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.

Build: work around Autoconf bug in AC_SEARCH_LIBS preventing both LAPACK and Tensorflow from being used together for sPuReMD.

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

PG-PuReMD: backport fixes from sPuReMD to control file parsing. Tools: formatting tweaks for MPI-GPU code.

PuReMD: disable debug prints during basic debugging (DEBUG -> DEBUG_FOCUS). Re-enable DUAL_SOLVER. Small buffer reworking around trajectory file (REG_TRAJ). Other code clean-up.

PG-PuReMD: remove outdated debugging and validation code (was performing host-only simulation with host+device simulation and comparing results).

PG-PuReMD: refactoring to unify CUDA code naming conventions and to simply code in cuda_system_props.cu.

PG-PuReMD: fix issue with portions of interaction lists not being initialized for Cuda_Init_Forces. Utilize more targeted debugging prints (DEBUG -> DEBUG_FOCUS). Other general code cleanup.

sPuReMD: fix issue with configure script nuking Tensorflow link variables when LAPACK link variables are set.

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.