sPuReMD: fix memory leak with ICHOLT preconditioner (droptol for OpenMP only) for charge solver. Default to Jacobi preconditioner. Resolve several compiler warnings around C strings (snprintf, etc.). Other code clean-up.

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.

PG-PuReMD: merge changes from sPuReMD and PuReMD for validation work for simulation accuracy. Small correction to lone pair energy calculation. PuReMD: code formatting changes to better align with sPuReMD. sPuReMD: fix issue with valence angle calculations not setting list indices under certain sitations (taking previous continue statement missed index assignment).

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

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.