_comparator pydefect.tests.analyzer.test_defect_structure_info pydefect.tests.analyzer.test_eigenvalue_plotter pydefect.tests.analyzer.test_grids pydefect.tests.analyzer.test_make_band_edge_states pydefect.tests.analyzer.test_make_calc_summary pydefect.tests.analyzer.test_make_defect_energy_info pydefect.tests.analyzer.test_make_defect_energy_summary pydefect.tests.analyzer.test_make_defect_structure_info pydefect.tests.analyzer.test_pinning_levels pydefect.tests.analyzer.test_refine_defect_structure pydefect.tests.analyzer.test_transition_levels pydefect.tests.analyzer.test_transition_levels_plotter pydefect.tests.analyzer.test_unitcell pydefect.tests.cli pydefect.tests.cli.test_main pydefect.tests.cli.test_main_functions pydefect.tests.cli.test_main_tools pydefect.tests.cli.test_main_util pydefect.tests.cli.test_main_util_functions pydefect.tests.cli.test_make_defect_vesta_file pydefect.tests.cli.vasp pydefect.tests.cli.vasp.test_get_defect_charge_state pydefect.tests.cli.vasp.test_main_vasp pydefect.tests.cli.vasp.test_main_vasp_functions pydefect.tests.cli.vasp.test_main_vasp_util pydefect.tests.cli.vasp.test_main_vasp_util_functions pydefect.tests.cli.vasp.test_make_band_edge_orbital_infos pydefect.tests.cli.vasp.test_make_calc_results pydefect.tests.cli.vasp.test_make_composition_energies_from_mp pydefect.tests.cli.vasp.test_make_defect_charge_info pydefect.tests.cli.vasp.test_make_efnv_correction pydefect.tests.cli.vasp.test_make_gkfo_correction pydefect.tests.cli.vasp.test_make_local_extrema pydefect.tests.cli.vasp.test_make_perfect_band_edge_state pydefect.tests.cli.vasp.test_make_poscars_from_query pydefect.tests.cli.vasp.test_make_unitcell pydefect.tests.conftest pydefect.tests.corrections pydefect.tests.corrections.test_efnv_correction pydefect.tests.corrections.test_efnv_performance pydefect.tests.corrections.test_ewald pydefect.tests.corrections.test_gkfo_correction pydefect.tests.corrections.test_site_potential_plotter pydefect.tests.helpers pydefect.tests.input_maker pydefect.tests.input_maker.test_append_interstitial pydefect.tests.input_maker.test_complex_defect_entries_make pydefect.tests.input_maker.test_complex_defect_set pydefect.tests.input_maker.test_defect pydefect.tests.input_maker.test_defect_entries_maker pydefect.tests.input_maker.test_defect_entry pydefect.tests.input_maker.test_defect_set pydefect.tests.input_maker.test_defect_set_maker pydefect.tests.input_maker.test_local_extrema pydefect.tests.input_maker.test_manual_supercell_maker pydefect.tests.input_maker.test_supercell pydefect.tests.input_maker.test_supercell_info pydefect.tests.input_maker.test_supercell_maker pydefect.util pydefect.util.coords pydefect.util.error_classes pydefect.util.mp_tools pydefect.util.prepare_names pydefect.util.structure_tools

monoclinic() (in module pydefect.tests.conftest) most_isotropic_supercell (pydefect.input_maker.supercell.Supercells property) most_neutral_concentration (pydefect.analyzer.concentration.concentration.ConcentrationByFermiLevel property) mp_query_mock() (in module pydefect.tests.cli.vasp.test_make_composition_energies_from_mp) MplTLData (class in pydefect.analyzer.transition_levels_plotter) MpQuery (class in pydefect.util.mp_tools) multiplicity (pydefect.input_maker.supercell_info.SupercellInfo property)

N

n (pydefect.analyzer.concentration.concentration.CarrierConcentration attribute) name (pydefect.analyzer.concentration.concentration.DefectConcentration attribute) (pydefect.analyzer.defect_energy.DefectEnergyInfo attribute) (pydefect.analyzer.transition_levels.TransitionLevel attribute) (pydefect.input_maker.complex_defect_set.ComplexDefect attribute) (pydefect.input_maker.defect.Defect attribute) (pydefect.input_maker.defect_entry.DefectEntry attribute) neighbor_atom_indices (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) neighbor_cutoff_factor (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) neighboring_atom_indices (pydefect.util.structure_tools.Coordination attribute) neighboring_atom_indices() (pydefect.analyzer.defect_structure_comparator.DefectStructureComparator method) net_abs_ratio (pydefect.analyzer.concentration.concentration.Concentration property) net_charge (pydefect.analyzer.concentration.concentration.CarrierConcentration property) (pydefect.analyzer.concentration.concentration.Concentration property) (pydefect.analyzer.concentration.concentration.DefectConcentration property)

next_Ef_to_neutral_concentration() (pydefect.analyzer.concentration.concentration.ConcentrationByFermiLevel method) next_x_y_combination() (pydefect.input_maker.supercell.TetragonalSupercells static method) NoCalculatedPotentialSiteError NoCorrection (class in pydefect.corrections.no_correction) NoElectronicConvError NoElementEnergyError NoIonicConvError NotPrimitiveError num_atom_differences() (in module pydefect.analyzer.make_defect_energy_info) num_electron_in_cbm() (in module pydefect.analyzer.make_band_edge_states) num_hole_in_vbm() (in module pydefect.analyzer.make_band_edge_states)

O

occupation (pydefect.analyzer.band_edge_states.EdgeInfo property) (pydefect.analyzer.band_edge_states.LocalizedOrbital attribute) (pydefect.analyzer.band_edge_states.OrbitalInfo attribute) occupied_deep_state (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) only_digits() (in module pydefect.util.prepare_names) orb_infos() (in module pydefect.tests.analyzer.test_make_band_edge_states) orbital_diff() (in module pydefect.analyzer.make_band_edge_states) orbital_info (pydefect.analyzer.band_edge_states.EdgeInfo attribute) orbital_info() (in module pydefect.tests.analyzer.test_band_edge_states)

orbital_infos (pydefect.analyzer.band_edge_states.BandEdgeOrbitalInfos attribute) OrbitalInfo (class in pydefect.analyzer.band_edge_states) orbitals (pydefect.analyzer.band_edge_states.EdgeInfo property) (pydefect.analyzer.band_edge_states.LocalizedOrbital attribute) (pydefect.analyzer.band_edge_states.OrbitalInfo attribute) original_pos (pydefect.analyzer.defect_structure_info.Displacement attribute) ortho_conventional() (in module pydefect.tests.conftest) out_atom (pydefect.input_maker.defect.SimpleDefect property) oxidation_state() (in module pydefect.database.database)

