doped
Module contents
doped
is a python package for managing solid-state defect calculations,
with functionality to generate defect structures and relevant competing phases
(for chemical potentials), interface with ShakeNBreak
(https://shakenbreak.readthedocs.io) for defect structure-searching (see
https://www.nature.com/articles/s41524-023-00973-1), write VASP input files for
defect supercell calculations, and automatically parse and analyse the results.
- doped.get_mp_context()[source]
Get a multiprocessing context that is compatible with the current OS.
- doped.pool_manager(processes: int | None = None)[source]
Context manager for
multiprocessing
Pool
, to throw a clearer error message whenRuntimeError
s are raisedmultiprocessing
withindoped
is used in a python script.See https://doped.readthedocs.io/en/latest/Troubleshooting.html#errors-with-python-scripts
- Parameters:
processes (int | None) – Number of processes to use with
Pool
. IfNone
, will usemp.cpu_count() - 1
(i.e. one less than the number of available CPUs).- Yields:
Pool – A
Pool
object with the specified number of processes.
Submodules
- doped.analysis module
- doped.chemical_potentials module
ChemicalPotentialGrid
CompetingPhases
CompetingPhasesAnalyzer
combine_extrinsic()
get_MP_summary_docs()
get_X_poor_limit()
get_X_rich_limit()
get_and_set_competing_phase_name()
get_chempots_from_phase_diagram()
get_doped_chempots_from_entries()
get_entries()
get_entries_in_chemsys()
make_molecular_entry()
make_molecule_in_a_box()
prune_entries_to_border_candidates()
- doped.core module
Defect
DefectEntry
DefectEntry.as_dict()
DefectEntry.bulk_entry
DefectEntry.bulk_entry_energy
DefectEntry.bulk_site_concentration
DefectEntry.bulk_supercell
DefectEntry.calculation_metadata
DefectEntry.charge_state
DefectEntry.charge_state_guessing_log
DefectEntry.conv_cell_frac_coords
DefectEntry.conventional_structure
DefectEntry.corrected_energy
DefectEntry.corrections
DefectEntry.corrections_metadata
DefectEntry.defect
DefectEntry.defect_supercell
DefectEntry.defect_supercell_site
DefectEntry.degeneracy_factors
DefectEntry.entry_id
DefectEntry.equilibrium_concentration()
DefectEntry.equiv_conv_cell_frac_coords
DefectEntry.equivalent_supercell_sites
DefectEntry.formation_energy()
DefectEntry.from_dict()
DefectEntry.from_json()
DefectEntry.get_ediff()
DefectEntry.get_eigenvalue_analysis()
DefectEntry.get_freysoldt_correction()
DefectEntry.get_kumagai_correction()
DefectEntry.is_shallow
DefectEntry.name
DefectEntry.plot_site_displacements()
DefectEntry.sc_defect_frac_coords
DefectEntry.sc_entry
DefectEntry.sc_entry_energy
DefectEntry.to_json()
DefectEntry.wyckoff
Interstitial
Substitution
Vacancy
doped_defect_from_pmg_defect()
guess_and_set_oxi_states_with_timeout()
guess_and_set_struct_oxi_states()
is_shallow()
- doped.corrections module
- doped.generation module
DefectsGenerator
charge_state_probability()
closest_site_info()
get_defect_entry_from_defect()
get_defect_name_from_defect()
get_defect_name_from_entry()
get_ideal_supercell_matrix()
get_interstitial_sites()
get_neighbour_distances_and_symbols()
get_oxi_probabilities()
get_stol_equiv_dist()
get_vacancy_charge_states()
guess_defect_charge_states()
name_defect_entries()
sort_defect_entries()
- doped.thermodynamics module
DefectThermodynamics
DefectThermodynamics.add_entries()
DefectThermodynamics.all_stable_entries
