doped
See the DeepWiki site for an overview of the codebase and workflow diagrams.
Modules
- doped.analysis module
- doped.chemical_potentials module
ChemicalPotentialGridCompetingPhasesCompetingPhases.as_dict()CompetingPhases.convergence_setup()CompetingPhases.entries_dictCompetingPhases.from_dict()CompetingPhases.get_kpoint_convergence_sets()CompetingPhases.get_relaxation_sets()CompetingPhases.get_singlepoint_sets()CompetingPhases.metallic_entriesCompetingPhases.molecular_entriesCompetingPhases.nonmetallic_entriesCompetingPhases.vasp_std_setup()CompetingPhases.write_kpoint_convergence_files()CompetingPhases.write_relaxation_files()CompetingPhases.write_singlepoint_files()
CompetingPhasesAnalyzerCompetingPhasesAnalyzer.as_dict()CompetingPhasesAnalyzer.calculate_chempots()CompetingPhasesAnalyzer.chempot_gridCompetingPhasesAnalyzer.entries_dictCompetingPhasesAnalyzer.from_dict()CompetingPhasesAnalyzer.get_formation_energy_df()CompetingPhasesAnalyzer.plot_chempot_heatmap()CompetingPhasesAnalyzer.to_LaTeX_table()
entries_from_chempot_limits()get_MP_summary_dicts()get_X_poor_limit()get_X_rich_limit()get_X_rich_poor_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()plot_chempot_heatmap()prune_entries_to_border_candidates()
- doped.core module
DefectDefectEntryDefectEntry.as_dict()DefectEntry.bulk_entry_energyDefectEntry.bulk_site_concentrationDefectEntry.corrected_energyDefectEntry.equilibrium_concentration()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_shallowDefectEntry.plot_site_displacements()DefectEntry.sc_entry_energyDefectEntry.to_json()
InterstitialSubstitutionVacancydoped_defect_from_pmg_defect()get_oxi_probabilities()guess_and_set_oxi_states_with_timeout()guess_and_set_struct_oxi_states()is_shallow()most_common_oxi()remove_site_oxi_state()template_defect_entry_from_structures()
- doped.corrections module
- doped.generation module
DefectsGeneratorcharge_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_stol_equiv_dist()get_vacancy_charge_states()guess_defect_charge_states()name_defect_entries()sort_defect_entries()
- doped module (
__init__.py) - doped.thermodynamics module
DefectThermodynamicsDefectThermodynamics.add_entries()DefectThermodynamics.all_stable_entriesDefectThermodynamics.all_unstable_entriesDefectThermodynamics.as_dict()DefectThermodynamics.bulk_dosDefectThermodynamics.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_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.plot_chempot_heatmap()DefectThermodynamics.print_transition_levels()DefectThermodynamics.prune_to_stable_entries()DefectThermodynamics.to_json()DefectThermodynamics.unstable_entries
FermiSolverbold_print()get_doping()get_e_h_concs()get_fermi_dos()get_interpolated_chempots()get_rich_poor_limit_dict()group_defects_by_distance()group_defects_by_name()group_defects_by_type_and_distance()name_defect_cluster()raw_energy_from_chempots()scissor_dos()
- doped.utils package
- Submodules
- doped.utils.configurations module
- doped.utils.displacements module
- doped.utils.efficiency module
DopedTopographyAnalyzerDopedVacancyGeneratorHashabledictStructureMatcher_scan_stol()array_to_tuple()cache_ready_PeriodicSite__eq__()cache_species()cached_Structure_eq_func()cached_allclose()doped_Composition_eq_func()doped_Structure__eq__()fast_Composition_eq()get_all_distances()get_dist_equiv_stol()get_element_indices()get_element_min_max_bond_length_dict()get_min_stol_for_s1_s2()get_voronoi_nodes()
- doped.utils.eigenvalues module
- doped.utils.legacy_corrections module
- doped.utils.parsing module
check_atom_mapping_far_from_defect()find_archived_fname()find_missing_idx()find_nearest_coords()get_coords_and_idx_of_species()get_core_potentials_from_outcar()get_defect_type_and_composition_diff()get_defect_type_site_idxs_and_unrelaxed_structure()get_dimer_bonds()get_locpot()get_magnetization_from_vasprun()get_matching_site()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()total_charge_from_vasprun()
- doped.utils.plotting module
- doped.utils.stenciling module
- doped.utils.supercells module
- doped.utils.symmetry module
apply_symm_op_to_site()apply_symm_op_to_struct()are_equivalent_lattices()cached_simplify()cached_solve()cluster_coords()cluster_sites_by_dist_tol()doped_cluster_frac_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_min_dist_between_equiv_sites()get_orientational_degeneracy()get_primitive_structure()get_sga()get_sga_and_symprec()get_spglib_conv_structure()get_wyckoff()get_wyckoff_dict_from_sgn()get_wyckoff_label_and_equiv_coord_list()group_order_from_schoenflies()is_periodic_image()point_symmetry_from_defect()point_symmetry_from_defect_entry()point_symmetry_from_site()point_symmetry_from_structure()schoenflies_from_hermann()summed_dist()swap_axes()translate_structure()
- Module contents
- doped.vasp module
DefectDictSetDefectRelaxSetDefectRelaxSet.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