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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

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Fixes uninitialized bits occurring in the PaddedNumAtoms regions by properly constructing them. This should hopefully get rid of some of the NaN errors we've been seeing.