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PG-PuReMD: remove outdated debugging and validation code (was performing host-only simulation with host+device simulation and comparing results).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

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).

PuReMD: clean-up of heuristic for dynamically determining when to recompute the preconditioner for the charge solver.

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.