Index

_

_BilbaoCS_conv_cell_vector_mapping (doped.core.DefectEntry attribute)

_get_entries_kwargs (doped.chemical_potentials.CompetingPhases attribute)

A

add_charge_states() (doped.generation.DefectsGenerator method) add_entries() (doped.thermodynamics.DefectThermodynamics method) all_entries (doped.thermodynamics.DefectThermodynamics attribute) all_stable_entries (doped.thermodynamics.DefectThermodynamics property) all_unstable_entries (doped.thermodynamics.DefectThermodynamics property) apply_corrections() (doped.analysis.DefectParser method) apply_s2_to_s1_transformation() (in module doped.utils.configurations) apply_symm_op_to_site() (in module doped.utils.symmetry) apply_symm_op_to_struct() (in module doped.utils.symmetry)

are_equivalent_lattices() (in module doped.utils.symmetry) array_to_tuple() (in module doped.utils.efficiency) as_dict() (doped.chemical_potentials.ChemicalPotentialGrid method) (doped.chemical_potentials.CompetingPhases method) (doped.chemical_potentials.CompetingPhasesAnalyzer method) (doped.core.Defect method) (doped.generation.DefectsGenerator method) (doped.thermodynamics.DefectThermodynamics method) (doped.vasp.DefectsSet method)

B

backend (doped.thermodynamics.FermiSolver attribute) band_edge_properties_from_vasprun() (in module doped.utils.eigenvalues) band_gap (doped.thermodynamics.DefectThermodynamics attribute) bold_print() (in module doped.thermodynamics) bulk_dos (doped.thermodynamics.DefectThermodynamics property) bulk_entry (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) (doped.core.DefectEntry attribute) bulk_entry_energy (doped.core.DefectEntry property) bulk_formula (doped.thermodynamics.DefectThermodynamics attribute) bulk_site_concentration (doped.core.DefectEntry property) bulk_structure (doped.chemical_potentials.CompetingPhases attribute)

bulk_supercell (doped.core.DefectEntry attribute) (doped.generation.DefectsGenerator attribute) (doped.vasp.DefectRelaxSet attribute) (doped.vasp.DefectsSet attribute) bulk_vasp_gam (doped.vasp.DefectRelaxSet property) (doped.vasp.DefectsSet attribute) bulk_vasp_ncl (doped.vasp.DefectRelaxSet property) (doped.vasp.DefectsSet attribute) bulk_vasp_nkred_std (doped.vasp.DefectRelaxSet property) (doped.vasp.DefectsSet attribute) bulk_vasp_std (doped.vasp.DefectRelaxSet property) (doped.vasp.DefectsSet attribute)

C

cache_ready_Site__eq__() (in module doped.utils.efficiency) cache_species() (in module doped.utils.efficiency) cached_allclose() (in module doped.utils.efficiency) cached_simplify() (in module doped.utils.symmetry) cached_solve() (in module doped.utils.symmetry) cached_Structure_eq_func() (in module doped.utils.efficiency) calc_displacements_ellipsoid() (in module doped.utils.displacements) calc_site_displacements() (in module doped.utils.displacements) calculate_chempots() (doped.chemical_potentials.CompetingPhasesAnalyzer method) calculation_metadata (doped.core.DefectEntry attribute) cell_metric() (in module doped.utils.supercells) charge_state (doped.core.DefectEntry attribute) charge_state_guessing_log (doped.core.DefectEntry attribute) charge_state_probability() (in module doped.generation) charges (doped.utils.plotting.TransitionLevel attribute) check_and_set_defect_entry_name() (in module doped.analysis) check_atom_mapping_far_from_defect() (in module doped.utils.parsing) check_compatibility (doped.thermodynamics.DefectThermodynamics attribute) ChemicalPotentialGrid (class in doped.chemical_potentials) chempot_grid (doped.chemical_potentials.CompetingPhasesAnalyzer property) chempots (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) (doped.thermodynamics.DefectThermodynamics property)

