Improvements for the hardwall function.

Bonds to which the hardwall restraint is applied are now
decided based on listed bond interactions and not just atom
numbers.  This is a much more robust approach.  Issues with
parallelization remain; scaling past 4 threads/CPUs always
crashes in this function.  Future update will correct this once
I have tracked down the root of the problem.

Change-Id: Id9148866740ee70f09ae546da119a99085a5a5c0