molssi-seamm/lammps_step: Bugfix: MDI stress not calculated and error catching

MDI requires an option in fix mdi/qm for it to request the virial; it is not automatic for e.g. NPT calculations. The code now adds the keywords for periodic calculations but not molecular ones. Added code to catch errors in the analysis of the GPU performance in cases where data is missing or cannot be interpreted correctly, so that calculation continues without error. Fixed an issue returning the stdout and stderr from the LAMMPS/MDI calculation. LAMMPS logs to stdout and MDI to stderr to keep the streams separate.