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.chem_limitsCompetingPhasesAnalyzer.cplap_input()CompetingPhasesAnalyzer.from_csv()CompetingPhasesAnalyzer.from_vaspruns()CompetingPhasesAnalyzer.intrinsic_chem_limitsCompetingPhasesAnalyzer.intrinsic_phase_diagramCompetingPhasesAnalyzer.to_LaTeX_table()CompetingPhasesAnalyzer.to_csv()
ExtrinsicCompetingPhasescombine_extrinsic()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.entry_idDefectEntry.equiv_conv_cell_frac_coordsDefectEntry.equivalent_supercell_sitesDefectEntry.from_json()DefectEntry.get_freysoldt_correction()DefectEntry.get_kumagai_correction()DefectEntry.nameDefectEntry.sc_defect_frac_coordsDefectEntry.sc_entryDefectEntry.to_json()DefectEntry.wyckoff
InterstitialSubstitutionVacancydoped_defect_from_pmg_defect()
- 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_oxi_probabilities()guess_defect_charge_states()name_defect_entries()
- doped.plotting module
- doped.utils package
- 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()
DefectsSetdeep_dict_update()scaled_ediff()
- doped.VASP_sets