Index

_

__add_poscar_to_curr_prop_inst() (kim_tools.test_driver.core.SingleCrystalTestDriver method) __calc (kim_tools.test_driver.core.KIMTestDriver attribute) __files_to_ignore_in_output (kim_tools.test_driver.core.KIMTestDriver attribute) __files_to_keep_in_output (kim_tools.test_driver.core.KIMTestDriver attribute) __kim_model_name (kim_tools.test_driver.core.KIMTestDriver attribute) __nominal_crystal_structure_npt (kim_tools.test_driver.core.SingleCrystalTestDriver attribute) __output_property_instances (kim_tools.test_driver.core.KIMTestDriver attribute) __times_called (kim_tools.test_driver.core.KIMTestDriver attribute) __token (kim_tools.test_driver.core.KIMTestDriver attribute) _abc_impl (kim_tools.test_driver.core.KIMTestDriver attribute) (kim_tools.test_driver.core.SingleCrystalTestDriver attribute) _add_common_crystal_genome_keys_to_current_property_instance() (in module kim_tools.test_driver.core) _add_file_to_current_property_instance() (kim_tools.test_driver.core.KIMTestDriver method) _add_key_to_current_property_instance() (in module kim_tools.test_driver.core) (kim_tools.test_driver.core.KIMTestDriver method) _add_property_instance() (in module kim_tools.test_driver.core) (kim_tools.test_driver.core.KIMTestDriver method) _add_property_instance_and_common_crystal_genome_keys() (in module kim_tools.test_driver.core) (kim_tools.test_driver.core.SingleCrystalTestDriver method) _archive_aux_files() (kim_tools.test_driver.core.KIMTestDriver method) _calc (kim_tools.test_driver.core.KIMTestDriver property) _calculate() (kim_tools.test_driver.core.KIMTestDriver method)

_check_space_group() (in module kim_tools.symmetry_util.core) _compare_Atoms() (kim_tools.aflow_util.core.AFLOW method) _compare_noncrystallographic_fields() (in module kim_tools.test_driver.core) _compare_poscars() (kim_tools.aflow_util.core.AFLOW method) _get_atoms() (kim_tools.test_driver.core.SingleCrystalTestDriver method) _get_cell_cauchy_stress() (kim_tools.test_driver.core.SingleCrystalTestDriver method) _get_mass_density() (kim_tools.test_driver.core.SingleCrystalTestDriver method) _get_nominal_crystal_structure_npt() (kim_tools.test_driver.core.SingleCrystalTestDriver method) _get_optional_source_value() (in module kim_tools.test_driver.core) _get_pressure() (kim_tools.test_driver.core.SingleCrystalTestDriver method) _get_serialized_property_instances() (kim_tools.test_driver.core.KIMTestDriver method) _get_supported_lammps_atom_style() (kim_tools.test_driver.core.KIMTestDriver method) _get_temperature() (kim_tools.test_driver.core.SingleCrystalTestDriver method) _glob_with_exceptions() (in module kim_tools.test_driver.core) _init_output_dir() (kim_tools.test_driver.core.KIMTestDriver method) _set_serialized_property_instances() (kim_tools.test_driver.core.KIMTestDriver method) (kim_tools.test_driver.core.SingleCrystalTestDriver method) _setup() (kim_tools.test_driver.core.KIMTestDriver method) (kim_tools.test_driver.core.SingleCrystalTestDriver method) _update_nominal_parameter_values() (kim_tools.test_driver.core.SingleCrystalTestDriver method) _update_optional_key_in_property_dict() (in module kim_tools.test_driver.core) _verify_unchanged_symmetry() (kim_tools.test_driver.core.SingleCrystalTestDriver method)

A

add_si_units() (in module kim_tools.kimunits) AFLOW (class in kim_tools.aflow_util.core) AFLOW.AFLOWNotFoundException AFLOW.ChangedSymmetryException AFLOW.FailedToMatchException AFLOW.FailedToSolveException

aflow_command() (kim_tools.aflow_util.core.AFLOW method) aflow_executable (kim_tools.aflow_util.core.AFLOW attribute) (kim_tools.test_driver.core.SingleCrystalTestDriver attribute) aflow_work_dir (kim_tools.aflow_util.core.AFLOW attribute) are_in_same_wyckoff_set() (in module kim_tools.symmetry_util.core) atom_outside_cell_along_nonperiodic_dim() (in module kim_tools.ase.core)

