GitLab

License header changes; force duplication factor to 4; fixed potential problem w/ Shake -- if no constraints, pgm crashes

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.

Added Platform::getDefaultPluginDirectory().  Plugins are now installed into .../openmm/lib/plugins.

(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.

Minor fixes to some recent changes that prevented compilation (Mark looked at these). This code still has never been tested, at least on Windows.

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