kim_tools package
Subpackages
- kim_tools.aflow_util package
- Submodules
- kim_tools.aflow_util.core module
random()IncorrectSpaceGroupExceptionIncorrectSpeciesExceptionInconsistentWyckoffExceptionEquivalentEqnSetEquivalentAtomSetwrite_tmp_poscar_from_atoms_and_run_function()check_number_of_atoms()split_parameter_array()internal_parameter_sort_key()get_equivalent_atom_sets_from_prototype_and_atom_map()get_stoich_reduced_list_from_prototype()build_abstract_formula_from_stoich_reduced_list()get_wyckoff_lists_from_prototype()get_atom_indices_for_each_wyckoff_orb()get_all_equivalent_labels()prototype_labels_are_equivalent()find_species_permutation_between_prototype_labels()get_space_group_number_from_prototype()get_pearson_symbol_from_prototype()get_bravais_lattice_from_prototype()read_shortnames()get_real_to_virtual_species_map()solve_for_aflow_cell_params_from_primitive_ase_cell_params()AFLOWAFLOW.aflow_executableAFLOW.aflow_work_dirAFLOW.npAFLOW.AFLOWNotFoundExceptionAFLOW.ChangedSymmetryExceptionAFLOW.FailedToMatchExceptionAFLOW.FailedToSolveExceptionAFLOW.aflow_command()AFLOW.write_poscar_from_prototype()AFLOW.build_atoms_from_prototype()AFLOW.compare_materials_dir()AFLOW.get_aflow_version()AFLOW.compare_to_prototypes()AFLOW.get_prototype_designation_from_file()AFLOW.get_prototype_designation_from_atoms()AFLOW.get_library_prototype_label_and_shortname_from_file()AFLOW.get_library_prototype_label_and_shortname_from_atoms()AFLOW._compare_poscars()AFLOW._compare_Atoms()AFLOW.get_basistransformation_rotation_originshift_atom_map_from_atoms()AFLOW.get_param_names_from_prototype()AFLOW.get_equation_sets_from_prototype()AFLOW.solve_for_params_of_known_prototype()AFLOW.confirm_atoms_unrotated_when_cells_aligned()AFLOW.confirm_unrotated_prototype_designation()
- Module contents
- kim_tools.ase package
- Submodules
- kim_tools.ase.core module
KIMASEErrorremove_species_not_supported_by_ASE()randomize_species()fractional_coords_transformation()atom_outside_cell_along_nonperiodic_dim()randomize_positions()get_isolated_energy_per_atom()rescale_to_get_nonzero_energy()check_if_atoms_interacting_energy()check_if_atoms_interacting_force()check_if_atoms_interacting()rescale_to_get_nonzero_forces()perturb_until_all_forces_sizeable()get_model_species_minimum_cutoff()get_model_energy_cutoff()generate_fcc_compute_energy()fcc_atoms_in_supercell()local_edge_detection()filter_good_alat()find_working_configuration_FCC()
- Module contents
- kim_tools.symmetry_util package
- Submodules
- kim_tools.symmetry_util.core module
IncorrectCrystallographyExceptionIncorrectNumAtomsExceptionPeriodExtensionException_check_space_group()cartesian_to_fractional_itc_rotation_from_ase_cell()fractional_to_cartesian_itc_rotation_from_ase_cell()cartesian_rotation_is_in_point_group()get_cell_from_poscar()are_in_same_wyckoff_set()space_group_numbers_are_enantiomorphic()get_wyck_pos_xform_under_normalizer()get_bravais_lattice_from_space_group()get_formal_bravais_lattice_from_space_group()get_primitive_wyckoff_multiplicity()get_symbolic_cell_from_formal_bravais_lattice()get_change_of_basis_matrix_to_conventional_cell_from_formal_bravais_lattice()change_of_basis_atoms()get_possible_primitive_shifts()get_primitive_genpos_ops()transform_atoms()reduce_and_avg()voigt_to_full_symb()full_to_voigt_symb()rotate_tensor_symb()fit_voigt_tensor_to_cell_and_space_group_symb()fit_voigt_tensor_and_error_to_cell_and_space_group()fit_voigt_tensor_to_cell_and_space_group()get_smallest_nn_dist()FixProvidedSymmetry
- kim_tools.symmetry_util.elasticity module
- Module contents
- kim_tools.test_driver package
- Submodules
- kim_tools.test_driver.core module
