GitLab

Platform specific header files get installed.  This allows plugins to be built with just an OpenMM installation, not a full source tree.

Moved SFMT into libraries folder, and restructured it to allow multiple independent random number generators

Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.

Implemented setting random seed for reference platform, as well as adding it as an option to BrownianIntegrator and AndersenThermostat.

Lots of mystical CMake incantations to make Cuda platform compile both static and dynamic libraries correctly

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

Continuing to implement ReferencePlatform (implemented kinetic energy calculation and LangevinIntegrator)

Created a test case for StandardMMForceFieldImpl's findExclusions() method.  Fixed some bugs that it found.  Created a CMake script and configured it for building and running test cases.