I'll be happy to help. Although I can dig it up from internet resources, it would help me if you could provide an example LAMMPS structure to work with. It doesn't have to be the one you plan to study, just some example. Or email me the real structure privately.
It could also be interesting to create an export filter for the Builder, so that one can build structures in VNL and then easily run them in LAMMPS.
Btw, in ATK 13.8 (but more so even in 14.2) we are adding a similar classical simulation engine as LAMMPS into ATK, so it will be possible to use ATK for the whole thing, hopefully.