P

p (pydefect.analyzer.concentration.concentration.CarrierConcentration attribute) p_edge_state() (in module pydefect.tests.analyzer.test_make_band_edge_states) p_ratio (pydefect.analyzer.band_edge_states.EdgeInfo property) params (pydefect.input_maker.local_extrema.VolumetricDataLocalExtrema attribute) parchg() (in module pydefect.tests.cli.vasp.test_make_defect_charge_info) parse_args_main() (in module pydefect.cli.main) parse_args_main_util() (in module pydefect.cli.main_util) parse_args_main_vasp() (in module pydefect.cli.vasp.main_vasp) parse_args_main_vasp_util() (in module pydefect.cli.vasp.main_vasp_util) parse_dirs() (in module pydefect.cli.main_tools) participation_ratio (pydefect.analyzer.band_edge_states.LocalizedOrbital attribute) (pydefect.analyzer.band_edge_states.OrbitalInfo attribute) pc_1st_term (pydefect.corrections.gkfo_correction.GkfoCorrection property) pc_2nd_term (pydefect.corrections.gkfo_correction.GkfoCorrection attribute) pc_potential (pydefect.corrections.efnv_correction.PotentialSite attribute) perfect_band_edge_state() (in module pydefect.tests.analyzer.test_band_edge_states) PerfectBandEdgeState (class in pydefect.analyzer.band_edge_states) perturb_structure() (in module pydefect.input_maker.defect_entries_maker) perturbed_coords (pydefect.input_maker.defect_entry.PerturbedSite attribute) perturbed_site_indices (pydefect.input_maker.defect_entry.DefectEntry property) perturbed_site_symmetry (pydefect.input_maker.defect_entry.DefectEntry attribute) perturbed_sites (pydefect.input_maker.defect_entry.DefectEntry attribute) perturbed_structure (pydefect.input_maker.defect_entry.DefectEntry attribute) PerturbedSite (class in pydefect.input_maker.defect_entry) phase_diagram (pydefect.chem_pot_diag.chem_pot_diag.RelativeEnergies property) piled_tl_energy_widths (pydefect.analyzer.transition_levels_plotter.MplTLData attribute) pinning_level (pydefect.analyzer.concentration.concentration.ConcentrationByFermiLevel property) pinning_level() (pydefect.analyzer.defect_energy.SingleChargeEnergies method) pinning_levels (pydefect.analyzer.concentration.concentration.Concentration property) (pydefect.analyzer.concentration.concentration.ConcentrationByFermiLevel attribute) (pydefect.analyzer.defect_energy.ChargeEnergies property) pinning_levels_from_charge_energies() (in module pydefect.analyzer.pinning_levels) plot_carrier_concentrations() (in module pydefect.cli.main_util_functions) plot_chem_pot_diag() (in module pydefect.cli.main_functions) plot_defect_concentrations() (in module pydefect.cli.main_util_functions) plot_defect_energy() (in module pydefect.cli.main_functions) plot_multiple_pns() (in module pydefect.analyzer.concentration.plot_concentration) plot_pn() (in module pydefect.analyzer.concentration.plot_concentration) point_charge_correction (pydefect.corrections.efnv_correction.ExtendedFnvCorrection attribute) polygons (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag attribute) pop_interstitial_from_supercell_info() (in module pydefect.cli.main_functions) potential (pydefect.corrections.efnv_correction.PotentialSite attribute) PotentialPlotterMplSettings (class in pydefect.corrections.site_potential_plotter) potentials (pydefect.analyzer.calc_results.CalcResults attribute) PotentialSite (class in pydefect.corrections.efnv_correction) pprint_equiv_atoms (pydefect.input_maker.supercell_info.SimpleSite property) prettify_names() (in module pydefect.util.prepare_names) pretty_coords() (in module pydefect.util.coords) pretty_orbital() (in module pydefect.analyzer.band_edge_states) print_a_to_file_x() (in module pydefect.tests.cli.test_main_tools) pydefect module pydefect.analyzer module pydefect.analyzer.band_edge_states module pydefect.analyzer.calc_results module pydefect.analyzer.calc_summary module pydefect.analyzer.concentration module pydefect.analyzer.concentration.concentration module pydefect.analyzer.concentration.degeneracy module pydefect.analyzer.concentration.distribution_function module pydefect.analyzer.concentration.make_concentration module pydefect.analyzer.concentration.plot_concentration module pydefect.analyzer.defect_charge_info module pydefect.analyzer.defect_energy module pydefect.analyzer.defect_energy_plotter module pydefect.analyzer.defect_energy_util module pydefect.analyzer.defect_structure_comparator module pydefect.analyzer.defect_structure_info module pydefect.analyzer.eigenvalue_plotter module pydefect.analyzer.grids module pydefect.analyzer.make_band_edge_states module pydefect.analyzer.make_calc_summary module pydefect.analyzer.make_defect_energy_info module pydefect.analyzer.make_defect_energy_summary module pydefect.analyzer.make_defect_structure_info module pydefect.analyzer.pinning_levels module pydefect.analyzer.refine_defect_structure module pydefect.analyzer.transition_levels module pydefect.analyzer.transition_levels_plotter module pydefect.analyzer.unitcell module pydefect.chem_pot_diag module pydefect.chem_pot_diag.chem_pot_diag module pydefect.chem_pot_diag.cpd_plotter module pydefect.cli module pydefect.cli.main module pydefect.cli.main_functions module pydefect.cli.main_print_json module pydefect.cli.main_tools module pydefect.cli.main_util module pydefect.cli.main_util_functions module pydefect.cli.make_defect_vesta_file module pydefect.cli.vasp module pydefect.cli.vasp.get_defect_charge_state module pydefect.cli.vasp.main_vasp module pydefect.cli.vasp.main_vasp_functions module pydefect.cli.vasp.main_vasp_util module pydefect.cli.vasp.main_vasp_util_functions module pydefect.cli.vasp.make_band_edge_orbital_infos module pydefect.cli.vasp.make_calc_results module pydefect.cli.vasp.make_composition_energies_from_mp module pydefect.cli.vasp.make_defect_charge_info module pydefect.cli.vasp.make_efnv_correction module pydefect.cli.vasp.make_gkfo_correction module pydefect.cli.vasp.make_local_extrema module pydefect.cli.vasp.make_perfect_band_edge_state module pydefect.cli.vasp.make_poscars_from_query module pydefect.cli.vasp.make_unitcell module pydefect.cli.vasp.molecules module pydefect.cli.vasp.molecules.molecules module pydefect.corrections module pydefect.corrections.abstract_correction module pydefect.corrections.efnv_correction module pydefect.corrections.ewald module pydefect.corrections.gkfo_correction module pydefect.corrections.no_correction module pydefect.corrections.site_potential_plotter module pydefect.database module pydefect.database.database module pydefect.defaults module pydefect.error module

