GitLab

Optimization to nonbonded forces: replaced divides by multiplies when applying periodic boundary conditions

Moved SFMT into libraries folder, and restructured it to allow multiple independent random number generators

Allow parameter specification of platforms to be compared

Removed ALREADY_MODIFIED_PATH variable in gpu sniffer link stanza, which I am pretty sure would not have worked as desired.

Modified link path in platforms/cuda/CMakeLists.txt to increase likelihood that CUDA_HAVE_GPU flag will be set.

Including installing Test<Platform>HarmonicBondForce tests.

Changed link line for gpu sniffing program so it works on Windows with new single FindCuda location.

FindCUDA.cmake.

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.