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()

Get a multiprocessing context that is compatible with the current OS.

doped.pool_manager(processes: int | None = None)

Context manager for multiprocessing Pool, to throw a clearer error message when RuntimeErrors are raised multiprocessing within doped 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. If None, will use mp.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
  • DefectParser
    • DefectParser.apply_corrections()
    • DefectParser.from_paths()
    • DefectParser.load_FNV_data()
    • DefectParser.load_and_check_calculation_metadata()
    • DefectParser.load_bulk_gap_data()
    • DefectParser.load_eFNV_data()
  • DefectsParser
    • DefectsParser.defect_dict
    • DefectsParser.get_defect_thermodynamics()
  • check_and_set_defect_entry_name()
  • defect_entry_from_paths()
  • defect_from_structures()
  • defect_name_from_structures()
  • guess_defect_position()
• doped.chemical_potentials module
  • ChemicalPotentialGrid
    • ChemicalPotentialGrid.get_grid()
    • ChemicalPotentialGrid.grid_from_dataframe()
  • CompetingPhases
    • CompetingPhases.convergence_setup()
    • CompetingPhases.metallic_entries
    • CompetingPhases.molecular_entries
    • CompetingPhases.nonmetallic_entries
    • CompetingPhases.vasp_std_setup()
  • CompetingPhasesAnalyzer
    • CompetingPhasesAnalyzer.as_dict()
    • CompetingPhasesAnalyzer.calculate_chempots()
    • CompetingPhasesAnalyzer.from_dict()
    • CompetingPhasesAnalyzer.get_formation_energy_df()
    • CompetingPhasesAnalyzer.plot_chempot_heatmap()
    • CompetingPhasesAnalyzer.to_LaTeX_table()
  • 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
    • Defect.as_dict()
    • Defect.defect_site
    • Defect.element_changes
    • Defect.from_json()
    • Defect.get_charge_states()
    • Defect.get_supercell_structure()
    • Defect.to_json()
    • Defect.volume
  • 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
  • get_freysoldt_correction()
  • get_kumagai_correction()
  • plot_FNV()
• doped.generation module
  • DefectsGenerator
    • DefectsGenerator.add_charge_states()
    • DefectsGenerator.as_dict()
    • DefectsGenerator.defect_generator_info()
    • DefectsGenerator.from_dict()
    • DefectsGenerator.from_json()
    • DefectsGenerator.remove_charge_states()
    • DefectsGenerator.to_json()
  • 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
    • FermiSolver.equilibrium_solve()
    • FermiSolver.interpolate_chempots()
    • FermiSolver.optimise()
    • FermiSolver.pseudo_equilibrium_solve()
    • FermiSolver.scan_chemical_potential_grid()
    • FermiSolver.scan_chempots()
    • FermiSolver.scan_dopant_concentration()
    • FermiSolver.scan_temperature()
  • 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
    • StructureMatcher_scan_stol()
    • get_dist_equiv_stol()
    • get_element_indices()
    • get_element_min_max_bond_length_dict()
    • get_min_stol_for_s1_s2()
    • get_path_structures()
    • get_s2_like_s1()
    • orient_s2_like_s1()
    • write_path_structures()
  • doped.utils.displacements module
    • calc_displacements_ellipsoid()
    • calc_site_displacements()
    • plot_displacements_ellipsoid()
    • plot_site_displacements()
  • doped.utils.efficiency module
    • DopedTopographyAnalyzer
    • Hashabledict
    • cache_ready_PeriodicSite__eq__()
    • cached_Structure_eq_func()
    • cached_allclose()
    • doped_Composition_eq_func()
    • doped_Structure__eq__()
    • fast_Composition_eq()
    • get_voronoi_nodes()
  • doped.utils.eigenvalues module
    • band_edge_properties_from_vasprun()
    • get_band_edge_info()
    • get_eigenvalue_analysis()
    • make_band_edge_orbital_infos()
    • make_perfect_band_edge_state_from_vasp()
  • doped.utils.legacy_corrections module
    • get_murphy_image_charge_correction()
    • lany_zunger_corrected_defect_dict()
  • 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
    • format_defect_name()
    • formation_energy_plot()
    • get_colormap()
    • get_legend_font_size()
    • get_linestyles()
    • plot_chemical_potential_table()
  • doped.utils.stenciling module
    • get_defect_in_supercell()
    • is_within_frac_bounds()
  • doped.utils.supercells module
    • cell_metric()
    • find_ideal_supercell()
    • find_optimal_cell_shape()
    • get_min_image_distance()
    • get_pmg_cubic_supercell_dict()
    • min_dist()
  • 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
    • DefectDictSet.incar
    • DefectDictSet.nelect
    • DefectDictSet.write_input()
  • 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
    • DefectsSet.write_files()
  • DopedDictSet
    • DopedDictSet.incar
    • DopedDictSet.kpoints
    • DopedDictSet.poscar
    • DopedDictSet.potcar
  • DopedKpoints
  • deep_dict_update()
  • scaled_ediff()
• doped.VASP_sets