├── .circleci └── config.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── .buildinfo ├── .nojekyll ├── _images │ ├── NaCl_final_eigenvalues.png │ ├── NaCl_initial_eigenvalues.png │ ├── correction.pdf │ ├── correction.png │ ├── correction_pdf_MgSe_Va_Mg_2.png │ ├── cpd_BaSnO3.png │ ├── cpd_MgAl2O4.pdf │ ├── cpd_MgAl2O4.png │ ├── cpd_MgO.png │ ├── eigenvalues.pdf │ ├── eigenvalues.png │ ├── eigenvalues_MgSe_Va_Mg_0.png │ ├── eigenvalues_final.pdf │ ├── eigenvalues_final.png │ ├── eigenvalues_initial.pdf │ ├── eigenvalues_initial.png │ ├── energy_A.pdf │ ├── energy_A.png │ ├── energy_MgSe_A.png │ ├── flowchart.png │ ├── gkfo_correction.pdf │ ├── gkfo_correction.png │ ├── pydefect.pdf │ ├── pydefect.png │ └── seqdiag-99ce4c7713db7a3fc03cae37a298ce6102d9dc71.png ├── _static │ ├── basic.css │ ├── css │ │ ├── badge_only.css │ │ ├── fonts │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── fontawesome-webfont.woff2 │ │ │ ├── lato-bold-italic.woff │ │ │ ├── lato-bold-italic.woff2 │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-normal-italic.woff │ │ │ ├── lato-normal-italic.woff2 │ │ │ ├── lato-normal.woff │ │ │ └── lato-normal.woff2 │ │ └── theme.css │ ├── debug.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── fonts │ │ ├── FontAwesome.otf │ │ ├── Lato │ │ │ ├── lato-bold.eot │ │ │ ├── lato-bold.ttf │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-bolditalic.eot │ │ │ ├── lato-bolditalic.ttf │ │ │ ├── lato-bolditalic.woff │ │ │ ├── lato-bolditalic.woff2 │ │ │ ├── lato-italic.eot │ │ │ ├── lato-italic.ttf │ │ │ ├── lato-italic.woff │ │ │ ├── lato-italic.woff2 │ │ │ ├── lato-regular.eot │ │ │ ├── lato-regular.ttf │ │ │ ├── lato-regular.woff │ │ │ └── lato-regular.woff2 │ │ ├── Roboto-Slab-Bold.woff │ │ ├── Roboto-Slab-Bold.woff2 │ │ ├── Roboto-Slab-Light.woff │ │ ├── Roboto-Slab-Light.woff2 │ │ ├── Roboto-Slab-Regular.woff │ │ ├── Roboto-Slab-Regular.woff2 │ │ ├── Roboto-Slab-Thin.woff │ │ ├── Roboto-Slab-Thin.woff2 │ │ ├── RobotoSlab │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ └── roboto-slab-v7-regular.woff2 │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ ├── fontawesome-webfont.woff2 │ │ ├── lato-bold-italic.woff │ │ ├── lato-bold-italic.woff2 │ │ ├── lato-bold.woff │ │ ├── lato-bold.woff2 │ │ ├── lato-normal-italic.woff │ │ ├── lato-normal-italic.woff2 │ │ ├── lato-normal.woff │ │ └── lato-normal.woff2 │ ├── jquery-3.5.1.js │ ├── jquery.js │ ├── js │ │ ├── badge_only.js │ │ ├── html5shiv-printshiv.min.js │ │ ├── html5shiv.min.js │ │ ├── modernizr.min.js │ │ ├── theme.js │ │ └── versions.