httk.atomistic.species

Species definition for httk-atomistic, mirroring the OPTIMADE species entry.

Classes

Species

A chemical species occupying one or more sites, mirroring the OPTIMADE species object.

Module Contents

class httk.atomistic.species.Species

A chemical species occupying one or more sites, mirroring the OPTIMADE species object.

A species has a name (unique within a structure; it need not be a chemical symbol), a list of chemical_symbols composing it, and a matching list of concentration values. Each chemical symbol is an element symbol, or one of the pseudo-symbols "X" (unknown) or "vacancy". The optional mass, attached, nattached, and original_name fields carry the remaining OPTIMADE species information; attached and nattached must be given together and share their length.

name: str

chemical_symbols: tuple[str, Ellipsis]

concentration: tuple[float, Ellipsis]

mass: tuple[float, Ellipsis] | None = None

original_name: str | None = None

attached: tuple[str, Ellipsis] | None = None

nattached: tuple[int, Ellipsis] | None = None

property is_single_element: bool

Whether this species is a single, unattached, real chemical element.

True only for a species composed of exactly one element symbol (not "X" or "vacancy") with no attached particles. Such species are the ones that can be represented as a bare atomic number in the primitive representation.

classmethod create(obj: Species | dict[str, Any]) → Species

Return a Species from either an existing Species (returned unchanged) or an OPTIMADE species dict.