pydefect.input_maker module pydefect.input_maker.append_interstitial module pydefect.input_maker.complex_defect_entries_make module pydefect.input_maker.complex_defect_set module pydefect.input_maker.defect module pydefect.input_maker.defect_entries_maker module pydefect.input_maker.defect_entry module pydefect.input_maker.defect_set module pydefect.input_maker.defect_set_maker module pydefect.input_maker.local_extrema module pydefect.input_maker.manual_supercell_maker module pydefect.input_maker.supercell module pydefect.input_maker.supercell_info module pydefect.input_maker.supercell_maker module pydefect.tests module pydefect.tests.analyzer module pydefect.tests.analyzer.concentration module pydefect.tests.analyzer.concentration.test_concentration module pydefect.tests.analyzer.concentration.test_degeneracy module pydefect.tests.analyzer.concentration.test_distribution_function module pydefect.tests.analyzer.concentration.test_make_concentration module pydefect.tests.analyzer.concentration.test_plot_concentration module pydefect.tests.analyzer.test_band_edge_states module pydefect.tests.analyzer.test_calc_results module pydefect.tests.analyzer.test_calc_summary module pydefect.tests.analyzer.test_defect_charge_info module pydefect.tests.analyzer.test_defect_energy module pydefect.tests.analyzer.test_defect_energy_plotter module pydefect.tests.analyzer.test_defect_energy_util module pydefect.tests.analyzer.test_defect_structure_comparator module pydefect.tests.analyzer.test_defect_structure_info module pydefect.tests.analyzer.test_eigenvalue_plotter module pydefect.tests.analyzer.test_grids module pydefect.tests.analyzer.test_make_band_edge_states module pydefect.tests.analyzer.test_make_calc_summary module pydefect.tests.analyzer.test_make_defect_energy_info module pydefect.tests.analyzer.test_make_defect_energy_summary module pydefect.tests.analyzer.test_make_defect_structure_info module pydefect.tests.analyzer.test_pinning_levels module pydefect.tests.analyzer.test_refine_defect_structure module pydefect.tests.analyzer.test_transition_levels module pydefect.tests.analyzer.test_transition_levels_plotter module pydefect.tests.analyzer.test_unitcell module pydefect.tests.cli module pydefect.tests.cli.test_main module pydefect.tests.cli.test_main_functions module pydefect.tests.cli.test_main_tools module pydefect.tests.cli.test_main_util module pydefect.tests.cli.test_main_util_functions module pydefect.tests.cli.test_make_defect_vesta_file module pydefect.tests.cli.vasp module pydefect.tests.cli.vasp.test_get_defect_charge_state module pydefect.tests.cli.vasp.test_main_vasp module pydefect.tests.cli.vasp.test_main_vasp_functions module pydefect.tests.cli.vasp.test_main_vasp_util module pydefect.tests.cli.vasp.test_main_vasp_util_functions module pydefect.tests.cli.vasp.test_make_band_edge_orbital_infos module pydefect.tests.cli.vasp.test_make_calc_results module pydefect.tests.cli.vasp.test_make_composition_energies_from_mp module pydefect.tests.cli.vasp.test_make_defect_charge_info module pydefect.tests.cli.vasp.test_make_efnv_correction module pydefect.tests.cli.vasp.test_make_gkfo_correction module pydefect.tests.cli.vasp.test_make_local_extrema module pydefect.tests.cli.vasp.test_make_perfect_band_edge_state module pydefect.tests.cli.vasp.test_make_poscars_from_query module pydefect.tests.cli.vasp.test_make_unitcell module pydefect.tests.conftest module pydefect.tests.corrections module pydefect.tests.corrections.test_efnv_correction module pydefect.tests.corrections.test_efnv_performance module pydefect.tests.corrections.test_ewald module pydefect.tests.corrections.test_gkfo_correction module pydefect.tests.corrections.test_site_potential_plotter module pydefect.tests.helpers module pydefect.tests.input_maker module pydefect.tests.input_maker.test_append_interstitial module pydefect.tests.input_maker.test_complex_defect_entries_make module pydefect.tests.input_maker.test_complex_defect_set module pydefect.tests.input_maker.test_defect module pydefect.tests.input_maker.test_defect_entries_maker module pydefect.tests.input_maker.test_defect_entry module pydefect.tests.input_maker.test_defect_set module pydefect.tests.input_maker.test_defect_set_maker module pydefect.tests.input_maker.test_local_extrema module pydefect.tests.input_maker.test_manual_supercell_maker module pydefect.tests.input_maker.test_supercell module pydefect.tests.input_maker.test_supercell_info module pydefect.tests.input_maker.test_supercell_maker module pydefect.util module pydefect.util.coords module pydefect.util.error_classes module pydefect.util.mp_tools module pydefect.util.prepare_names module pydefect.util.structure_tools module PydefectError, [1]

Q

quantities (pydefect.input_maker.local_extrema.CoordInfo attribute)

R

r_lattice_set() (pydefect.corrections.ewald.Ewald method) r_vector_nums (pydefect.corrections.ewald.Ewald property) radial_dist (pydefect.analyzer.defect_charge_info.AveChargeDensityDist attribute) radius (pydefect.analyzer.band_edge_states.LocalizedOrbital attribute) (pydefect.input_maker.local_extrema.VolumetricDataAnalyzeParams attribute) random_3d_vector() (in module pydefect.input_maker.defect_entries_maker) redistribute_concentration() (in module pydefect.analyzer.concentration.make_concentration) refine_defect_structure() (in module pydefect.analyzer.refine_defect_structure) rel_chem_pots (pydefect.analyzer.defect_energy.DefectEnergySummary attribute) RelativeEnergies (class in pydefect.chem_pot_diag.chem_pot_diag)

remove_collisions() (pydefect.cli.vasp.make_local_extrema.ChargeDensityAnalyzer method) remove_digits() (in module pydefect.util.prepare_names) remove_dot() (in module pydefect.analyzer.defect_structure_info) remove_higher_energy_comp() (in module pydefect.cli.vasp.make_composition_energies_from_mp) removed (pydefect.analyzer.defect_structure_comparator.SiteDiff attribute) removed_by_sub (pydefect.analyzer.defect_structure_comparator.SiteDiff attribute) removed_indices (pydefect.analyzer.defect_structure_comparator.DefectStructureComparator property) replaced_sites (pydefect.input_maker.complex_defect_set.ComplexDefect attribute) rhombohedral() (in module pydefect.tests.conftest) RhombohedralSupercells (class in pydefect.input_maker.supercell)

S

same (pydefect.analyzer.defect_structure_info.SymmRelation attribute) same_atom_charge_io() (pydefect.analyzer.calc_summary.SingleCalcSummary method) same_config_from_init (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) (pydefect.analyzer.defect_structure_info.DefectStructureInfo property) same_structure (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) sanitize_matrix() (in module pydefect.cli.main_tools) screen_defect_set() (in module pydefect.input_maker.defect_set) screen_simple_defect() (in module pydefect.input_maker.defect) screened_defect_energies() (pydefect.analyzer.defect_energy.DefectEnergySummary method) self_pot (pydefect.corrections.ewald.Ewald property) shifted_distance_data() (pydefect.analyzer.grids.Grids method) shifted_final_structure (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) shortest_distance (pydefect.util.structure_tools.Distances property) show_convergence_warning() (pydefect.analyzer.calc_results.CalcResults method) show_dist() (pydefect.analyzer.defect_charge_info.DefectChargeInfo method) show_pinning_levels() (in module pydefect.cli.main_util_functions) show_u_values() (in module pydefect.cli.main_util_functions) simple_cubic() (in module pydefect.tests.conftest) simple_cubic_2x1x1() (in module pydefect.tests.conftest) simple_cubic_2x2x2() (in module pydefect.tests.conftest) SimpleDefect (class in pydefect.input_maker.defect) SimpleSite (class in pydefect.input_maker.supercell_info) single_charge_energies() (in module pydefect.tests.analyzer.test_defect_energy) single_summaries (pydefect.analyzer.calc_summary.CalcSummary attribute) single_summary() (in module pydefect.tests.analyzer.test_calc_summary) SingleCalcSummary (class in pydefect.analyzer.calc_summary) SingleChargeEnergies (class in pydefect.analyzer.defect_energy) site (pydefect.analyzer.concentration.degeneracy.Degeneracy attribute) site_diff (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) site_diff() (in module pydefect.tests.analyzer.test_defect_structure_comparator) site_diff_from_initial (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) site_index (pydefect.input_maker.supercell_info.SimpleSite attribute) site_symmetry (pydefect.input_maker.defect_entry.DefectEntry attribute) (pydefect.input_maker.local_extrema.CoordInfo attribute) (pydefect.input_maker.supercell_info.Interstitial attribute) (pydefect.input_maker.supercell_info.SimpleSite attribute) SiteDiff (class in pydefect.analyzer.defect_structure_comparator) SitePotentialMplPlotter (class in pydefect.corrections.site_potential_plotter) SitePotentialPlotter (class in pydefect.corrections.site_potential_plotter) sites (pydefect.corrections.efnv_correction.ExtendedFnvCorrection attribute) (pydefect.input_maker.supercell_info.SupercellInfo attribute) sort_sites_by_integrated_chg() (pydefect.cli.vasp.make_local_extrema.ChargeDensityAnalyzer method) source (pydefect.chem_pot_diag.chem_pot_diag.CompositionEnergy attribute) space_group (pydefect.input_maker.supercell_info.SupercellInfo attribute)

