Index

A

add_constant_chempot_line() (StabilityDiagram method), [1] add_heatmap() (StabilityDiagram method), [1] add_points() (StabilityDiagram method), [1] add_reservoirs() (StabilityDiagram method), [1] Advanced append() (DefectConcentrations method), [1] (DefectsAnalysis method), [1]

are_chempots_delta (Reservoirs property), [1] as_dict() (Chempots method), [1] (DefectConcentrations method), [1] (DefectEntry method), [1] (DefectsAnalysis method), [1] (PressureReservoirs method), [1] (Reservoirs method), [1] (ThermoData method), [1]

B

binding_energy() (DefectsAnalysis method), [1] bulk_specie (Substitution property), [1] bulk_structure (Defect property), [1] (DefectComplex property), [1] (DefectEntry property), [1]

bulk_volume (Defect property), [1] (DefectComplex property), [1]

C

calculate_single_chempot() (PDHandler method), [1] carrier_concentrations() (DefectsAnalysis method), [1] charge (Defect property), [1] (DefectComplex property), [1] (DefectEntry property), [1] charge_transition_levels() (DefectsAnalysis method), [1] chempot_ideal_gas() (in module defermi.chempots.core) Chempots (class in defermi.chempots.core), [1] chempots (DefectsAnalysis property), [1] Conductivity (class in defermi.thermodynamics), [1] constant_chempot_line() (StabilityDiagram method), [1] contribs (MPDatabase.MPRester property), [1] convert_conc_from_weight_to_cm3() (in module defermi.tools.utils)

copy() (Chempots method), [1] (DefectConcentrations method), [1] (DefectsAnalysis method), [1] (Reservoirs method), [1] (SingleDefConc method), [1] corrections (DefectEntry property), [1] create_def_structure_for_visualization() (in module defermi.structure) create_interstitial_structures() (in module defermi.structure) create_interstitials() (in module defermi.generator) create_substitution_structures() (in module defermi.structure) create_substitutions() (in module defermi.generator) create_vacancies() (in module defermi.generator) create_vacancy_structures() (in module defermi.structure)

D

data (DefectEntry property), [1] decode_object_from_json() (in module defermi.tools.utils) Defect (class in defermi.defects), [1] defect (DefectEntry property), [1] defect_composition (Defect property), [1] (DefectComplex property), [1] (Interstitial property), [1] (Polaron property), [1] (Substitution property), [1] (Vacancy property), [1] defect_concentration() (DefectEntry method), [1] defect_concentration_function (DefectEntry property), [1] defect_concentrations() (DefectsAnalysis method), [1] defect_finder() (in module defermi.structure) defect_names (DefectComplex property), [1] defect_site_index (Defect property), [1] (Interstitial property), [1] (Polaron property), [1] (Substitution property), [1] (Vacancy property), [1] defect_specie (DefectEntry property), [1] defect_structure (Defect property), [1] (DefectComplex property), [1] defect_type (DefectEntry property), [1] DefectComplex (class in defermi.defects), [1] DefectConcentrations (class in defermi.analysis), [1] DefectEntry (class in defermi.entries), [1] defects (Defect property), [1] (DefectComplex property), [1] DefectsAnalysis (class in defermi.analysis), [1] DefectThermodynamics (class in defermi.thermodynamics), [1] defermi.analysis module defermi.chempots module defermi.chempots.core module defermi.chempots.generator module defermi.chempots.oxygen module defermi.chempots.phase_diagram module defermi.chempots.reservoirs module defermi.chempots.tests module defermi.chempots.tests.test_chempots module defermi.chempots.tests.test_generator module defermi.chempots.tests.test_oxygen module

defermi.chempots.tests.test_phase_diagram module defermi.chempots.tests.test_reservoirs module defermi.cli module defermi.cli.inputs module defermi.cli.main module defermi.corrections module defermi.corrections.freysoldt module defermi.corrections.kumagai module defermi.defects module defermi.elasticity module defermi.electronic_structure module defermi.entries module defermi.generator module defermi.plotter module defermi.structure module defermi.thermodynamics module defermi.tools module defermi.tools.materials_project module defermi.tools.structure module defermi.tools.tests module defermi.tools.tests.test_materials_project module defermi.tools.utils module deform_lattice() (in module defermi.tools.structure) delta_atoms (Defect property), [1] (DefectComplex property), [1] (DefectEntry property), [1] (Interstitial property), [1] (Polaron property), [1] (Substitution property), [1] (Vacancy property), [1]

