Skip to content

defects

Common defect workflows.

has_deps module-attribute 

has_deps = (
    find_spec("shakenbreak") is not None
    and find_spec("pymatgen.analysis.defects") is not None
)

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 
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
@subflow
@requires(
    has_deps,
    "shakenbreak and pymatgen-analysis-defects must be installed. 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.
    """
    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