httk.atomistic.models.protostructure¶

The assigned-species geometrical-classification family.

Submodules¶

Attributes¶

ProtostructureLike

Classes¶

`ProtostructureAPI`	The common interface for standard-setting occupied Wyckoff positions.
`ProtostructureBackend`	Backend root for standard-setting assigned-species classification keys.
`WyckoffOccupation`	Store one Wyckoff orbit occupied by one possibly disordered species.
`Protostructure`	Store a standard-setting space group and its occupied Wyckoff positions.
`ProtostructureViewBase`	Base class for views presenting protostructure backends.

Package Contents¶

class httk.atomistic.models.protostructure.ProtostructureAPI¶

Bases: 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.

property spacegroup: httk.atomistic.symmetry.spacegroup.Spacegroup¶

Abstractmethod:

Return the standard-setting space group.

property occupations: tuple[httk.atomistic.models.protostructure.occupation.WyckoffOccupation, Ellipsis]¶

Abstractmethod:

Return the occupied Wyckoff positions in canonical order.

property representative: FundamentalDomainStructure | None¶

Return an optional retained exact representative.

property discriminator: str | None¶

Return an optional geometrical-class discriminator.

similar(other, delta)¶

Return whether two protostructures have compatible geometry within delta.

The base identity (space group, occupations, and any discriminators present on both) must agree; when both sides retain a geometrical representative, their total Cartesian atom travel must not exceed delta. A protostructure-like other (a view, a backend, or a label string) is erased to a value first.

Parameters:

other (httk.atomistic.models.protostructure.like.ProtostructureLike) – The protostructure-like value to compare against.
delta (float) – The non-negative finite Cartesian travel budget.

Returns:

Whether the two values are compatible within delta.

Raises:

TypeError – If delta is not a real number.
ValueError – If delta is negative or non-finite.

Return type:

bool

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.

Returns:: The standard-setting multiplicity for each occupation.
Return type:: tuple[int, Ellipsis]

property nsites_conventional: int¶

Return the total number of sites in the standard conventional cell.

Returns:: The conventional-cell site count.
Return type:: int

property formula: httk.atomistic.models.formula.formula_view.ChemicalFormulaView¶

Return a reduced formula at the standard conventional-cell scale.

Returns:: The conventional-cell reduced formula view.
Return type:: httk.atomistic.models.formula.formula_view.ChemicalFormulaView

property anonymous_formula: httk.atomistic.models.formula.formulatype_view.FormulatypeView¶

Return a reduced anonymous formula at the standard conventional-cell scale.

Returns:: The conventional-cell anonymous formula view.
Return type:: httk.atomistic.models.formula.formulatype_view.FormulatypeView

property label: httk.atomistic.models.protostructure.label.ProtostructureLabel¶

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 aflow_label). Any faithful render is the protostructure label; the canonical protostructure label comes from a normalizer-canonical protostructure.

Returns:: The protostructure label view.
Return type:: httk.atomistic.models.protostructure.label.ProtostructureLabel

property aflow_label: str¶

Return the AFLOW-style label of this protostructure.

Unlike 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.

Returns:: The AFLOW-style label text.
Return type:: str

property protostructure: Self¶

Return this protostructure value.

class httk.atomistic.models.protostructure.ProtostructureBackend(backend, **hints)¶

Bases: httk.core.Backend[ProtostructureBackend], httk.atomistic.models.protostructure.api.ProtostructureAPI

Backend root for standard-setting assigned-species classification keys.

backend_classes: ClassVar[list[type[httk.core.Backend[Any]]]]¶

type httk.atomistic.models.protostructure.ProtostructureLike = httk.atomistic.models.protostructure.backend.ProtostructureBackend | httk.atomistic.models.protostructure.view_base.ProtostructureViewBase | httk.atomistic.models.protostructure.protostructure.Protostructure | str¶

class httk.atomistic.models.protostructure.WyckoffOccupation¶

Store one Wyckoff orbit occupied by one possibly disordered species.

Parameters:

wyckoff – The Wyckoff letter in the standard setting.
species – The real species occupying the orbit.

wyckoff: str¶

species: httk.atomistic.models.species.species.Species¶

class httk.atomistic.models.protostructure.Protostructure(spacegroup=None, occupations=None, *, representative=None, discriminator=None)¶

Bases: httk.atomistic.models.protostructure.backend.ProtostructureBackend

Store a standard-setting space group and its occupied Wyckoff positions.

The base value is provenance-independent: recognition and derivation return a base Protostructure, so a value recognized from a structure compares equal to one built by hand or parsed from a label. Multiplicities, composition, and formula derivations are defined at the standard-setting conventional-cell scale, even when the source used to recognize it was stored in a volume-scaled setting.

A geometrical representative and/or a discriminator are optional refinements, present only when the user constructs the value with them; recognition never attaches them. They participate in equality and content identity: equality covers the space group, the occupations, the discriminator, and the representative when present, so two values sharing space group, occupations, and discriminator but differing in representative are not equal.

Parameters:

spacegroup (httk.atomistic.symmetry.spacegroup.Spacegroup | int | None) – The standard-setting space group or its IT number.
occupations (collections.abc.Sequence[httk.atomistic.models.protostructure.occupation.WyckoffOccupation | tuple[str, Any]] | None) – The occupied Wyckoff positions and their species.
representative (httk.atomistic.models.structure.asu.FundamentalDomainStructure | None) – An optional exact standard-setting class anchor.
discriminator (str | None) – An optional external class discriminator.

kind: ClassVar[str] = 'protostructure'¶

property spacegroup: httk.atomistic.symmetry.spacegroup.Spacegroup¶

Return the standard-setting space group.

property occupations: tuple[httk.atomistic.models.protostructure.occupation.WyckoffOccupation, Ellipsis]¶

Return the canonical occupied Wyckoff positions.

property representative: httk.atomistic.models.structure.asu.FundamentalDomainStructure | None¶

Return an optional retained exact representative.

property discriminator: str | None¶

Return an optional geometrical-class discriminator.

class httk.atomistic.models.protostructure.ProtostructureViewBase¶

Bases: httk.core.View[httk.atomistic.models.protostructure.backend.ProtostructureBackend]

Base class for views presenting protostructure backends.