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.

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

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

1) Added DLL export macros to many classes; enough to get tests to compile
2) Cosmetic changes to reduce warnings in Visual Studio:
   a) change many "for (int i ="... to "for (size_t i ="... to avoid unsigned mismatch warnings
   b) included many explicit static_cast<OpenMMReal>() casts to document places where double->float conversion warnings occur

Added INCLUDE(Dart) to OpenMM CMakeLists.txt

Continuing to implement ReferencePlatform (implemented GBSA kernels, added test case for SHAKE and fixed some bugs in it)

Continuing to implement ReferencePlatform (implemented kinetic energy calculation and LangevinIntegrator)