Index

_

__array_finalize__() (aiida_atomistic.data.structure.utils.ObservedArray method) __len__() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) __repr__() (aiida_atomistic.data.structure.kind.Kind method) (aiida_atomistic.data.structure.models.StructureBaseModel method) (aiida_atomistic.data.structure.site.Site method) (aiida_atomistic.data.structure.structure.StructureBuilder method) (aiida_atomistic.data.structure.structure.StructureData method) (aiida_atomistic.data.structure.StructureBuilder method) (aiida_atomistic.data.structure.StructureData method) (aiida_atomistic.data.StructureBuilder method) (aiida_atomistic.data.StructureData method) __setattr__() (aiida_atomistic.data.structure.models.ImmutableStructureModel method) __setitem__() (aiida_atomistic.data.structure.site.FrozenList method) (aiida_atomistic.data.structure.utils.ObservedArray method) __str__() (aiida_atomistic.data.structure.structure.StructureBuilder method) (aiida_atomistic.data.structure.structure.StructureData method) (aiida_atomistic.data.structure.StructureBuilder method) (aiida_atomistic.data.structure.StructureData method) (aiida_atomistic.data.StructureBuilder method) (aiida_atomistic.data.StructureData method) _adjust_default_cell() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _atomic_masses (in module aiida_atomistic.data.structure.constants) (in module aiida_atomistic.data.structure.getter_mixin) (in module aiida_atomistic.data.structure.setter_mixin) (in module aiida_atomistic.data.structure.utils) _atomic_numbers (in module aiida_atomistic.data.structure.constants) (in module aiida_atomistic.data.structure.getter_mixin) (in module aiida_atomistic.data.structure.setter_mixin) (in module aiida_atomistic.data.structure.utils) _check_valid_sites() (in module aiida_atomistic.data.structure.utils) _COMPUTED_PROPERTIES (in module aiida_atomistic.data.structure.constants) _CONVERSION_PLURAL_SINGULAR (in module aiida_atomistic.data.structure.constants) _create_symbols_tuple() (in module aiida_atomistic.data.structure.utils) _create_weights_tuple() (in module aiida_atomistic.data.structure.utils) _DEFAULT_CELL (in module aiida_atomistic.data.structure.constants) (in module aiida_atomistic.data.structure.getter_mixin) (in module aiida_atomistic.data.structure.setter_mixin) (in module aiida_atomistic.data.structure.utils) _DEFAULT_PBC (in module aiida_atomistic.data.structure.constants) _DEFAULT_PROPERTIES (in module aiida_atomistic.data.structure.setter_mixin) _DEFAULT_THRESHOLDS (in module aiida_atomistic.data.structure.getter_mixin) (in module aiida_atomistic.data.structure.setter_mixin) _DEFAULT_VALUES (in module aiida_atomistic.data.structure.constants) (in module aiida_atomistic.data.structure.setter_mixin) _dimensionality_label (in module aiida_atomistic.data.structure.utils) _from_pymatgen_molecule() (aiida_atomistic.data.structure.getter_mixin.GetterMixin class method) _from_pymatgen_structure() (aiida_atomistic.data.structure.getter_mixin.GetterMixin class method) _get_dimensionality() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _get_object_ase() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _get_object_phonopyatoms() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _get_object_pymatgen() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _get_object_pymatgen_molecule() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method)