specie (pydefect.analyzer.defect_structure_info.Displacement attribute) (pydefect.corrections.efnv_correction.PotentialSite attribute) spherical_dist() (pydefect.analyzer.grids.Grids method) spin (pydefect.analyzer.concentration.degeneracy.Degeneracy attribute) StandardEnergies (class in pydefect.chem_pot_diag.chem_pot_diag) states (pydefect.analyzer.band_edge_states.BandEdgeStates attribute) std_rel_energies (pydefect.chem_pot_diag.chem_pot_diag.CompositionEnergies property) str_header (pydefect.analyzer.concentration.concentration.Concentration property) (pydefect.analyzer.concentration.concentration.DefectConcentration property) str_int_to_int() (in module pydefect.cli.main_tools) str_list (pydefect.analyzer.concentration.concentration.Concentration property) (pydefect.analyzer.concentration.concentration.DefectConcentration property) (pydefect.input_maker.complex_defect_set.ComplexDefect property) (pydefect.input_maker.defect.Defect property) stripe_numbers() (in module pydefect.input_maker.supercell_info) structure (pydefect.analyzer.calc_results.CalcResults attribute) (pydefect.input_maker.defect_entry.DefectEntry attribute) (pydefect.input_maker.supercell_info.SupercellInfo attribute) structure_comparator() (in module pydefect.tests.analyzer.test_defect_structure_comparator) structure_comparator_periodic_issue() (in module pydefect.tests.analyzer.test_defect_structure_comparator) structures() (in module pydefect.tests.conftest) subgroup (pydefect.analyzer.defect_structure_info.SymmRelation attribute) substituted (pydefect.analyzer.defect_structure_info.DefectType attribute) sum_alignment_term (pydefect.corrections.gkfo_correction.GkfoCorrection property) sum_chg_dens_distribution() (pydefect.analyzer.defect_charge_info.DefectChargeInfo method) sum_pc_correction (pydefect.corrections.gkfo_correction.GkfoCorrection property) Supercell (class in pydefect.input_maker.supercell) supercell_cbm (pydefect.analyzer.defect_energy.DefectEnergySummary attribute) (pydefect.analyzer.transition_levels.TransitionLevels attribute) supercell_info() (in module pydefect.tests.conftest) (in module pydefect.tests.input_maker.test_complex_defect_entries_make) supercell_vbm (pydefect.analyzer.defect_energy.DefectEnergySummary attribute) (pydefect.analyzer.transition_levels.TransitionLevels attribute) SupercellError SupercellInfo (class in pydefect.input_maker.supercell_info) SupercellMaker (class in pydefect.input_maker.supercell_maker) Supercells (class in pydefect.input_maker.supercell) supergroup (pydefect.analyzer.defect_structure_info.SymmRelation attribute) symm_relation (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) (pydefect.analyzer.defect_structure_info.DefectStructureInfo property) symmetry_relation() (in module pydefect.analyzer.defect_structure_info) SymmRelation (class in pydefect.analyzer.defect_structure_info) symprec (pydefect.analyzer.defect_structure_info.DefectStructureInfo attribute) system (pydefect.analyzer.unitcell.Unitcell attribute)

