GitLab

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

The differences in the Ewald energies between the Reference and Cuda platforms were traced to roundoff error in the 
computation of the Vdw and Coulomb ixns for the short-range energy contribution (verified using double precision in the sum); the vdw and Coulomb terms are now accumulated separately and then added to the total energy