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.  

When computing kinetic energy, make sure the shifted velocities are perpendicular to the constraints

Reduced memory use for random numbers, eliminated unnecessary calculation when generating random numbers

When converting to fixed point, multiply by 0x100000000 instead of 0xFFFFFFFF.  This should be (very very slightly) more accurate, since its reciprocal can be exactly represented in floating point.