PG-PuReMD: fix performance logging code around GPU code. Rearrange header files to allow some preprocessor definitions to be defined via options in configure script. Rework Autoconf and Automake code to allow passing flags directly to nvcc compiler wrapper (for CUDA code). Enable C11 and C++11 standard targets during compilation.

PG-PuReMD: replace deprecated CUDA warp-level primitives with modern ones. Fix issue with modern GPU microarchitectures using incorrect code paths (post-Kepler). Other code clean-up.

PG-PuReMD: include missing header file in Automake make file (includes file in distribution tarball).

PG-PuReMD: remove outdated debugging and validation code (was performing host-only simulation with host+device simulation and comparing results).

sPuReMD: fix issue with configure script nuking Tensorflow link variables when LAPACK link variables are set.

sPuReMD: refactoring to better align with PuReMD code. PuReMD: backport sPuReMD changes from validation efforts against Fortran ReaxFF code.

Build toos: refactor to remove recurisve Makefiles. Fix issue with OpenMP flags being overridden when user supplied value for CFLAGS variable.