T

T (pydefect.analyzer.concentration.concentration.ConcentrationByFermiLevel attribute) t_all_sorted_points (pydefect.analyzer.defect_energy.CrossPoints property) T_before_quench (pydefect.analyzer.concentration.concentration.ConcentrationByFermiLevel attribute) t_boundary_points (pydefect.analyzer.defect_energy.CrossPoints property) t_inner_cross_points (pydefect.analyzer.defect_energy.CrossPoints property) target (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag attribute) (pydefect.chem_pot_diag.chem_pot_diag.TargetVertices attribute) target_coords (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag property) target_element_chem_pot() (in module pydefect.chem_pot_diag.chem_pot_diag) target_vertices_dict (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag attribute) TargetVertex (class in pydefect.chem_pot_diag.chem_pot_diag) TargetVertices (class in pydefect.chem_pot_diag.chem_pot_diag) test() (in module pydefect.tests.corrections.test_efnv_performance) test_actual_files() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_add_atom_to_structure() (in module pydefect.tests.input_maker.test_defect_entries_maker) test_add_interstitial() (in module pydefect.tests.input_maker.test_append_interstitial) test_add_interstitial2() (in module pydefect.tests.input_maker.test_append_interstitial) test_add_interstitial_not_primitive_error() (in module pydefect.tests.input_maker.test_append_interstitial) test_add_interstitials() (in module pydefect.tests.cli.test_main_functions) test_add_interstitials_from_local_extrema() (in module pydefect.tests.cli.test_main_util) (in module pydefect.tests.cli.test_main_util_functions) test_anchor_atom_coords() (in module pydefect.tests.input_maker.test_defect_entry) test_anchor_atom_index() (in module pydefect.tests.input_maker.test_defect_entry) test_append_interstitial() (in module pydefect.tests.cli.test_main) test_atom_mapping_to_perfect() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_average_diele_const() (in module pydefect.tests.analyzer.test_unitcell) test_average_masses() (in module pydefect.tests.analyzer.test_unitcell) test_band_edge_eigenvalues_msonable() (in module pydefect.tests.analyzer.test_band_edge_states) test_band_edge_eigenvalues_to_json_file() (in module pydefect.tests.analyzer.test_band_edge_states) test_band_edge_orbital_info_energies_occupations() (in module pydefect.tests.analyzer.test_band_edge_states) test_band_edge_orbital_info_json_roundtrip() (in module pydefect.tests.analyzer.test_band_edge_states) test_band_edge_orbital_info_repr() (in module pydefect.tests.analyzer.test_band_edge_states) test_band_edge_orbital_infos() (in module pydefect.tests.cli.vasp.test_main_vasp) test_band_edge_states() (in module pydefect.tests.cli.test_main) test_band_edge_states_band_indices() (in module pydefect.tests.analyzer.test_band_edge_states) test_band_edge_states_has_donor_phs() (in module pydefect.tests.analyzer.test_band_edge_states) test_band_edge_states_json_roundtrip() (in module pydefect.tests.analyzer.test_band_edge_states) test_band_edge_states_str() (in module pydefect.tests.analyzer.test_band_edge_states) test_band_edge_states_str2() (in module pydefect.tests.analyzer.test_band_edge_states) test_boltzmann_dist() (in module pydefect.tests.analyzer.concentration.test_distribution_function) test_calc_charge_state() (in module pydefect.tests.cli.vasp.test_main_vasp_util) (in module pydefect.tests.cli.vasp.test_main_vasp_util_functions) test_calc_defect_charge_info() (in module pydefect.tests.cli.vasp.test_main_vasp_util) test_calc_defect_concentrations() (in module pydefect.tests.cli.test_main_util_functions) test_calc_defect_structure_info() (in module pydefect.tests.cli.test_main_functions) test_calc_grids() (in module pydefect.tests.cli.vasp.test_main_vasp_util) (in module pydefect.tests.cli.vasp.test_main_vasp_util_functions) test_calc_max_sphere_radius() (in module pydefect.tests.cli.vasp.test_make_efnv_correction) test_calc_results() (in module pydefect.tests.cli.vasp.test_main_vasp) test_calc_results_json_roundtrip() (in module pydefect.tests.analyzer.test_calc_results) test_calc_results_show_convergence_warning() (in module pydefect.tests.analyzer.test_calc_results) test_calc_results_str() (in module pydefect.tests.analyzer.test_calc_results) test_calc_summary_msonable() (in module pydefect.tests.analyzer.test_calc_summary) test_calc_summary_str() (in module pydefect.tests.analyzer.test_calc_summary) test_calc_u_value() (in module pydefect.tests.analyzer.test_defect_energy_util) test_calc_u_value_with_shallow() (in module pydefect.tests.analyzer.test_defect_energy_util) test_carrier_concentration_net_charge() (in module pydefect.tests.analyzer.concentration.test_concentration) test_carrier_concentration_str() (in module pydefect.tests.analyzer.concentration.test_concentration) test_cb_dos() (in module pydefect.tests.analyzer.concentration.test_make_concentration) test_center_1d_periodic_quantity() (in module pydefect.tests.cli.vasp.test_make_defect_charge_info) test_charge_dist_json_roundtrip() (in module pydefect.tests.analyzer.test_defect_charge_info) test_charge_energies_cross_points() (in module pydefect.tests.analyzer.test_defect_energy) test_charge_energies_energy_at_ef() (in module pydefect.tests.analyzer.test_defect_energy) test_charge_energies_energy_range() (in module pydefect.tests.analyzer.test_defect_energy) test_charge_energies_pinning_level() (in module pydefect.tests.analyzer.test_defect_energy) test_charge_energies_pinning_levels() (in module pydefect.tests.analyzer.test_defect_energy) test_charge_set() (in module pydefect.tests.input_maker.test_defect_set) test_check_site_structure_consistency() (in module pydefect.tests.input_maker.test_manual_supercell_maker) test_complex_defect_set() (in module pydefect.tests.input_maker.test_complex_defect_set) test_composition_energies_from_mp() (in module pydefect.tests.cli.test_main_util_functions) test_con_by_Ef_str() (in module pydefect.tests.analyzer.concentration.test_concentration) test_concentration_by_fermi_level() (in module pydefect.tests.analyzer.concentration.test_concentration) test_concentration_by_fermi_level_msonable() (in module pydefect.tests.analyzer.concentration.test_make_concentration) test_concentration_str() (in module pydefect.tests.analyzer.concentration.test_concentration) test_concentrations() (in module pydefect.tests.analyzer.concentration.test_concentration) test_create_supercell() (in module pydefect.tests.input_maker.test_manual_supercell_maker) (in module pydefect.tests.input_maker.test_supercell_maker) test_create_supercell_2() (in module pydefect.tests.input_maker.test_manual_supercell_maker) test_create_supercell_generate_supercell_info() (in module pydefect.tests.input_maker.test_supercell_maker) test_create_supercell_matrix() (in module pydefect.tests.input_maker.test_supercell_maker) test_create_supercell_raise_not_primitive_error() (in module pydefect.tests.input_maker.test_supercell_maker) test_create_supercell_tetragonal() (in module pydefect.tests.input_maker.test_supercell_maker) test_cross_points() (in module pydefect.tests.analyzer.test_defect_energy) test_cross_points_e_max_energies_dicts() (in module pydefect.tests.analyzer.test_defect_energy) test_data_files() (in module pydefect.tests.conftest) test_def_str_info_defect_type() (in module pydefect.tests.analyzer.test_defect_structure_info) test_defect_center_periodicity() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_defect_charge_info_are_localized() (in module pydefect.tests.analyzer.test_defect_charge_info) test_defect_charge_info_half_charge_radius() (in module pydefect.tests.analyzer.test_defect_charge_info) test_defect_charge_info_json_roundtrip() (in module pydefect.tests.analyzer.test_defect_charge_info) test_defect_charge_info_repr() (in module