GitLab

Including installing Test<Platform>HarmonicBondForce tests.

based on the FindCUDA.cmake that was in the platforms/cuda/cuda-make directory.
Setting of CUDA_NVCC_FLAGS is now in top-level CMakeLists.txt, in case I ever figure out how
to get this working with the cmake 2.8 installed system version of FindCUDA.cmake.
Before this change, there were three separate FindCUDA.cmake areas.  Now there is just one.

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

So far tested only on GPU-having windows machine.

Exported some symbols from Cuda plugin, for use by external NML plugin.
  cudaOpenMMInitializeIntegration, gpuSetConstants, CudaPlatform
  (but I couldn't figure out how to export kGenerateRandoms)
Also turned off TestRandomCuda on Windows, since it always fails and makes the dashboard look bad.
Renamed InitializeIntegration method to cudaOpenMMInitializeIntegration, now that symbol is being exported.

Increased the tolerance on two tests that started failing when we switched the reference platform to double precision

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

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