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 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.

sPuReMD: change inline functions to be generated for each translational unit. Begin adding vectorization support via OpenMP SIMD.

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: begin merging code from LAMMPS USER-REAXC-OMP/USER-OMP. Fix ACKS2 charge matrix coefficients.

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

PG-PuReMD: fix include guards, resolve implicit function declarations, fix inline issues with GCC v5 (C99 std). Other general code clean-up.

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: refactor preconditioning using control file parameters. Add ILUT_PAR precondioner method. Fix control file parsing bugs.

sPuReMD: begin refactoring data structures from array of structs to struct or arrays (sparse_matrix).

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

sPuReMD: fix SuperLU build and code. Fix ILU_PAR (compute factors separately). Move diagonal preconditioner computation. Refactor precondition computations. General code clean-up.