sPuReMD: add checks on string and file handling. Rewrite PDB writing to be line-by-line. Other refactoring.

sPuReMD: remove debug prints. Default to no good initial guess for out of range values for spline extrapolation.

sPuReMD: move NaN checks on system energy to after logging. This allows better diagnostics for, e.g., the potential logging.

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

sPuReMD: fix GMRES bug introduced from previous refactoring. Explicitly link OpenMP for library. Refactoring to remove global variables. Remove unnecessary OpenMP barriers after single regions.

sPuReMD: split into library and driver for, e.g., optimization integration. Fix bug with interaction lists being allocated for hydrogen bonds when no hydorgen atoms present. Fix minimum allocation size of 3-body lists (uncovered with small lithium geometries). Refactor naming of conflicting data structures. Update .gitignore.

PG-PuReMD: fix error due to function prototype change. PuReMD: fix issues with GCC new inline behavior, fix reax_list bugs. sPuReMD: change exit code to zero.

sPuReMD: add safe memory allocation functions. Fix issue with certain parameters for shielded van der Waals interactions not being correctly initialized. Other general refactoring.

sPuReMD: further OpenMP work on force computations and interaction lists. Minor data structure scope changes. Fix numereous non-critical memory leaks. Add tear-down code. Other general refactoring.

Add minor checks to PG-PuReMD and PuReMD. Major refactoring of sPuReMD: backport much of PuReMD code and add CUSTOM geo format.