B

build_abstract_formula_from_stoich_reduced_list() (in module kim_tools.aflow_util.core)

build_atoms_from_prototype() (kim_tools.aflow_util.core.AFLOW method)

C

calc_bulk() (in module kim_tools.symmetry_util.elasticity) cartesian_rotation_is_in_point_group() (in module kim_tools.symmetry_util.core) cartesian_to_fractional_itc_rotation_from_ase_cell() (in module kim_tools.symmetry_util.core) change_of_basis_atoms() (in module kim_tools.symmetry_util.core) check_if_atoms_interacting() (in module kim_tools.ase.core) check_if_atoms_interacting_energy() (in module kim_tools.ase.core) check_if_atoms_interacting_force() (in module kim_tools.ase.core) check_kimpy_call() (in module kim_tools.vc.core) check_number_of_atoms() (in module kim_tools.aflow_util.core) check_units_util() (in module kim_tools.kimunits)

coeff_matrix_list (kim_tools.aflow_util.core.EquivalentEqnSet attribute) compare_materials_dir() (kim_tools.aflow_util.core.AFLOW method) compare_to_prototypes() (kim_tools.aflow_util.core.AFLOW method) confirm_atoms_unrotated_when_cells_aligned() (kim_tools.aflow_util.core.AFLOW method) confirm_unrotated_prototype_designation() (kim_tools.aflow_util.core.AFLOW method) const_terms_list (kim_tools.aflow_util.core.EquivalentEqnSet attribute) convert() (in module kim_tools.kimunits) convert_list() (in module kim_tools.kimunits) convert_units() (in module kim_tools.kimunits) crystal_input_from_test_generator_line() (in module kim_tools.test_driver.core)

D

deduplicate_property_instances() (kim_tools.test_driver.core.SingleCrystalTestDriver method)

detect_unique_crystal_structures() (in module kim_tools.test_driver.core)

E

EquivalentAtomSet (class in kim_tools.aflow_util.core)

EquivalentEqnSet (class in kim_tools.aflow_util.core)

F

fcc_atoms_in_supercell() (in module kim_tools.ase.core) filter_good_alat() (in module kim_tools.ase.core) find_nearest_isotropy() (in module kim_tools.symmetry_util.elasticity) find_species_permutation_between_prototype_labels() (in module kim_tools.aflow_util.core) find_working_configuration_FCC() (in module kim_tools.ase.core) fit_voigt_tensor_and_error_to_cell_and_space_group() (in module kim_tools.symmetry_util.core) fit_voigt_tensor_to_cell_and_space_group() (in module kim_tools.symmetry_util.core)

fit_voigt_tensor_to_cell_and_space_group_symb() (in module kim_tools.symmetry_util.core) FixProvidedSymmetry (class in kim_tools.symmetry_util.core) frac_position_list (kim_tools.aflow_util.core.EquivalentAtomSet attribute) fractional_coords_transformation() (in module kim_tools.ase.core) fractional_to_cartesian_itc_rotation_from_ase_cell() (in module kim_tools.symmetry_util.core) full_to_voigt_symb() (in module kim_tools.symmetry_util.core) function_of_matrix() (in module kim_tools.symmetry_util.elasticity)

