sPuReMD: output PDB files according to write_freq value in control file in addition to outputting to the trajectory file. Small tweak to PDB output format to be in compliance with specification.

sPuReMD: fix issue with runs using restart files overwriting velocities to zero. Change behavor to warn if conflicting conditions exist for generating initial atom velocities. Revert formatting change of pressure logs. Enable pressure file logging when compute_pressure = 1.

sPuReMD: add control file parameter to compute atomic system pressure for non-NPT ensembles. Fix issues with isotropic NPT ensemble (incorrect pressure and temperature scalers). Change atomic position remapping behavior to include upper boundaries of the simulation box (shared memory code only). Other code clean-up.

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

sPuReMD: corrections to external pressure calculations for NPT-type ensemble simulations (use correct periodic images between reneighboring steps). Other code clean-up.

sPuReMD: fix issue with torsion & conjugation forces being incorrect due to rel_box arithmetic being wrong (incorrect directions for position vectors). Redesign atomic distance and position update functions to support both periodic boundary conditions and non-periodic boundary conditions.  Behavior change: let random_velocity parameter in control file take precedent over specifying a non-zero initial temperature value. Other code clean-up.

sPuReMD: disable debug prints (DEBUG -> DEBUG_FOCUS). Small tweaks to valence angle code to better match reference. Other code clean-up.

sPuReMD: refine BiCGStab implementation to not falsely report numeric breakdown. TODO: decide on correct checks for level of precision in numeric breakdown checks.

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 deadlock condition in BiCGStab (global shared variables in Norm and Dot functions could overwritten in some multi-threaded runs). Remove debugging prints.

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: small updates to Python wrapper (data structure changes). Fix issue with system energies not being computed for step 0 with the wrapper.

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.

PuReMD: code refactoring to remove global variables (similar to sPuReMD). sPuReMD: minor refactoring to match naming conventions of PuReMD.

sPuReMD: fix issue with SMALL_BOX_SUPPORT incorrectly computing pairwise atomic distances for periodic self-images. Fix issue with integer vector sum function (used in bond order and torsion interactions).

sPuReMD: remove global variable (array of function pointers for printing bonded interactions during debugging).

sPuReMD: improvements for building in debug mode (add assertion support for run-time checks). Fix issue with Verlet list recomputation logic being incorrect. Fixes to be string comparisons.

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: add safety check for BGF input files (CRYSTX). Remove compiler warnings when enabling DEBUG_FOCUS.

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: fixes to SAI preconditioner to correctly apply threshold to negative entries and to handle EE/ACKS2 cases when a threshold value of 1.0 is chosen.

sPuReMD: fix bug with diagonal scaling during FG_ICHOL/FG_ILUT producing incorrect factorizations when diagonal entries were negative.

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