pwtools.crys.pbc_wrap_coords

pwtools.crys.pbc_wrap_coords(coords_frac, copy=True, mask=[True, True, True], xyz_axis=-1)[source]

Apply periodic boundary conditions to array of fractional coords.

Wrap atoms with fractional coords > 1 or < 0 into the cell.

Parameters:

  • coords_frac (array 2d or 3d) – fractional coords, if 3d then one axis is assumed to be a time axis and the array is a MD trajectory or such

  • copy (bool) – Copy coords_frac before applying pbc.

  • mask (sequence of bools, len = 3 for x,y,z) – Apply pbc only x, y or z. E.g. [True, True, False] would not wrap the z coordinate.

  • xyz_axis (the axis of coords_frac where the indices 0,1,2 pull out the x,y,z) – coords. For a usual 2d array of coords with shape (natoms,3), xyz_axis=1 (= last axis = -1). For a 3d array (natoms, nstep, 3), xyz_axis=2 (also -1).

Returns:

coords_frac – Array with all values in [0,1] except for those where mask[i]=False.

Return type:

array_like(coords_frac)

Notes

About the copy arg: If copy=False, then this is an in-place operation and the array in the global scope is modified! In fact, then these do the same:

>>> a = pbc_wrap_coords(a, copy=False)
>>> pbc_wrap_coords(a, copy=False)