G

generate_fcc_compute_energy() (in module kim_tools.ase.core) get_aflow_version() (kim_tools.aflow_util.core.AFLOW method) get_all_equivalent_labels() (in module kim_tools.aflow_util.core) get_atom_indices_for_each_wyckoff_orb() (in module kim_tools.aflow_util.core) (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_atoms_from_crystal_structure() (in module kim_tools.test_driver.core) get_basistransformation_rotation_originshift_atom_map_from_atoms() (kim_tools.aflow_util.core.AFLOW method) get_bravais_lattice_from_prototype() (in module kim_tools.aflow_util.core) get_bravais_lattice_from_space_group() (in module kim_tools.symmetry_util.core) get_cell_from_poscar() (in module kim_tools.symmetry_util.core) get_change_of_basis_matrix_to_conventional_cell_from_formal_bravais_lattice() (in module kim_tools.symmetry_util.core) get_crystal_structure_from_atoms() (in module kim_tools.test_driver.core) get_deduplicated_property_instances() (in module kim_tools.test_driver.core) get_equation_sets_from_prototype() (kim_tools.aflow_util.core.AFLOW method) get_equivalent_atom_sets_from_prototype_and_atom_map() (in module kim_tools.aflow_util.core) get_formal_bravais_lattice_from_space_group() (in module kim_tools.symmetry_util.core) get_input_rotation() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_isolated_energy_per_atom() (in module kim_tools.ase.core) (kim_tools.test_driver.core.KIMTestDriver method) get_kim_model_supported_species_and_codes() (in module kim_tools.vc.core) get_library_prototype_label_and_shortname_from_atoms() (kim_tools.aflow_util.core.AFLOW method) get_library_prototype_label_and_shortname_from_file() (kim_tools.aflow_util.core.AFLOW method) get_model_energy_cutoff() (in module kim_tools.ase.core) get_model_species_minimum_cutoff() (in module kim_tools.ase.core)

get_nominal_a() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_nominal_library_prototype_label() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_nominal_parameter_names() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_nominal_parameter_values() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_nominal_prototype_label() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_nominal_short_name() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_nominal_space_group_number() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_nominal_stoichiometric_species() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_nominal_stoichiometry() (kim_tools.test_driver.core.SingleCrystalTestDriver method) get_param_names_from_prototype() (kim_tools.aflow_util.core.AFLOW method) get_pearson_symbol_from_prototype() (in module kim_tools.aflow_util.core) get_poscar_from_crystal_structure() (in module kim_tools.test_driver.core) get_possible_primitive_shifts() (in module kim_tools.symmetry_util.core) get_primitive_genpos_ops() (in module kim_tools.symmetry_util.core) get_primitive_wyckoff_multiplicity() (in module kim_tools.symmetry_util.core) get_prototype_designation_from_atoms() (kim_tools.aflow_util.core.AFLOW method) get_prototype_designation_from_file() (kim_tools.aflow_util.core.AFLOW method) get_real_to_virtual_species_map() (in module kim_tools.aflow_util.core) get_smallest_nn_dist() (in module kim_tools.symmetry_util.core) get_space_group_number_from_prototype() (in module kim_tools.aflow_util.core) get_stoich_reduced_list_from_prototype() (in module kim_tools.aflow_util.core) get_supported_lammps_atom_style() (in module kim_tools.test_driver.core) get_symbolic_cell_from_formal_bravais_lattice() (in module kim_tools.symmetry_util.core) get_wyck_pos_xform_under_normalizer() (in module kim_tools.symmetry_util.core) get_wyckoff_lists_from_prototype() (in module kim_tools.aflow_util.core)

I

InconsistentWyckoffException IncorrectCrystallographyException IncorrectNumAtomsException IncorrectSpaceGroupException

IncorrectSpeciesException indep_elast_compon_names_and_values_from_voigt() (in module kim_tools.symmetry_util.elasticity) internal_parameter_sort_key() (in module kim_tools.aflow_util.core) islinear() (in module kim_tools.kimunits)

K

kim_model_name (kim_tools.test_driver.core.KIMTestDriver property) kim_tools module kim_tools.aflow_util module kim_tools.aflow_util.core module kim_tools.ase module kim_tools.ase.core module kim_tools.kimunits module kim_tools.symmetry_util module kim_tools.symmetry_util.core module

kim_tools.symmetry_util.elasticity module kim_tools.test_driver module kim_tools.test_driver.core module kim_tools.vc module kim_tools.vc.core module KIMASEError KimpyError KIMTestDriver (class in kim_tools.test_driver.core) KIMTestDriver.MissingModelError KIMTestDriver.NonKIMModelError KIMTestDriverError KIMVCError

