GitLab

Eliminate some VC++ build problems via the usual expedient of explicit casts from unsigned to signed and from double to float. TNT Arrays apparently can't be indexed with unsigned because VC++ finds something ambiguous then above their operator[] methods.

(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.

(2) I disabled the block of code in the main CMakeLists file that tries to second guess VC++'s choices for runtime libraries. This was required for me to get CUDA to work in VC 2005 where the compiler always chooses multithreaded libraries. I verified that Brook will still build this way, but I haven't tested it.

Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.

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

Stop trying to populate and delete third element of two-element particleList array in TestReferenceNeighborList.cpp.
Memory corruption awaits...

Implemented dynamic loading of platforms from DLLs.  Also fixed a lot of compilation errors and warnings under Windows.

 * capitalization of gpuTypes.h
 * various cmake issues

removed redundant qualification ‘ReferenceForce::’ on member ‘getDeltaRPeriodic’ to get compile on linux