_get_object_pymatgen_structure() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _get_one_kind_index() (aiida_atomistic.data.structure.hubbard_mixin.HubbardSetterMixin method) _get_symbol_indices() (aiida_atomistic.data.structure.hubbard_mixin.HubbardSetterMixin method) _get_valid_cell() (in module aiida_atomistic.data.structure.utils) _get_valid_pbc() (in module aiida_atomistic.data.structure.utils) _GLOBAL_PROPERTIES (in module aiida_atomistic.data.structure.constants) _MAGMOM_THRESHOLD (in module aiida_atomistic.data.structure.constants) _MASS_THRESHOLD (in module aiida_atomistic.data.structure.constants) (in module aiida_atomistic.data.structure.getter_mixin) (in module aiida_atomistic.data.structure.setter_mixin) (in module aiida_atomistic.data.structure.utils) _model (aiida_atomistic.data.structure.structure.StructureBuilder attribute) (aiida_atomistic.data.structure.structure.StructureData attribute) (aiida_atomistic.data.structure.StructureBuilder attribute) (aiida_atomistic.data.structure.StructureData attribute) (aiida_atomistic.data.StructureBuilder attribute) (aiida_atomistic.data.StructureData attribute) _mutable (aiida_atomistic.data.structure.kind.Kind attribute) (aiida_atomistic.data.structure.models.ImmutableStructureModel attribute) (aiida_atomistic.data.structure.models.MutableStructureModel attribute) (aiida_atomistic.data.structure.models.StructureBaseModel attribute) (aiida_atomistic.data.structure.site.FrozenSite attribute) (aiida_atomistic.data.structure.site.Site attribute) (aiida_atomistic.data.structure.structure.StructureBuilder attribute) (aiida_atomistic.data.structure.structure.StructureData attribute) (aiida_atomistic.data.structure.StructureBuilder attribute) (aiida_atomistic.data.structure.StructureData attribute) (aiida_atomistic.data.StructureBuilder attribute) (aiida_atomistic.data.StructureData attribute) _parse_xyz() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _prepare_chemdoodle() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _prepare_cif() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _prepare_xsf() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _prepare_xyz() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _properties (aiida_atomistic.data.structure.structure.StructureBuilder attribute) (aiida_atomistic.data.structure.structure.StructureData attribute) (aiida_atomistic.data.structure.StructureBuilder attribute) (aiida_atomistic.data.structure.StructureData attribute) (aiida_atomistic.data.StructureBuilder attribute) (aiida_atomistic.data.StructureData attribute) _serialize_array() (in module aiida_atomistic.data.structure.site) _SUM_THRESHOLD (in module aiida_atomistic.data.structure.constants) (in module aiida_atomistic.data.structure.getter_mixin) (in module aiida_atomistic.data.structure.setter_mixin) (in module aiida_atomistic.data.structure.utils) _valid_symbols (in module aiida_atomistic.data.structure.constants) (in module aiida_atomistic.data.structure.getter_mixin) (in module aiida_atomistic.data.structure.setter_mixin) (in module aiida_atomistic.data.structure.utils) _validate_array() (in module aiida_atomistic.data.structure.site) _validate_dimensionality() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) _validate_properties() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method)

A

aiida_atomistic.data module aiida_atomistic.data.structure module aiida_atomistic.data.structure.constants module aiida_atomistic.data.structure.getter_mixin module aiida_atomistic.data.structure.hubbard_mixin module aiida_atomistic.data.structure.hubbard_qe_utils module aiida_atomistic.data.structure.kind module

aiida_atomistic.data.structure.models module aiida_atomistic.data.structure.setter_mixin module aiida_atomistic.data.structure.site module aiida_atomistic.data.structure.structure module aiida_atomistic.data.structure.utils module alloy_list (aiida_atomistic.data.structure.site.Site property) append_atom() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) append_hubbard_parameter() (aiida_atomistic.data.structure.hubbard_mixin.HubbardSetterMixin method) ase_refine_cell() (in module aiida_atomistic.data.structure.utils) atom_kinds_to_html() (in module aiida_atomistic.data.structure.utils)

B

build_sites_from_expanded_properties() (in module aiida_atomistic.data.structure.utils)

C

calc_cell_volume() (in module aiida_atomistic.data.structure.utils) cell (aiida_atomistic.data.structure.getter_mixin.GetterMixin property) (aiida_atomistic.data.structure.models.StructureBaseModel attribute) cell_volume() (aiida_atomistic.data.structure.models.StructureBaseModel method) charge (aiida_atomistic.data.structure.site.Site attribute) charges() (aiida_atomistic.data.structure.models.StructureBaseModel method) check_is_alloy() (in module aiida_atomistic.data.structure.utils) check_kinds_match() (in module aiida_atomistic.data.structure.utils)

check_minimal_requirements() (aiida_atomistic.data.structure.models.StructureBaseModel method) (aiida_atomistic.data.structure.site.Site method) check_plugin_unsupported_props() (in module aiida_atomistic.data.structure.utils) classify_site_kinds() (in module aiida_atomistic.data.structure.utils) clear_hubbard_parameters() (aiida_atomistic.data.structure.hubbard_mixin.HubbardSetterMixin method) clear_sites() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) compress_properties_by_kind() (in module aiida_atomistic.data.structure.utils) create_automatic_kind_name() (in module aiida_atomistic.data.structure.utils), [1] custom (aiida_atomistic.data.structure.models.StructureBaseModel attribute)

