Better format the output files list

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

docs/source/user-guide/output_files.rst

@@ -13,55 +13,66 @@ File descriptions
 
 Below is a summary of all GCHP output files that you may encounter depending on your run directory configuration.
 
-:file:`gchp.YYYYMMSS_HHmmSSz.log`
+.. option:: gchp.YYYYMMSS_HHmmSSz.log
+
    Standard output log file of GCHP, including both GEOS-Chem and HEMCO. 
    The date in the filename is the start date of the simulation. 
    Using this file is technically optional since it appears only in the run script. 
    However, the advantage of sending GCHP standard output to this file is that the logs of consecutive runs will not be over-written due to the date in the filename. 
    Note that the file contains HEMCO log information as well as GEOS-Chem. 
    Unlike in GEOS-Chem Classic there is no :file:`HEMCO.log` in GCHP. 
 
-:file:`batch job file, e.g. slurm-jobid.out`
+.. option:: batch job file, e.g. slurm-jobid.out
+
    If you use a job scheduler to submit GCHP as a batch job then you will have a job log file. 
    This file will contain output from your job script unless sent to a different file. 
    If your run crashes then the MPI error messages and error traceback will also appear in this file.
 
-:file:`allPES.log`
+.. option:: `allPES.log
+
    GCHP logging output based on configuration in :file:`logging.yml`. 
    Treat this file as a debugging tool to help diagnose problems in MAPL, particularly the ExtData component of the model which handles input reading and regridding.
 
-:file:`logfile.000000.out`
+.. option:: logfile.000000.out
+
    Log file for advection. It includes information such as the domain stack size, stretched grid factors, and FV3 parameters used in the run.
 
-:file:`cap_restart`
+.. option:: cap_restart
+
    This file is both input and output. As an input file it contains the simulation start date. 
    After a successful run the content of the file is updated to the simulation end date. 
    As an output file it is therefore the input file for the next run if running GCHP simulations consecutively in time.
 
-:file:`Restarts/GEOSChem.Restart.YYYYMMDD_HHmmSSz.cN.nc4`
+.. option:: Restarts/GEOSChem.Restart.YYYYMMDD_HHmmSSz.cN.nc4
+
    GCHP restart file output at the end of the run. 
    This file is actually the GCHP end-of-run checkpoint file that is moved and renamed as part of the run script. 
    Unless including the code to do that in your run script you will instead get :file:`gcchem_internal_checkpoint` in the main run directory. 
    Moving and renaming is a better option because (1) it includes the datetime to prevent overwriting upon consecutive runs, (2) it enables using the :file:`gchp_restart.nc4` symbolic link in the main run directory to automatically point to the correct restart file based on start date and grid resolution, and (3) it minimizes clutter in the run directory. 
    Please note that the vertical level dimension in all GCHP restart files is positive down, meaning level 1 is top-of-atmosphere.
 
-:file:`gcchem_internal_checkpoint.YYYYMMDD_HHmmz.nc4`
+.. option:: gcchem_internal_checkpoint.YYYYMMDD_HHmmz.nc4
+
    Optional restart files output mid-run. In order to generate these you must configure the run directory to output with a specific frequency that is less than the duration of your run. Note that unlike the end-of-run restart file, these files are not copied to :file:`Restarts` in your run script and are not renamed.
 
-:file:`OutputDir/GEOSChem.HistoryCollectionName.YYYYMMDD_HHmmz.nc4`
+.. option:: OutputDir/GEOSChem.HistoryCollectionName.YYYYMMDD_HHmmz.nc4
+
    GCHP diagnostic data files. Each file contains the collection name configured in :file:`HISTORY.rc` and the datetime of the first data in the file. For time-averaged data files the datetime is the start of the averaging period. 
    Please note that the vertical level dimension in GCHP diagnostics files is collection-dependent. 
    Data are positive down, meaning level 1 is top-of-atmosphere, for the Emissions collection. 
    All other collections are positive up, meaning level 1 is surface.
 
-:file:`HistoryCollectionName.rcx`
-   Summary of settings used to generate data in each diagnostic collection file that is output.
+.. option:: HistoryCollectionName.rcx
+
+   Summary of settings in :file:`HISTORY.rc` per collection.
+
+.. option:: EGRESS
 
-:file:`EGRESS`
    This file is empty and can be ignored. It is an artifact of the MAPL software used in GCHP.
 
-:file:`warnings_and_errors.log`
-   This file is empty and can be ignored.
+.. option:: warnings_and_errors.log
+
+   This file is empty and can be ignored. It is an artifact of configuration in :file:`logging.yml`.
 
 Memory
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