updated creating a run directory and the glossary

docs/source/reference/glossary.rst

@@ -7,9 +7,21 @@ Terminology
 .. glossary::
    :sorted:
 
+   absolute path
+      The full path to a file, e.g., :file:`/example/foo/bar.txt`. An absolute path
+      should always start with :literal:`/`. As opposed to a :term:`relative path`.
+
+   relative path
+      The path to a file relative to the current working directory. For example, the relative path to
+      :file:`/example/foo/bar.txt` if your current working directory is :file:`/example` is :file:`foo/bar.txt`.
+      As opposed to an :term:`absolute path`.
+
    compile
       Generating an executable program from source code (which is in a plain-text format).
 
+   checkpoint file
+      See :term:`restart file`.
+
    build
       See :term:`compile`.
 
@@ -18,21 +30,22 @@ Terminology
       module files, and libraries are stored.
 
    run directory
-      A directory that stores a GEOS-Chem simulation. This directory contains configuration files, the simulations
-      ouptut, and sometimes input files like :term:`restart files <restart file>`.
+      The working directory for a GEOS-Chem simulation. A run directory houses the simulation's configuration 
+      files, the output directory (:file:`OutputDir`), and input files/links such as :term:`restart files <restart file>`
+      or input data directories.
 
    restart file
-      A NetCDF file with initial conditions for a simulation.
+      A NetCDF file with initial conditions for a simulation. Also called a :term:`checkpoint file` in GCHP.
 
    target face
       The face of a stretched-grid that is refined. The target face is centered on the target point.
 
    stretched-grid
       A cubed-sphere grid that is "stretched" to enhance the grid resolution in a region.
 
-   gridded-component
+   gridded component
       A formal model component. MAPL organizes model components with a `tree structure <https://en.wikipedia.org/wiki/Tree_structure>`_,
       and facilitates component interconnections.
 
    HISTORY
-      The MAPL :term:`gridded-component` that handles model output. All GCHP output diagnostics are facilitated by HISTORY.
+      The MAPL :term:`gridded component` that handles model output. All GCHP output diagnostics are facilitated by HISTORY.

docs/source/user-guide/rundir-init.rst

@@ -2,21 +2,34 @@
 Creating a Run Directory
 ========================
 
-GCHP run directories are created from within the source code.
-A new run directory should be created for each different version of GEOS-Chem you use. 
-Git version information is logged to file :file:`rundir.version` within the run directory upon creation.
-
-To create a run directory, navigate to the :file:`run/` subdirectory of the source code and execute shell script :file:`createRunDir.sh`.
+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.
+The gist of creating a run directory is simple: navigate to the :file:`run/` subdirectory, run :file:`./createRunDir.sh`,
+and answer the prompts:
 
 .. code-block:: console
 
    gcuser:~$ cd Code.GCHP/run
-   gcuser:~/Code.GCHP/run$
+   gcuser:~/Code.GCHP/run$ ./createRunDir.sh
+   ... <answer the prompts> ...
+   
+.. important::
+   Use :term:`absolute paths <absolute path>` when responding to prompts.
+
+Create a run directory. If you are unsure what a prompt is asking, see their explanations below, or ask a question 
+on GitHub. After creating a run directory, you can move on to the next section.
+
+-------------------------------------------------------------------------------------------
+
+.. _create_rundir_prompts:
+
+Explanations of Prompts
+-----------------------
 
-During the course of script execution you will be asked a series of questions:
+Below are detailed explanations of the prompts in :file:`./createRunDir.sh`.
 
 Enter ExtData path
-------------------
+^^^^^^^^^^^^^^^^^^
 
 The first time you create a GCHP run directory on your system you will be prompted for a path to GEOS-Chem shared data directories. 
 The path should include the name of your :file:`ExtData/` directory and should not contain symbolic links. 
@@ -31,7 +44,7 @@ When creating additional run directories you will only be prompted again if the
    -----------------------------------------------------------
 
 Choose a simulation type
-------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^
 
 Enter the integer number that is next to the simulation type you want to use.
 
@@ -60,7 +73,7 @@ If creating a full chemistry run directory you will be given additional options.
      8. RRTMG
 
 Choose meteorology source
--------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Enter the integer number that is next to the input meteorology source you would like to use.
 
@@ -73,7 +86,7 @@ Enter the integer number that is next to the input meteorology source you would
      2. GEOS-FP
 
 Enter run directory path
-------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^
 
 Enter the target path where the run directory will be stored. You will be prompted to enter a new path if the one you enter does not exist.
 
@@ -84,7 +97,7 @@ Enter the target path where the run directory will be stored. You will be prompt
    -----------------------------------------------------------
 
 Enter run directory name
-------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^
 
 Enter the run directory name, or accept the default. You will be prompted for a new name if a run directory of the same name already exists at the target path.
 
@@ -95,7 +108,7 @@ Enter the run directory name, or accept the default. You will be prompted for a
    -----------------------------------------------------------
 
 Enable version control (optional)
----------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Enter whether you would like your run directory tracked with git version control. 
 With version control you can keep track of exactly what you changed relative to the original settings.