E

elemental (DefectConcentrations property), [1] elements (DefectConcentrations property), [1] (DefectsAnalysis property), [1]

energy_diff (DefectEntry property), [1]

F

f0() (in module defermi.electronic_structure) fermi_dirac() (in module defermi.entries) filter_concentrations() (DefectConcentrations method), [1] filter_entries() (DefectsAnalysis method), [1] filter_reservoirs() (Reservoirs method), [1] find_structure() (MPDatabase.MPRester method), [1] format_composition() (in module defermi.tools.utils) format_legend_with_charge_kv() (in module defermi.defects) format_legend_with_charge_number() (in module defermi.defects) formation_energies() (DefectsAnalysis method), [1] formation_energy() (DefectEntry method), [1] formation_energy_function (DefectEntry property), [1] from_computed_entries() (DefectEntry static method), [1] from_dataframe() (DefectsAnalysis static method), [1] from_dict() (Chempots static method), [1] (DefectConcentrations class method), [1] (DefectEntry class method), [1] (DefectsAnalysis class method), [1] (PressureReservoirs class method), [1] (Reservoirs class method), [1] (ThermoData class method), [1]

from_file() (DefectsAnalysis static method), [1] from_json() (DefectsAnalysis static method), [1] (PressureReservoirs static method), [1] (Reservoirs static method), [1] (ThermoData static method), [1] from_pmg_elements() (Chempots static method), [1] from_string() (Defect static method), [1] (DefectComplex static method), [1] from_structures() (DefectEntry static method), [1] from_vasp_directories() (DefectEntry static method), [1] (DefectsAnalysis static method), [1]

G

generate_chempots_from_condition() (in module defermi.chempots.generator) generate_chempots_from_mp() (in module defermi.chempots.generator) generate_defect_structure() (DefectComplex method), [1] (Interstitial method), [1] (Polaron method), [1] (Substitution method), [1] (Vacancy method), [1] generate_elemental_chempots() (in module defermi.chempots.generator) generate_pressure_reservoirs_from_precursors() (in module defermi.chempots.generator) get_absolute() (Chempots method), [1] get_absolute_res_dict() (Reservoirs method), [1] get_all_boundaries_chempots() (PDHandler method), [1] get_atom_reference_data() (MPDatabase.MPRester method), [1] get_bandstructure_by_material_id() (MPDatabase.MPRester method), [1] get_barycenter_chemical_potentials_absolute() (in module defermi.chempots.oxygen) get_barycenter_chemical_potentials_relative() (in module defermi.chempots.oxygen) get_carrier_concentrations() (in module defermi.electronic_structure) get_charge_density_from_material_id() (MPDatabase.MPRester method), [1] get_charge_density_from_task_id() (MPDatabase.MPRester method), [1] get_charge_from_computed_entry() (in module defermi.tools.utils) get_charge_transition_level() (DefectsAnalysis method), [1] get_chempot_diagram() (PDHandler method), [1] get_chempots_reference() (PDHandler method), [1] get_cohesive_energy() (MPDatabase.MPRester method), [1] get_conductivities_from_thermodata() (Conductivity method), [1] get_conductivity() (Conductivity method), [1] get_database_version() (MPDatabase.MPRester method), [1] get_dataframe() (PDHandler method), [1] (Reservoirs method), [1] get_defect_from_string() (in module defermi.defects) get_delta_atoms() (in module defermi.defects) get_delta_atoms_from_comp() (in module defermi.defects) get_displacement_vectors() (in module defermi.tools.structure) get_distance_vector() (in module defermi.tools.structure) get_dos_by_material_id() (MPDatabase.MPRester method), [1] get_dos_from_effective_mass() (in module defermi.electronic_structure) get_dos_from_stable_composition() (MPDatabase method), [1] get_dos_object_from_json() (in module defermi.electronic_structure) get_download_info() (MPDatabase.MPRester method), [1] get_elastic_dipole_tensor() (in module defermi.elasticity) get_element_total() (DefectConcentrations method), [1] get_emmet_version() (MPDatabase.MPRester static method), [1] get_energies_from_comp() (PDHandler method), [1] get_energy_from_stable_comp() (PDHandler method), [1] get_entries() (MPDatabase method), [1] (MPDatabase.MPRester method), [1] get_entries_from_comp() (PDHandler method), [1] get_entries_from_compositions() (MPDatabase method), [1] get_entries_in_chemsys() (MPDatabase.MPRester method), [1] get_entry_by_material_id() (MPDatabase.MPRester method), [1] get_formation_energies_from_comp() (PDHandler method), [1] get_formation_energy_from_stable_comp() (PDHandler method), [1] get_freysoldt_correction_from_locpot() (in module defermi.corrections.freysoldt) get_furthest_neighbors() (in module defermi.tools.structure)

