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.

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

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 

All energies existing in Preview Release 3 now run on the GPU, new Ewald energy terms still use Reference implementation

- MingW, where "WIN32" is set by CMake but the compiler is not Microsoft's (should use _MSC_VER) in that case, and 
- in gcc 4.4 which is fussy about some issues that earlier versions were silent about, such as passing a string constant to a "char*" rather than a "const char*".
I also fixed a syntax error in CMakeLists that showed up in the OpenMM workshop for some unknown reason.

Brook is not currently building correctly; I think it has not yet been fully converted to the getTime() interface needed for variable step integrators.

(2) I disabled the block of code in the main CMakeLists file that tries to second guess VC++'s choices for runtime libraries. This was required for me to get CUDA to work in VC 2005 where the compiler always chooses multithreaded libraries. I verified that Brook will still build this way, but I haven't tested it.

Checked in explicit solvent implementation for Cuda platform (cutoffs, periodic boundary conditions, SETTLE)

Continuing to implement ReferencePlatform (implemented GBSA kernels, added test case for SHAKE and fixed some bugs in it)