PG-PuReMD: use a warp of threads for apply bond derivatives to forces and simplify these code paths.

PG-PuReMD: fix incorrect summations in kinetic energy and temperature calculation functions. Replace several hand-coded device-wide reduction kernels with CUB libary reduction.

PG-PuReMD: split bond and hbond initialization kernels for future optimizations. Cleanup CUDA code related to far neighbor list being in full format (remove unnecessary conditionals and arithmetic).

sPuReMD: enable setting the number of OpenMP threads via control file keyword or OpenMP environment variable (OMP_NUM_THREADS).

sPuReMD: make zlib dependency optional (trajectory file compression). PG-PuReMD: remove erroneous zlib header file inclusion.

sPuReMD: fix OpenMP compilation issue with specifications prior to 4.0 (behavior change regarding implicit shared attribute assignment to const variables).

QMMM interface related: ignore QM-MM bonds while forming bond lists, update charge matrix so that the total charge constraint only applies to QM atoms

PG-PuReMD: handle a few missed reductions in nonbonded interactions more efficiently. Clean-up bonded interactions functions and do not export kernels via header files. Increase C++ standard to c++14 for CUB (Thrust dependency). Continue with bundled CUB version and transition to version included with CUDA SDK in the future.

PG-PuReMD: use atomics for both partial energy and force accumulation (small reworks to reduce number of atomic operations). Remove several unneccesary cudaMemset calls. Other code clean-up.

Test: fix Python wrapper for QM/MM (interfaces out-of-date). Fix Fortran tester bugs. Add test artifacts.

sPuReMD: standardize QM/MM interface. Add test codes for QM/MM interface for AVE dataset in Python and Fortran.

sPuReMD: merge changes from branch 'new_setup'. Rework interface for geometry initialization without file I/O. Other code clean-up.