structuretoolkit.analyse.strain.Strain

class structuretoolkit.analyse.strain.Strain(structure: Atoms, ref_structure: Atoms, num_neighbors: int | None = None, only_bulk_type: bool = False)

Bases: object

Calculate local strain of each atom following the Lagrangian strain tensor:

>>> strain = (F.T*F - 1)/2

where F is the atomic deformation gradient.

Example:

>>> from ase.build import bulk
>>> import structuretoolkit as st
>>> bulk = bulk('Fe', cubic=True)
>>> structure = st.get_strain(bulk, np.random.random((3,3))*0.1, return_box=True)
>>> Strain(structure, bulk).strain

__init__(structure: Atoms, ref_structure: Atoms, num_neighbors: int | None = None, only_bulk_type: bool = False)

Parameters:

• structure (ase.atoms.Atoms) – Structure to calculate the strain values.

• ref_structure (ase.atoms.Atoms) – Reference bulk structure (against which the strain is calculated)

• num_neighbors (int) – Number of neighbors to take into account to calculate the local frame. If not specified, it is estimated based on cna analysis (only available if the bulk structure is bcc, fcc or hcp).

• only_bulk_type (bool) – Whether to calculate the strain of all atoms or only for those which cna considers has the same crystal structure as the bulk. Those which have a different crystal structure will get 0 strain.

Methods

__init__(structure, ref_structure[, ...])

param structure: Structure to calculate the

Attributes

coords	Local coordinates of each atom.
crystal_phase	Majority crystal phase calculated via common neighbor analysis.
num_neighbors	Number of neighbors to consider the local frame.
ref_coord	Reference local coordinates.
rotations	Rotation for each atom to find the correct pairs of coordinates.
strain	Calculate the strain value of each atom.

property coords: ndarray

Local coordinates of each atom.

Returns:

The local coordinates of each atom.

Return type:

np.ndarray

property crystal_phase: str

Majority crystal phase calculated via common neighbor analysis.

property num_neighbors: int

Number of neighbors to consider the local frame. Should be the coordination number.

property ref_coord: ndarray

Reference local coordinates.

Returns:

The reference local coordinates.

Return type:

np.ndarray

property rotations: ndarray

Rotation for each atom to find the correct pairs of coordinates.

Returns:

The rotation matrix for each atom.

Return type:

np.ndarray

property strain: ndarray

Calculate the strain value of each atom.

Returns:

The strain value of each atom.

Return type:

np.ndarray