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.  

Fixed error in updateNeighborListSize() when createInteractionKernel() has not been called (e.g. with AmoebaVdwForce)

CustomNonbondedForce.cpp, CudaNonbondedUtilities.cpp and CudaKernels.cpp are now fully reverted to 3478.

LPW attempted bugfixes: (1) Changed unit multipliers in AmoebaVdwForce::getParticleParameters (2) Sorted vectors in exclusionLists so it agrees with atomExclusions

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

Began implementing new mixed precision model that does integration in double precision and force evaluation in single precision

Continuing to implement new CUDA platform: constraints, LangevinIntegrator, BrownianIntegrator, VariableLangevinIntegrator, VariableVerletIntegrator