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── scripts │ │ ├── furo-extensions.js │ │ ├── furo.js │ │ ├── furo.js.LICENSE.txt │ │ └── furo.js.map │ ├── searchtools.js │ ├── skeleton.css │ ├── sphinx_highlight.js │ ├── styles │ │ ├── furo-extensions.css │ │ ├── furo-extensions.css.map │ │ ├── furo.css │ │ └── furo.css.map │ ├── underscore-1.3.1.js │ └── underscore.js ├── change_log.html ├── concentrations.html ├── doctrees │ ├── change_log.doctree │ ├── environment.pickle │ ├── first_principles_calc.doctree │ ├── hybrid_functional.doctree │ ├── index.doctree │ ├── introduction.doctree │ ├── tutorial.doctree │ └── vertical_transition_level.doctree ├── first_principles_calc.html ├── genindex.html ├── hybrid_functional.html ├── index.html ├── introduction.html ├── objects.inv ├── search.html ├── searchindex.js ├── tutorial.html └── vertical_transition_level.html ├── docs_rst ├── Makefile ├── NaCl_final_eigenvalues.png ├── NaCl_initial_eigenvalues.png ├── change_log.rst ├── concentrations.rst ├── conf.py ├── correction.pdf ├── correction.png ├── correction_pdf_MgSe_Va_Mg_2.png ├── cpd_BaSnO3.png ├── cpd_MgAl2O4.pdf ├── cpd_MgAl2O4.png ├── cpd_MgO.png ├── eigenvalues.pdf ├── eigenvalues.png ├── eigenvalues_MgSe_Va_Mg_0.png ├── eigenvalues_final.pdf ├── eigenvalues_final.png ├── eigenvalues_initial.pdf ├── eigenvalues_initial.png ├── energy.png ├── energy_A.pdf ├── energy_A.png ├── energy_MgSe_A.png ├── first_principles_calc.rst ├── flowchart.png ├── gkfo_correction.pdf ├── gkfo_correction.png ├── index.rst ├── make.bat ├── pydefect.pdf ├── pydefect.png ├── tutorial.rst └── vertical_transition_level.rst ├── pydefect ├── __init__.py ├── analyzer │ ├── __init__.py │ ├── _defect_charge_distribution.py │ ├── band_edge_states.py │ ├── calc_results.py │ ├── calc_summary.py │ ├── concentration │ │ ├── __init__.py │ │ ├── concentration.py │ │ ├── degeneracy.py │ │ ├── distribution_function.py │ │ ├── make_concentration.py │ │ └── plot_concentration.py │ ├── defect_charge_info.py │ ├── defect_energy.py │ ├── defect_energy_plotter.py │ ├── defect_energy_util.py │ ├── defect_structure_comparator.py │ ├── defect_structure_info.py │ ├── eigenvalue_plotter.py │ ├── grids.py │ ├── make_band_edge_states.py │ ├── make_calc_summary.py │ ├── make_defect_energy_info.py │ ├── make_defect_energy_summary.py │ ├── make_defect_structure_info.py │ ├── pinning_levels.py │ ├── refine_defect_structure.py │ ├── transition_levels.py │ ├── transition_levels_plotter.py │ └── unitcell.py ├── chem_pot_diag │ ├── __init__.py │ ├── chem_pot_diag.py │ └── cpd_plotter.py ├── cli │ ├── __init__.py │ ├── main.py │ ├── main_functions.py │ ├── main_print_json.py │ ├── main_tools.py │ ├── main_util.py │ ├── main_util_functions.py │ ├── make_defect_vesta_file.py │ └── vasp │ │ ├── __init__.py │ │ ├── get_defect_charge_state.py │ │ ├── main_vasp.py │ │ ├── main_vasp_functions.py │ │ ├── main_vasp_util.py │ │ ├── main_vasp_util_functions.py │ │ ├── make_band_edge_orbital_infos.py │ │ ├── make_calc_results.py │ │ ├── make_composition_energies_from_mp.py │ │ ├── make_defect_charge_info.py │ │ ├── make_efnv_correction.py │ │ ├── make_gkfo_correction.py │ │ ├── make_local_extrema.py │ │ ├── make_perfect_band_edge_state.py │ │ ├── make_poscars_from_query.py │ │ ├── make_unitcell.py │ │ └── molecules │ │ ├── H2 │ │ ├── POSCAR │ │ └── prior_info.yaml │ │ ├── H2O │ │ ├── POSCAR │ │ └── prior_info.yaml │ │ ├── N2 │ │ ├── POSCAR │ │ └── prior_info.yaml │ │ ├── NH3 │ │ ├── POSCAR │ │ └── prior_info.yaml │ │ ├── NO2 │ │ ├── POSCAR │ │ └── prior_info.yaml │ │ ├── O2 │ │ ├── POSCAR │ │ └── prior_info.yaml │ │ ├── __init__.py │ │ ├── molecule_data.yaml │ │ └── molecules.py ├── corrections │ ├── __init__.py │ ├── abstract_correction.py │ ├── efnv_correction.py │ ├── ewald.py │ ├── gkfo_correction.py │ ├── no_correction.py │ └── site_potential_plotter.py ├── database │ ├── __init__.py │ ├── database.py │ ├── electronegativity.yaml │ ├── oxidation_state.yaml │ └── rcore.yaml ├── defaults.py ├── error.py ├── input_maker │ ├── __init__.py │ ├── append_interstitial.py │ ├── complex_defect_entries_make.py │ ├── complex_defect_set.py │ ├── defect.py │ ├── defect_entries_maker.py │ ├── defect_entry.py │ ├── defect_set.py │ ├── defect_set_maker.py │ ├── local_extrema.py │ ├── manual_supercell_maker.py │ ├── supercell.py │ ├── supercell_info.py │ └── supercell_maker.py ├── tests │ ├── __init__.py │ ├── analyzer │ │ ├── PARCHG.0125.ALLK │ │ ├── __init__.py │ │ ├── band_edge_database │ │ │ └── NaCl │ │ │ │ ├── Va_Na1_-1_edge_characters.json │ │ │ │ ├── Va_Na1_0_edge_characters.json │ │ │ │ ├── Va_Na1_1_edge_characters.json │ │ │ │ └── perfect_edge_characters.json │ │ ├── band_edge_eigenvalues.json │ │ ├── concentration │ │ │ ├── __init__.py │ │ │ ├── test_concentration.py │ │ │ ├── test_degeneracy.py │ │ │ ├── test_distribution_function.py │ │ │ ├── test_make_concentration.py │ │ │ └── test_plot_concentration.py │ │ ├── test_band_edge_states.py │ │ ├── test_calc_results.py │ │ ├── test_calc_summary.py │ │ ├── test_defect_charge_info.py │ │ ├── test_defect_energy.py │ │ ├── test_defect_energy_plotter.py │ │ ├── test_defect_energy_util.py │ │ ├── test_defect_structure_comparator.py │ │ ├── test_defect_structure_info.py │ │ ├── test_eigenvalue_plotter.py │ │ ├── test_grids.py │ │ ├── test_make_band_edge_states.py │ │ ├── test_make_calc_summary.py │ │ ├── test_make_defect_energy_info.py │ │ ├── test_make_defect_energy_summary.py │ │ ├── test_make_defect_structure_info.py │ │ ├── test_pinning_levels.py │ │ ├── test_refine_defect_structure.py │ │ ├── test_transition_levels.py │ │ ├── test_transition_levels_plotter.py │ │ └── test_unitcell.py │ ├── chem_pot_diag │ │ ├── test_chem_pot_diag.py │ │ └── test_cpd_plotter.py │ ├── cli │ │ ├── __init__.py │ │ ├── test_main.py │ │ ├── test_main_functions.py │ │ ├── test_main_tools.py │ │ ├── test_main_util.py │ │ ├── test_main_util_functions.py │ │ ├── test_make_defect_vesta_file.py │ │ └── vasp │ │ │ ├── __init__.py │ │ │ ├── test_get_defect_charge_state.py │ │ │ ├── test_main_vasp.py │ │ │ ├── test_main_vasp_functions.py │ │ │ ├── test_main_vasp_util.py │ │ │ ├── test_main_vasp_util_functions.py │ │ │ ├── test_make_band_edge_orbital_infos.py │ │ │ ├── test_make_calc_results.py │ │ │ ├── test_make_composition_energies_from_mp.py │ │ │ ├── test_make_defect_charge_info.py │ │ │ ├── test_make_efnv_correction.py │ │ │ ├── test_make_gkfo_correction.py │ │ │ ├── test_make_local_extrema.py │ │ │ ├── test_make_perfect_band_edge_state.py │ │ │ ├── test_make_poscars_from_query.py │ │ │ ├── test_make_unitcell.py │ │ │ └── vasp_files │ │ │ ├── H2_CHGCAR │ │ │ ├── KInO2_Va_O_2 │ │ │ ├── Va_O1_2 │ │ │ │ ├── calc_results.json │ │ │ │ └── defect_entry.json │ │ │ ├── perfect_calc_results.json │ │ │ ├── pydefect.yaml │ │ │ └── unitcell.json │ │ │ ├── MgO_2x2x2_perfect │ │ │ ├── OUTCAR │ │ │ ├── PROCAR │ │ │ └── vasprun.xml │ │ │ ├── MgO_VaO_+_to_2+_transition │ │ │ ├── final_2+ │ │ │ │ ├── OUTCAR-finish │ │ │ │ ├── POSCAR-finish │ │ │ │ └── calc_results.json │ │ │ ├── initial_+ │ │ │ │ ├── OUTCAR-finish │ │ │ │ ├── POSCAR-finish │ │ │ │ ├── calc_results.json │ │ │ │ ├── correction.json │ │ │ │ ├── correction.pdf │ │ │ │ └── defect_entry.json │ │ │ └── unitcell.json │ │ │ ├── MgO_conv_Va_O_0 │ │ │ ├── CONTCAR │ │ │ ├── OUTCAR │ │ │ └── vasprun.xml │ │ │ ├── NaMgF3_AECCAR0 │ │ │ ├── NaMgF3_AECCAR2 │ │ │ ├── NaMgF3_CHG │ │ │ ├── NaMgF3_LOCPOT │ │ │ └── unitcell_Ne_solid │ │ │ ├── OUTCAR-band │ │ │ ├── OUTCAR-dielectric │ │ │ └── vasprun-band.xml │ ├── conftest.py │ ├── corrections │ │ ├── NaCl_Va_Na_-1_correction.json │ │ ├── __init__.py │ │ ├── gkfo_correction.json │ │ ├── test_efnv_correction.py │ │ ├── test_efnv_performance.py │ │ ├── test_ewald.py │ │ ├── test_gkfo_correction.py │ │ └── test_site_potential_plotter.py │ ├── database │ │ └── test_database.py │ ├── helpers │ │ └── __init__.py │ ├── input_maker │ │ ├── __init__.py │ │ ├── test_append_interstitial.py │ │ ├── test_complex_defect_entries_make.py │ │ ├── test_complex_defect_set.py │ │ ├── test_defect.py │ │ ├── test_defect_entries_maker.py │ │ ├── test_defect_entry.py │ │ ├── test_defect_set.py │ │ ├── test_defect_set_maker.py │ │ ├── test_local_extrema.py │ │ ├── test_manual_supercell_maker.py │ │ ├── test_supercell.py │ │ ├── test_supercell_info.py │ │ └── test_supercell_maker.py │ ├── pytest.ini │ ├── test_data_files │ │ └── Na3AgO2 │ │ │ ├── con_by_Ef_A_300K.json │ │ │ ├── defect_energy_summary.json │ │ │ ├── degeneracies.yaml │ │ │ └── total_dos.json │ └── util │ │ ├── test_coords.py │ │ ├── test_mp_tools.py │ │ ├── test_prepare_names.py │ │ └── test_structure_tools.py └── util │ ├── __init__.py │ ├── coords.py │ ├── error_classes.py │ ├── mp_tools.py │ ├── prepare_names.py │ └── structure_tools.py 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