GitLab

move the plugin to its own project.
This change might also simplify pyopenmm nightly test issues.

day when we try it on Windows.
Added "-isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5" to Mac compile flags,
to possibly help run on Leopard.

Incorporate Normal Mode Langevin openmm code from Chris Sweet as a plugin.  (compiles on windows, but no actual testing done)

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.

Free energy plugin added
Plugin will not run w/ Obc or GB/VI forces unless line 2004 of gpu.cpp (gpu->sim.totalNonbondOutputBuffers  = 2*gpu->sim.nonbondOutputBuffers;) is commented in -- working on removing this constraint
Also unit tests for GB/VI currently fail 

Better search for svnversion.exe on Windows

Deleted all the old hand-generated wrappers.

Created CMake script for generating API wrappers.  Also updated the wrapper scripts to handle vector<double>.

Examples: now builds CWrappers as a library; modified C builds to use it; added visual studio project to build Argon example in Fortran.
System.h: addForce() wasn't returning the index.

I'm checking in very early attempts at OpenMM Hello World examples so Chris and I can work on them together.

(2) I disabled the block of code in the main CMakeLists file that tries to second guess VC++'s choices for runtime libraries. This was required for me to get CUDA to work in VC 2005 where the compiler always chooses multithreaded libraries. I verified that Brook will still build this way, but I haven't tested it.

because virgin computers without CUDA generate loads of errors trying
to find CUDA on cmake run.

Modified FindBrook.cmake to be a bit more specific about finding BROOK_INCLUDE_DIR, so it finds on my computer