We have python scripts help unwrap VASP MD coordinate output (XDATCAR) and calculate the mean square displacement (MSD) of each atom type in the structure. First script xdatcar2xyz.py is a general purpose XDATCAR to xyz converter. is used to convert XDATCAR (currently only the most recent XDATCAR format of VASP). The second script msd.py can process any XYZ file given the lattice vectors, and write element-wise decomposed MSD and unwrapped coordinates.
Scripts can be obtained by sending an e-mail to M. Aykol (aykol (at) u.northwestern.edu).