GitLab

Converted the routine for identifying molecules from a recursion to a loop.  This avoids stack overflows with very long linear molecules.

Platform specific header files get installed.  This allows plugins to be built with just an OpenMM installation, not a full source tree.

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.

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

Workaround for Nvidia compiler bug where compute level 1.2 processors try to compile double precision code

On Fermi, store forces as 64 bit fixed point and update with atomic operations.  Also various other minor optimizations.

Change suggested by Tony Tye to simplify debugging by including all compilation options in the kernel source

Switched back to always using the bundled cl.hpp, since the previous code didn't work on some OpenCL implementations

OpenCL kernels are now stored into a C++ class at build time rather than installing them as text files.