GitLab

Converted the array containing atom block indices for the neighbor list from ushort2 to int.  This removes the hard limit of 2 million atoms.

Fixes a hard to catch bug when a boundingBoxSize increases in size in between a timestep, but does not trigger a rebuild of the neighbourlist. Affects the usage of singlePeriodicCopy in nonbonded force.  

OpenCLArray is no longer templatized and doesn't provide a host buffer.  This is in preparation for adding mixed/double precision support.

On Fermi, store forces as 64 bit fixed point and update with atomic operations.  Also various other minor optimizations.

Fixed bug when CustomGBForce was told to use exclusions, but didn't have any exclusions.  (See bug 1519.)

Reduced number of force buffers to one per work group.  Increased work group size for nonbonded interactions.