Skip to content

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,
        0.0,
    ),
    symmetry: bool = False,
) -> list[Atoms]

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, 0.0) ) –

    strain values to apply to each shear mode.

  • symmetry (bool, default: False ) –

    whether or not to use symmetry reduction

Returns:

  • list[Atoms] –

    All generated deformed structures

Source code in quacc/atoms/deformation.py 
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
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, 0.0),
    symmetry: bool = False,
) -> list[Atoms]:
    """
    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
    -------
    list[Atoms]
        All generated deformed structures
    """
    struct = AseAtomsAdaptor.get_structure(atoms)

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

    return [structure.to_ase_atoms() for structure in deformed_set]