chempots_df (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) closest_site_info() (in module doped.generation) cluster_coords() (in module doped.utils.symmetry) cluster_sites_by_dist_tol() (in module doped.utils.symmetry) clustered_defect_entries (doped.thermodynamics.DefectThermodynamics attribute) clustered_defect_entries_by_type (doped.thermodynamics.DefectThermodynamics attribute) compare_incar_tags() (in module doped.utils.parsing) compare_kpoints() (in module doped.utils.parsing) compare_potcar_symbols() (in module doped.utils.parsing) CompetingPhases (class in doped.chemical_potentials) CompetingPhasesAnalyzer (class in doped.chemical_potentials) composition (doped.chemical_potentials.CompetingPhases attribute) (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) conn_x (doped.utils.plotting.TransitionLevelLabel attribute) conn_y (doped.utils.plotting.TransitionLevelLabel attribute) conv_cell_frac_coords (doped.core.DefectEntry attribute) conventional_structure (doped.core.DefectEntry attribute) (doped.generation.DefectsGenerator attribute) convergence_set (in module doped.chemical_potentials) convergence_setup() (doped.chemical_potentials.CompetingPhases method) corrected_energy (doped.core.DefectEntry property) corrections (doped.core.DefectEntry attribute) corrections_metadata (doped.core.DefectEntry attribute)

D

deep_dict_update() (in module doped.vasp) default_defect_relax_set (in module doped.vasp) default_defect_set (in module doped.vasp) default_energy_affecting_incar_tags (in module doped.utils.parsing) default_get_entries_kwargs (in module doped.chemical_potentials) default_HSE_set (in module doped.vasp) default_potcar_dict (in module doped.vasp) default_relax_set (in module doped.vasp) Defect (class in doped.core) defect (doped.core.DefectEntry attribute) defect_and_info_from_structures() (in module doped.analysis) defect_charge_map (doped.thermodynamics.DefectThermodynamics attribute) defect_dict (doped.analysis.DefectsParser attribute) defect_entries (doped.generation.DefectsGenerator attribute) (doped.thermodynamics.DefectThermodynamics property) (doped.vasp.DefectsSet attribute) defect_from_structures() (in module doped.analysis) defect_generator_info() (doped.generation.DefectsGenerator method) defect_names (doped.thermodynamics.DefectThermodynamics property) defect_sets (doped.vasp.DefectsSet attribute) defect_site (doped.core.Defect property) defect_site_from_structures() (in module doped.analysis) defect_structure_from_sites() (in module doped.core) defect_supercell (doped.core.DefectEntry attribute) (doped.vasp.DefectRelaxSet attribute) defect_supercell_site (doped.core.DefectEntry attribute) defect_thermodynamics (doped.thermodynamics.FermiSolver attribute) DefectDictSet (class in doped.vasp) DefectEntry (class in doped.core) DefectParser (class in doped.analysis) DefectRelaxSet (class in doped.vasp) defects (doped.generation.DefectsGenerator attribute) DefectsGenerator (class in doped.generation) DefectsParser (class in doped.analysis) DefectsSet (class in doped.vasp) DefectThermodynamics (class in doped.thermodynamics) degeneracy_factors (doped.core.DefectEntry attribute) dist_tol (doped.thermodynamics.DefectThermodynamics property) doped module doped.analysis module

doped.chemical_potentials module doped.core module doped.corrections module doped.generation module doped.thermodynamics module doped.utils module doped.utils.configurations module doped.utils.displacements module doped.utils.efficiency module doped.utils.eigenvalues module doped.utils.legacy_corrections module doped.utils.parsing module doped.utils.plotting module doped.utils.stenciling module doped.utils.supercells module doped.utils.symmetry module doped.vasp module doped_cluster_frac_coords() (in module doped.utils.symmetry) doped_Composition_eq_func() (in module doped.utils.efficiency) doped_defect_from_pmg_defect() (in module doped.core) doped_plot_style() (in module doped.utils.plotting) doped_Structure__eq__() (in module doped.utils.efficiency) DopedDictSet (class in doped.vasp) DopedTopographyAnalyzer (class in doped.utils.efficiency) DopedVacancyGenerator (class in doped.utils.efficiency)