get_ion_entries() (MPDatabase.MPRester method), [1] get_ion_reference_data() (MPDatabase.MPRester method), [1] get_ion_reference_data_for_chemsys() (MPDatabase.MPRester method), [1] get_kumagai_correction() (in module defermi.corrections.kumagai) get_kumagai_correction_from_structures() (in module defermi.corrections.kumagai) get_latex_table() (Reservoirs method), [1] get_material_id_from_task_id() (MPDatabase.MPRester method), [1] get_material_id_references() (MPDatabase.MPRester method), [1] get_material_ids() (MPDatabase.MPRester method), [1] get_multiplicity() (Defect method), [1] (DefectComplex method), [1] (Interstitial method), [1] (Polaron method), [1] (Substitution method), [1] (Vacancy method), [1] get_object_feature() (in module defermi.tools.utils) get_object_from_json() (in module defermi.tools.utils) get_oxygen_chempot_from_pO2() (in module defermi.chempots.oxygen) get_oxygen_chempot_standard_finite_temperature() (in module defermi.chempots.oxygen) get_oxygen_evolution() (MPDatabase.MPRester method), [1] get_oxygen_pressure_reservoirs() (in module defermi.chempots.oxygen) get_phase_boundaries_chempots() (PDHandler method), [1] get_phase_boundaries_compositions() (PDHandler method), [1] get_phase_diagram_from_chemsys() (MPDatabase method), [1] get_phonon_bandstructure_by_material_id() (MPDatabase.MPRester method), [1] get_phonon_dos_by_material_id() (MPDatabase.MPRester method), [1] get_plot() (PDHandler method), [1] (Reservoirs method), [1] (StabilityDiagram method), [1] get_pO2_quenched_thermodata() (DefectThermodynamics method), [1] get_pO2_thermodata() (DefectThermodynamics method), [1] get_pourbaix_entries() (MPDatabase.MPRester method), [1] get_pressure_reservoirs_from_phase_diagram() (in module defermi.chempots.oxygen) get_pressure_reservoirs_from_precursors() (in module defermi.chempots.oxygen) get_referenced() (Chempots method), [1] get_referenced_res_dict() (Reservoirs method), [1] get_relaxation_volume() (in module defermi.elasticity) get_single_point_quenched_thermodata() (DefectThermodynamics method), [1] get_single_point_thermodata() (DefectThermodynamics method), [1] get_site_in_bulk() (Substitution method), [1] get_specific_pressures() (ThermoData method), [1] get_stability() (MPDatabase.MPRester method), [1] get_stability_diagram() (PDHandler method), [1] get_stable_energy_pfu_from_composition() (MPDatabase method), [1] get_stable_entry_from_comp() (PDHandler method), [1] get_stable_entry_from_composition() (MPDatabase method), [1] get_structure() (MPDatabase method), [1] get_structure_by_material_id() (MPDatabase.MPRester method), [1] get_structures() (MPDatabase.MPRester method), [1] get_task_ids_associated_with_material_id() (MPDatabase.MPRester method), [1] get_trajectory_for_visualization() (in module defermi.structure) get_variable_species_quenched_thermodata() (DefectThermodynamics method), [1] get_variable_species_thermodata() (DefectThermodynamics method), [1] get_wulff_shape() (MPDatabase.MPRester method), [1] Getting started

I

Interstitial (class in defermi.defects), [1] is_site_in_structure() (in module defermi.tools.structure) is_site_in_structure_coords() (in module defermi.tools.structure)

items() (Chempots method), [1] (Reservoirs method), [1] (SingleDefConc method), [1] (ThermoData method), [1]

K

keys() (Chempots method), [1] (Reservoirs method), [1] (SingleDefConc method), [1] (ThermoData method), [1]

