Index

A

add_charge_states() (doped.generation.DefectsGenerator method) add_entries() (doped.thermodynamics.DefectThermodynamics method) all_stable_entries (doped.thermodynamics.DefectThermodynamics property) all_unstable_entries (doped.thermodynamics.DefectThermodynamics property) apply_corrections() (doped.analysis.DefectParser method) 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) are_equivalent_molecules() (in module doped.complexes) as_dict() (doped.chemical_potentials.CompetingPhasesAnalyzer method) (doped.core.Defect method) (doped.core.DefectEntry method) (doped.generation.DefectsGenerator method) (doped.thermodynamics.DefectThermodynamics method)

B

band_edge_properties_from_vasprun() (in module doped.utils.eigenvalues) bold_print() (in module doped.thermodynamics) bulk_dos (doped.thermodynamics.DefectThermodynamics property) bulk_entry (doped.core.DefectEntry attribute) bulk_entry_energy (doped.core.DefectEntry property)

bulk_site_concentration (doped.core.DefectEntry property) bulk_supercell (doped.core.DefectEntry attribute) bulk_vasp_gam (doped.vasp.DefectRelaxSet property) bulk_vasp_ncl (doped.vasp.DefectRelaxSet property) bulk_vasp_nkred_std (doped.vasp.DefectRelaxSet property) bulk_vasp_std (doped.vasp.DefectRelaxSet property)

C

cache_ready_PeriodicSite__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) check_and_set_defect_entry_name() (in module doped.analysis) check_atom_mapping_far_from_defect() (in module doped.utils.parsing)

ChemicalPotentialGrid (class in doped.chemical_potentials) chempot_grid (doped.chemical_potentials.CompetingPhasesAnalyzer property) chempots (doped.thermodynamics.DefectThermodynamics property) classify_vacancy_geometry() (in module doped.complexes) closest_site_info() (in module doped.generation) cluster_coords() (in module doped.utils.symmetry) cluster_sites_by_dist_tol() (in module doped.utils.symmetry) combine_extrinsic() (in module doped.chemical_potentials) CompetingPhases (class in doped.chemical_potentials) CompetingPhasesAnalyzer (class in doped.chemical_potentials) conv_cell_frac_coords (doped.core.DefectEntry attribute) conventional_structure (doped.core.DefectEntry attribute) 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) Defect (class in doped.core) defect (doped.core.DefectEntry attribute) defect_and_info_from_structures() (in module doped.analysis) defect_dict (doped.analysis.DefectsParser attribute) defect_entries (doped.thermodynamics.DefectThermodynamics property) defect_entry_from_paths() (in module doped.analysis) defect_from_structures() (in module doped.analysis) defect_generator_info() (doped.generation.DefectsGenerator method) defect_name_from_structures() (in module doped.analysis) defect_names (doped.thermodynamics.DefectThermodynamics property) defect_site (doped.core.Defect property) defect_supercell (doped.core.DefectEntry attribute) defect_supercell_site (doped.core.DefectEntry attribute) DefectDictSet (class in doped.vasp) DefectEntry (class in doped.core) DefectParser (class in doped.analysis) DefectRelaxSet (class in doped.vasp) 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.complexes 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_Structure__eq__() (in module doped.utils.efficiency) DopedDictSet (class in doped.vasp) DopedKpoints (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) entries_from_chempot_limits() (in module doped.chemical_potentials)

entry_id (doped.core.DefectEntry attribute) equilibrium_concentration() (doped.core.DefectEntry method) equiv_conv_cell_frac_coords (doped.core.DefectEntry attribute) equivalent_supercell_sites (doped.core.DefectEntry attribute)

F

fast_Composition_eq() (in module doped.utils.efficiency) FermiSolver (class in doped.thermodynamics) find_archived_fname() (in module doped.utils.parsing) find_ideal_supercell() (in module doped.utils.supercells) find_optimal_cell_shape() (in module doped.utils.supercells) format_defect_name() (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.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) from_paths() (doped.analysis.DefectParser class method)

