PG-PuReMD: fix host-device transfers for charge solver code (SpMV data transfer sizes). Remove unused code. Other general code clean-up.

PG-PuReMD: fix issue with divergent MPI_Reduce calls by multiple MPI processes (timing logging code). Add run-time MPI routine error checking. Fix issue with upper limit of hydrogen atoms allowed being hard-coded in GPU code (use dynamic memory allocation instead). Other code clean-up.

PG-PuReMD: clean-up MPI custom datatype initialization and error reporting. Avoid truncations in buffer size calculations. Other code clean-up.

sPuReMD: finalize corrections for pressure calculations. Change output units from GPa to ATMs. Other formatting changes.

PG-PuReMD: improve memory management around temporary storage space on both the host and device (i.e., scratch space).

PG-PuReMD: replace deprecated CUDA warp-level primitives with modern ones. Fix issue with modern GPU microarchitectures using incorrect code paths (post-Kepler). Other code clean-up.

PG-PuReMD: include missing header file in Automake make file (includes file in distribution tarball).

PG-PuReMD: revert to 1 thread per atom implementation in nonbonded energy and force calculations in order to correct issue with forces being incorrectly calculated (revisit 1 warp per atom implementation later). Disable charge matrix row-wise sorting. Other general code clean-up.

PG-PuReMD: corrections to van der Waals and Coulomb energies calculations (far neighbor list in full format, not half). Fix QEq charge matrix initialization (full format). Other refactoring and code clean-up.

PG-PuReMD: fix issue with SpMVs operations using incorrect row-wise bounds (end pointer incorrect in light of sparse_matrix struct 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.

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.