Fix memory allocation issues related to API usage (setup => cleanup but no simulate) as detailed in Issue #9.

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

sPuReMD: small updates to Python wrapper (data structure changes). Fix issue with system energies not being computed for step 0 with the wrapper.

sPuReMD: backport changes for reax_list, struct declaration/definition separation, interaction_function.

sPuReMD: separate total energy computation and fix Python driver bug with structure definition for ctypes. Allow disabling file logging during simulation.