httk.atomistic.models.bareprotostructure ======================================== .. py:module:: httk.atomistic.models.bareprotostructure .. autoapi-nested-parse:: The assigned-species Wyckoff-only classification family. Submodules ---------- .. toctree:: :maxdepth: 1 /reference/autoapi/httk/atomistic/models/bareprotostructure/api/index /reference/autoapi/httk/atomistic/models/bareprotostructure/backend/index /reference/autoapi/httk/atomistic/models/bareprotostructure/bareprotostructure/index /reference/autoapi/httk/atomistic/models/bareprotostructure/label/index /reference/autoapi/httk/atomistic/models/bareprotostructure/label_string/index /reference/autoapi/httk/atomistic/models/bareprotostructure/like/index /reference/autoapi/httk/atomistic/models/bareprotostructure/projected/index /reference/autoapi/httk/atomistic/models/bareprotostructure/recognized/index /reference/autoapi/httk/atomistic/models/bareprotostructure/view/index /reference/autoapi/httk/atomistic/models/bareprotostructure/view_base/index Attributes ---------- .. autoapisummary:: httk.atomistic.models.bareprotostructure.BareProtostructureLike Classes ------- .. autoapisummary:: httk.atomistic.models.bareprotostructure.WyckoffOccupation httk.atomistic.models.bareprotostructure.BareProtostructureAPI httk.atomistic.models.bareprotostructure.BareProtostructureBackend httk.atomistic.models.bareprotostructure.BareProtostructure httk.atomistic.models.bareprotostructure.BareProtostructureViewBase Package Contents ---------------- .. py:class:: WyckoffOccupation Store one Wyckoff orbit occupied by one possibly disordered species. :param wyckoff: The Wyckoff letter in the standard setting. :param species: The real species occupying the orbit. .. py:attribute:: wyckoff :type: str .. py:attribute:: species :type: httk.atomistic.models.species.species.Species .. py:class:: BareProtostructureAPI Bases: :py:obj:`abc.ABC` The common interface for standard-setting occupied Wyckoff positions. Composition and formula derivations from this interface use the standard-setting conventional-cell scale, independently of the setting or transform of a source structure from which a protostructure was recognized. .. py:property:: spacegroup :type: httk.atomistic.symmetry.spacegroup.Spacegroup :abstractmethod: Return the standard-setting space group. .. py:property:: occupations :type: tuple[httk.atomistic.models.protostructure.occupation.WyckoffOccupation, ...] :abstractmethod: Return the occupied Wyckoff positions in canonical order. .. py:method:: multiplicities() Return tabulated standard-setting multiplicities for each occupation. These are deliberately not multiplicities from a source structure's transform; they define the provenance-independent conventional-cell scale of this value. :return: The standard-setting multiplicity for each occupation. .. py:property:: nsites_conventional :type: int Return the total number of sites in the standard conventional cell. :return: The conventional-cell site count. .. py:property:: formula :type: httk.atomistic.models.formula.formula_view.ChemicalFormulaView Return a reduced formula at the standard conventional-cell scale. :return: The conventional-cell reduced formula view. .. py:property:: anonymous_formula :type: httk.atomistic.models.formula.formulatype_view.FormulatypeView Return a reduced anonymous formula at the standard conventional-cell scale. :return: The conventional-cell anonymous formula view. .. py:property:: label :type: httk.atomistic.models.bareprotostructure.label.BareProtostructureLabel Return the httk protostructure label of this protostructure. The label's unsuffixed part orders classes by their Wyckoff letters, so it is the prototype label of the erased anonymous prototype; the suffix lists the class species names. This is NOT an AFLOW label: AFLOW orders classes alphabetically by element (see :attr:`aflow_label`). Any faithful render is *the* protostructure label; the *canonical* protostructure label comes from a normalizer-canonical protostructure. :return: The protostructure label view. .. py:property:: aflow_label :type: str Return the AFLOW-style label of this protostructure. Unlike :attr:`label`, AFLOW orders classes alphabetically by element symbol and reassigns the anonymous symbols in that order, so the unsuffixed prefix depends on the chemistry. Provided for interoperability only. :return: The AFLOW-style label text. .. py:property:: bare_protostructure :type: Self Return this protostructure value. .. py:class:: BareProtostructureBackend(backend, **hints) Bases: :py:obj:`httk.core.Backend`\ [\ :py:obj:`BareProtostructureBackend`\ ], :py:obj:`httk.atomistic.models.bareprotostructure.api.BareProtostructureAPI` Backend root for standard-setting assigned-species classification keys. .. py:attribute:: backend_classes :type: ClassVar[list[type[httk.core.Backend[Any]]]] .. py:class:: BareProtostructure(spacegroup, occupations) Bases: :py:obj:`httk.atomistic.models.bareprotostructure.backend.BareProtostructureBackend` Store only standard-setting Wyckoff occupations, without geometrical refinement. :param spacegroup: The standard-setting space group or its IT number. :param occupations: Occupied Wyckoff positions and their assigned species. .. py:attribute:: kind :type: ClassVar[str] :value: 'bare_protostructure' .. py:property:: spacegroup :type: httk.atomistic.symmetry.spacegroup.Spacegroup Return the standard-setting space group. .. py:property:: occupations :type: tuple[httk.atomistic.models.protostructure.occupation.WyckoffOccupation, ...] Return the canonical occupied Wyckoff positions. .. py:type:: BareProtostructureLike :canonical: httk.atomistic.models.bareprotostructure.backend.BareProtostructureBackend | httk.atomistic.models.bareprotostructure.view_base.BareProtostructureViewBase | httk.atomistic.models.bareprotostructure.bareprotostructure.BareProtostructure | str | httk.atomistic.models.protostructure.backend.ProtostructureBackend | httk.atomistic.models.protostructure.view_base.ProtostructureViewBase | httk.atomistic.models.bareprototype.view_base.BarePrototypeViewBase | httk.atomistic.models.prototype.view_base.PrototypeViewBase | httk.atomistic.models.structure.backend.StructureBackend | httk.atomistic.models.structure.view.StructureView .. py:class:: BareProtostructureViewBase Bases: :py:obj:`httk.core.View`\ [\ :py:obj:`httk.atomistic.models.bareprotostructure.backend.BareProtostructureBackend`\ ] Base class for views presenting protostructure backends.