Index

A

add_charge_states() (doped.generation.DefectsGenerator method) all_stable_entries (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram property) all_unstable_entries (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram property) apply_corrections() (doped.analysis.DefectParser method)

are_equal() (doped.utils.legacy_pmg.PointDefectComparator method) as_dict() (doped.core.Defect method) (doped.core.DefectEntry method) (doped.generation.DefectsGenerator method) (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram method)

B

bold_print() (in module doped.analysis) bulk_composition (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) bulk_entry (doped.core.DefectEntry attribute) bulk_supercell (doped.core.DefectEntry attribute) (doped.generation.DefectsGenerator attribute) (doped.vasp.DefectRelaxSet attribute) bulk_vasp_gam (doped.vasp.DefectRelaxSet attribute) (doped.vasp.DefectRelaxSet property)

bulk_vasp_ncl (doped.vasp.DefectRelaxSet attribute) (doped.vasp.DefectRelaxSet property) bulk_vasp_nkred_std (doped.vasp.DefectRelaxSet attribute) (doped.vasp.DefectRelaxSet property) bulk_vasp_std (doped.vasp.DefectRelaxSet attribute) (doped.vasp.DefectRelaxSet property)

C

calculate_chempots() (doped.chemical_potentials.CompetingPhasesAnalyzer method) calculation_metadata (doped.core.DefectEntry attribute) charge_state (doped.core.DefectEntry attribute) charge_state_guessing_log (doped.core.DefectEntry attribute) check_and_set_defect_entry_name() (in module doped.analysis) chem_limits (doped.chemical_potentials.CompetingPhasesAnalyzer property) closest_site_info() (in module doped.generation) 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) (doped.generation.DefectsGenerator 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) cplap_input() (doped.chemical_potentials.CompetingPhasesAnalyzer method)

D

data (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) deep_dict_update() (in module doped.vasp) Defect (class in doped.core) defect (doped.core.DefectEntry attribute) defect_concentrations() (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram method) defect_dict (doped.analysis.DefectsParser attribute) defect_entries (doped.generation.DefectsGenerator attribute) (doped.vasp.DefectsSet attribute) 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_sets (doped.vasp.DefectsSet attribute) defect_supercell (doped.core.DefectEntry attribute) (doped.vasp.DefectRelaxSet attribute) defect_supercell_site (doped.core.DefectEntry attribute) defect_types (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram property) DefectDictSet (class in doped.vasp) DefectEntry (class in doped.core) DefectParser (class in doped.analysis) DefectPhaseDiagram (class in doped.utils.legacy_pmg.thermodynamics) 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) doped module

doped.analysis module doped.chemical_potentials module doped.core module doped.corrections module doped.generation module doped.plotting module doped.utils module doped.utils.legacy_pmg module doped.utils.legacy_pmg.thermodynamics module doped.utils.parsing module doped.utils.wyckoff module doped.vasp module doped_defect_from_pmg_defect() (in module doped.core) dpd_from_defect_dict() (in module doped.analysis) dpd_transition_levels() (in module doped.analysis)

E

elemental (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) entry_id (doped.core.DefectEntry attribute) equiv_conv_cell_frac_coords (doped.core.DefectEntry attribute)

equivalent_supercell_sites (doped.core.DefectEntry attribute) extrinsic_species (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) ExtrinsicCompetingPhases (class in doped.chemical_potentials)

F

find_archived_fname() (in module doped.utils.parsing) find_stable_charges() (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram method) formation_energy_df (doped.chemical_potentials.CompetingPhasesAnalyzer attribute) formation_energy_plot() (in module doped.plotting) formation_energy_table() (in module doped.analysis) from_csv() (doped.chemical_potentials.CompetingPhasesAnalyzer method)

from_dict() (doped.generation.DefectsGenerator class method) (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram class method) from_json() (doped.core.Defect class method) (doped.core.DefectEntry class method) (doped.generation.DefectsGenerator class method) from_paths() (doped.analysis.DefectParser class method) from_vaspruns() (doped.chemical_potentials.CompetingPhasesAnalyzer method)

