GitLab

All platforms now handle nonbonded exceptions in a consistent way (they ignore cutoffs and periodic boundary conditions).  Also started OpenCL implementation of CustomHbondForce.

Code surrounding 'RealOpenMMType == 0' will be removed 
once confirmed free-energy plugin code does not break

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

Incorporate Normal Mode Langevin openmm code from Chris Sweet as a plugin.  (compiles on windows, but no actual testing done)

Added a version of Platform::getPlatform() that looks up platforms by name.  Added a Context constructor that allows platform-specific properties to be specified.

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.

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 

Restructured how force and energy computations are done to make it easier to write plugins for the CUDA platform