_glob_with_exceptions()get_supported_lammps_atom_style()_get_optional_source_value()_update_optional_key_in_property_dict()minimize_wrapper()_add_property_instance()_add_key_to_current_property_instance()KIMTestDriverErrorKIMTestDriverKIMTestDriver.__kim_model_nameKIMTestDriver.__calcKIMTestDriver.__output_property_instancesKIMTestDriver.__files_to_keep_in_outputKIMTestDriver.__files_to_ignore_in_outputKIMTestDriver.__tokenKIMTestDriver.__times_calledKIMTestDriver.NonKIMModelErrorKIMTestDriver.MissingModelErrorKIMTestDriver._setup()KIMTestDriver._init_output_dir()KIMTestDriver._archive_aux_files()KIMTestDriver._calculate()KIMTestDriver._add_property_instance()KIMTestDriver._add_key_to_current_property_instance()KIMTestDriver._add_file_to_current_property_instance()KIMTestDriver._get_supported_lammps_atom_style()KIMTestDriver.kim_model_nameKIMTestDriver.property_instancesKIMTestDriver._calcKIMTestDriver.modelKIMTestDriver._get_serialized_property_instances()KIMTestDriver._set_serialized_property_instances()KIMTestDriver.write_property_instances_to_file()KIMTestDriver.get_isolated_energy_per_atom()KIMTestDriver._abc_impl
_add_common_crystal_genome_keys_to_current_property_instance()_add_property_instance_and_common_crystal_genome_keys()get_crystal_structure_from_atoms()get_poscar_from_crystal_structure()get_atoms_from_crystal_structure()SingleCrystalTestDriverSingleCrystalTestDriver.__nominal_crystal_structure_nptSingleCrystalTestDriver.aflow_executableSingleCrystalTestDriver._setup()SingleCrystalTestDriver._update_nominal_parameter_values()SingleCrystalTestDriver._verify_unchanged_symmetry()SingleCrystalTestDriver.__add_poscar_to_curr_prop_inst()SingleCrystalTestDriver._add_property_instance_and_common_crystal_genome_keys()SingleCrystalTestDriver._get_temperature()SingleCrystalTestDriver._get_cell_cauchy_stress()SingleCrystalTestDriver._get_pressure()SingleCrystalTestDriver._get_mass_density()SingleCrystalTestDriver._get_nominal_crystal_structure_npt()SingleCrystalTestDriver.deduplicate_property_instances()SingleCrystalTestDriver._set_serialized_property_instances()SingleCrystalTestDriver._get_atoms()SingleCrystalTestDriver.get_nominal_prototype_label()SingleCrystalTestDriver.get_nominal_space_group_number()SingleCrystalTestDriver.get_nominal_stoichiometric_species()SingleCrystalTestDriver.get_nominal_stoichiometry()SingleCrystalTestDriver.get_nominal_a()SingleCrystalTestDriver.get_nominal_parameter_names()SingleCrystalTestDriver.get_nominal_parameter_values()SingleCrystalTestDriver.get_nominal_short_name()SingleCrystalTestDriver.get_nominal_library_prototype_label()SingleCrystalTestDriver.get_atom_indices_for_each_wyckoff_orb()SingleCrystalTestDriver.get_input_rotation()SingleCrystalTestDriver._abc_impl
query_crystal_structures()detect_unique_crystal_structures()_compare_noncrystallographic_fields()get_deduplicated_property_instances()crystal_input_from_test_generator_line()
- Module contents
- kim_tools.vc package
Submodules
kim_tools.kimunits module
Simple wrapper for executable for converting arbitrary units to SI units
Copyright (c) 2014-2022, Regents of the University of Minnesota. All rights reserved.
This software may be distributed as-is, without modification.
- kim_tools.kimunits.check_units_util()
Figure out if units (first choice) or gunits (second choice) works with the options that we use
- Return type:
- kim_tools.kimunits.linear_fit(x, y)
Perform a linear fit between x,y, returning the average error for each data point as well. This is written this way so as to not add a numpy dependency
- kim_tools.kimunits.islinear(unit, to_unit=None)
Detect if the conversion from unit to to_unit is a linear map. Apparently the units utility is float precision, so if error is less than 1e-7 we know it is linear.
- kim_tools.kimunits.convert_units(from_value, from_unit, wanted_unit=None, suppress_unit=False)
Works with 'units' utility
- kim_tools.kimunits.convert(from_value, from_unit, wanted_unit=None, suppress_unit=False)
Works with 'units' utility
- kim_tools.kimunits.convert_list(x, from_unit, to_unit=None, convert=<function convert_units>, dofit=True)
Thread conversion over a list, or list of lists
- kim_tools.kimunits.add_si_units(doc, convert=<function convert_units>)
Given a document, add all of the appropriate si-units fields