sPuReMD: fix Coulomb energy calculations for QM/MM mode. Indicate QEq model not supported with QM/MM mode. Add Fortran interface for QM/MM mode.

sPuReMD: add QMMM library interface for external codes (e.g., Amber). Rework file I/O parsing to jive with multiple consecutive simulation code changes. Improve file parser error checking (numeric types). Other code clean-up.

sPuReMD: fixes for multiple consecutive simulation codepath. Reorganization to this codepath (some data structure now carry a flag to designation their allocation state). Fix bug in force field parser (atom type not truncated correctly). Charge sparse_matrix structs to be non-pointers to jive with new allocation state flag. Other code clean-up.

sPuReMD: finalize sPuReMD multiple consecutive simulation code (for integration with other codebases).

sPuReMD: add functionality to run multiple MD simulations (for usage via integration with external codebases).

sPuReMD: resolve OpenMP build errors with GCC v10 (behavior changes for function arguments). Suppress possibly unitialized variable warnings for BiCGStab.

sPuReMD: finalize corrections for pressure calculations. Change output units from GPa to ATMs. Other formatting changes.

PuReMD: backport changes for interaction function calculations. sPuReMD: alignment with PuReMD code.

sPuReMD: replace OpenMP critical sections on ext_press with thread-local storage and subsequent reduction (ext_press_local). Other code clean-up.

sPuReMD: add support for using the Tensorflow machine learning library to prediction initial guesses for the charge solver using the long short-term memory model (LSTM) via frozen models in GraphDef files.

sPuReMD: fix small formatting issue with writing out PDB formatted files. Fix issue with bond restrictions when running with BGF formatted geometry files. Respect buffer size of snprintf calls.

sPuReMD: fix issue with far neighbor list being incorrectly generated on MD steps where the list was not being computed (issue with atomic distances being incorrectly computed for peroidic neighbors). Disable several debugging print statements (DEBUG -> DEBUG_FOCUS). Other code clean-up.

sPuReMD: fix issue with certain preconditioners not being initialized for runs using restart files. Fix issue with part of simulation box struct not being initialized for runs using restart files (box->min). Other code clean-up from debugging issues with SMALL_BOX_SUPPORT.

sPuReMD: fix issues with using sizeof with dynamically allocated pointers. Change OpenMP schedule policies for linear algebra code. PuReMD: correct discrepancy with charge matrix construction. Enable dual solver for charges by default.

sPuReMD: refactoring to better align with PuReMD code. PuReMD: backport sPuReMD changes from validation efforts against Fortran ReaxFF code.

sPuReMD: complete fine-grained Cholesky implementation. TODO: fix numeric breakdowns with water 6540 atom system.

sPuReMD: workarounds for memory issues with ILUT factors. Implement ILU(0) and call when selecting ILUT with a droptol of 0.

sPuReMD: fix issue with hbonds list indices not being reset correctly. Small algebraic rearrangements of valence angle calculations to match Fortran ReaxFF code (no numeric changes). Fix issue with rvec_isZero being incorrect. Fix issue with debugging arrays for TEST_FORCES not having indicies initialized. Other clean-up work.

sPuReMD: re-enable SMALL_BOX_SUPPORT. Fix issue with far nbrs list being incorrectly generated for small boxes (missing nbr ID). Fix issue with ACKS2 matrix being incorrect for small boxes due to multiple non-zeros being added for each perioidic image of an atom (accumulate instead). Add missing ACKS2-specific energy and forces term. Clean-up far nbr list estimation and generation code for small boxes. Do not add far list struct entries unless the atom is below the specified cutoff.

sPuReMD: fix ILUTP bug with order of permutation matrix application. Refactor dense vector permutation code (GC, ILUTP).

PG-PuReMD: begin merging preconditioner code from sPuReMD. Make data structures between sPuReMD and PG-PuReMD consistent. Update control file parsing.

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: 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.