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.