L

label (Defect property), [1] (DefectComplex property), [1] (DefectEntry property), [1]

M

main() (in module defermi.cli.main) maxwell_boltzmann() (in module defermi.electronic_structure) (in module defermi.entries) merge_entries() (DefectsAnalysis method), [1] module defermi.analysis defermi.chempots defermi.chempots.core defermi.chempots.generator defermi.chempots.oxygen defermi.chempots.phase_diagram defermi.chempots.reservoirs defermi.chempots.tests defermi.chempots.tests.test_chempots defermi.chempots.tests.test_generator defermi.chempots.tests.test_oxygen defermi.chempots.tests.test_phase_diagram defermi.chempots.tests.test_reservoirs defermi.cli defermi.cli.inputs defermi.cli.main defermi.corrections defermi.corrections.freysoldt defermi.corrections.kumagai defermi.defects defermi.elasticity defermi.electronic_structure defermi.entries defermi.generator defermi.plotter defermi.structure defermi.thermodynamics defermi.tools defermi.tools.materials_project defermi.tools.structure defermi.tools.tests defermi.tools.tests.test_materials_project defermi.tools.utils

mp_rester (MPDatabase property), [1] MPDatabase (class in defermi.tools.materials_project), [1] MPDatabase.MPRester (class in defermi.tools.materials_project), [1] mu (Chempots property), [1] multiplicity (Defect property), [1] (DefectComplex property), [1] (DefectEntry property), [1]

N

name (Defect property), [1] (DefectComplex property), [1] (DefectEntry property), [1] (Interstitial property), [1] (Polaron property), [1] (Substitution property), [1] (Vacancy property), [1]

names (DefectConcentrations property), [1]

P

PDHandler (class in defermi.chempots.phase_diagram), [1] plot_binding_energies() (DefectsAnalysis method), [1] (in module defermi.plotter) plot_brouwer_diagram() (DefectsAnalysis method), [1] plot_charge_transition_levels() (in module defermi.plotter) plot_ctl() (DefectsAnalysis method), [1] plot_doping_diagram() (DefectsAnalysis method), [1] plot_formation_energies() (DefectsAnalysis method), [1] (in module defermi.plotter) plot_pO2_vs_concentrations() (in module defermi.plotter)

plot_pO2_vs_conductivity() (in module defermi.plotter) plot_pO2_vs_fermi_level() (in module defermi.plotter) plot_variable_species_vs_concentrations() (in module defermi.plotter) plot_variable_species_vs_conductivity() (in module defermi.plotter) plot_variable_species_vs_fermi_level() (in module defermi.plotter) plot_x_vs_concentrations() (in module defermi.plotter) plot_x_vs_conductivity() (in module defermi.plotter) plot_x_vs_fermi_level() (in module defermi.plotter) Polaron (class in defermi.defects), [1] PressureReservoirs (class in defermi.chempots.reservoirs), [1]

Q

query() (MPDatabase.MPRester method), [1]

R

rattle_atoms() (in module defermi.tools.structure) relaxation_volume() (DefectEntry method), [1] remove_oxidation_state_from_site() (in module defermi.tools.structure) Reservoirs (class in defermi.chempots.reservoirs), [1] reset_all_custom_functions() (DefectsAnalysis method), [1]

reset_defect_concentration_function() (DefectEntry method), [1] reset_defect_concentration_functions() (DefectsAnalysis method), [1] reset_formation_energy_function() (DefectEntry method), [1] reset_formation_energy_functions() (DefectsAnalysis method), [1] run_import_vasp() (in module defermi.cli.inputs)

S

save_object_as_json() (in module defermi.tools.utils) select_concentrations() (DefectConcentrations method), [1] select_entries() (DefectsAnalysis method), [1] select_objects() (in module defermi.tools.utils) set_bulk_volume() (Defect method), [1] set_charge() (Defect method), [1] (DefectComplex method), [1] (DefectEntry method), [1] set_corrections() (DefectEntry method), [1] set_data() (DefectEntry method), [1] (ThermoData method), [1] set_defect_concentration_function() (DefectEntry method), [1] set_defect_concentration_functions() (DefectsAnalysis method), [1] set_formation_energy_function() (DefectEntry method), [1] set_formation_energy_functions() (DefectsAnalysis method), [1] set_label() (Defect method), [1] (DefectComplex method), [1] (DefectEntry method), [1] set_multiplicity() (Defect method), [1] (DefectComplex method), [1] (DefectEntry method), [1] set_to_absolute() (Reservoirs method), [1] set_to_referenced() (Reservoirs method), [1] setUp() (TestChempots method), [1] (TestMPDatabase method), [1] (TestPDHandler method), [1] (TestReservoirs method), [1] setup_import() (in module defermi.cli.inputs) setup_import_vasp() (in module defermi.cli.inputs) SingleDefConc (class in defermi.analysis), [1]

