defects

Utility functions for dealing with defects.

has_deps module-attribute

has_deps = True

get_defect_entry_from_defect

get_defect_entry_from_defect(
    defect: Defect,
    defect_supercell: Structure,
    defect_charge: int,
) -> DefectEntry

Function to generate DefectEntry object from Defect object.

Parameters:

• defect (Defect) –

  defect object

• defect_supercell (Structure) –

  defect supercell

• defect_charge (int) –

  charge state of defect

Returns:

• DefectEntry –

  defect entry

Source code in quacc/atoms/defects.py

def get_defect_entry_from_defect(
    defect: Defect, defect_supercell: Structure, defect_charge: int
) -> DefectEntry:
    """
    Function to generate DefectEntry object from Defect object.

    Parameters
    ----------
    defect
        defect object
    defect_supercell
        defect supercell
    defect_charge
        charge state of defect

    Returns
    -------
    DefectEntry
        defect entry
    """
    from pymatgen.analysis.defects.thermo import DefectEntry  # skipcq: PYL-W0621

    # Find defect's fractional coordinates and remove it from supercell
    for site in defect_supercell:
        if site.species.elements[0].symbol == DummySpecies().symbol:
            dummy_site = site
            break
    defect_supercell.remove(dummy_site)

    computed_structure_entry = ComputedStructureEntry(
        structure=defect_supercell,
        energy=0.0,  # needs to be set, so set to 0.0
    )

    return DefectEntry(
        defect=defect,
        charge_state=defect_charge,
        sc_entry=computed_structure_entry,
        sc_defect_frac_coords=dummy_site.frac_coords,
    )

make_defects_from_bulk

make_defects_from_bulk(
    atoms: Atoms,
    defect_gen: (
        AntiSiteGenerator
        | ChargeInterstitialGenerator
        | InterstitialGenerator
        | SubstitutionGenerator
        | VacancyGenerator
        | VoronoiInterstitialGenerator
    ) = VacancyGenerator,
    defect_charge: int = 0,
    sc_mat: NDArray | None = None,
    min_atoms: int = 80,
    max_atoms: int = 240,
    min_length: float = 10.0,
    force_diagonal: bool = False,
    **defect_gen_kwargs
) -> list[Atoms]

Function to make defects from a bulk atoms object.

Parameters:

• atoms (Atoms) –

  bulk atoms

• defect_gen (AntiSiteGenerator | ChargeInterstitialGenerator | InterstitialGenerator | SubstitutionGenerator | VacancyGenerator | VoronoiInterstitialGenerator, default: VacancyGenerator ) –

  defect generator

• defect_charge (int, default: 0 ) –

  charge state of defect

• sc_mat (NDArray | None, default: None ) –

  supercell matrix

• min_atoms (int, default: 80 ) –

  minimum number of atoms in supercell

• max_atoms (int, default: 240 ) –

  maximum number of atoms in supercell

• min_length (float, default: 10.0 ) –

  minimum length of supercell

• force_diagonal (bool, default: False ) –

  force supercell to be diagonal

• **defect_gen_kwargs –

  keyword arguments to pass to the pymatgen.analysis.defects.generators get_defects() method

Returns:

• list[Atoms] –

  All generated defects

Source code in quacc/atoms/defects.py

@requires(
    has_deps, "Missing defect dependencies. Please run pip install quacc[defects]"
)
def make_defects_from_bulk(
    atoms: Atoms,
    defect_gen: (
        AntiSiteGenerator
        | ChargeInterstitialGenerator
        | InterstitialGenerator
        | SubstitutionGenerator
        | VacancyGenerator
        | VoronoiInterstitialGenerator
    ) = VacancyGenerator,
    defect_charge: int = 0,
    sc_mat: NDArray | None = None,
    min_atoms: int = 80,
    max_atoms: int = 240,
    min_length: float = 10.0,
    force_diagonal: bool = False,
    **defect_gen_kwargs,
) -> list[Atoms]:
    """
    Function to make defects from a bulk atoms object.

    Parameters
    ----------
    atoms
        bulk atoms
    defect_gen
        defect generator
    defect_charge
        charge state of defect
    sc_mat
        supercell matrix
    min_atoms
        minimum number of atoms in supercell
    max_atoms
        maximum number of atoms in supercell
    min_length
        minimum length of supercell
    force_diagonal
        force supercell to be diagonal
    **defect_gen_kwargs
        keyword arguments to pass to the pymatgen.analysis.defects.generators
        get_defects() method

    Returns
    -------
    list[Atoms]
        All generated defects
    """
    # Use pymatgen-analysis-defects and ShakeNBreak to generate defects
    struct = AseAtomsAdaptor.get_structure(atoms)

    # Make all the defects
    defects = defect_gen().get_defects(struct, **defect_gen_kwargs)
    final_defects = []
    for defect in defects:
        defect.user_charges = [defect_charge]

        # Generate the supercell for a defect
        defect_supercell = defect.get_supercell_structure(
            sc_mat=sc_mat,
            dummy_species=DummySpecies(),
            min_atoms=min_atoms,
            max_atoms=max_atoms,
            min_length=min_length,
            force_diagonal=force_diagonal,
        )

        # Generate DefectEntry object from Defect object
        defect_entry = get_defect_entry_from_defect(
            defect=defect,
            defect_supercell=defect_supercell,
            defect_charge=defect_charge,
        )

        # Instantiate class to apply rattle and bond distortion to all defects
        dist = Distortions([defect_entry])

        # Apply rattle and bond distortion to all defects
        defect_dict, distortion_metadata = dist.apply_distortions()
        defect_symbol = next(iter(distortion_metadata["defects"].keys()))
        distortion_dict = defect_dict[defect_symbol]["charges"][defect_charge][
            "structures"
        ]["distortions"]

        # Make atoms objects and store defect stats
        for distortions, defect_struct in distortion_dict.items():
            final_defect = defect_struct.to_ase_atoms()
            defect_stats = {
                "defect_symbol": defect_symbol,
                "defect_charge": defect_charge,
                "distortions": distortions,
                "bulk": atoms,
                "defect": defect,
            }
            final_defect.info["defect_stats"] = defect_stats
            final_defects.append(final_defect)
    return final_defects