L

linear_fit() (in module kim_tools.kimunits)

local_edge_detection() (in module kim_tools.ase.core)

M

map_to_Kelvin() (in module kim_tools.symmetry_util.elasticity) minimize_wrapper() (in module kim_tools.test_driver.core) model (kim_tools.test_driver.core.KIMTestDriver property) module kim_tools kim_tools.aflow_util kim_tools.aflow_util.core kim_tools.ase kim_tools.ase.core kim_tools.kimunits kim_tools.symmetry_util kim_tools.symmetry_util.core kim_tools.symmetry_util.elasticity kim_tools.test_driver kim_tools.test_driver.core kim_tools.vc kim_tools.vc.core

N

np (kim_tools.aflow_util.core.AFLOW attribute)

P

param_names (kim_tools.aflow_util.core.EquivalentEqnSet attribute) PeriodExtensionException perturb_until_all_forces_sizeable() (in module kim_tools.ase.core)

prep_symm_map() (kim_tools.symmetry_util.core.FixProvidedSymmetry method) property_instances (kim_tools.test_driver.core.KIMTestDriver property) prototype_labels_are_equivalent() (in module kim_tools.aflow_util.core)

Q

query_crystal_structures() (in module kim_tools.test_driver.core)

R

random() (in module kim_tools.aflow_util.core) randomize_positions() (in module kim_tools.ase.core) randomize_species() (in module kim_tools.ase.core) read_shortnames() (in module kim_tools.aflow_util.core) reduce_and_avg() (in module kim_tools.symmetry_util.core)

remove_species_not_supported_by_ASE() (in module kim_tools.ase.core) rescale_to_get_nonzero_energy() (in module kim_tools.ase.core) rescale_to_get_nonzero_forces() (in module kim_tools.ase.core) rotate_tensor_symb() (in module kim_tools.symmetry_util.core) rwrite() (kim_tools.vc.core.VerificationCheck method)

S

setup_and_run_vc() (in module kim_tools.vc.core) SingleCrystalTestDriver (class in kim_tools.test_driver.core) solve_for_aflow_cell_params_from_primitive_ase_cell_params() (in module kim_tools.aflow_util.core) solve_for_params_of_known_prototype() (kim_tools.aflow_util.core.AFLOW method)

space_group_numbers_are_enantiomorphic() (in module kim_tools.symmetry_util.core) species (kim_tools.aflow_util.core.EquivalentAtomSet attribute) (kim_tools.aflow_util.core.EquivalentEqnSet attribute) split_parameter_array() (in module kim_tools.aflow_util.core)

T

todict() (kim_tools.symmetry_util.core.FixProvidedSymmetry method)

transform_atoms() (in module kim_tools.symmetry_util.core)

U

UnitConversion

V

vc_letter_grade_machine_precision() (in module kim_tools.vc.core) vc_stripall() (in module kim_tools.vc.core) VerificationCheck (class in kim_tools.vc.core)

voigt_elast_class() (in module kim_tools.symmetry_util.elasticity) voigt_elast_compon_eqn() (in module kim_tools.symmetry_util.elasticity) voigt_elast_struct_svg() (in module kim_tools.symmetry_util.elasticity) voigt_to_full_symb() (in module kim_tools.symmetry_util.core)

W

write_aux_ase_atoms() (kim_tools.vc.core.VerificationCheck method) write_aux_string() (kim_tools.vc.core.VerificationCheck method) write_aux_x_y() (kim_tools.vc.core.VerificationCheck method) write_poscar_from_prototype() (kim_tools.aflow_util.core.AFLOW method)

write_property_instances_to_file() (kim_tools.test_driver.core.KIMTestDriver method) write_results() (kim_tools.vc.core.VerificationCheck method) write_tmp_poscar_from_atoms_and_run_function() (in module kim_tools.aflow_util.core) wyckoff_letter (kim_tools.aflow_util.core.EquivalentAtomSet attribute) (kim_tools.aflow_util.core.EquivalentEqnSet attribute)