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
CompetingPhases
CompetingPhasesAnalyzer
CompetingPhasesAnalyzer.bulk_composition
CompetingPhasesAnalyzer.elemental
CompetingPhasesAnalyzer.extrinsic_species
CompetingPhasesAnalyzer.data
CompetingPhasesAnalyzer.formation_energy_df
CompetingPhasesAnalyzer.calculate_chempots()
CompetingPhasesAnalyzer.chem_limits
CompetingPhasesAnalyzer.cplap_input()
CompetingPhasesAnalyzer.from_csv()
CompetingPhasesAnalyzer.from_vaspruns()
CompetingPhasesAnalyzer.intrinsic_chem_limits
CompetingPhasesAnalyzer.intrinsic_phase_diagram
CompetingPhasesAnalyzer.to_LaTeX_table()
CompetingPhasesAnalyzer.to_csv()
ExtrinsicCompetingPhases
combine_extrinsic()
get_chempots_from_phase_diagram()
make_molecule_in_a_box()
- doped.core module
Defect
DefectEntry
DefectEntry.as_dict()
DefectEntry.bulk_entry
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.entry_id
DefectEntry.equiv_conv_cell_frac_coords
DefectEntry.equivalent_supercell_sites
DefectEntry.from_json()
DefectEntry.get_freysoldt_correction()
DefectEntry.get_kumagai_correction()
DefectEntry.name
DefectEntry.sc_defect_frac_coords
DefectEntry.sc_entry
DefectEntry.to_json()
DefectEntry.wyckoff
Interstitial
Substitution
Vacancy
doped_defect_from_pmg_defect()
- doped.generation module
DefectsGenerator
DefectsGenerator.defect_entries
DefectsGenerator.defects
DefectsGenerator.primitive_structure
DefectsGenerator.supercell_matrix
DefectsGenerator.bulk_supercell
DefectsGenerator.conventional_structure
DefectsGenerator.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
DefectDictSet
DefectRelaxSet
DefectRelaxSet.vasp_gam
DefectRelaxSet.vasp_nkred_std
DefectRelaxSet.vasp_std
DefectRelaxSet.vasp_ncl
DefectRelaxSet.defect_supercell
DefectRelaxSet.bulk_supercell
DefectRelaxSet.poscar_comment
DefectRelaxSet.bulk_vasp_gam
DefectRelaxSet.bulk_vasp_nkred_std
DefectRelaxSet.bulk_vasp_std
DefectRelaxSet.bulk_vasp_ncl
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
deep_dict_update()
scaled_ediff()
- doped.VASP_sets