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.  

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.

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.

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

NonbondedForce::updateParametersInContext() is more tolerant about what changes to exceptions it allows