GitLab

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.

Checked in explicit solvent implementation for Cuda platform (cutoffs, periodic boundary conditions, SETTLE)

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.