G

generate() (doped.utils.efficiency.DopedVacancyGenerator method) generate_complex_from_defect_sites() (in module doped.complexes) 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_complex_defect_multiplicity() (in module doped.complexes) 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_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_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_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() (in module doped.thermodynamics) get_doping_windows() (doped.thermodynamics.DefectThermodynamics method) get_dQ() (in module doped.utils.configurations) get_e_h_concs() (in module doped.thermodynamics) 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_equivalent_complex_defect_sites_in_primitive() (in module doped.complexes) get_es_energy() (in module doped.complexes) 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_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) get_mp_processes() (in module doped) 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_rich_poor_limit_dict() (in module doped.thermodynamics) get_s2_like_s1() (in module doped.utils.configurations) get_sga() (in module doped.utils.symmetry) get_sga_and_symprec() (in module doped.utils.symmetry) get_site_mappings() (in module doped.utils.parsing) get_spglib_conv_structure() (in module doped.utils.symmetry) get_split_vacancies() (in module doped.complexes) get_split_vacancies_by_geometry() (in module doped.complexes) get_split_vacancies_from_database() (in module doped.complexes) get_split_vacancies_from_electrostatics() (in module doped.complexes) get_stol_equiv_dist() (in module doped.generation) get_supercell_structure() (doped.core.Defect method) get_symmetries_and_degeneracies() (doped.thermodynamics.DefectThermodynamics method) get_transition_levels() (doped.thermodynamics.DefectThermodynamics method) get_vacancy_charge_states() (in module doped.generation) 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) 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

Hashabledict (class in doped.utils.efficiency)

I

incar (doped.vasp.DefectDictSet property) (doped.vasp.DopedDictSet property) interpolate_chempots() (doped.thermodynamics.FermiSolver method) Interstitial (class in doped.core)

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)

K

kpoints (doped.vasp.DopedDictSet property)

L

lany_zunger_corrected_defect_dict() (in module doped.utils.legacy_corrections) 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)

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.complexes 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) molecule_from_sites() (in module doped.complexes) most_common_oxi() (in module doped.core)

N

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

name_defect_entries() (in module doped.generation) nelect (doped.vasp.DefectDictSet property) nonmetallic_entries (doped.chemical_potentials.CompetingPhases property)

O

optimise() (doped.thermodynamics.FermiSolver method)

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

P

parse_projected_eigen() (in module doped.utils.parsing) 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)

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) poscar (doped.vasp.DopedDictSet property) potcar (doped.vasp.DopedDictSet property) print_transition_levels() (doped.thermodynamics.DefectThermodynamics method) prune_entries_to_border_candidates() (in module doped.chemical_potentials) prune_to_stable_entries() (doped.thermodynamics.DefectThermodynamics method)

R

raw_energy_from_chempots() (in module doped.thermodynamics) remove_charge_states() (doped.generation.DefectsGenerator method)

remove_site_oxi_state() (in module doped.core) 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) schoenflies_from_hermann() (in module doped.utils.symmetry)

scissor_dos() (in module doped.thermodynamics) shallow_dopant_binding_energy() (in module doped.analysis) sort_defect_entries() (in module doped.generation) spin_degeneracy_from_vasprun() (in module doped.utils.parsing) StructureMatcher_scan_stol() (in module doped.utils.efficiency) Substitution (class in doped.core) summed_rms_dist() (in module doped.utils.symmetry) suppress_logging() (in module doped) swap_axes() (in module doped.utils.symmetry)

T

to_json() (doped.core.Defect method) (doped.core.DefectEntry method) (doped.generation.DefectsGenerator method) (doped.thermodynamics.DefectThermodynamics method)

to_LaTeX_table() (doped.chemical_potentials.CompetingPhasesAnalyzer method) total_charge_from_vasprun() (in module doped.utils.parsing) translate_structure() (in module doped.utils.symmetry)

U

unstable_entries (doped.thermodynamics.DefectThermodynamics property)

V

Vacancy (class in doped.core) 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) volume (doped.core.Defect property)

W

write_all() (doped.vasp.DefectRelaxSet method) write_files() (doped.vasp.DefectsSet method) write_gam() (doped.vasp.DefectRelaxSet method) write_input() (doped.vasp.DefectDictSet method)

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