E

el_refs (doped.thermodynamics.DefectThermodynamics property) element_changes (doped.core.Defect property) elemental_diatomic_bond_lengths (in module doped.chemical_potentials) elemental_energies (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) elements (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) entries (doped.chemical_potentials.CompetingPhases attribute) (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) entries_dict (doped.chemical_potentials.CompetingPhases property) (doped.chemical_potentials.CompetingPhasesAnalyzer property)

entries_from_chempot_limits() (in module doped.chemical_potentials) equilibrium_concentration() (doped.core.DefectEntry method) equiv_conv_cell_frac_coords (doped.core.DefectEntry attribute) equivalent_supercell_sites (doped.core.DefectEntry attribute) extrinsic_elements (doped.chemical_potentials.CompetingPhases attribute) (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) extrinsic_entries (doped.chemical_potentials.CompetingPhases attribute) (doped.chemical_potentials.CompetingPhasesAnalyzer attribute)

F

faded (doped.utils.plotting.TransitionLevel attribute) fast_Composition_eq() (in module doped.utils.efficiency) FclusterCriterion (in module doped.utils.symmetry) FermiSolver (class in doped.thermodynamics) find_archived_fname() (in module doped.utils.parsing) find_ideal_supercell() (in module doped.utils.supercells) find_missing_idx() (in module doped.utils.parsing) find_nearest_coords() (in module doped.utils.parsing) format_defect_name() (in module doped.utils.plotting) format_defect_names() (in module doped.utils.plotting) formation_energy() (doped.core.DefectEntry method) formation_energy_plot() (in module doped.utils.plotting) from_dataframe() (doped.chemical_potentials.ChemicalPotentialGrid class method)

from_dict() (doped.chemical_potentials.ChemicalPotentialGrid class method) (doped.chemical_potentials.CompetingPhases class method) (doped.chemical_potentials.CompetingPhasesAnalyzer class method) (doped.core.DefectEntry class method) (doped.generation.DefectsGenerator class method) (doped.thermodynamics.DefectThermodynamics class method) from_json() (doped.core.Defect class method) (doped.core.DefectEntry class method) (doped.generation.DefectsGenerator class method) (doped.thermodynamics.DefectThermodynamics class method) (doped.vasp.DefectRelaxSet class method) (doped.vasp.DefectsSet class method) from_paths() (doped.analysis.DefectParser class method)

G

generate() (doped.utils.efficiency.DopedVacancyGenerator method) get_all_distances() (in module doped.utils.efficiency) get_all_equiv_sites() (in module doped.utils.symmetry) get_and_set_competing_phase_name() (in module doped.chemical_potentials) get_band_edge_info() (in module doped.utils.eigenvalues) get_BCS_conventional_structure() (in module doped.utils.symmetry) get_charge_states() (doped.core.Defect method) get_chempots_from_phase_diagram() (in module doped.chemical_potentials) get_clean_structure() (in module doped.utils.symmetry) get_colormap() (in module doped.utils.plotting) get_colors() (in module doped.utils.plotting) get_constrained_grid() (doped.chemical_potentials.ChemicalPotentialGrid method) get_conv_cell_site() (in module doped.utils.symmetry) get_coords_and_idx_of_species() (in module doped.utils.parsing) get_core_potentials_from_outcar() (in module doped.utils.parsing) get_defect_colors_and_linestyles() (in module doped.utils.plotting) get_defect_entry_from_defect() (in module doped.generation) get_defect_in_supercell() (in module doped.utils.stenciling) get_defect_name_from_defect() (in module doped.generation) get_defect_name_from_entry() (in module doped.generation) get_defect_site_orig_oxi_state() (in module doped.generation) get_defect_thermodynamics() (doped.analysis.DefectsParser method) get_defect_type_and_composition_diff() (in module doped.utils.parsing) get_defect_type_and_site_indices() (in module doped.utils.parsing) get_defect_type_palette() (in module doped.utils.plotting) get_dimer_bonds() (in module doped.utils.parsing) get_dist_equiv_stol() (in module doped.utils.efficiency) get_distance_matrix() (in module doped.utils.symmetry) get_dopability_limits() (doped.thermodynamics.DefectThermodynamics method) get_doped_chempots_from_entries() (in module doped.chemical_potentials) get_doping_windows() (doped.thermodynamics.DefectThermodynamics method) get_dQ() (in module doped.utils.configurations) get_ediff() (doped.core.DefectEntry method) get_eigenvalue_analysis() (doped.core.DefectEntry method) (in module doped.utils.eigenvalues) get_element_indices() (in module doped.utils.efficiency) get_element_min_max_bond_length_dict() (in module doped.utils.efficiency) get_entries() (in module doped.chemical_potentials) get_entries_in_chemsys() (in module doped.chemical_potentials) get_equilibrium_concentrations() (doped.thermodynamics.DefectThermodynamics method) get_equilibrium_fermi_level() (doped.thermodynamics.DefectThermodynamics method) get_equiv_frac_coords_in_primitive() (in module doped.utils.symmetry) get_fermi_dos() (in module doped.thermodynamics) get_fermi_level_and_concentrations() (doped.thermodynamics.DefectThermodynamics method) get_formation_energies() (doped.thermodynamics.DefectThermodynamics method) get_formation_energy() (doped.thermodynamics.DefectThermodynamics method) get_formation_energy_df() (doped.chemical_potentials.CompetingPhasesAnalyzer method) get_freysoldt_correction() (doped.core.DefectEntry method) (in module doped.corrections) get_grid() (doped.chemical_potentials.ChemicalPotentialGrid method) get_ideal_supercell_matrix() (in module doped.generation) get_interpolated_chempots() (in module doped.thermodynamics) get_interstitial_sites() (in module doped.generation) get_kpoint_convergence_sets() (doped.chemical_potentials.CompetingPhases method)

get_kumagai_correction() (doped.core.DefectEntry method) (in module doped.corrections) get_legend_font_size() (in module doped.utils.plotting) get_linestyles() (in module doped.utils.plotting) get_locpot() (in module doped.utils.parsing) get_magnetization_from_vasprun() (in module doped.utils.parsing) get_matching_site() (in module doped.utils.parsing) get_min_dist_between_equiv_sites() (in module doped.utils.symmetry) get_min_image_distance() (in module doped.utils.supercells) get_min_stol_for_s1_s2() (in module doped.utils.efficiency) get_mp_context() (in module doped.utils) get_mp_processes() (in module doped.utils) get_MP_summary_dicts() (in module doped.chemical_potentials) get_multiplicity() (doped.core.Defect method) get_murphy_image_charge_correction() (in module doped.utils.legacy_corrections) get_neighbour_distances_and_symbols() (in module doped.generation) get_nelect_from_vasprun() (in module doped.utils.parsing) get_neutral_nelect_from_vasprun() (in module doped.utils.parsing) get_orientational_degeneracy() (in module doped.utils.symmetry) get_outcar() (in module doped.utils.parsing) get_oxi_probabilities() (in module doped.core) get_path_structures() (in module doped.utils.configurations) get_pmg_cubic_supercell_dict() (in module doped.utils.supercells) get_primitive_structure() (in module doped.utils.symmetry) get_procar() (in module doped.utils.parsing) get_quenched_fermi_level_and_concentrations() (doped.thermodynamics.DefectThermodynamics method) get_relaxation_sets() (doped.chemical_potentials.CompetingPhases method) get_rich_poor_limit_dict() (in module doped.thermodynamics) get_sga() (in module doped.utils.symmetry) get_sga_and_symprec() (in module doped.utils.symmetry) get_singlepoint_sets() (doped.chemical_potentials.CompetingPhases method) get_site_mappings() (in module doped.utils.parsing) get_spglib_conv_structure() (in module doped.utils.symmetry) get_stol_equiv_dist() (in module doped.generation) get_supercell_structure() (doped.core.Defect method) get_symmetries_and_degeneracies() (doped.thermodynamics.DefectThermodynamics method) get_transformation_from_s2_to_s1() (in module doped.utils.configurations) get_transition_levels() (doped.thermodynamics.DefectThermodynamics method) get_vasprun() (in module doped.utils.parsing) get_voronoi_nodes() (in module doped.utils.efficiency) get_wigner_seitz_radius() (in module doped.utils.parsing) get_wyckoff() (in module doped.utils.symmetry) get_wyckoff_dict_from_sgn() (in module doped.utils.symmetry) get_wyckoff_label_and_equiv_coord_list() (in module doped.utils.symmetry) get_X_poor_limit() (in module doped.chemical_potentials) get_X_rich_limit() (in module doped.chemical_potentials) get_X_rich_poor_limit() (in module doped.chemical_potentials) group_defects_by_distance() (in module doped.thermodynamics) group_defects_by_name() (in module doped.thermodynamics) group_defects_by_type_and_distance() (in module doped.thermodynamics) group_order_from_schoenflies() (in module doped.utils.symmetry) guess_and_set_oxi_states_with_timeout() (in module doped.core) guess_and_set_struct_oxi_states() (in module doped.core) guess_defect_charge_states() (in module doped.generation) guess_defect_position() (in module doped.analysis)

