GitLab

All energies existing in Preview Release 3 now run on the GPU, new Ewald energy terms still use Reference implementation

In calcForces() kReduceBornSumAndForces kernel is not needed since Born radii/Obc chain term now calculated prior to calculation of forces
Modified kCalculateObcGbsaBornSum kernel loop to match that in kCalculateCDLJObcGbsaForces1; Born sums are zero w/o mods

(2) Changed erfc.cpp to a header file which defines missing erf() and erfc() as static functions when using VC++ but otherwise does nothing.
(3) Replaced all nonstandard uses of real() and imag() methods as lvalues; instead work directly with the complex values.
(4) Fixed a bug in TestFindExclusions which was caught by VC++'s extensive STL debug mode self-examination.

There are still problems in hilbert.c and not all CUDA tests pass.

Implemented the Ewald summation method in the reference platform. Preliminary cuda prototype is included.

Implemented setting random seed for reference platform, as well as adding it as an option to BrownianIntegrator and AndersenThermostat.

Checked in explicit solvent implementation for Cuda platform (cutoffs, periodic boundary conditions, SETTLE)

Optimization: introduced a kernel to clear forces at the start of each time step rather than relying on the stream