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    "# Helpful command line tools\n",
    "\n",
    "## Navigating the filesystem\n",
    "- `less FILENAME`: Show the contents of a text file\n",
    "    - Scroll up and down in file with arrow keys or page-up, page-down\n",
    "    - Exit by pressing `q`\n",
    "- `ls DIRECTORY`: List the contents of a directory\n",
    "- `cd DIRECTORY`: Change into directory `DIRECTORY`\n",
    "    - *Note*: Typing `cd` with no directory name given will change to your home directory\n",
    "- `cp FILENAME DESTINATION`: Copy a file from `FILENAME` to `DESTINATION`\n",
    "    - *Note*: To copy a directory you must include the `-r` flag. For example, `cp -r DIRECTORY DESTINATION`"
   ]
  },
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   "metadata": {},
   "source": [
    "## Running DOUAR jobs\n",
    "\n",
    "### Editing and running a new job\n",
    "To run a new simulation with DOUAR you should do the following:\n",
    "```bash\n",
    "cd\n",
    "cd douar/inputs\n",
    "cp OLDMODEL.txt NEWMODEL.txt\n",
    "nano NEWMODEL.txt\n",
    "```\n",
    "*(edit parameters)*\n",
    "```bash\n",
    "~/bin/submitdouar.sh -i ~/douar/inputs/NEWMODEL.txt -n 32\n",
    "```"
   ]
  },
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   "source": [
    "### Monitoring job status/cancelling a job\n",
    "\n",
    "- `squeue`: Show a list of models running on the geo-hpcc cluster\n",
    "- `scancel JOB_ID`: Cancel a job running on the cluster"
   ]
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   "source": [
    "### Postprocessing job output\n",
    "To create the `VTK` files for visualization in **ParaView**, you can do the following:\n",
    "\n",
    "```bash\n",
    "cd /globalscratch/introgm[N]/douar/NEWMODEL_yymmddhhmmss/OUT\n",
    "~/bin/process_outbin.sh -n NUM\n",
    "```\n",
    "\n",
    "*(tranfer* `.vtk` *files using WinSCP or scp)*\n",
    "\n",
    "*(Visualize data in ParaView)*\n",
    "\n",
    "where `[N]` in `introgm[N]` should be replaced with your user number and `NUM` is the frequency of VTK output to produce. For example, `~/bin/process_outbin.sh -n 5` would produce output for every 5th DOUAR time step."
   ]
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