sPuReMD: refactor and clean up preconditioner application code (level scheduling, graph coloring, Jacobi iteration). Conditionally change charge matrix for setting up preconditioner for ICHOLT and ILU(T).

sPuReMD: fix issue with graph coloring causing sporadic failures in solver convergence for EE and ACKS2. Conditionally change the charge matrix for ICHOLT and ILU(T) preconditioning. Refactor graph coloring code.

sPuReMD: fix bug in GMRES where vector inputs and outputs to apply_preconditioner were being overwritten. Refactor OpenMP code in GMRES.

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.

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: fix linear solver to work with no preconditioner. Fix issue when precondition recomputation frequency is zero. Other misc. changes.

sPuReMD: enable debug builds. Fix compilation issues when optimizations disabled (-O0). Fix graph coloring data structure management.

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

sPuReMD: expand domain-based QEq matrix cut-off and add control file parameter. Update control file.

sPuReMD: refactor tri solve level sched memory management. Change OpenMP thread scheduling policy to static. Modify logging output format.

sPuReMD: fix diagonal preconditioner computation and level scheduling application. Modify preconditioner logic to compute and cache sparsity-based info. Update run script.