pydefect.tests.analyzer.test_defect_charge_info) test_defect_charge_info_show_dist() (in module pydefect.tests.analyzer.test_defect_charge_info) test_defect_charge_info_sum_chg_dens_distribution() (in module pydefect.tests.analyzer.test_defect_charge_info) test_defect_charge_info_uniform_half_charge_radius() (in module pydefect.tests.analyzer.test_defect_charge_info) test_defect_concentration() (in module pydefect.tests.analyzer.concentration.test_concentration) test_defect_concentration_str() (in module pydefect.tests.analyzer.concentration.test_concentration) test_defect_energies_mpl_plot() (in module pydefect.tests.analyzer.test_defect_energy_plotter) test_defect_energies_mpl_settings() (in module pydefect.tests.analyzer.test_defect_energy_plotter) test_defect_energy_infos() (in module pydefect.tests.cli.test_main) test_defect_energy_summary() (in module pydefect.tests.cli.test_main) test_defect_energy_summary_charge_energies() (in module pydefect.tests.analyzer.test_defect_energy) test_defect_energy_summary_exclude_defects() (in module pydefect.tests.analyzer.test_defect_energy) test_defect_energy_summary_json_roundtrip() (in module pydefect.tests.analyzer.test_defect_energy) test_defect_energy_summary_latexified_title() (in module pydefect.tests.analyzer.test_defect_energy) test_defect_energy_summary_str() (in module pydefect.tests.analyzer.test_defect_energy) test_defect_entries() (in module pydefect.tests.cli.vasp.test_main_vasp) test_defect_entries_interstitials() (in module pydefect.tests.input_maker.test_defect_entries_maker) test_defect_entries_maker() (in module pydefect.tests.input_maker.test_defect_entries_maker) test_defect_entries_maker_from_sites() (in module pydefect.tests.input_maker.test_complex_defect_entries_make) test_defect_entries_maker_insert_host_atoms() (in module pydefect.tests.input_maker.test_defect_entries_maker) test_defect_entry() (in module pydefect.tests.input_maker.test_defect_entry) test_defect_entry_str() (in module pydefect.tests.input_maker.test_defect_entry) test_defect_hashable() (in module pydefect.tests.input_maker.test_defect) test_defect_msonable() (in module pydefect.tests.input_maker.test_defect) test_defect_name_and_charges() (in module pydefect.tests.input_maker.test_defect) test_defect_set() (in module pydefect.tests.input_maker.test_defect_set) test_defect_set_maker() (in module pydefect.tests.input_maker.test_defect_set_maker) test_defect_set_maker_dopants() (in module pydefect.tests.input_maker.test_defect_set_maker) test_defect_set_maker_electroneg_diff() (in module pydefect.tests.input_maker.test_defect_set_maker) test_defect_set_maker_oxi_state() (in module pydefect.tests.input_maker.test_defect_set_maker) test_defect_set_maker_screening() (in module pydefect.tests.input_maker.test_defect_set_maker) test_defect_set_msonable() (in module pydefect.tests.input_maker.test_defect_set) test_defect_set_w_options() (in module pydefect.tests.cli.test_main) test_defect_set_wo_options() (in module pydefect.tests.cli.test_main) test_defect_site_diff_pot() (in module pydefect.tests.corrections.test_efnv_correction) test_defect_site_msonable() (in module pydefect.tests.corrections.test_efnv_correction) test_defect_structure_analyzer_defect_center() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_defect_structure_info() (in module pydefect.tests.cli.test_main) test_defect_structure_info_json_roundtrip() (in module pydefect.tests.analyzer.test_defect_structure_info) test_defect_type() (in module pydefect.tests.analyzer.test_defect_structure_info) test_defect_vesta_file() (in module pydefect.tests.cli.test_make_defect_vesta_file) test_defect_vesta_file_w_options() (in module pydefect.tests.cli.test_main_util) test_defect_vesta_file_wo_options() (in module pydefect.tests.cli.test_main_util) test_degeneracies() (in module pydefect.tests.analyzer.concentration.test_degeneracy) test_degeneracies_yaml_round_trip() (in module pydefect.tests.analyzer.concentration.test_degeneracy) test_dos_carrier_type() (in module pydefect.tests.analyzer.concentration.test_make_concentration) test_effective_ionic_diele_const() (in module pydefect.tests.analyzer.test_unitcell) test_efnv_correction() (in module pydefect.tests.cli.test_main) test_energy_total_correction() (in module pydefect.tests.analyzer.test_defect_energy) test_energy_yaml() (in module pydefect.tests.analyzer.test_defect_energy) test_energy_yaml2() (in module pydefect.tests.analyzer.test_defect_energy) test_ewald() (in module pydefect.tests.corrections.test_ewald) test_ewald_lattice_set() (in module pydefect.tests.corrections.test_ewald) test_ewald_real() (in module pydefect.tests.corrections.test_ewald) test_ewald_rec() (in module pydefect.tests.corrections.test_ewald) test_ewald_vector_nums() (in module pydefect.tests.corrections.test_ewald) test_ewald_xyz() (in module pydefect.tests.corrections.test_ewald) test_extended_fnv_correction_alignment_correction() (in module pydefect.tests.corrections.test_efnv_correction) (in module pydefect.tests.corrections.test_gkfo_correction) test_extended_fnv_correction_ave_pot_diff() (in module pydefect.tests.corrections.test_efnv_correction) test_extended_fnv_correction_correction_dict() (in module pydefect.tests.corrections.test_efnv_correction) test_extended_fnv_correction_correction_energy() (in module pydefect.tests.corrections.test_efnv_correction) (in module pydefect.tests.corrections.test_gkfo_correction) test_extended_fnv_correction_msonable() (in module pydefect.tests.corrections.test_efnv_correction) test_extrema_coords() (in module pydefect.tests.cli.vasp.test_make_local_extrema) test_fermi_dirac() (in module pydefect.tests.analyzer.concentration.test_distribution_function) test_find_inequivalent_coords() (in module pydefect.tests.cli.vasp.test_make_local_extrema) test_fold_coords() (in module pydefect.tests.analyzer.test_make_defect_structure_info) test_from_file() (in module pydefect.tests.input_maker.test_defect_set) test_from_yaml() (in module pydefect.tests.input_maker.test_complex_defect_set) test_full_name() (in module pydefect.tests.input_maker.test_defect_entry) test_gkfo_correction() (in module pydefect.tests.cli.test_main_util) test_gkfo_correction_charge() (in module pydefect.tests.corrections.test_gkfo_correction) test_gkfo_correction_defect_region_radius() (in module pydefect.tests.corrections.test_gkfo_correction) test_gkfo_correction_pc_1st_term() (in module pydefect.tests.corrections.test_gkfo_correction) test_gkfo_correction_sum_pc_correction() (in module pydefect.tests.corrections.test_gkfo_correction) test_gkfo_site_potential_plotter() (in module pydefect.tests.corrections.test_site_potential_plotter) test_grids_from_chgcar() (in module pydefect.tests.analyzer.test_grids) test_grids_joblib_roundtrip() (in module pydefect.tests.analyzer.test_grids) test_grids_np_save_load_roundtrip() (in module pydefect.tests.analyzer.test_grids) test_hashable() (in module pydefect.tests.input_maker.test_defect_entry) test_interstitial() (in module pydefect.tests.input_maker.test_supercell_info) test_is_correction() (in module pydefect.tests.corrections.test_gkfo_correction) test_json_round_trip() (in module pydefect.tests.input_maker.test_supercell_info) test_json_roundtrip() (in module pydefect.tests.input_maker.test_defect_entry) test_judge_defect_type() (in module pydefect.tests.analyzer.test_defect_structure_info) test_kpt_idx() (in module pydefect.tests.analyzer.test_band_edge_states) test_local_extrema_append_sites_to_supercell_info() (in module pydefect.tests.input_maker.test_local_extrema) test_local_extrema_append_sites_to_supercell_info2() (in module pydefect.tests.input_maker.test_local_extrema) test_local_extrema_json_roundtrip() (in module pydefect.tests.input_maker.test_local_extrema) test_local_extrema_str() (in module pydefect.tests.input_maker.test_local_extrema)

