PG-PuReMD: more code clean-up and re-organization.

PG-PuReMD/src/allocate.c

PG-PuReMD/src/comm_tools.c

PG-PuReMD/src/control.c

PG-PuReMD/src/cuda_environment.cu

PG-PuReMD/src/cuda_init_md.cu

PG-PuReMD/src/cuda_init_md.h

PG-PuReMD/src/cuda_utils.cu

PG-PuReMD/src/init_md.c

PG-PuReMD/src/integrate.c

PG-PuReMD/src/parallelreax.c

PG-PuReMD/src/reax_types.h

PG-PuReMD/src/reset_tools.c