apply_pbc

dislocation_tools.io.lammps_formats.apply_pbc(dof, periodic_boundary, image_distances, mode)

Apply periodic boundary conditions.

Parameters

• dof_chunk (array-like) – atomic coordinates

• periodic_boundary (list) – element i = True if boundary in direction i is periodic

• image_distances (list) – distance that must be subtracted from x, y, or z-coordinates to wrap them across the periodic boundaries. None if boundary is not periodic.

• mode (str) – ‘wrap’ to wrap coordinates, ‘unwrap’ to unwrap

Returns

dof_chunk – atomic coordinates with pbc applied

Return type

numpy.ndarray

Notes

Triclinic boxes are not fully supported. In this case, only the non-inclinced direction can be periodic.