test_make_band_edge_orb_infos_and_eigval_plot() (in module pydefect.tests.cli.vasp.test_main_vasp_functions) test_make_band_edge_orbital_infos() (in module pydefect.tests.cli.vasp.test_make_band_edge_orbital_infos) test_make_band_edge_state() (in module pydefect.tests.analyzer.test_make_band_edge_states) test_make_band_edge_state_w_defect_charge_info() (in module pydefect.tests.analyzer.test_make_band_edge_states) test_make_band_edge_state_wo_participation_ratio() (in module pydefect.tests.analyzer.test_make_band_edge_states) test_make_band_edge_states() (in module pydefect.tests.cli.test_main_functions) test_make_calc_results() (in module pydefect.tests.cli.vasp.test_main_vasp_functions) test_make_calc_results_from_vasp_results() (in module pydefect.tests.cli.vasp.test_make_calc_results) test_make_calc_summary() (in module pydefect.tests.analyzer.test_make_calc_summary) test_make_carrier_concentrations() (in module pydefect.tests.analyzer.concentration.test_make_concentration) test_make_charge_dist() (in module pydefect.tests.cli.vasp.test_make_defect_charge_info) test_make_chem_pot_diag_from_mp() (in module pydefect.tests.cli.vasp.test_make_composition_energies_from_mp) test_make_chem_pot_diag_from_mp_yaml() (in module pydefect.tests.cli.vasp.test_make_composition_energies_from_mp) test_make_competing_phase_dirs() (in module pydefect.tests.cli.vasp.test_main_vasp_functions) test_make_composition_energies() (in module pydefect.tests.cli.vasp.test_main_vasp_functions) test_make_cpd_and_vertices() (in module pydefect.tests.cli.test_main_functions) test_make_cpd_and_vertices_options() (in module pydefect.tests.cli.test_main) test_make_cpd_options() (in module pydefect.tests.cli.test_main_util) test_make_def_str_info_same_config_from_init() (in module pydefect.tests.analyzer.test_defect_structure_info) test_make_def_str_info_symm_rel() (in module pydefect.tests.analyzer.test_defect_structure_info) test_make_defect_charge_info() (in module pydefect.tests.cli.vasp.test_make_defect_charge_info) test_make_defect_charge_info_main() (in module pydefect.tests.cli.vasp.test_main_vasp_util_functions) test_make_defect_energy_info() (in module pydefect.tests.analyzer.test_make_defect_energy_info) test_make_defect_energy_summary() (in module pydefect.tests.analyzer.test_make_defect_energy_summary) test_make_defect_entries() (in module pydefect.tests.cli.vasp.test_main_vasp_functions) test_make_defect_entry() (in module pydefect.tests.cli.vasp.test_main_vasp_util) (in module pydefect.tests.input_maker.test_defect_entry) test_make_defect_entry_main() (in module pydefect.tests.cli.vasp.test_main_vasp_util_functions) test_make_defect_set() (in module pydefect.tests.cli.test_main_functions) test_make_defect_structure_info() (in module pydefect.tests.analyzer.test_make_defect_structure_info) test_make_defect_structure_info2() (in module pydefect.tests.analyzer.test_make_defect_structure_info) test_make_defect_vesta_file() (in module pydefect.tests.cli.test_main_util_functions) test_make_degeneracy() (in module pydefect.tests.analyzer.concentration.test_degeneracy) test_make_efnv_correction() (in module pydefect.tests.cli.vasp.test_make_efnv_correction) test_make_efnv_correction_from_vasp() (in module pydefect.tests.cli.test_main_functions) test_make_gkfo_correction() (in module pydefect.tests.cli.vasp.test_make_gkfo_correction) test_make_gkfo_correction_from_vasp() (in module pydefect.tests.cli.test_main_util_functions) test_make_local_extrema() (in module pydefect.tests.cli.vasp.test_main_vasp_functions) test_make_local_extrema_from_volumetric_data() (in module pydefect.tests.cli.vasp.test_make_local_extrema) test_make_local_extrema_w_options() (in module pydefect.tests.cli.vasp.test_main_vasp) test_make_local_extrema_wo_options() (in module pydefect.tests.cli.vasp.test_main_vasp) test_make_parchg_dir() (in module pydefect.tests.cli.vasp.test_main_vasp_util) (in module pydefect.tests.cli.vasp.test_main_vasp_util_functions) test_make_perfect_band_edge_state_from_vasp() (in module pydefect.tests.cli.vasp.test_make_perfect_band_edge_state) test_make_poscars_from_query() (in module pydefect.tests.cli.vasp.test_make_poscars_from_query) test_make_poscars_w_options() (in module pydefect.tests.cli.vasp.test_main_vasp) test_make_poscars_wo_options() (in module pydefect.tests.cli.vasp.test_main_vasp) test_make_recommended_supercell() (in module pydefect.tests.cli.test_main_functions) test_make_recommended_supercell2() (in module pydefect.tests.cli.test_main_functions) test_make_site_diff() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_make_site_diff_wo_diff() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_make_sites_from_yaml() (in module pydefect.tests.input_maker.test_manual_supercell_maker) test_make_sites_from_yaml_w_error() (in module pydefect.tests.input_maker.test_manual_supercell_maker) test_make_standard_and_relative_energies() (in module pydefect.tests.cli.test_main_functions) test_make_standard_and_relative_energies_options() (in module pydefect.tests.cli.test_main) test_make_supercell_from_matrix() (in module pydefect.tests.cli.test_main_functions) test_make_supercell_w_options() (in module pydefect.tests.cli.test_main) test_make_supercell_wo_options() (in module pydefect.tests.cli.test_main) test_make_transition_levels() (in module pydefect.tests.analyzer.test_transition_levels) test_make_unitcell() (in module pydefect.tests.cli.vasp.test_main_vasp_functions) test_matrix_from_x_y() (in module pydefect.tests.input_maker.test_supercell) test_msonable() (in module pydefect.tests.corrections.test_ewald) (in module pydefect.tests.input_maker.test_defect_entry) test_neighboring_atom_indices() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_next_Ef_to_neutral_concentration() (in module pydefect.tests.analyzer.concentration.test_concentration) test_next_x_y_combination() (in module pydefect.tests.input_maker.test_supercell) test_num_atom_diff() (in module pydefect.tests.analyzer.test_make_defect_energy_info) test_num_electron_in_cbm() (in module pydefect.tests.analyzer.test_make_band_edge_states) test_num_hole_in_vbm() (in module pydefect.tests.analyzer.test_make_band_edge_states) test_orbital_diff() (in module pydefect.tests.analyzer.test_make_band_edge_states) test_orbital_info_msonable() (in module pydefect.tests.analyzer.test_band_edge_states) test_parse_dirs() (in module pydefect.tests.cli.test_main_tools) test_parse_dirs_fail() (in module pydefect.tests.cli.test_main_tools) test_parse_dirs_file() (in module pydefect.tests.cli.test_main_tools) test_parse_dirs_skip_when_output_file_exist() (in module pydefect.tests.cli.test_main_tools) test_perfect_band_edge_state() (in module pydefect.tests.cli.vasp.test_main_vasp) test_perfect_edge_state_json_roundtrip() (in module pydefect.tests.analyzer.test_band_edge_states) test_perturbed_site_indices() (in module pydefect.tests.input_maker.test_defect_entry) test_perturbed_structure() (in module pydefect.tests.input_maker.test_defect_entries_maker) test_pinning_level() (in module pydefect.tests.analyzer.concentration.test_concentration) test_pinning_levels_from_charge_energies() (in module pydefect.tests.analyzer.test_pinning_levels) test_plot() (in module pydefect.tests.analyzer.test_eigenvalue_plotter) test_plot_chem_pot_diag() (in module pydefect.tests.cli.test_main_functions) test_plot_concentration() (in module pydefect.tests.analyzer.concentration.test_plot_concentration) test_plot_cpd_options() (in module pydefect.tests.cli.test_main) test_plot_defect_concentration() (in module pydefect.tests.analyzer.concentration.test_plot_concentration) test_plot_defect_formation_energy() (in module pydefect.tests.cli.test_main) test_plot_wo_spin() (in module pydefect.tests.analyzer.test_eigenvalue_plotter) test_pop_interstitial() (in module pydefect.tests.cli.test_main) test_pop_interstitials() (in module pydefect.tests.cli.test_main_functions) test_pop_interstitials_pop_all() (in module pydefect.tests.cli.test_main_functions) test_pretty_orbital() (in module pydefect.tests.analyzer.test_band_edge_states) test_random_3d_vector() (in module pydefect.tests.input_maker.test_defect_entries_maker) test_redistribute_concentration() (in module pydefect.tests.analyzer.concentration.test_make_concentration) test_refine_defect_poscar() (in module pydefect.tests.cli.vasp.test_main_vasp_util) test_refine_poscar() (in module pydefect.tests.cli.vasp.test_main_vasp_util_functions) test_remove_higher_energy_comp() (in module pydefect.tests.cli.vasp.test_make_composition_energies_from_mp) test_repr() (in module pydefect.tests.analyzer.test_defect_structure_info) (in module pydefect.tests.corrections.test_efnv_correction) (in module pydefect.tests.corrections.test_gkfo_correction) test_rhombohedral_supercell_info() (in module pydefect.tests.input_maker.test_supercell_maker) test_rhombohedral_supercells() (in module pydefect.tests.input_maker.test_supercell) test_sanitize_matrix_1_input_value() (in module pydefect.tests.cli.test_main_tools) test_sanitize_matrix_3_input_values() (in module pydefect.tests.cli.test_main_tools) test_sanitize_matrix_9_input_values() (in module pydefect.tests.cli.test_main_tools) test_sanitize_matrix_raise_error_for_improper_matrix_element_length() (in module pydefect.tests.cli.test_main_tools) test_screen_defect() (in module pydefect.tests.input_maker.test_defect) test_screen_defect_set() (in module pydefect.tests.input_maker.test_defect_set) test_shift_distance_data() (in module pydefect.tests.analyzer.test_grids) test_shift_distance_data2() (in module pydefect.tests.analyzer.test_grids) test_show_pinning_levels() (in module pydefect.tests.cli.test_main_util_functions) test_show_transition_levels() (in module pydefect.tests.analyzer.test_transition_levels) test_show_u_values() (in module pydefect.tests.cli.test_main_util) (in module pydefect.tests.cli.test_main_util_functions) test_simple_defect() (in module pydefect.tests.input_maker.test_defect) test_simple_defect_hashable() (in module pydefect.tests.input_maker.test_defect) test_simple_defect_msonable() (in module pydefect.tests.input_maker.test_defect) test_single_calc_summary_msonable() (in module pydefect.tests.analyzer.test_calc_summary) test_single_calc_summary_properties() (in module pydefect.tests.analyzer.test_calc_summary) test_site_diff() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_site_diff_is_no_diff() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_site_diff_msonable() (in module pydefect.tests.analyzer.test_defect_structure_comparator) test_site_potential_plotter_with_actual_file() (in module pydefect.tests.corrections.test_site_potential_plotter) test_site_potential_plotter_with_simple_example() (in module pydefect.tests.corrections.test_site_potential_plotter) test_spglib_cyclic_behavior() (in module pydefect.tests.input_maker.test_supercell_maker) test_spherical_dist() (in module pydefect.tests.analyzer.test_grids) test_str_int_to_int() (in module pydefect.tests.cli.test_main_tools) test_supercell() (in module pydefect.tests.input_maker.test_supercell) test_supercell_average_angle() (in module pydefect.tests.input_maker.test_supercell) test_supercell_info_distances() (in module pydefect.tests.input_maker.test_supercell_info) test_supercell_info_from_dict() (in module pydefect.tests.input_maker.test_supercell_info) test_supercell_info_interstitials_distances() (in module pydefect.tests.input_maker.test_supercell_info) test_supercell_info_msonable() (in module pydefect.tests.input_maker.test_supercell_info) test_supercell_info_str() (in module pydefect.tests.input_maker.test_supercell_info) test_supercell_info_wo_symmetry_info() (in module pydefect.tests.input_maker.test_supercell_info) test_supercell_species_order() (in module pydefect.tests.input_maker.test_supercell) test_supercells() (in module pydefect.tests.input_maker.test_supercell) test_supercells_raise_no_supercell_error() (in module pydefect.tests.input_maker.test_supercell) test_symmetrize_defect_structure() (in module pydefect.tests.analyzer.test_refine_defect_structure) test_symmetrize_defect_structure_2() (in module pydefect.tests.analyzer.test_refine_defect_structure) test_symmetrize_defect_structure_wo_anchor() (in module pydefect.tests.analyzer.test_refine_defect_structure) test_symmetry_relation() (in module pydefect.tests.analyzer.test_defect_structure_info) test_tetragonal_supercells() (in module pydefect.tests.input_maker.test_supercell) test_to_yaml() (in module pydefect.tests.input_maker.test_defect_set) test_transformation_matrix() (in module pydefect.tests.input_maker.test_supercell_maker) test_transition_levels_msonable() (in module pydefect.tests.analyzer.test_transition_levels) test_unitcell() (in module pydefect.tests.analyzer.test_unitcell) (in module pydefect.tests.cli.vasp.test_main_vasp) (in module pydefect.tests.cli.vasp.test_make_unitcell) test_vb_dos() (in module pydefect.tests.analyzer.concentration.test_make_concentration) test_yaml_roundtrip() (in module pydefect.tests.analyzer.test_unitcell) tetra_close_to_cubic() (in module pydefect.tests.conftest) TetragonalSupercells (class in pydefect.input_maker.supercell) threshold_abs (pydefect.input_maker.local_extrema.VolumetricDataAnalyzeParams attribute) threshold_frac (pydefect.input_maker.local_extrema.VolumetricDataAnalyzeParams attribute) title (pydefect.analyzer.defect_energy.DefectEnergySummary attribute) tl_energy_widths (pydefect.analyzer.transition_levels_plotter.MplTLData attribute) to_istructure() (in module pydefect.input_maker.defect_entries_maker) to_json_file() (pydefect.corrections.abstract_correction.Correction method) to_phase_diagram() (pydefect.chem_pot_diag.chem_pot_diag.CompositionEnergies method) to_prior_info() (pydefect.input_maker.defect_entry.DefectEntry method) to_target_vertices (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag property) to_yaml() (pydefect.analyzer.defect_energy.DefectEnergies method) (pydefect.analyzer.defect_energy.DefectEnergyInfo method) (pydefect.chem_pot_diag.chem_pot_diag.CompositionEnergies method) (pydefect.chem_pot_diag.chem_pot_diag.CpdAbstractEnergies method) (pydefect.chem_pot_diag.chem_pot_diag.TargetVertices method) (pydefect.input_maker.defect_set.DefectSet method) to_yaml_file() (pydefect.analyzer.unitcell.Unitcell method) tol (pydefect.input_maker.local_extrema.VolumetricDataAnalyzeParams attribute) total_concentration (pydefect.analyzer.concentration.concentration.DefectConcentration property) total_correction (pydefect.analyzer.defect_energy.DefectEnergy property) TotalDos (class in pydefect.analyzer.concentration.make_concentration) transformation_matrix (pydefect.input_maker.supercell_info.SupercellInfo attribute) (pydefect.input_maker.supercell_maker.SupercellMaker property) transition_levels (pydefect.analyzer.transition_levels.TransitionLevels attribute) transition_levels() (in module pydefect.tests.analyzer.test_transition_levels) TransitionLevel (class in pydefect.analyzer.transition_levels) TransitionLevels (class in pydefect.analyzer.transition_levels) TransitionLevelsMplPlotter (class in pydefect.analyzer.transition_levels_plotter) transpose() (in module pydefect.chem_pot_diag.cpd_plotter) typical_defect_name() (in module pydefect.util.prepare_names)

