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
• 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.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()
• doped.corrections module
• doped.generation module
• doped.thermodynamics module
• doped.utils package
  • Submodules
  • doped.utils.displacements module
  • 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()
    • defect_charge_from_vasprun()
    • find_archived_fname()
    • find_idx_of_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
    • cell_metric()
    • find_ideal_supercell()
    • find_optimal_cell_shape()
    • get_min_image_distance()
    • get_pmg_cubic_supercell_dict()
  • 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_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()
    • point_symmetry_from_defect()
    • point_symmetry_from_defect_entry()
    • schoenflies_from_hermann()
    • summed_rms_dist()
    • swap_axes()
    • translate_structure()
  • Module contents
• doped.vasp module
• doped.VASP_sets