GitLab

* Began creating common compute framework to unify code between CUDA and OpenCL

* Began OpenCL implementation of common compute framework

* Common implementation of CMMotionRemover

* CUDA implementation of common compute interface

* Converted HarmonicBondForce to common compute API

* Converted standard bonded forces to common compute API

* Converted ExpressionUtilities to common compute API

* Created ComputeParameterSet

* Converted custom bonded forces to common compute API

* Converted CustomCentroidBondForce to common compute API

* Converted CustomManyParticleForce to common compute API

* Moved lots of duplicate code from CudaContext and OpenCLContext to ComputeContext

* Converted GayBerneForce to common compute API

* Removed obsolete kernels

* Converted verlet integrators to common compute API

* Converted Langevin and Brownian integrators to common compute API

* Converted CustomIntegrator to common compute API

* Converted CustomNonbondedForce to common compute API

* Removed uses of a deprecated API

* Fixed failing test cases

* Converted GBSAOBCForce to common compute API

* Began converting CustomGBForce to common compute API

* Finished converting CustomGBForce to common compute API

* Merged duplicated code in CudaIntegrationUtilities and OpenCLIntegrationUtilities

* Converted RMSDForce and AndersenThermostat to common compute API

* Converted CustomHbondForce to common compute API

* Merged scripts for encoding kernel sources

* Converted Drude plugin to common compute API

* Fixed errors in CMake scripts

* Attempt at fixing errors on Windows

* Added discussion of common compute API to developer guide

* Added Windows export macro for common classes

* Fixed error in CMMotionRemover

* Ubdated travis to newer Ubuntu version

* Fixed errors on CPU OpenCL

* Fixed Windows linking errors

* Added missing pragma for 32 bit atomics

* Replaced long long with mm_long

* More fixes to Windows linking

* Bug fix

Useful when cuda is not installed in the default location.

Changed CMake scripts to work correctly if the FFTW threading support was built into the main library instead of a separate library

Modified OpenCL include search path for Linux.

Unify FindOpenCL.cmake files to one location, under cmake_modules.
Other changes to permit building with nvidia opencl on Windows.

Including installing Test<Platform>HarmonicBondForce tests.

Added modern findpackagehandlestandardargs technique to FindCUDA.cmake, to permit configuration on machine
with no cuda installed.

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.

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.

Incorporate apple-specific OpenCL include directory from the other FindOpenCL.cmake in the platforms/opencl CMakeLists.txt file.
TODO - in future use only one FindOpenCL.cmake file.

Reorganized platform analysis in NML init method.
Failed attempt to get OPENMM_PLUGIN_DIR working for NML test.

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

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.