GitLab

Integrators control when atom reordering gets done, instead of having it happen automatically when forces are evaluated.  This simplifies some code, and also improves unintuitive behavior with CustomIntegrator.

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.  

CudaApplyConstraintsKernel::apply() did not set the context as current, leading to errors when using multiple contexts

Fixed potential energy discrepancies in large systems between CUDA and Reference platform. The energy calculation now uses the same method as that of reciprocalConvolution so it mirrors the reference implementation. OpenCL is fine.  

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.

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

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

Committing FFTWs to work with complex conjugate arrays. Decoupled energy and force calculation into two separate kernels.