GitLab

Simplified constraint code.  In the process, this fixed a bug that caused bubbles to appear in water when running on Fermi GPUs.

Optimization to nonbonded forces: replaced divides by multiplies when applying periodic boundary conditions

Use a consistent (and more accurate) value for electric constant everywhere.  Also cleaned up handling of constants and units in various places.

Mods to get Free energy plugin libs to compile on Windows; still problem w/ kCalculateLocalSoftcoreForces.cu
and hence OpenMMFreeEnergyCuda lib

Redesigned CustomNonbondedForce to eliminate combining rules and allow the expression to directly use parameters for individual particles.

replaced w/ the "KISS" (Keep It Simple Stupid) random number generator implemented in rng.h & rng.cpp

Free energy plugin added
Plugin will not run w/ Obc or GB/VI forces unless line 2004 of gpu.cpp (gpu->sim.totalNonbondOutputBuffers  = 2*gpu->sim.nonbondOutputBuffers;) is commented in -- working on removing this constraint
Also unit tests for GB/VI currently fail