GitLab

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

All platforms now handle nonbonded exceptions in a consistent way (they ignore cutoffs and periodic boundary conditions).  Also started OpenCL implementation of CustomHbondForce.

Increased the tolerance on two tests that started failing when we switched the reference platform to double precision

Use a consistent (and more accurate) value for electric constant everywhere.  Also cleaned up handling of constants and units in various places.

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.