GEOS-Chem v11-01 Online User's Guide

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1. Introduction

1.1 Overview

GEOS-Chem Community Mission: to advance understanding of human and natural influences on the environment
through a comprehensive, state-of-the-science, readily accessible global model of atmospheric composition.

GEOS-Chem is a global 3-D chemical transport model (CTM) for atmospheric composition driven by meteorological input from the Goddard Earth Observing System (GEOS) of the NASA Global Modeling Assimilation Office (GMAO). It is applied by research groups around the world to a wide range of atmospheric composition problems. Scientific direction of the model is provided by the GEOS-Chem Steeting Committee and by User Working Groups. The model is managed by the GEOS-Chem Support Team, based at Harvard University and Dalhousie University.

This User's Guide provides information and instructions for installing and running GEOS-Chem v11-01. Much of the GEOS-Chem documentation has been moved to the GEOS-Chem online wiki located at http://wiki.geos-chem.org/. Wiki hyperlinks are provided throughout this guide directing you to where you can find in-depth information on different GEOS-Chem topics. We encourage you to explore the GEOS-Chem wiki to supplement the information provided in this User's Guide and to access the most up-to-date information available for GEOS-Chem. If you are new to GEOS-Chem, please read the GEOS-Chem welcome letter for new users as well as the GEOS-Chem Overview for a brief description of GEOS-Chem and how it is managed.

This User's Guide is arranged as follows:

Chapter Description
1. Introduction (This page) Provides a brief overview of GEOS-Chem v11-01 and guidelines for how to be an active and responsible participant in the GEOS-Chem community.
2. Requirements for Installing GEOS-Chem

Lists required software packages that you need to run GEOS-Chem.

3. The NetCDF Library Describes how to load the netCDF library on your system.
4. The GEOS-Chem Shared Data Directories Describes how to download the shared data directories for the emissions and meteorology data that drive GEOS-Chem simulations.

5. The GEOS-Chem Source Code Directory

Describes how to download the GEOS-Chem source code.
6. The GEOS-Chem Run Directories Describes how to generate run directories for the various GEOS-Chem simulations and the input and output files of GEOS-Chem.

7. Compiling GEOS-Chem

Describes how to compile the GEOS-Chem source code into an executable file.

8. Coding and Debugging

Lists resources for writing efficient code and for debugging GEOS-Chem.
9. GEOS-Chem Components Describes the various components that make up GEOS-Chem (e.g. transport, chemistry).
10. GEOS-Chem Species Describes the GEOS-Chem species that are used in each type of simulation and how you can add new species to an existing simulation.

11. Meteorological Fields

Describes the meteorological data fields used by GEOS-Chem.
12. Horizontal and Vertical Grids Describes the horizontal and vertical grids used by GEOS-Chem.
13. Diagnostics Describes the diagnostics generated by GEOS-Chem.
14. GEOS-Chem Reference Contains links to the reference guides that are automatically generated from the GEOS-Chem source code and the GEOS-Chem coding style guide.
15. GEOS-Chem Version History Lists new features in each GEOS-Chem version.
16. High Performance GEOS-Chem Describes the development of an MPI implementation for GEOS-Chem.

1.2 Participation in the GEOS-Chem User Community

Development of the GEOS-Chem model and its adjoint is a grass-roots activity by individual scientists pursuing their own research interests and sharing their work for the benefit of all. Being a GEOS-Chem user therefore comes with expectations and responsibilities. Please read and follow the guidelines below to help us maintain an active and vibrant GEOS-Chem community.

  1. Send an email to geos-chem-support [at] as.harvard.edu containing a paragraph describing how you and the other members of your research group plan to use GEOS-Chem. We will add this to the GEOS-Chem People and Projects web page. Registering your group helps us to accurately track how many research groups are using GEOS-Chem.

  2. Subscribe to the general GEOS-Chem email list and to an email list of one or more Working Groups. The general GEOS-Chem email list is where we make announcements about new model releases, bugs and fixes, and other information of interest to the entire GEOS-Chem community. In addition, each GEOS-Chem Working Group has its own email list that group members use to discuss various aspects of model development and validation. Please see the Subscribing to the GEOS-Chem email lists wiki page for instructions.

  3. We encourage you to join a Working Group that is most relevant to your area of research. The Working Groups foster communication and collaboration between GEOS-Chem users and they identify priorities for model development to the GEOS-Chem Steering Committee. Please take a moment to introduce yourself to any relevant Working Group via email.

  4. Adhere to the list of best practices. In particular, if you discover a problem (e.g. bugs, missing files, numerical issues, etc.), please alert the GEOS-Chem Support Team right away. Other GEOS-Chem users will most certainly benefit from your discovery!

  5. We encourage you to send us your timing results from a 7-day time test. This will allow us to keep a list of how the model is performing across several different platform/compiler combinations. We will post this information on the GEOS-Chem performance wiki page.

  6. Please read the GEOS-Chem Credits and References page containing guidelines for giving appropriate credit to developers through co-authorship or citation. You may also refer to the Narrative Description of the GEOS-Chem Model wiki page for assistance with correctly citing relevant model components of the current standard version of GEOS-Chem in your publications.

1.3 New features in v11-01

See the following pages for a list of new features in GEOS-Chem v11-01 and for details on the 1-month and 1-year benchmark simulations used to validate this version.

1.4 Bugs and Technical Issues Fixed in v11-01

GEOS-Chem v11-01 contains fixes and for several bugs and technical issues. If you have been using an older version of GEOS-Chem (e.g. v10-01, v9-02), please check this list to see if any outstanding issues have since been resolved.

A few issues still remain unresolved (or cannot be resolved due to compiler bugs, etc.). For more information, please see:

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