Fix memory allocation issues related to API usage (setup => cleanup but no simulate) as detailed in Issue #9.

sPuReMD: add QMMM library interface for external codes (e.g., Amber). Rework file I/O parsing to jive with multiple consecutive simulation code changes. Improve file parser error checking (numeric types). Other code clean-up.

sPuReMD: finalize sPuReMD multiple consecutive simulation code (for integration with other codebases).

Tools: add PuReMD custom geometry replication to geo_tool.py. Remove older awk scripts. Fix issue with silica 6000 atom PDB file (CRYST1 lines not 70 characters).

Tools: update run_sim.py to generate more robust Slurm and Torque/PBS job scripts with the MPI+CUDA code (added extra option for specifying additional flags to be used with the command used to invoking the mpi+x code).

Tools: fix geometry file extension auto-detection for run_md_custom. Add missing restart-related control file keywords.

Tools: fix geo_format for run_md_custom (geo file is mandatory, so the file type extension should always happen).

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

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

sPuReMD: small updates to Python wrapper (data structure changes). Fix issue with system energies not being computed for step 0 with the wrapper.

PuReMD-old: fix issue where nonbonded time was incorrect when energy_update_freq > 1. Update tools/run_sim.py to include both total simulation time and mean time per step.

PuReMD-old: increase precision in log file to 4 decimal places for select fields. Merge MPI log parsing logic.

PuReMD-old: back-port run_sim.py from master branch. Update control file parsing to ignore sPuReMD/PG-PuReMD options.

sPuReMD: add missing header files when distributing (make dist). Fix OpenMP bug with ACKS2 geometry-dependent force contribution. Fix small OpenMP compilation issue. Update tools/run_sim.py to respect geo_format parameter and infer if not present for md_run_custom.