U

u_values_from_defect_energies() (in module pydefect.analyzer.defect_energy_util) uniform_half_charge_radius (pydefect.analyzer.defect_charge_info.DefectChargeInfo property) unique_point_group() (in module pydefect.analyzer.defect_structure_info) unit_cell (pydefect.input_maker.local_extrema.VolumetricDataLocalExtrema attribute) Unitcell (class in pydefect.analyzer.unitcell) unitcell() (in module pydefect.tests.analyzer.test_unitcell)

unitcell_structure (pydefect.input_maker.supercell_info.SupercellInfo attribute) unknown (pydefect.analyzer.defect_structure_info.DefectType attribute) unoccupied_deep_state (pydefect.analyzer.calc_summary.SingleCalcSummary attribute) unstable_comp_info (pydefect.chem_pot_diag.chem_pot_diag.RelativeEnergies property) unstable_compounds (pydefect.chem_pot_diag.chem_pot_diag.RelativeEnergies property) UnstableTargetError

V

vacancy (pydefect.analyzer.defect_structure_info.DefectType attribute) vacancy_split (pydefect.analyzer.defect_structure_info.DefectType attribute) vasp_files() (in module pydefect.tests.conftest) VBDos (class in pydefect.analyzer.concentration.make_concentration) vbm (pydefect.analyzer.concentration.make_concentration.TotalDos attribute) (pydefect.analyzer.unitcell.Unitcell attribute) vbm_hole_occupation (pydefect.analyzer.band_edge_states.BandEdgeState attribute) vbm_info (pydefect.analyzer.band_edge_states.BandEdgeState attribute) (pydefect.analyzer.band_edge_states.PerfectBandEdgeState attribute)

vbm_orbital_diff (pydefect.analyzer.band_edge_states.BandEdgeState attribute) vertex_elements (pydefect.chem_pot_diag.chem_pot_diag.ChemPotDiag attribute) vertices (pydefect.chem_pot_diag.chem_pot_diag.TargetVertices attribute) vol_params() (in module pydefect.tests.conftest) volume (pydefect.analyzer.concentration.make_concentration.TotalDos attribute) VolumetricDataAnalyzeParams (class in pydefect.input_maker.local_extrema) VolumetricDataLocalExtrema (class in pydefect.input_maker.local_extrema)

W

wyckoff_letter (pydefect.input_maker.supercell_info.SimpleSite attribute)

X

xyz() (pydefect.corrections.ewald.Ewald static method)