Moving plotting output section to user guide and clean up user guide …

…names Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
geoschem · Jun 22, 2022 · 89cc57d · 89cc57d
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Showing 9 changed files with 17 additions and 22 deletions.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -57,6 +57,7 @@ with Spack, as well as how to use Spack to install GCHP's dependencies if needed
    user-guide/running.rst
    user-guide/rundir-config.rst
    user-guide/output_files.rst
+   supplement/plotting-output.rst
 
 .. toctree::
    :maxdepth: 1
@@ -66,7 +67,6 @@ 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
-   supplement/plotting-output.rst
    stretched-grid.rst
    supplement/satellite-overpass.rst
    geos-chem-shared-docs/supplemental-guides/bashdatacatalog.rst

diff --git a/docs/source/user-guide/compiling.rst b/docs/source/user-guide/compiling.rst
@@ -11,8 +11,8 @@
 
 .. _building_gchp:
 
-Compiling GCHP
-==============
+Compile
+=======
 
 There are three steps to building GCHP. The first is configuring your build, which is done with :program:`cmake`; 
 the second step is compiling, which is done with :program:`make`. The third step is install, which is also done with :program:`make`.

diff --git a/docs/source/user-guide/downloading.rst b/docs/source/user-guide/downloading.rst
@@ -1,7 +1,7 @@
 .. _downloading_gchp:
 
-Downloading GCHP
-================
+Download to model
+=================
 
 The GCHP source code is hosted at https://github.com/geoschem/GCHP. Clone 
 the repository:

diff --git a/docs/source/user-guide/getting-input-data.rst b/docs/source/user-guide/getting-input-data.rst
@@ -1,7 +1,7 @@
 .. _downloading_input_data:
 
-Downloading Input Data
-======================
+Download Input Data
+===================
 
 Input data for GEOS-Chem is available at http://geoschemdata.wustl.edu/ExtData/.
 

diff --git a/docs/source/user-guide/output_files.rst b/docs/source/user-guide/output_files.rst
@@ -6,8 +6,7 @@ A successful GCHP run produces three categories of output files: diagnostics, re
 .. note::
    It is important to be aware that GCHP 3D data files in this version of GCHP have two different vertical dimension conventions. Restart files and Emissions diagnostic files are defined with top-of-atmospheric level equal to 1. All other data files, meaning all diagnostic files that are not Emissions collections, are defined with surface level equal to 1. This means files may be vertically flipped relative to each other. This should be taken into account when doing data visualization and analysis using these files.
 
-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`
    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. 
@@ -39,9 +38,3 @@ Descriptions
 :file:`warnings_and_errors.log`
    This file is empty and can be ignored.
 
-Data visualization and post-processing
---------------------------------------
-
-With the exception of the restart file, all GCHP output netCDF files may be viewed with Panoply software freely available from NASA GISS. In addition, the GEOS-Chem python package GCPy is fully functional with GCHP output files. 
-
-
diff --git a/docs/source/supplement/plotting-output.rst → docs/source/user-guide/plotting-output.rst b/docs/source/supplement/plotting-output.rst → docs/source/user-guide/plotting-output.rst
@@ -2,6 +2,8 @@
 Plotting GCHP Output
 ====================
 
+With the exception of the restart file, all GCHP output netCDF files may be viewed with Panoply software freely available from NASA GISS. In addition, python works very well with all GCHP output.
+
 Panoply
 -------
 
@@ -73,4 +75,4 @@ Here is a basic example of plotting cubed-sphere data:
 .. note:: 
 
    The grid-box corners should be used with :code:`pcolormesh()` because the grid-boxes are not regular (it's a curvilinear grid).
-   This is why we use :code:`corner_lats` and :code:`corner_lons` in the example above.
+   This is why we use :code:`corner_lats` and :code:`corner_lons` in the example above.
diff --git a/docs/source/user-guide/rundir-config.rst b/docs/source/user-guide/rundir-config.rst
@@ -1,7 +1,7 @@
 
 
-Run Directory Configuration
-===========================
+Configure a run
+===============
 
 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`. Use the rest of this guide to get acquainted with the configuration files and hone in on what to change based on what you would like to do.
 

diff --git a/docs/source/user-guide/rundir-init.rst b/docs/source/user-guide/rundir-init.rst
@@ -1,7 +1,7 @@
 .. _creating_a_run_directory:
 
-Creating a Run Directory
-========================
+Create a Run Directory
+======================
 
 Run directories are created with the :file:`createRunDir.sh` script in the :file:`run/` subdirectory of the source code.
 Run directories are version-specific, so you need to create new run directories for every GEOS-Chem version.

diff --git a/docs/source/user-guide/running.rst b/docs/source/user-guide/running.rst
@@ -1,8 +1,8 @@
 
 .. _running_gchp:
 
-Running GCHP
-============
+Run the model
+=============
 
 .. note::
    Another useful resource for instructions on running GCHP is our `YouTube tutorial <https://www.youtube.com/watch?v=K6frcfCjpds>`_.