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.
Submodules
- doped.analysis module
- doped.chemical_potentials module
CompetingPhasesCompetingPhasesAnalyzerCompetingPhasesAnalyzer.bulk_compositionCompetingPhasesAnalyzer.elementalCompetingPhasesAnalyzer.extrinsic_speciesCompetingPhasesAnalyzer.dataCompetingPhasesAnalyzer.formation_energy_dfCompetingPhasesAnalyzer.calculate_chempots()CompetingPhasesAnalyzer.chempotsCompetingPhasesAnalyzer.from_csv()CompetingPhasesAnalyzer.from_vaspruns()CompetingPhasesAnalyzer.intrinsic_chempotsCompetingPhasesAnalyzer.intrinsic_phase_diagramCompetingPhasesAnalyzer.to_LaTeX_table()CompetingPhasesAnalyzer.to_csv()
ExtrinsicCompetingPhasescombine_extrinsic()get_X_poor_limit()get_X_rich_limit()get_chempots_from_phase_diagram()make_molecule_in_a_box()
- doped.core module
DefectDefectEntryDefectEntry.as_dict()DefectEntry.bulk_entryDefectEntry.bulk_supercellDefectEntry.calculation_metadataDefectEntry.charge_stateDefectEntry.charge_state_guessing_logDefectEntry.conv_cell_frac_coordsDefectEntry.conventional_structureDefectEntry.corrected_energyDefectEntry.correctionsDefectEntry.corrections_metadataDefectEntry.defectDefectEntry.defect_supercellDefectEntry.defect_supercell_siteDefectEntry.degeneracy_factorsDefectEntry.entry_idDefectEntry.equilibrium_concentration()DefectEntry.equiv_conv_cell_frac_coordsDefectEntry.equivalent_supercell_sitesDefectEntry.formation_energy()DefectEntry.from_dict()DefectEntry.from_json()DefectEntry.get_eigenvalue_analysis()DefectEntry.get_freysoldt_correction()DefectEntry.get_kumagai_correction()DefectEntry.nameDefectEntry.plot_site_displacements()DefectEntry.sc_defect_frac_coordsDefectEntry.sc_entryDefectEntry.to_json()DefectEntry.wyckoff
InterstitialSubstitutionVacancydoped_defect_from_pmg_defect()
- doped.corrections module
- doped.generation module
DefectsGeneratorDefectsGenerator.defect_entriesDefectsGenerator.defectsDefectsGenerator.primitive_structureDefectsGenerator.supercell_matrixDefectsGenerator.bulk_supercellDefectsGenerator.conventional_structureDefectsGenerator.add_charge_states()DefectsGenerator.as_dict()DefectsGenerator.defect_generator_info()DefectsGenerator.from_dict()DefectsGenerator.from_json()DefectsGenerator.remove_charge_states()DefectsGenerator.to_json()
closest_site_info()get_defect_entry_from_defect()get_defect_name_from_defect()get_defect_name_from_entry()get_ideal_supercell_matrix()get_oxi_probabilities()guess_defect_charge_states()name_defect_entries()
- doped.thermodynamics module
DefectThermodynamicsDefectThermodynamics.add_entries()DefectThermodynamics.all_stable_entriesDefectThermodynamics.all_unstable_entriesDefectThermodynamics.as_dict()DefectThermodynamics.chempotsDefectThermodynamics.defect_entriesDefectThermodynamics.defect_namesDefectThermodynamics.dist_tolDefectThermodynamics.el_refsDefectThermodynamics.from_dict()DefectThermodynamics.from_json()DefectThermodynamics.get_dopability_limits()DefectThermodynamics.get_doping_windows()DefectThermodynamics.get_equilibrium_concentrations()DefectThermodynamics.get_equilibrium_fermi_level()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.to_json()
bold_print()get_e_h_concs()get_rich_poor_limit_dict()group_defects_by_distance()group_defects_by_name()scissor_dos()
- doped.utils package
- Submodules
- doped.utils.displacements module
- doped.utils.legacy_corrections module
- doped.utils.parsing module
check_atom_mapping_far_from_defect()defect_charge_from_vasprun()find_archived_fname()find_nearest_coords()get_coords_and_idx_of_species()get_defect_site_idxs_and_unrelaxed_structure()get_defect_type_and_composition_diff()get_interstitial_site_and_orientational_degeneracy()get_locpot()get_magnetization_from_vasprun()get_nelect_from_vasprun()get_neutral_nelect_from_vasprun()get_orientational_degeneracy()get_outcar()get_procar()get_site_mapping_indices()get_vasprun()parse_projected_eigen_no_mag()reorder_s1_like_s2()simple_spin_degeneracy_from_charge()suppress_logging()
- doped.utils.plotting module
- doped.utils.supercells module
- doped.utils.symmetry module
apply_symm_op_to_site()apply_symm_op_to_struct()get_BCS_conventional_structure()get_clean_structure()get_conv_cell_site()get_primitive_structure()get_spglib_conv_structure()get_wyckoff()get_wyckoff_dict_from_sgn()get_wyckoff_label_and_equiv_coord_list()group_order_from_schoenflies()point_symmetry()point_symmetry_from_defect()point_symmetry_from_defect_entry()schoenflies_from_hermann()swap_axes()
- Module contents
- doped.vasp module
DefectDictSetDefectRelaxSetDefectRelaxSet.vasp_gamDefectRelaxSet.vasp_nkred_stdDefectRelaxSet.vasp_stdDefectRelaxSet.vasp_nclDefectRelaxSet.defect_supercellDefectRelaxSet.bulk_supercellDefectRelaxSet.poscar_commentDefectRelaxSet.bulk_vasp_gamDefectRelaxSet.bulk_vasp_nkred_stdDefectRelaxSet.bulk_vasp_stdDefectRelaxSet.bulk_vasp_nclDefectRelaxSet.bulk_vasp_gamDefectRelaxSet.bulk_vasp_nclDefectRelaxSet.bulk_vasp_nkred_stdDefectRelaxSet.bulk_vasp_stdDefectRelaxSet.vasp_gamDefectRelaxSet.vasp_nclDefectRelaxSet.vasp_nkred_stdDefectRelaxSet.vasp_stdDefectRelaxSet.write_all()DefectRelaxSet.write_gam()DefectRelaxSet.write_ncl()DefectRelaxSet.write_nkred_std()DefectRelaxSet.write_std()
DefectsSetDopedDictSetDopedKpointsdeep_dict_update()scaled_ediff()
- doped.VASP_sets