D

dimensionality() (aiida_atomistic.data.structure.models.StructureBaseModel method)

E

efficient_copy() (in module aiida_atomistic.data.structure.utils)

ensure_numpy_array() (aiida_atomistic.data.structure.site.Site class method)

F

formula (aiida_atomistic.data.structure.getter_mixin.GetterMixin property) formula() (aiida_atomistic.data.structure.models.StructureBaseModel method) freeze_nested() (in module aiida_atomistic.data.structure.site) freeze_pbc() (aiida_atomistic.data.structure.models.ImmutableStructureModel class method) freeze_sites() (aiida_atomistic.data.structure.models.StructureBaseModel method) from_ase() (aiida_atomistic.data.structure.getter_mixin.GetterMixin class method) from_ase_atom() (aiida_atomistic.data.structure.site.Site class method)

from_builder() (aiida_atomistic.data.structure.structure.StructureData class method) (aiida_atomistic.data.structure.StructureData class method) (aiida_atomistic.data.StructureData class method) from_file() (aiida_atomistic.data.structure.getter_mixin.GetterMixin class method) from_pymatgen() (aiida_atomistic.data.structure.getter_mixin.GetterMixin class method) FrozenList (class in aiida_atomistic.data.structure.site) FrozenSite (class in aiida_atomistic.data.structure.site)

G

generate_kinds() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_cif() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_composition() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_default_tolerances() (aiida_atomistic.data.structure.site.Site class method) get_defined_properties() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_description() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_dimensionality() (in module aiida_atomistic.data.structure.utils) get_formula() (in module aiida_atomistic.data.structure.utils) get_formula_from_symbol_list() (in module aiida_atomistic.data.structure.utils) get_formula_group() (in module aiida_atomistic.data.structure.utils) get_hubbard_card() (aiida_atomistic.data.structure.hubbard_qe_utils.HubbardUtils method) get_hubbard_file() (aiida_atomistic.data.structure.hubbard_qe_utils.HubbardUtils method) get_hubbard_for_supercell() (aiida_atomistic.data.structure.hubbard_qe_utils.HubbardUtils method) get_hubbard_indices() (in module aiida_atomistic.data.structure.hubbard_qe_utils) get_hubbard_list() (aiida_atomistic.data.structure.hubbard_mixin.HubbardGetterMixin method) get_index_and_translation() (in module aiida_atomistic.data.structure.hubbard_qe_utils)

get_kind() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_kind_names() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_magmom_coord() (aiida_atomistic.data.structure.site.Site method) get_pymatgen_molecule() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_pymatgen_structure() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_pymatgen_version() (in module aiida_atomistic.data.structure.utils) get_queryable_properties() (aiida_atomistic.data.structure.getter_mixin.GetterMixin class method) get_supercell_atomic_index() (in module aiida_atomistic.data.structure.hubbard_qe_utils) get_supported_properties() (aiida_atomistic.data.structure.getter_mixin.GetterMixin class method) get_symbols_set() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) get_symbols_string() (in module aiida_atomistic.data.structure.utils) get_value() (aiida_atomistic.data.structure.structure.StructureData method) (aiida_atomistic.data.structure.StructureData method) (aiida_atomistic.data.StructureData method) GetterMixin (class in aiida_atomistic.data.structure.getter_mixin) group_symbols() (in module aiida_atomistic.data.structure.utils)

