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deformation

Utility functions for dealing with deformations.

make_deformations_from_bulk 

make_deformations_from_bulk(
    atoms: Atoms,
    norm_strains: Sequence[float] = (
        -0.01,
        -0.005,
        0.005,
        0.01,
    ),
    shear_strains: Sequence[float] = (
        -0.06,
        -0.03,
        0.03,
        0.06,
    ),
    symmetry: bool = False,
) -> DeformedStructureSet

Function to generate deformed structures from a bulk atoms object.

Parameters:

  • atoms (Atoms) –

    bulk atoms

  • norm_strains (Sequence[float], default: (-0.01, -0.005, 0.005, 0.01) ) –

    strain values to apply to each normal mode.

  • shear_strains (Sequence[float], default: (-0.06, -0.03, 0.03, 0.06) ) –

    strain values to apply to each shear mode.

  • symmetry (bool, default: False ) –

    whether or not to use symmetry reduction

Returns:

  • DeformedStructureSet –

    A pymatgen DeformedStructureSet with information on the deformed structures and their strains, useful for fitting later.

Source code in quacc/atoms/deformation.py 
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def make_deformations_from_bulk(
    atoms: Atoms,
    norm_strains: Sequence[float] = (-0.01, -0.005, 0.005, 0.01),
    shear_strains: Sequence[float] = (-0.06, -0.03, 0.03, 0.06),
    symmetry: bool = False,
) -> DeformedStructureSet:
    """
    Function to generate deformed structures from a bulk atoms object.

    Parameters
    ----------
    atoms
        bulk atoms
    norm_strains
        strain values to apply to each normal mode.
    shear_strains
        strain values to apply to each shear mode.
    symmetry
        whether or not to use symmetry reduction

    Returns
    -------
    DeformedStructureSet
        A pymatgen DeformedStructureSet with information on the deformed
        structures and their strains, useful for fitting later.
    """
    struct = AseAtomsAdaptor.get_structure(atoms)  # type: ignore

    return DeformedStructureSet(
        struct,
        norm_strains=norm_strains,
        shear_strains=shear_strains,
        symmetry=symmetry,
    )