Split up rundir configuration in two; move stretched grid to supplements

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

docs/source/index.rst

@@ -55,9 +55,10 @@ with Spack, as well as how to use Spack to install GCHP's dependencies if needed
    user-guide/rundir-init.rst
    user-guide/getting-input-data.rst
    user-guide/running.rst
+   user-guide/configuration-files.rst
    user-guide/rundir-config.rst
    user-guide/output_files.rst
-   supplement/plotting-output.rst
+   user-guide/plotting-output.rst
 
 .. toctree::
    :maxdepth: 1
@@ -67,7 +68,7 @@ with Spack, as well as how to use Spack to install GCHP's dependencies if needed
    supplement/setting-up-aws-parallelcluster.rst
    supplement/caching-input-data.rst
    supplement/containers.rst
-   stretched-grid.rst
+   supplement/stretched-grid.rst
    supplement/satellite-overpass.rst
    geos-chem-shared-docs/supplemental-guides/bashdatacatalog.rst
    geos-chem-shared-docs/supplemental-guides/using-kpp-with-gc.rst

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

@@ -0,0 +1,68 @@
+
+
+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`.
+
+.. contents:: Table of contents
+    :depth: 4
+
+---------------------------------------------------------------------------------------------------
+
+Configuration files
+-------------------
+
+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:
+
+.. toctree::
+   :maxdepth: 1
+
+   config-files/GCHP_rc.rst
+   config-files/CAP_rc.rst
+   config-files/ExtData_rc.rst
+   config-files/geoschem_config_yml.rst
+   config-files/HEMCO_Config_rc.rst
+   config-files/input_nml.rst
+   config-files/logging_yml.rst
+   config-files/HISTORY_rc.rst
+   config-files/HEMCO_Diagn_rc.rst
+
+The run directory also includes bash script :file:`setCommonRunningSetting.sh` to edit commonly changed run-time settings from one place, making the run configuration process for GCHP more manageable.
+
+
+.. _setcommonrunsettings_sh:
+
+: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.
+
+.. _GCHP_rc:
+
+: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).
+
+: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`.      
+
+: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`.
+
+: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`.
+
+:file:`HISTORY.rc`
+   Config file for the MAPL History component. 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`.
+

docs/source/user-guide/downloading.rst

@@ -1,7 +1,7 @@
 .. _downloading_gchp:
 
-Download to model
-=================
+Download the model
+==================
 
 The GCHP source code is hosted at https://github.com/geoschem/GCHP. Clone 
 the repository: