pwtools.crys.coord_trans3d

pwtools.crys.coord_trans3d(coords, old=None, new=None, copy=True, axis=-1, timeaxis=0)[source]

Special case version for debugging mostly. It does the loop for the general case where coords+old+new are 3d arrays (e.g. variable cell MD trajectory).

This may be be slow for large nstep. All other cases (coords has arbitrary many dimensions, i.e. ndarray + old/new are fixed) are covered by coord_trans(). Also some special cases may be possible to solve with np.dot() alone if the transformation simplifes. Check your math.

Parameters:

  • coords (3d array) – one axis (axis) must have length-M vectors, another (timeaxis) must be length nstep

  • old (2d arrays, two axes must be of equal length)

  • new (2d arrays, two axes must be of equal length)

  • copy (see coord_trans())

  • axis (axis where length-M vecs are placed if the timeaxis is removed)

  • timeaxis (time axis along which 2d arrays are aligned)

Examples

M = 3
coords : (nstep,natoms,3)
old,new : (nstep,3,3)
timeaxis = 0
axis = 1 == -1 (remove timeaxis -> 2d slices (natoms,3) and (3,3) -> axis=1)