H

ha (doped.utils.plotting.TransitionLevelLabel attribute)

Hashabledict (class in doped.utils.efficiency)

I

incar (doped.vasp.DefectDictSet property) (doped.vasp.DopedDictSet property) Interstitial (class in doped.core) intrinsic_chempots (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) intrinsic_chempots_df (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) intrinsic_elements (doped.chemical_potentials.CompetingPhases attribute) (doped.chemical_potentials.CompetingPhasesAnalyzer attribute)

intrinsic_entries (doped.chemical_potentials.CompetingPhases attribute) intrinsic_MP_doc_dicts (doped.chemical_potentials.CompetingPhases attribute) intrinsic_phase_diagram (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) is_periodic_image() (in module doped.utils.symmetry) is_shallow (doped.core.DefectEntry property) is_shallow() (in module doped.core) is_within_frac_bounds() (in module doped.utils.stenciling)

J

json_name (doped.vasp.DefectsSet attribute)

json_obj (doped.vasp.DefectsSet attribute)

K

kpoints (doped.vasp.DopedDictSet property)

L

label (doped.utils.plotting.TransitionLevelLabel attribute) label_w (doped.utils.plotting.TransitionLevelLabel attribute) lany_zunger_corrected_defect_dict() (in module doped.utils.legacy_corrections) LinkageMethod (in module doped.utils.symmetry)

load_and_check_calculation_metadata() (doped.analysis.DefectParser method) load_bulk_gap_data() (doped.analysis.DefectParser method) load_eFNV_data() (doped.analysis.DefectParser method) load_FNV_data() (doped.analysis.DefectParser method) local_point_symmetry() (in module doped.utils.symmetry)

M

make_band_edge_orbital_infos() (in module doped.utils.eigenvalues) make_molecular_entry() (in module doped.chemical_potentials) make_molecule_in_a_box() (in module doped.chemical_potentials) make_perfect_band_edge_state_from_vasp() (in module doped.utils.eigenvalues) metallic_entries (doped.chemical_potentials.CompetingPhases property) min_dist() (in module doped.utils.supercells) module doped doped.analysis doped.chemical_potentials doped.core doped.corrections doped.generation doped.thermodynamics doped.utils doped.utils.configurations doped.utils.displacements doped.utils.efficiency doped.utils.eigenvalues doped.utils.legacy_corrections doped.utils.parsing doped.utils.plotting doped.utils.stenciling doped.utils.supercells doped.utils.symmetry doped.vasp

molecular_entries (doped.chemical_potentials.CompetingPhases property) most_common_oxi() (in module doped.core) MP_bulk_computed_entry (doped.chemical_potentials.CompetingPhases attribute) MP_doc_dicts (doped.chemical_potentials.CompetingPhases attribute) MP_full_pd (doped.chemical_potentials.CompetingPhases attribute) MP_full_pd_entries (doped.chemical_potentials.CompetingPhases attribute) MP_intrinsic_full_pd_entries (doped.chemical_potentials.CompetingPhases attribute) MPRESTER_PROPERTY_DATA (in module doped.chemical_potentials) MPRESTER_SUMMARY_DATA (in module doped.chemical_potentials)

