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defects

Common defect workflows.

has_pmg_defects module-attribute 

has_pmg_defects = bool(
    find_spec("pymatgen.analysis.defects")
)

has_shakenbreak module-attribute 

has_shakenbreak = bool(find_spec('shakenbreak'))

bulk_to_defects_subflow 

bulk_to_defects_subflow(
    atoms: Atoms,
    relax_job: Job,
    static_job: Job | None = None,
    make_defects_kwargs: dict[str, Any] | None = None,
) -> list[dict]

Workflow consisting of:

  1. Defect generation

  2. Defect relaxations

  3. Defect statics (optional)

Parameters:

Returns:

  • list[dict] –

    List of dictionary of results.

Source code in quacc/recipes/common/defects.py 
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@subflow
@requires(
    has_pmg_defects,
    "Missing pymatgen-analysis-defects. Please run pip install quacc[defects]",
)
@requires(has_shakenbreak, "Missing shakenbreak. Please run pip install quacc[defects]")
def bulk_to_defects_subflow(
    atoms: Atoms,
    relax_job: Job,
    static_job: Job | None = None,
    make_defects_kwargs: dict[str, Any] | None = None,
) -> list[dict]:
    """
    Workflow consisting of:

    1. Defect generation

    2. Defect relaxations

    3. Defect statics (optional)

    Parameters
    ----------
    atoms
        Atoms object for the structure.
    relax_job
        The relaxation function.
    static_job
        The static function.
    make_defects_kwargs
        Keyword arguments for [quacc.atoms.defects.make_defects_from_bulk][]

    Returns
    -------
    list[dict]
        List of dictionary of results.
    """
    make_defects_kwargs = make_defects_kwargs or {}
    defects = make_defects_from_bulk(atoms, **make_defects_kwargs)

    results = []
    for defect in defects:
        result = relax_job(defect)

        if static_job is not None:
            result = static_job(result["atoms"])

        results.append(result)

    return results