Granular systems have high stress/energy when they are overlapped,
b/c the push-off contact forces are so large. If you build a system
with overlaps, you will have that problem. If you use fix deform
it is easy to induce lots of overlaps. I don’t think
there is an error with “too many contacts” in current LAMMPS,
though it does indicate you probably have a lot of overlaps (in
the older version).
Are you using the current version?
Steve