G

get_BCS_conventional_structure() (in module doped.utils.wyckoff) get_chempots_from_phase_diagram() (in module doped.chemical_potentials) get_conv_cell_site() (in module doped.utils.wyckoff) get_defect_entry_from_defect() (in module doped.generation) get_defect_name_from_defect() (in module doped.generation) get_defect_name_from_entry() (in module doped.generation) get_defect_site_idxs_and_unrelaxed_structure() (in module doped.utils.parsing) get_defect_type_and_composition_diff() (in module doped.utils.parsing) get_dopability_limits() (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram method) get_freysoldt_correction() (doped.core.DefectEntry method) (in module doped.corrections) get_kumagai_correction() (doped.core.DefectEntry method) (in module doped.corrections)

get_locpot() (in module doped.utils.parsing) get_outcar() (in module doped.utils.parsing) get_oxi_probabilities() (in module doped.generation) get_primitive_structure() (in module doped.utils.wyckoff) get_site_mapping_indices() (in module doped.utils.parsing) get_spglib_conv_structure() (in module doped.utils.wyckoff) get_supercell_structure() (doped.core.Defect method) get_vasprun() (in module doped.utils.parsing) get_wyckoff() (in module doped.utils.wyckoff) get_wyckoff_dict_from_sgn() (in module doped.utils.wyckoff) get_wyckoff_label_and_equiv_coord_list() (in module doped.utils.wyckoff) guess_defect_charge_states() (in module doped.generation)

H

herm2sch() (in module doped.generation)

I

incar (doped.vasp.DefectDictSet property) Interstitial (class in doped.core)

intrinsic_chem_limits (doped.chemical_potentials.CompetingPhasesAnalyzer property) intrinsic_phase_diagram (doped.chemical_potentials.CompetingPhasesAnalyzer property)

J

json_name (doped.vasp.DefectsSet attribute)

json_obj (doped.vasp.DefectsSet attribute)

K

kpoints (doped.vasp.DefectDictSet property)

L

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_molecule_in_a_box() (in module doped.chemical_potentials) module doped doped.analysis doped.chemical_potentials doped.core doped.corrections doped.generation doped.plotting doped.utils doped.utils.legacy_pmg doped.utils.legacy_pmg.thermodynamics doped.utils.parsing doped.utils.wyckoff doped.vasp

N

name (doped.core.DefectEntry attribute)

name_defect_entries() (in module doped.generation)

P

plot() (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram method) plot_FNV() (in module doped.corrections) PointDefectComparator (class in doped.utils.legacy_pmg)

poscar (doped.vasp.DefectDictSet property) poscar_comment (doped.vasp.DefectRelaxSet attribute) potcar (doped.vasp.DefectDictSet property) primitive_structure (doped.generation.DefectsGenerator attribute)

R

remove_charge_states() (doped.generation.DefectsGenerator method)

reorder_s1_like_s2() (in module doped.utils.parsing)

S

sc_defect_frac_coords (doped.core.DefectEntry attribute) sc_entry (doped.core.DefectEntry attribute) scaled_ediff() (in module doped.vasp) solve_for_fermi_energy() (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram method)

solve_for_non_equilibrium_fermi_energy() (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram method) Substitution (class in doped.core) suggest_charges() (doped.utils.legacy_pmg.thermodynamics.DefectPhaseDiagram method) supercell_matrix (doped.generation.DefectsGenerator attribute) swap_axes() (in module doped.utils.wyckoff)

T

to_csv() (doped.chemical_potentials.CompetingPhasesAnalyzer method) to_json() (doped.core.Defect method) (doped.core.DefectEntry method) (doped.generation.DefectsGenerator method)

to_LaTeX_table() (doped.chemical_potentials.CompetingPhasesAnalyzer method)

V

Vacancy (class in doped.core) vasp_gam (doped.vasp.DefectRelaxSet attribute) (doped.vasp.DefectRelaxSet property) vasp_ncl (doped.vasp.DefectRelaxSet attribute) (doped.vasp.DefectRelaxSet property)

vasp_nkred_std (doped.vasp.DefectRelaxSet attribute) (doped.vasp.DefectRelaxSet property) vasp_std (doped.vasp.DefectRelaxSet attribute) (doped.vasp.DefectRelaxSet property) vasp_std_setup() (doped.chemical_potentials.CompetingPhases method)

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_std() (doped.vasp.DefectRelaxSet method) wyckoff (doped.core.DefectEntry attribute)