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Index
A
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B
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C
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D
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E
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F
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G
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I
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J
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K
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L
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M
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N
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P
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R
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S
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T
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V
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W
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)
as_dict() (doped.core.Defect method)
(doped.core.DefectEntry method)
(doped.generation.DefectsGenerator method)
(doped.thermodynamics.DefectThermodynamics method)
B
bold_print() (in module doped.thermodynamics)
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)
(doped.vasp.DefectsSet attribute)
bulk_vasp_ncl (doped.vasp.DefectRelaxSet attribute)
(doped.vasp.DefectRelaxSet property)
(doped.vasp.DefectsSet attribute)
bulk_vasp_nkred_std (doped.vasp.DefectRelaxSet attribute)
(doped.vasp.DefectRelaxSet property)
(doped.vasp.DefectsSet attribute)
bulk_vasp_std (doped.vasp.DefectRelaxSet attribute)
(doped.vasp.DefectRelaxSet property)
(doped.vasp.DefectsSet attribute)
C
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)
check_and_set_defect_entry_name() (in module doped.analysis)
check_atom_mapping_far_from_defect() (in module doped.utils.parsing)
chempots (doped.chemical_potentials.CompetingPhasesAnalyzer property)
(doped.thermodynamics.DefectThermodynamics 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)
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_charge_from_vasprun() (in module doped.utils.parsing)
defect_dict (doped.analysis.DefectsParser attribute)
defect_entries (doped.generation.DefectsGenerator attribute)
(doped.thermodynamics.DefectThermodynamics property)
(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_names (doped.thermodynamics.DefectThermodynamics property)
defect_sets (doped.vasp.DefectsSet attribute)
defect_supercell (doped.core.DefectEntry attribute)
(doped.vasp.DefectRelaxSet 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)
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.displacements
module
doped.utils.legacy_corrections
module
doped.utils.parsing
module
doped.utils.plotting
module
doped.utils.supercells
module
doped.utils.symmetry
module
doped.vasp
module
doped_defect_from_pmg_defect() (in module doped.core)
DopedDictSet (class in doped.vasp)
DopedKpoints (class in doped.vasp)
E
el_refs (doped.thermodynamics.DefectThermodynamics property)
elemental (doped.chemical_potentials.CompetingPhasesAnalyzer attribute)
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)
extrinsic_species (doped.chemical_potentials.CompetingPhasesAnalyzer attribute)
ExtrinsicCompetingPhases (class in doped.chemical_potentials)
F
find_archived_fname() (in module doped.utils.parsing)
find_ideal_supercell() (in module doped.utils.supercells)
find_nearest_coords() (in module doped.utils.parsing)
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_df (doped.chemical_potentials.CompetingPhasesAnalyzer attribute)
from_csv() (doped.chemical_potentials.CompetingPhasesAnalyzer method)
from_dict() (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)
from_vaspruns() (doped.chemical_potentials.CompetingPhasesAnalyzer method)
G
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_conv_cell_site() (in module doped.utils.symmetry)
get_coords_and_idx_of_species() (in module doped.utils.parsing)
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_thermodynamics() (doped.analysis.DefectsParser method)
get_defect_type_and_composition_diff() (in module doped.utils.parsing)
get_dopability_limits() (doped.thermodynamics.DefectThermodynamics method)
get_doping_windows() (doped.thermodynamics.DefectThermodynamics method)
get_e_h_concs() (in module doped.thermodynamics)
get_eigenvalue_analysis() (doped.core.DefectEntry method)
get_equilibrium_concentrations() (doped.thermodynamics.DefectThermodynamics method)
get_equilibrium_fermi_level() (doped.thermodynamics.DefectThermodynamics method)
get_formation_energies() (doped.thermodynamics.DefectThermodynamics method)
get_formation_energy() (doped.thermodynamics.DefectThermodynamics method)
get_freysoldt_correction() (doped.core.DefectEntry method)
(in module doped.corrections)
get_ideal_supercell_matrix() (in module doped.generation)
get_interstitial_site_and_orientational_degeneracy() (in module doped.utils.parsing)
get_kumagai_correction() (doped.core.DefectEntry method)
(in module doped.corrections)
get_locpot() (in module doped.utils.parsing)
get_magnetization_from_vasprun() (in module doped.utils.parsing)
get_min_image_distance() (in module doped.utils.supercells)
get_murphy_image_charge_correction() (in module doped.utils.legacy_corrections)
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.parsing)
get_outcar() (in module doped.utils.parsing)
get_oxi_probabilities() (in module doped.generation)
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_site_mapping_indices() (in module doped.utils.parsing)
get_spglib_conv_structure() (in module doped.utils.symmetry)
get_supercell_structure() (doped.core.Defect method)
get_symmetries_and_degeneracies() (doped.thermodynamics.DefectThermodynamics method)
get_transition_levels() (doped.thermodynamics.DefectThermodynamics method)
get_vasprun() (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_order_from_schoenflies() (in module doped.utils.symmetry)
guess_defect_charge_states() (in module doped.generation)
I
incar (doped.vasp.DefectDictSet property)
(doped.vasp.DopedDictSet property)
Interstitial (class in doped.core)
intrinsic_chempots (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.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_molecule_in_a_box() (in module doped.chemical_potentials)
module
doped
doped.analysis
doped.chemical_potentials
doped.core
doped.corrections
doped.generation
doped.thermodynamics
doped.utils
doped.utils.displacements
doped.utils.legacy_corrections
doped.utils.parsing
doped.utils.plotting
doped.utils.supercells
doped.utils.symmetry
doped.vasp
N
name (doped.core.DefectEntry attribute)
name_defect_entries() (in module doped.generation)
nelect (doped.vasp.DefectDictSet property)
P
parse_projected_eigen_no_mag() (in module doped.utils.parsing)
plot() (doped.thermodynamics.DefectThermodynamics method)
plot_FNV() (in module doped.corrections)
plot_site_displacements() (doped.core.DefectEntry method)
(in module doped.utils.displacements)
point_symmetry() (in module doped.utils.symmetry)
point_symmetry_from_defect() (in module doped.utils.symmetry)
point_symmetry_from_defect_entry() (in module doped.utils.symmetry)
poscar (doped.vasp.DopedDictSet property)
poscar_comment (doped.vasp.DefectRelaxSet attribute)
potcar (doped.vasp.DopedDictSet property)
primitive_structure (doped.generation.DefectsGenerator attribute)
print_transition_levels() (doped.thermodynamics.DefectThermodynamics method)
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)
schoenflies_from_hermann() (in module doped.utils.symmetry)
scissor_dos() (in module doped.thermodynamics)
simple_spin_degeneracy_from_charge() (in module doped.utils.parsing)
Substitution (class in doped.core)
supercell_matrix (doped.generation.DefectsGenerator attribute)
suppress_logging() (in module doped.utils.parsing)
swap_axes() (in module doped.utils.symmetry)
T
to_csv() (doped.chemical_potentials.CompetingPhasesAnalyzer method)
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)
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)
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