structuretoolkit.common.helper.get_wrapped_coordinates

structuretoolkit.common.helper.get_wrapped_coordinates#

structuretoolkit.common.helper.get_wrapped_coordinates(structure: Atoms, positions: ndarray, epsilon: float = 1e-08) → ndarray[source]#

Return coordinates in wrapped in the periodic cell

Parameters:

  • positions (list/numpy.ndarray) – Positions

  • epsilon (float) – displacement to add to avoid wrapping of atoms at borders

Returns:

Wrapped positions

Return type:

numpy.ndarray