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.

PuReMD: begin EE and ACKS2 charge model implementation. Refactor charge solvers in order to enable optimizated communication for sparse matrix structure (specifically around SpMV operations). Other general refactoring.

Tools: add function to apply Gaussian noise to atomic positions in order to generate a new structure file.

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.