H

has_ase (in module aiida_atomistic.data.structure.getter_mixin) (in module aiida_atomistic.data.structure.setter_mixin) has_ase() (in module aiida_atomistic.data.structure.utils) has_pymatgen (in module aiida_atomistic.data.structure.getter_mixin) (in module aiida_atomistic.data.structure.setter_mixin) has_pymatgen() (in module aiida_atomistic.data.structure.utils) has_spglib() (in module aiida_atomistic.data.structure.utils) has_vacancies (aiida_atomistic.data.structure.getter_mixin.GetterMixin property) (aiida_atomistic.data.structure.site.Site property)

has_vacancies() (aiida_atomistic.data.structure.models.StructureBaseModel method) (in module aiida_atomistic.data.structure.utils) hubbard (aiida_atomistic.data.structure.models.StructureBaseModel attribute) hubbard_structure (aiida_atomistic.data.structure.hubbard_qe_utils.HubbardUtils property) HubbardGetterMixin (class in aiida_atomistic.data.structure.hubbard_mixin) HubbardSetterMixin (class in aiida_atomistic.data.structure.hubbard_mixin) HubbardUtils (class in aiida_atomistic.data.structure.hubbard_qe_utils)

I

ImmutableStructureModel (class in aiida_atomistic.data.structure.models) initialize_intersites_hubbard() (aiida_atomistic.data.structure.hubbard_mixin.HubbardSetterMixin method) initialize_onsites_hubbard() (aiida_atomistic.data.structure.hubbard_mixin.HubbardSetterMixin method) is_alloy (aiida_atomistic.data.structure.getter_mixin.GetterMixin property) (aiida_atomistic.data.structure.site.Site property)

is_alloy() (aiida_atomistic.data.structure.models.StructureBaseModel method) is_collinear (aiida_atomistic.data.structure.getter_mixin.GetterMixin property) is_intersite_hubbard() (in module aiida_atomistic.data.structure.hubbard_qe_utils) is_to_reorder() (aiida_atomistic.data.structure.hubbard_qe_utils.HubbardUtils method) is_valid_symbol() (in module aiida_atomistic.data.structure.utils)

K

Kind (class in aiida_atomistic.data.structure.kind) kind_name (aiida_atomistic.data.structure.site.Site attribute)

kind_names() (aiida_atomistic.data.structure.models.StructureBaseModel method) kinds (aiida_atomistic.data.structure.getter_mixin.GetterMixin property) kinds() (aiida_atomistic.data.structure.models.StructureBaseModel method)

M

magmom (aiida_atomistic.data.structure.site.Site attribute) magmoms() (aiida_atomistic.data.structure.models.StructureBaseModel method) magnetization (aiida_atomistic.data.structure.site.Site attribute) magnetizations() (aiida_atomistic.data.structure.models.StructureBaseModel method) mass (aiida_atomistic.data.structure.site.Site attribute) masses() (aiida_atomistic.data.structure.models.StructureBaseModel method) model_config (aiida_atomistic.data.structure.models.ImmutableStructureModel attribute) (aiida_atomistic.data.structure.models.StructureBaseModel attribute) (aiida_atomistic.data.structure.site.FrozenSite attribute) (aiida_atomistic.data.structure.site.Site attribute) module aiida_atomistic.data aiida_atomistic.data.structure aiida_atomistic.data.structure.constants aiida_atomistic.data.structure.getter_mixin aiida_atomistic.data.structure.hubbard_mixin aiida_atomistic.data.structure.hubbard_qe_utils aiida_atomistic.data.structure.kind aiida_atomistic.data.structure.models aiida_atomistic.data.structure.setter_mixin aiida_atomistic.data.structure.site aiida_atomistic.data.structure.structure aiida_atomistic.data.structure.utils

MutableStructureModel (class in aiida_atomistic.data.structure.models)

N

name (aiida_atomistic.data.structure.kind.Kind property)

NumpyArray (in module aiida_atomistic.data.structure.site)

O

ObservedArray (class in aiida_atomistic.data.structure.utils)

order_k() (in module aiida_atomistic.data.structure.utils)

