GitLab

Variable time step integrators correctly report the size of the last step taken.  Also improved accuracy of integration unit tests.

Refactored ForceImpl, lots of KernelImpl subclasses, and other related classes to avoid redundant calculations when requesting a State with both forces and energies

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

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

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