Update output date and config file tables

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

docs/source/user-guide/configuration-files.rst

@@ -6,7 +6,7 @@ Configuration files
 All GCHP run directories have default simulation-specific run-time settings that are set in the configuration files. The many configuration files in GCHP can be overwhelming.
 However, you should be able to accomplish most if not all of what you wish to configure from one place in :file:`setCommonRunSettings.sh`. That file is a bash script used to configure settings in other files from one place.
 
-This section gives an overview of all run directory configuration files used at run-time in GCHP. More information about each file can be found in the below list of links for core configuration files:
+This section gives an overview of all run directory configuration files used at run-time in GCHP. Detailed information about each file can be found in the below list of links for core configuration files:
 
 .. toctree::
    :maxdepth: 1
@@ -21,36 +21,50 @@ This section gives an overview of all run directory configuration files used at
    config-files/HISTORY_rc.rst
    config-files/HEMCO_Diagn_rc.rst
 
-:file:`setCommonRunSettings.sh`
 
-   This file is a bash script that includes commonly changed run settings. It makes it easier to manage configuring GCHP since settings can be changed from one file rather than across multiple configuration files. When this file is executed it updates settings in other configuration files, overwriting what is there. Please get very familiar with the options in :file:`setCommonRunSettings.sh` and be conscientious about not updating the same setting elsewhere.
+For a quick overview of all configuration files read the table below.
 
-.. _GCHP_rc:
+:file:`setCommonRunSettings.sh`
+   This file is a bash script that includes commonly changed run settings. 
+   It makes it easier to manage configuring GCHP since settings can be changed from one file rather than across multiple configuration files. 
+   When this file is executed it updates settings in other configuration files, overwriting what is there. 
+   Please get very familiar with the options in :file:`setCommonRunSettings.sh` and be conscientious about not updating the same setting elsewhere.
 
 :file:`GCHP.rc`
    Controls high-level aspects of the simulation, including grid type and resolution, core distribution, stretched-grid parameters, timesteps, and restart filename.
 
 :file:`CAP.rc`
-   Controls parameters used by the highest level gridded component (CAP). This includes simulation run time information, name of the Root gridded component (GCHP), config filenames for Root and History, and toggles for certain MAPL logging utilities (timers, memory, and import/export name printing).
+   Controls parameters used by the highest level gridded component (CAP). 
+   This includes simulation run time information, name of the Root gridded component (GCHP), config filenames for Root and History, and toggles for certain MAPL logging utilities (timers, memory, and import/export name printing).
 
 :file:`ExtData.rc`
-   Config file for the MAPL ExtData component. Specifies input variable information, including name, regridding method, read frequency, offset, scaling, and file path. All GCHP imports must be specified in this file. Toggles at the top of the file enable MAPL ExtData debug prints and using most recent year if current year of data is unavailable. Default values may be used by specifying file path :file:`/dev/null`.      
+   Config file for the MAPL ExtData component. 
+   Specifies input variable information, including name, regridding method, read frequency, offset, scaling, and file path. All GCHP imports must be specified in this file. 
+   Toggles at the top of the file enable MAPL ExtData debug prints and using most recent year if current year of data is unavailable. 
+   Default values may be used by specifying file path :file:`/dev/null`.      
 
 :file:`geoschem_config.yml`
    Primary config file for GEOS-Chem. Same file format as in GEOS-Chem Classic but containing only options relevant to GCHP.
 
 :file:`HEMCO_Config.rc`
-   Contains emissions information used by HEMCO. Same function as in GEOS-Chem Classic except only HEMCO name, species, scale IDs, category, and hierarchy are used. Diagnostic frequency, file path, read frequency, and units are ignored, and are instead stored in GCHP config file :file:`ExtData.rc`. All HEMCO variables listed in :file:`HEMCO_Config.rc` for enabled emissions must also have an entry in :file:`ExtData.rc`.
+   Contains emissions information used by HEMCO. 
+   Same function as in GEOS-Chem Classic except only HEMCO name, species, scale IDs, category, and hierarchy are used. 
+   Diagnostic frequency, file path, read frequency, and units are ignored, and are instead stored in GCHP config file :file:`ExtData.rc`. 
+   All HEMCO variables listed in :file:`HEMCO_Config.rc` for enabled emissions must also have an entry in :file:`ExtData.rc`.
 
 :file:`input.nml`
    Namelist used in advection for domain stack size and stretched grid parameters.
 
 :file:`logging.yml`
-   Config file for the NASA pFlogger package included in GCHP for logging. This package uses a hierarchy of loggers, such as info, warnings, error, and debug, to extract non-GEOS-Chem information about GCHP runs and print it to log file :file:`allPEs.log`.
+   Config file for the NASA pFlogger package included in GCHP for logging. 
+   This package uses a hierarchy of loggers, such as info, warnings, error, and debug, to extract non-GEOS-Chem information about GCHP runs and print it to log file :file:`allPEs.log`.
 
 :file:`HISTORY.rc`
-   Config file for the MAPL History component. Configures diagnostic output from GCHP.
+   Config file for the MAPL History component. 
+   It configures diagnostic output from GCHP.
 
 :file:`HEMCO_Diagn.rc`
-   Contains information mapping :file:`HISTORY.rc` diagnostic names to HEMCO containers. Same function as in GEOS-Chem Classic except that not all items in :file:`HEMCO_Diagn.rc` will be output; only emissions listed in :file:`HISTORY.rc` will be included in diagnostics. All GCHP diagnostics listed in :file:`HISTORY.rc` that start with Emis, Hco, or Inv must have a corresponding entry in :file:`HEMCO_Diagn.rc`.
+   Contains information mapping :file:`HISTORY.rc` diagnostic names to HEMCO containers. 
+   Same function as in GEOS-Chem Classic except that not all items in :file:`HEMCO_Diagn.rc` will be output; only emissions listed in :file:`HISTORY.rc` will be included in diagnostics. 
+   All GCHP diagnostics listed in :file:`HISTORY.rc` that start with Emis, Hco, or Inv must have a corresponding entry in :file:`HEMCO_Diagn.rc`.
 

docs/source/user-guide/output_files.rst

@@ -9,25 +9,41 @@ A successful GCHP run produces three categories of output files: diagnostics, re
 Below is a summary of all GCHP output files that you may encounter depending on your run directory configuration.
 
 :file:`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. 
+   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`
-   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.
+   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`
-   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.
+   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`
    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`
-   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.
+   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`
-   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.
+   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:`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.
+   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.