sPuReMD: backport efforts for SMALL_BOX_SUPPORT from OGOLEM version of code and conditionally compile. Remove unused code. Other code clean-up.

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

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: fix complaints by Valgrind for indexing before head of array pointer (i.e., passed as function parameters).

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.

sPuReMD: complete preconditioner application using level scheduling with permutations based on graph coloring.