N

name (doped.core.DefectEntry attribute) name_defect_cluster() (in module doped.thermodynamics) name_defect_entries() (in module doped.generation)

neg_meta (doped.utils.plotting.TransitionLevel attribute) nelect (doped.vasp.DopedDictSet property) nonmetallic_entries (doped.chemical_potentials.CompetingPhases property)

O

optimise() (doped.thermodynamics.FermiSolver method)

orient_s2_like_s1() (in module doped.utils.configurations)

P

ParameterOrderWarning parse_projected_eigen() (in module doped.utils.parsing) parse_symmetry_and_degeneracy_metadata() (in module doped.analysis) parsed_folders (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) patch_vise_for_windows() (in module doped.utils) PETROFF10_EXTENDED_40 (in module doped.utils.plotting) phase_diagram (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) plot() (doped.thermodynamics.DefectThermodynamics method) plot_chemical_potential_table() (in module doped.utils.plotting) plot_chempot_heatmap() (doped.chemical_potentials.CompetingPhasesAnalyzer method) (doped.thermodynamics.DefectThermodynamics method) (in module doped.chemical_potentials) plot_displacements_ellipsoid() (in module doped.utils.displacements) plot_FNV() (in module doped.corrections) plot_site_displacements() (doped.core.DefectEntry method) (in module doped.utils.displacements)

plot_transition_levels() (doped.thermodynamics.DefectThermodynamics method) point_symmetry_from_defect() (in module doped.utils.symmetry) point_symmetry_from_defect_entry() (in module doped.utils.symmetry) point_symmetry_from_site() (in module doped.utils.symmetry) point_symmetry_from_structure() (in module doped.utils.symmetry) pool_manager() (in module doped.utils) pos_meta (doped.utils.plotting.TransitionLevel attribute) poscar (doped.vasp.DopedDictSet property) potcar (doped.vasp.DopedDictSet property) prim_interstitial_coords_mult_and_equiv_coords (doped.generation.DefectsGenerator attribute) primitive_structure (doped.generation.DefectsGenerator attribute) print_transition_levels() (doped.thermodynamics.DefectThermodynamics method) prune_entries_to_border_candidates() (in module doped.chemical_potentials) prune_to_expected_polymorphs() (in module doped.chemical_potentials) prune_to_stable_entries() (doped.thermodynamics.DefectThermodynamics method) py_sc_fermi_dos (doped.thermodynamics.FermiSolver property)

R

raw_energy_from_chempots() (in module doped.thermodynamics) recognised_post_interstitial_strings (in module doped.utils.plotting) recognised_post_vacancy_strings (in module doped.utils.plotting) recognised_pre_interstitial_strings (in module doped.utils.plotting)

recognised_pre_vacancy_strings (in module doped.utils.plotting) remove_charge_states() (doped.generation.DefectsGenerator method) remove_site_oxi_state() (in module doped.core) remove_translation_drift() (in module doped.utils.symmetry) reorder_s2_like_s1() (in module doped.utils.parsing)

