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phonons

Atoms handling with Phonopy.

has_phonopy module-attribute 

has_phonopy = bool(find_spec('phonopy'))

get_atoms_supercell_by_phonopy 

get_atoms_supercell_by_phonopy(
    atoms: Atoms,
    supercell_matrix: tuple[
        tuple[int, int, int],
        tuple[int, int, int],
        tuple[int, int, int],
    ],
) -> Atoms

Get the supercell of an ASE atoms object using a supercell matrix.

Parameters:

Returns:

  • Atoms –

    ASE atoms object of the supercell.

Source code in quacc/atoms/phonons.py 
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@requires(has_phonopy, "Phonopy not installed.")
def get_atoms_supercell_by_phonopy(
    atoms: Atoms,
    supercell_matrix: tuple[
        tuple[int, int, int], tuple[int, int, int], tuple[int, int, int]
    ],
) -> Atoms:
    """
    Get the supercell of an ASE atoms object using a supercell matrix.

    Parameters
    ----------
    atoms
        ASE atoms object.
    supercell_matrix
        The supercell matrix to use.

    Returns
    -------
    Atoms
        ASE atoms object of the supercell.
    """

    return phonopy_atoms_to_ase_atoms(
        get_supercell(
            get_phonopy_structure(Structure.from_ase_atoms(atoms)), supercell_matrix
        )
    )

get_phonopy 

get_phonopy(
    atoms: Atoms,
    min_lengths: (
        float | tuple[float, float, float] | None
    ) = None,
    supercell_matrix: (
        NDArray
        | tuple[
            tuple[int, int, int],
            tuple[int, int, int],
            tuple[int, int, int],
        ]
        | None
    ) = None,
    symprec: float = 1e-05,
    displacement: float = 0.01,
    phonopy_kwargs: dict | None = None,
) -> Phonopy

Convert an ASE atoms object to a phonopy object with displacements generated.

Parameters:

  • atoms (Atoms) –

    ASE atoms object.

  • min_lengths (float | tuple[float, float, float] | None, default: None ) –

    Minimum length of each lattice dimension (A).

  • supercell_matrix (NDArray | tuple[tuple[int, int, int], tuple[int, int, int], tuple[int, int, int]] | None, default: None ) –

    The supercell matrix to use. If specified, it will override any value specified by min_lengths.

  • symprec (float, default: 1e-05 ) –

    Precision for symmetry detection.

  • displacement (float, default: 0.01 ) –

    Atomic displacement (A).

  • phonopy_kwargs (dict | None, default: None ) –

    Additional kwargs to pass to the Phonopy class.

Returns:

  • Phonopy –

    Phonopy object

Source code in quacc/atoms/phonons.py 
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@requires(has_phonopy, "Phonopy not installed.")
def get_phonopy(
    atoms: Atoms,
    min_lengths: float | tuple[float, float, float] | None = None,
    supercell_matrix: (
        NDArray
        | tuple[tuple[int, int, int], tuple[int, int, int], tuple[int, int, int]]
        | None
    ) = None,
    symprec: float = 1e-5,
    displacement: float = 0.01,
    phonopy_kwargs: dict | None = None,
) -> Phonopy:
    """
    Convert an ASE atoms object to a phonopy object with displacements generated.

    Parameters
    ----------
    atoms
        ASE atoms object.
    min_lengths
        Minimum length of each lattice dimension (A).
    supercell_matrix
        The supercell matrix to use. If specified, it will override any
        value specified by `min_lengths`.
    symprec
        Precision for symmetry detection.
    displacement
        Atomic displacement (A).
    phonopy_kwargs
        Additional kwargs to pass to the Phonopy class.

    Returns
    -------
    Phonopy
        Phonopy object
    """
    phonopy_kwargs = phonopy_kwargs or {}

    if supercell_matrix is None and min_lengths is not None:
        supercell_matrix = np.diag(
            np.round(np.ceil(min_lengths / atoms.cell.lengths()))
        )

    phonon = Phonopy(
        get_phonopy_structure(Structure.from_ase_atoms(atoms)),
        symprec=symprec,
        supercell_matrix=supercell_matrix,
        **phonopy_kwargs,
    )
    phonon.generate_displacements(distance=displacement)

    return phonon

phonopy_atoms_to_ase_atoms 

phonopy_atoms_to_ase_atoms(
    phonopy_atoms: PhonopyAtoms,
) -> Atoms

Convert a phonopy atoms object to an ASE atoms object.

Parameters:

  • phonopy_atoms (PhonopyAtoms) –

    Phonopy atoms object

Returns:

  • Atoms –

    ASE atoms object

Source code in quacc/atoms/phonons.py 
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def phonopy_atoms_to_ase_atoms(phonopy_atoms: PhonopyAtoms) -> Atoms:
    """
    Convert a phonopy atoms object to an ASE atoms object.

    Parameters
    ----------
    phonopy_atoms
        Phonopy atoms object

    Returns
    -------
    Atoms
        ASE atoms object
    """
    pmg_structure = get_pmg_structure(phonopy_atoms)
    return pmg_structure.to_ase_atoms()