matdomain-structure

Immutable, source-neutral values for one exact crystallographic structure occurrence. The package preserves the input cell and caller-provided site sequence, provides deterministic canonical bytes and digests, and exposes one explicit site-wrapping transformation.

Python 3.12 or newer is required. Install the published distribution with:

pip install matdomain-structure

From this workspace, install it directly with:

python -m pip install -e ./packages/matdomain-structure

from matdomain.structure import Lattice, Site, Species, StructureValue

structure = StructureValue(
    lattice=Lattice(matrix=((3.0, 0.0, 0.0), (0.0, 3.0, 0.0), (0.0, 0.0, 3.0))),
    periodic_axes=(True, True, True),
    sites=(
        Site(fractional_coordinates=(0.0, 0.0, 0.0), species=(Species(kind="element", symbol="Li", occupancy=1.0),)),
    ),
)

digest = structure.canonical_digest()
wrapped = structure.wrap_sites_to_unit_cell()

Lattice rows are measured in angstroms, and each periodic-axis flag applies to the corresponding lattice row. Charge is measured in elementary-charge units and is None when unknown. Fractional coordinates are retained exactly until wrap_sites_to_unit_cell() is called; that operation wraps only periodic axes and reports every site whose coordinate representative changed.

Each site has at least one non-vacancy component and occupancy totaling one within an absolute tolerance of 1e-8. Partial occupancy uses one explicit vacancy component. Site order remains input order; species within a site are canonicalized by identity, including optional isotope mass number, oxidation state, and spin. The versioned canonical bytes are the exact Python wire profile returned by canonical_bytes() and contain no product provenance or scene data. Spin is the optional idealized species value represented by pymatgen, not a calculated site magnetic moment.

This distribution versions independently and uses tags of the form matdomain-structure-vX.Y.Z. The workspace release workflow checks and builds both distributions but publishes only the package named by the tag.

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Credits

Author: CMPDC

License expression

MIT
View SPDX License List

Requires

Python >=3.12

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