structuretoolkit.common.helper.get_extended_positions

structuretoolkit.common.helper.get_extended_positions#

structuretoolkit.common.helper.get_extended_positions(structure: Atoms, width: float, return_indices: bool = False, norm_order: int = 2, positions: ndarray | None = None)[source]#

Get all atoms in the boundary around the supercell which have a distance to the supercell boundary of less than dist

Parameters:

  • width (float) – width of the buffer layer on every periodic box side within which all atoms across periodic boundaries are chosen.

  • return_indices (bool) – Whether or not return the original indices of the appended atoms.

  • norm_order (int) – Order of Lp-norm.

  • positions (numpy.ndarray) – Positions for which the extended positions are returned. If None, the atom positions of the structure are used.

Returns:

Positions of all atoms in the extended box, indices of atoms in

their original option (if return_indices=True)

Return type:

numpy.ndarray