S

sc_defect_frac_coords (doped.core.DefectEntry attribute) sc_entry (doped.core.DefectEntry attribute) sc_entry_energy (doped.core.DefectEntry property) scaled_ediff() (in module doped.vasp) scan_chemical_potential_grid() (doped.thermodynamics.FermiSolver method) scan_chempots() (doped.thermodynamics.FermiSolver method) scan_dopant_concentration() (doped.thermodynamics.FermiSolver method) scan_temperature() (doped.thermodynamics.FermiSolver method) sch_symbols (in module doped.utils.symmetry) schoenflies_from_hermann() (in module doped.utils.symmetry) schoenflies_from_spacegroup_number() (in module doped.utils.symmetry) schoenflies_from_structure() (in module doped.utils.symmetry) scissor_dos() (in module doped.thermodynamics) shade_band_edges() (in module doped.utils.plotting)

shallow_dopant_binding_energy() (in module doped.analysis) single_extrinsic_phase_limits (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) singlepoint_incar_settings (in module doped.vasp) skip_dos_check (doped.thermodynamics.DefectThermodynamics attribute) (doped.thermodynamics.FermiSolver attribute) sort_defect_entries() (in module doped.generation) spin_degeneracy_from_vasprun() (in module doped.utils.parsing) stable_entries (doped.thermodynamics.DefectThermodynamics attribute) stencil_target_cell_from_big_cell() (in module doped.utils.stenciling) StructureMatcher_scan_stol() (in module doped.utils.efficiency) Substitution (class in doped.core) summed_dist() (in module doped.utils.symmetry) supercell_matrix (doped.generation.DefectsGenerator attribute) suppress_logging() (in module doped.utils) swap_axes() (in module doped.utils.symmetry)

T

template_defect_entry_from_structures() (in module doped.core) TL_eV (doped.utils.plotting.TransitionLevel attribute) (doped.utils.plotting.TransitionLevelLabel attribute) to_json() (doped.core.Defect method) (doped.core.DefectEntry method) (doped.generation.DefectsGenerator method) (doped.thermodynamics.DefectThermodynamics method) (doped.vasp.DefectRelaxSet method) (doped.vasp.DefectsSet method)

to_LaTeX_table() (doped.chemical_potentials.CompetingPhasesAnalyzer method) total_charge_from_vasprun() (in module doped.utils.parsing) transition_level_diagram() (in module doped.utils.plotting) transition_level_map (doped.thermodynamics.DefectThermodynamics attribute) transition_levels (doped.thermodynamics.DefectThermodynamics attribute) TransitionLevel (class in doped.utils.plotting) TransitionLevelLabel (class in doped.utils.plotting) translate_structure() (in module doped.utils.symmetry)

U

unstable_entries (doped.thermodynamics.DefectThermodynamics property)

unstable_host (doped.chemical_potentials.CompetingPhasesAnalyzer attribute)

V

va (doped.utils.plotting.TransitionLevelLabel attribute) Vacancy (class in doped.core) VARIANT_LINESTYLES (in module doped.utils.plotting) vasp_gam (doped.vasp.DefectRelaxSet property) vasp_ncl (doped.vasp.DefectRelaxSet property) vasp_nkred_std (doped.vasp.DefectRelaxSet property)

vasp_std (doped.vasp.DefectRelaxSet property) vasp_std_setup() (doped.chemical_potentials.CompetingPhases method) vasprun_paths (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) vbm (doped.thermodynamics.DefectThermodynamics attribute) vise_handling() (in module doped.utils) volume (doped.core.Defect property) (doped.thermodynamics.FermiSolver property)

W

warn_once() (in module doped.utils) write_all() (doped.vasp.DefectRelaxSet method) write_files() (doped.vasp.DefectsSet method) write_gam() (doped.vasp.DefectRelaxSet method) write_input() (doped.vasp.DopedDictSet method) write_kpoint_convergence_files() (doped.chemical_potentials.CompetingPhases method)

write_ncl() (doped.vasp.DefectRelaxSet method) write_nkred_std() (doped.vasp.DefectRelaxSet method) write_path_structures() (in module doped.utils.configurations) write_relaxation_files() (doped.chemical_potentials.CompetingPhases method) write_singlepoint_files() (doped.chemical_potentials.CompetingPhases method) write_std() (doped.vasp.DefectRelaxSet method) wyckoff (doped.core.DefectEntry attribute)

X

X (doped.chemical_potentials.CompetingPhases attribute)

x (doped.utils.plotting.TransitionLevelLabel attribute)

Y

y (doped.utils.plotting.TransitionLevelLabel attribute)