GitLab

Fix SWIG 3 support for the Python wrappers.

See swig/swig#387 for a discussion.  It would actually be nice to *not* set the
"compactdefaultargs" feature globally, since that would allow us to actually see
the real API at the Python level the same as you would see by looking at the C++
header files. But this is the only way to support both SWIG 2 and SWIG 3 easily
and avoid a lot of retooling for the SWIG input code generator.

Enabled OpenCL on OS X

Fixed a bug in OpenCL FFT

Optimization to OpenCL FFT

Fixed compilation error with latest version of SWIG

OpenCL FFT stores only non-redundant elements

Optimizations to CPU platform

Apparently CHARMM PSF files (particularly those printed by VMD's psfgen) can
have an insertion code tacked on to the end of the residue number, meaning that
casting to an integer will invariably fail.  We can't just ignore the insertion
code, though, since it will differentiate from the residues that came before and
after (which will likely have the same number -- same general idea as insertion
codes from PDB files). So instead we pull the insertion code off of the residue
number and extend the Residue object to accommodate that.

This is the port of the fix from ParmEd: ParmEd/ParmEd#98

I added a test for this case.

Implemented an optimized real-to-complex FFT

OpenCL FFT supports real-to-complex transforms

Fixed a performance regression on AMD GPUs

More fixes to OpenCL with CPU device

Fixed errors using OpenCL with CPU device

Parallelized extraction of inverse matrix for CCMA