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Test: fix Python wrapper for QM/MM (interfaces out-of-date).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.

sPuReMD: fix BGF parser to correctly remap atom coordinates to internal simulation box boundaries. Fix reax_list to handle case when total interactions is zero instead of terminating program.

sPuReMD: rework Fortran F90 interfaces for Amber specifics and declare this interface for such usage.

sPuReMD: fix Coulomb energy calculations for QM/MM mode. Indicate QEq model not supported with QM/MM mode. Add Fortran interface for QM/MM mode.

sPuReMD: add QMMM library interface for external codes (e.g., Amber). Rework file I/O parsing to jive with multiple consecutive simulation code changes. Improve file parser error checking (numeric types). Other code clean-up.

sPuReMD: fixes for multiple consecutive simulation codepath. Reorganization to this codepath (some data structure now carry a flag to designation their allocation state). Fix bug in force field parser (atom type not truncated correctly). Charge sparse_matrix structs to be non-pointers to jive with new allocation state flag. Other code clean-up.

sPuReMD: finalize sPuReMD multiple consecutive simulation code (for integration with other codebases).

PG-PuReMD: fix BGF parser for >1 process (correct atom counts within local simulation box boundaries).