There is a shift in materials simulations from ideal single crystals to
crystals made of several grains, with boundaries resulting in
interest in automated approaches to sample preparation from many
directions. Its part of my EU FP7 SimPhoNy project, and included in
some of our modules (especially NCAD,
not yet published). A recent manuscript by P. Lazic
presented a code (CELLMATCH) to combine to unit cells into a supercell for a graphene system, and its substrate with
DFT calculations with VASP.