GitLab

In Born radii calculation for particle i, removed factor of lambda associated w/ particle i

Padded atom entries in Born radii memory now initialized to zero
launch bounds guards now included for several kernels

Moved AMOEBA include files to plugins/amoeba/openmmapi/include/openmm to be consistent w/ outlay other plugins, ...

Refactored ForceImpl, lots of KernelImpl subclasses, and other related classes to avoid redundant calculations when requesting a State with both forces and energies

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.

Downgraded recent cmake changes to ghastly compliance with cmake 2.4, for the benefit of the simtk dart server.

Modified Cuda FreeEnergy plugin to use a different windows export macro than main openmm library and cuda library.
Modified CUDA_NVCC_FLAGS to be consistent with Peter's latest version in all three locations they are defined.
Added "-Xcompiler '/MD'" to CUDA_NVCC_FLAGS on Windows to avoid link error in Cuda FreeEnergy plugin.

Export CudaFreeEnergyKernelFactory symbols to avoid link error in test program.

Still doesn't build on windows, but might help with linux (todo next)

Fixed uninitialized value problem with setting box vectors.  This caused sporadic multithreading issues on Linux platforms.

Removed static variables in CudaFreeEnergyKernels.cpp
Moved declaration of global feSim to within method where actually used  in kCalculateNonbondedSoftcore.cu

Replace Platform::getPlatform by Platform::getPlatformByName where necessary, due to recently changed interface.

Removed cruft from Cmake file
Modified the way platform is specified in TstFreeEnergyCudaUsingParameterFile.cpp

removed some cruft

Fixed bug: was calling kReduceObcGbsaSoftcoreBornForces instead of kReduceGBVISoftcoreBornForces in GB/VI force calculation