GitLab

Added a version of Platform::getPlatform() that looks up platforms by name.  Added a Context constructor that allows platform-specific properties to be specified.

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 

Restructured how force and energy computations are done to make it easier to write plugins for the CUDA platform

(1) Made Platform::loadPluginLibrary() for Windows leave the end user alone if a failure occurs -- was throwing up an error box.
(2) Made Platform::loadPluginsFromDirectory() on Windows find only .dll's. 

Added Platform::getDefaultPluginDirectory().  Plugins are now installed into .../openmm/lib/plugins.

Implemented the Ewald summation method in the reference platform. Preliminary cuda prototype is included.

Optimization: introduced a kernel to clear forces at the start of each time step rather than relying on the stream

Implemented dynamic loading of platforms from DLLs.  Also fixed a lot of compilation errors and warnings under Windows.

Changed how kernels get initialized.  StandardMMForceField now has you set the 1-4 interactions explicitly.  CMMotionRemover allows the removal frequency to be set.

1) Added DLL export macros to many classes; enough to get tests to compile
2) Cosmetic changes to reduce warnings in Visual Studio:
   a) change many "for (int i ="... to "for (size_t i ="... to avoid unsigned mismatch warnings
   b) included many explicit static_cast<OpenMMReal>() casts to document places where double->float conversion warnings occur