working directory for FILE-IO files

[nathanfranklin]

Currently the working directory of where the input and output files is for lammps is the tmp directory. Maybe this should be the working directory or configured by the user.

[ahashibon]

how about a $SIMPHONY_RUNDIR or something similar as an environment variable setting where the jobs are run? Default could be something like $HOME/.simphony/WRAPPER(opt)/JOB_ID1 etc...