Catch overlapping atoms between grains

[stefanbringuier]

Currently no pruning or checking of distance between atoms in two different grains is performed. This can be will be problematic if the final polycrystal result in an unphysical configurations. In the Grains class, the method pruneoverlap(self,criteria) needs to be completed. The primary approach should be to limit the checking all atoms in the simulation box; we just need to check atoms at the boundaries between grains.

• [ ] Write function to identify grain boundary atoms
• [x] Method to prune unphysical atomic configurations at grain boundaries.

[stefanbringuier]

This pruning feature has been addressed with the most recent Commit 48229cf4e2654da9a7e2e40b12b36b487cba3b98