site (Defect property), [1] site_concentration_in_cm3 (Defect property), [1] (DefectComplex property), [1] site_in_bulk (Substitution property), [1] sites (DefectComplex property), [1] solve_fermi_level() (DefectsAnalysis method), [1] solve_intrinsic_fermi_level() (in module defermi.electronic_structure) solve_phase_boundary_chempots() (PDHandler method), [1] sort_entries() (DefectsAnalysis method), [1] sort_objects() (in module defermi.tools.utils) sort_sites_to_ref_coords() (in module defermi.tools.structure) specie (Defect property), [1] StabilityDiagram (class in defermi.chempots.phase_diagram), [1] stable (DefectConcentrations property), [1] stable_charges() (DefectsAnalysis method), [1] structure (DefectEntry property), [1] Substitution (class in defermi.defects), [1] symbol (Defect property), [1] (DefectComplex property), [1] (DefectEntry property), [1] (Interstitial property), [1] (Polaron property), [1] (Substitution property), [1] (Vacancy property), [1] symbol_charge (DefectEntry property), [1] symbol_kroger (DefectEntry property), [1] symbol_with_charge (Defect property), [1] (DefectComplex property), [1] symbol_with_charge_kv (Defect property), [1] (DefectComplex property), [1]

T

table() (DefectsAnalysis method), [1] test_absolute_referenced() (TestChempots method), [1] (TestReservoirs method), [1] test_as_dict_from_dict() (TestChempots method), [1] (TestReservoirs method), [1] test_boundary_chempots() (TestPDHandler method), [1] test_calculate_single_chempot() (TestPDHandler method), [1] test_chempot_from_pO2() (in module defermi.chempots.tests.test_oxygen) test_chempot_ideal_gas() (in module defermi.chempots.tests.test_chempots) test_entries() (TestPDHandler method), [1] test_generate_chempots_from_mp() (in module defermi.chempots.tests.test_generator) test_generate_pressure_reservoirs_from_precursors() (in module defermi.chempots.tests.test_generator) test_get_entries() (TestMPDatabase method), [1] test_get_phase_boundary_chempots() (TestPDHandler method), [1] test_get_structure() (TestMPDatabase method), [1] test_mu_refs() (TestReservoirs method), [1] test_oxygen_pressure_reservoirs() (TestOxygenReservoirs method), [1] test_pmg_elements() (TestChempots method), [1]

test_to_json_from_json() (TestReservoirs method), [1] TestChempots (class in defermi.chempots.tests.test_chempots), [1] TestMPDatabase (class in defermi.tools.tests.test_materials_project), [1] TestOxygenReservoirs (class in defermi.chempots.tests.test_oxygen), [1] TestPDHandler (class in defermi.chempots.tests.test_phase_diagram), [1] TestReservoirs (class in defermi.chempots.tests.test_reservoirs), [1] ThermoData (class in defermi.thermodynamics), [1] thermodata (DefectsAnalysis property), [1] to_dataframe() (DefectsAnalysis method), [1] to_file() (DefectsAnalysis method), [1] to_json() (DefectsAnalysis method), [1] (Reservoirs method), [1] (ThermoData method), [1] to_pmg_elements() (Chempots method), [1] total (DefectConcentrations property), [1] type (Defect property), [1] (DefectComplex property), [1] types (DefectsAnalysis property), [1]

U

update() (Chempots method), [1] (Reservoirs method), [1]

V

Vacancy (class in defermi.defects), [1] values() (Chempots method), [1] (Reservoirs method), [1] (SingleDefConc method), [1] (ThermoData method), [1]

view_structures_with_ase() (in module defermi.tools.structure)

W

write_extxyz_file() (in module defermi.tools.structure)

write_extxyz_for_visualization() (in module defermi.structure) write_xdatcar_from_structures() (in module defermi.tools.structure)