httk.atomistic.models.structure.symops

A structure represented by a CIF site’s own complete symmetry operations.

Classes

SymopsStructure

Represent a magCIF cell, listed sites, and its complete symmetry-operation list.

Module Contents

class httk.atomistic.models.structure.symops.SymopsStructure(cell, sites, species, species_at_sites, symops, *, site_moments=None, bns_number=None, bns_label=None, chemical_composition=None, chemical_formula_descriptive=None, chemical_formula_hill=None, optimization_type=None, immutable_id=None, last_modified=None, charge=None)

Bases: httk.atomistic.models.structure.semantics.StructureSemanticsMixin, httk.atomistic.models.structure.backend.StructureBackend

Represent a magCIF cell, listed sites, and its complete symmetry-operation list.

The operations are taken as declared. They are not checked for group closure: magCIF lists complete coset representatives, and an incomplete list consequently under-expands. Expansion is exact and deduplicates only by normalized fractional coordinates, species, and exact transformed moments.

Parameters:

• cell (httk.atomistic.models.cell.like.CellLike) – The cell geometry.

• sites (httk.atomistic.models.sites.like.SitesLike) – The listed site coordinates.

• species (collections.abc.Sequence[httk.atomistic.models.species.like.SpeciesLike]) – The distinct species definitions.

• species_at_sites (collections.abc.Sequence[str]) – The species name occupying each listed site.

• symops (collections.abc.Sequence[str | httk.atomistic.symmetry.affine_operation.AffineOperation | tuple[httk.atomistic.symmetry.affine_operation.AffineOperation, int]]) – The declared spatial or magnetic symmetry operations.

• site_moments (httk.atomistic.models.moments.like.SiteMomentsLike | None) – Optional moments aligned with the listed sites.

• bns_number (str | None) – Optional Belov–Neronova–Smirnova number.

• bns_label (str | None) – Optional Belov–Neronova–Smirnova label.

• chemical_composition (Any) – Optional chemical composition metadata.

• chemical_formula_descriptive (str | None) – Optional descriptive chemical formula.

• chemical_formula_hill (str | None) – Optional Hill chemical formula.

• optimization_type (str | None) – Optional optimization provenance.

• immutable_id (str | None) – Optional immutable source identifier.

• last_modified (datetime.datetime | None) – Optional source modification timestamp.

• charge (fractions.Fraction | int | str | None) – An explicitly assigned charge for the cell content.

Raises:

• TypeError – If an input component or magnetic label has the wrong kind.

• ValueError – If component lengths, operations, or semantic values are invalid.

kind: ClassVar[str] = 'symops'

property cell: httk.atomistic.models.cell.cell.Cell

Expose the cell geometry.

Returns:

The exact cell.

Return type:

httk.atomistic.models.cell.cell.Cell

property listed_sites: httk.atomistic.models.sites.sites.Sites

Expose the sites before symmetry expansion.

Returns:

The listed site coordinates.

Return type:

httk.atomistic.models.sites.sites.Sites

property listed_species_at_sites: tuple[str, Ellipsis]

Expose species names before symmetry expansion.

Returns:

Listed site species names in input order.

Return type:

tuple[str, Ellipsis]

property listed_site_moments: httk.atomistic.models.moments.backend.SiteMomentsBackend | None

Expose moments before symmetry expansion.

Returns:

Listed site moments, or None when unstated.

Return type:

httk.atomistic.models.moments.backend.SiteMomentsBackend | None

property symops: tuple[tuple[httk.atomistic.symmetry.affine_operation.AffineOperation, int], Ellipsis]

Expose normalized spatial and time-reversal operations.

Returns:

Operation and time-reversal pairs in declaration order.

Return type:

tuple[tuple[httk.atomistic.symmetry.affine_operation.AffineOperation, int], Ellipsis]

property bns_number: str | None

Expose the Belov–Neronova–Smirnova number.

Returns:

The BNS number, or None when unstated.

Return type:

str | None

property bns_label: str | None

Expose the Belov–Neronova–Smirnova label.

Returns:

The BNS label, or None when unstated.

Return type:

str | None

property species: tuple[httk.atomistic.models.species.species.Species, Ellipsis]

Expose the distinct species.

Returns:

Species referenced by the listed sites.

Return type:

tuple[httk.atomistic.models.species.species.Species, Ellipsis]

property coordinate_precision: Any

Expose the listed-coordinate precision.

Returns:

The fractional coordinate precision.

Return type:

Any

property basis_precision: Any

Expose the cell-basis precision.

Returns:

The basis precision.

Return type:

Any

property periodicity: tuple[bool, bool, bool]

Expose the cell periodicity flags.

Returns:

Periodicity flags for the three cell directions.

Return type:

tuple[bool, bool, bool]

property molecular: bool

Expose whether the structure is molecular.

Returns:

Always False for this backend.

Return type:

bool

property site_coordinate_span: str

Expose the coordinate span of the listed sites.

Returns:

"unit_cell".

Return type:

str

property charge: fractions.Fraction | None

Expose the explicitly assigned charge.

Returns:

The charge, or None when unstated.

Return type:

fractions.Fraction | None

cartesian_sites()

Compute exact Cartesian positions for the expanded sites.

Returns:

Cartesian positions in the exact surd representation.

Return type:

httk.core.SurdVector

property sites: httk.atomistic.models.sites.sites.Sites

Expose the symmetry-expanded sites.

Returns:

Expanded site coordinates.

Return type:

httk.atomistic.models.sites.sites.Sites

property species_at_sites: tuple[str, Ellipsis]

Expose species names for the expanded sites.

Returns:

Expanded site species names in site order.

Return type:

tuple[str, Ellipsis]

property site_moments: httk.atomistic.models.moments.backend.SiteMomentsBackend | None

Expose moments transformed onto the expanded sites.

Returns:

Expanded site moments, or None when moments were unstated.

Return type:

httk.atomistic.models.moments.backend.SiteMomentsBackend | None