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ReadTheDocs update: Add dry-run section to QuickStart guide
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docs/source/getting-started/quick-start.rst
- Added a section about using a dry-run simulation to download data
  to the GEOS-Chem Classic Quickstart Guide

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>
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yantosca committed Jul 10, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
## [Unreleased] - TBD
### Added
- ReadTheDocs update for for Cloud-J input parameter `num_levs_with_cloud`
- ReadTheDocs update: add section about using a dry-run simulation to Quickstart Guide

## [14.4.1] - 2024-06-28
### Fixed
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91 changes: 72 additions & 19 deletions docs/source/getting-started/quick-start.rst
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Expand Up @@ -110,8 +110,8 @@ time.

For demonstration purposes, we will use a full chemistry simulation
run directory with the default name (:file:`gc_merra2_4x5_fullchem`).
The steps to setup and run other types of GEOS-Chem simulations follow
the same pattern as the examples shown below.
The steps to setup and run other types of GEOS-Chem Classic
simulations follow the same pattern as the examples shown below.

.. attention::

Expand All @@ -125,14 +125,14 @@ the same pattern as the examples shown below.
.. _quick-load:

========================
3. Load your Environment
3. Load your environment
========================

Prior to building GEOS-Chem always make sure all libraries and
environment variables are loaded. An easy way to do this is to write
an :ref:`environment file <env>` and load that file every time you
work with GEOS-Chem. To make this extra easy you can create a
symbolic link to your environment file within your run directory or
Always make sure that all libraries and environment variables are
loaded prior to building GEOS-Chem Classic. An easy way to do this is
to write an :ref:`environment file <env>` and load that file every
time you work with GEOS-Chem. To make this extra easy you can create
a symbolic link to your environment file within your run directory or
for reference. For example, do the following in your new run
directory to have a handy link to the environment you plan on using.

Expand All @@ -154,12 +154,12 @@ run directory you can easily load your environment.
4. Configure your build
=======================

You may build GEOS-Chem from within the run directory or from anywhere
else on your system. But we recommend that you always build GEOS-Chem
from within the run directory. This is convenient because it keeps
all build files in close proximity to where you will run the model.
For this purpose the GEOS-Chem run directory includes a build
directory called :file:`build/`.
You may build GEOS-Chem Classic from within the run directory or from
anywhere else on your system. But we recommend that you always build
GEOS-Chem Classic from within the run directory. This is convenient
because it keeps all build files in close proximity to where you will
run the model. For this purpose the GEOS-Chem run directory includes a
build directory called :file:`build/`.

First, navigate to the :file:`build/` folder of your run directory:

Expand Down Expand Up @@ -284,14 +284,67 @@ Please see our :ref:`customguide` Supplemental Guide to learn how you
can customize your simulation by activating alternate science options
in your simulations.

Once you are satisfied that your simulation settings are correct, you
may proceed to run GEOS-Chem.
.. _quick-dry-download:

======================
7. Download input data
======================

Before you can run your GEOS-Chem Classic simulation, you must first
:ref:`download the required input data <data>`. These data include:

- Meteorological fields (e.g. GEOS-FP, MERRA-2, GEOS-IT, or GCAP2)
- Emissions inventories
- Inputs for GEOS-Chem modules (e.g. Cloud-J)

.. tip::

If your institution has several GEOS-Chem users, then someone may
have already downloaded these data for you. If this is the case,
you may :ref:`start running your your GEOS-Chem Classic simulation
<quick-run>`.

The easiest way to download data is to perform a :ref:`dry-run
simulation <dry-run>`. This is a GEOS-Chem Classic simulation that
steps through time, but does not perform computations or read data
files from disk. Instead, the dry-run simulation prints a list of all
data files that the simulation would have read.

To start a dry-run simulation, type this command:

.. code-block:: console
$ ./gcclassic --dryrun | tee log.dryrun
This will generate the :file:`log.dryrun` log file, which contains the
list of data files to be downloaded.

Once the dry-run simulation has finished, use the
:file:`download_data.py` file (included in your run directory) to
:ref:`download the required data <dry-run-download>`. Type:

.. code-block:: console
$ ./download_data.py log.dryrun --washu
This will download data from the :option:`WashU` data portal. You
may also download from the :option:`Amazon` or :option:`Rochester`
data portals.

.. note::

Depending on your system, you might have to activate a Conda or
Mamba environment containing a version of Python before running the
:file:`download.data.py` script. Ask your sysadmin.

For more information about dry-run simulations, please see our
:ref:`dry-run` chapter.

.. _quick-run:

========================
7. Run GEOS-Chem Classic
========================
======================
8. Run your simulation
======================

If you used an :ref:`environment file <env>` to load software
libraries prior to building GEOS-Chem then you should load that file
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