DefectThermodynamics.all_unstable_entries
DefectThermodynamics.as_dict()
DefectThermodynamics.bulk_dos
DefectThermodynamics.chempots
DefectThermodynamics.defect_entries
DefectThermodynamics.defect_names
DefectThermodynamics.dist_tol
DefectThermodynamics.el_refs
DefectThermodynamics.from_dict()
DefectThermodynamics.from_json()
DefectThermodynamics.get_dopability_limits()
DefectThermodynamics.get_doping_windows()
DefectThermodynamics.get_equilibrium_concentrations()
DefectThermodynamics.get_equilibrium_fermi_level()
DefectThermodynamics.get_fermi_level_and_concentrations()
DefectThermodynamics.get_formation_energies()
DefectThermodynamics.get_formation_energy()
DefectThermodynamics.get_quenched_fermi_level_and_concentrations()
DefectThermodynamics.get_symmetries_and_degeneracies()
DefectThermodynamics.get_transition_levels()
DefectThermodynamics.plot()
DefectThermodynamics.print_transition_levels()
DefectThermodynamics.prune_to_stable_entries()
DefectThermodynamics.to_json()
DefectThermodynamics.unstable_entries
FermiSolver
bold_print()
get_doping()
get_e_h_concs()
get_fermi_dos()
get_rich_poor_limit_dict()
group_defects_by_distance()
group_defects_by_name()
group_defects_by_type_and_distance()
raw_energy_from_chempots()
scissor_dos()
- doped.utils package
- Submodules
- 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
check_atom_mapping_far_from_defect()
doped_entry_id()
find_archived_fname()
find_missing_idx()
find_nearest_coords()
get_coords_and_idx_of_species()
get_core_potentials_from_outcar()
get_defect_site_idxs_and_unrelaxed_structure()
get_defect_type_and_composition_diff()
get_defect_type_site_idxs_and_unrelaxed_structure()
get_locpot()
get_magnetisation_from_vasprun()
get_nelect_from_vasprun()
get_neutral_nelect_from_vasprun()
get_outcar()
get_procar()
get_site_mapping_indices()
get_vasprun()
get_wigner_seitz_radius()
parse_projected_eigen()
reorder_s1_like_s2()
spin_degeneracy_from_vasprun()
suppress_logging()
total_charge_from_vasprun()
- doped.utils.plotting module
- doped.utils.stenciling module
- doped.utils.supercells module
- doped.utils.symmetry module
apply_symm_op_to_site()
apply_symm_op_to_struct()
are_equivalent_sites()
cached_simplify()
cached_solve()
cluster_coords()
get_BCS_conventional_structure()
get_all_equiv_sites()
get_clean_structure()
get_conv_cell_site()
get_distance_matrix()
get_equiv_frac_coords_in_primitive()
get_interstitial_site_and_orientational_degeneracy()
get_min_dist_between_equiv_sites()
get_orientational_degeneracy()
get_primitive_structure()
get_sga()
get_spglib_conv_structure()
get_wyckoff()
get_wyckoff_dict_from_sgn()
get_wyckoff_label_and_equiv_coord_list()
group_order_from_schoenflies()
point_symmetry_from_defect()
point_symmetry_from_defect_entry()
point_symmetry_from_site()
point_symmetry_from_structure()
schoenflies_from_hermann()
summed_rms_dist()
swap_axes()
translate_structure()
- Module contents
- doped.vasp module
DefectDictSet
DefectRelaxSet
DefectRelaxSet.bulk_vasp_gam
DefectRelaxSet.bulk_vasp_ncl
DefectRelaxSet.bulk_vasp_nkred_std
DefectRelaxSet.bulk_vasp_std
DefectRelaxSet.vasp_gam
DefectRelaxSet.vasp_ncl
DefectRelaxSet.vasp_nkred_std
DefectRelaxSet.vasp_std
DefectRelaxSet.write_all()
DefectRelaxSet.write_gam()
DefectRelaxSet.write_ncl()
DefectRelaxSet.write_nkred_std()
DefectRelaxSet.write_std()
DefectsSet
DopedDictSet
DopedKpoints
deep_dict_update()
scaled_ediff()
- doped.VASP_sets