GitLab

Set NVCC_FLAGS to particular value in new cmake_modules/FindCUDA.cmake

removed some cruft

Turn on free energy plugin by default.
Better rule for when to default build OpenMM wrappers.
Several tweaks to advanced vs. non-advanced cmake variables.

So nightly builds can build CUDA and API wrappers when prerequisites are present.
While still being gentle on third party cmake builders.
New cmake_modules directory contains FindCUDA.cmake from cmake 2.8.0, and
Find OpenCL.cmake from platforms/OpenCL directory.

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

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

Added #include <typeinfo> to see if it removes errors associated w/ std::bad_cast on Linux Ubuntu 4.3.2

Changed ReferenceFreeEnergyPlatform name to ReferenceFreeEnergy
Removed references to ParameterFileName in GB/VI

Redesigned CustomNonbondedForce to eliminate combining rules and allow the expression to directly use parameters for individual particles.