Replica Exchange Statistical-Temperature Molecular Dynamics

via modification of temper module in LAMMPS.

TO DO:
[x] Make STMD restart 
{x] Add universe variable to each *.d file created by fix_stmd.cpp 
[x] Add any necessary RESTMD restart information to oREST.d and iREST.d 
[x] Obtain acceptance criteria for RESTMD from oREST.d and replace metropolis criteria in temper.cpp 
[x] Check velocity rescaling, verify acceptance criteria
[x] Ensure swaps take place correctly
[x] Benchmark algorithm, 60nm and 100nm implicit solvent lipid vesicles: http://i.imgur.com/Zx1QBLw.png 
[x] Clean out input/output for use by others
[x] Create example simulations, 500 LJ long-run results: https://imgur.com/a/931G4Tn
[ ] Create documentation
[ ] Prepare for LAMMPS release, last bugchecks!