GitLab

Kinetic energy when using Verlet is calculated as average of v_i-1 and v_i

Test use env variable OPENMM_PLUGIN_DIR to find plugin

Added export for Windows
Format change to accomadate Windows

Removed cubic/quartic per-atom parameters from AmoebaHarmonicBondForce

Modified out-of-plane bend force to improve stability
Redid arguments to kCalculateAmoebaCudaKirkwood to reduce lmem

Note that I'm also modifying pyopenmm to be aware of this change.

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.

Turn default to ON for nightly building Cuda FreeEnergy plugin, since it is desired for pyopenmm release.