P

parse_hubbard_dat() (aiida_atomistic.data.structure.hubbard_qe_utils.HubbardUtils method) pbc (aiida_atomistic.data.structure.getter_mixin.GetterMixin property) (aiida_atomistic.data.structure.models.ImmutableStructureModel attribute) (aiida_atomistic.data.structure.models.StructureBaseModel attribute) pop_atom() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) pop_hubbard_parameters() (aiida_atomistic.data.structure.hubbard_mixin.HubbardSetterMixin method) position (aiida_atomistic.data.structure.kind.Kind attribute) (aiida_atomistic.data.structure.site.Site attribute)

positions (aiida_atomistic.data.structure.kind.Kind attribute) positions() (aiida_atomistic.data.structure.models.StructureBaseModel method) properties (aiida_atomistic.data.structure.structure.StructureBuilder property) (aiida_atomistic.data.structure.structure.StructureData property) (aiida_atomistic.data.structure.StructureBuilder property) (aiida_atomistic.data.structure.StructureData property) (aiida_atomistic.data.StructureBuilder property) (aiida_atomistic.data.StructureData property)

R

rebuild_site_lists_from_kind_lists() (in module aiida_atomistic.data.structure.utils) remove_charges() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) remove_hubbard() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) remove_magmoms() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) remove_magnetizations() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method)

remove_masses() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) remove_property() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) remove_tot_charge() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) remove_weights() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) reorder_atoms() (aiida_atomistic.data.structure.hubbard_qe_utils.HubbardUtils method)

S

set_automatic_kind_name() (aiida_atomistic.data.structure.site.Site method) set_cell() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_cell_angles() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_cell_lengths() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_charges() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_hubbard_from_list() (aiida_atomistic.data.structure.hubbard_mixin.HubbardSetterMixin method) set_kind_names() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_magmoms() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_magnetizations() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_masses() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_pbc() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_symbols_and_weights() (in module aiida_atomistic.data.structure.utils) set_tot_charge() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_tot_magnetization() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) set_weights() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) SetterMixin (class in aiida_atomistic.data.structure.setter_mixin)

Site (class in aiida_atomistic.data.structure.site) site_indices (aiida_atomistic.data.structure.kind.Kind attribute) sites (aiida_atomistic.data.structure.getter_mixin.GetterMixin property) (aiida_atomistic.data.structure.models.ImmutableStructureModel attribute) (aiida_atomistic.data.structure.models.StructureBaseModel attribute) sites_from_kinds() (in module aiida_atomistic.data.structure.utils) StructureBaseModel (class in aiida_atomistic.data.structure.models) StructureBuilder (class in aiida_atomistic.data) (class in aiida_atomistic.data.structure) (class in aiida_atomistic.data.structure.structure) StructureData (class in aiida_atomistic.data) (class in aiida_atomistic.data.structure) (class in aiida_atomistic.data.structure.structure) symbol (aiida_atomistic.data.structure.site.Site attribute) symbols() (aiida_atomistic.data.structure.models.StructureBaseModel method) symop_fract_from_ortho() (in module aiida_atomistic.data.structure.utils) symop_ortho_from_fract() (in module aiida_atomistic.data.structure.utils)

T

to_ase() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) (aiida_atomistic.data.structure.site.Site method) to_dict() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) to_file() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) to_kinds_based() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method)

to_mutable() (aiida_atomistic.data.structure.structure.StructureData method) (aiida_atomistic.data.structure.StructureData method) (aiida_atomistic.data.StructureData method) to_pymatgen() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method) tot_charge (aiida_atomistic.data.structure.models.StructureBaseModel attribute) tot_magnetization (aiida_atomistic.data.structure.models.StructureBaseModel attribute)

U

update() (aiida_atomistic.data.structure.site.Site method)

update_kind() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method) update_sites() (aiida_atomistic.data.structure.setter_mixin.SetterMixin method)

V

validate_cell_shape() (aiida_atomistic.data.structure.models.StructureBaseModel class method) validate_kinds() (aiida_atomistic.data.structure.getter_mixin.GetterMixin method)

validate_sites() (aiida_atomistic.data.structure.models.StructureBaseModel method) validate_symbols_tuple() (in module aiida_atomistic.data.structure.utils) validate_weights_tuple() (in module aiida_atomistic.data.structure.utils)

W

weight (aiida_atomistic.data.structure.site.Site attribute)

weights() (aiida_atomistic.data.structure.models.StructureBaseModel method)