GEOS-Chem v10-01 Online User's Guide
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Welcome to the international GEOS-Chem user community! The GEOS-Chem model is a global three-dimensional model of tropospheric chemistry driven by assimilated meteorological observations from the Goddard Earth Observing System (GEOS) of the NASA Global Modeling Assimilation Office (GMAO). GEOS-Chem is being developed by personnel at Harvard University and other institutions in the Americas, Europe, and Asia. and is actively supported by the GEOS-Chem Support Team.
In this GEOS-Chem User's Guide you will find information and resources necessary for using GEOS-Chem v10-01. Much of the GEOS-Chem documentation has recently migrated to the GEOS-Chem online wiki located at http://wiki.geos-chem.org/. Wiki hyperlinks are provided throughout the User's 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 v10-01 as well as past versions.
The GEOS-Chem v10-01 Online User's Guide is arranged as follows:
Chapter 1: Introduction provides a brief overview of GEOS-Chem v10-01, a list of basic computing requirements, and guidelines for how to be an active and responsible participant in the GEOS-Chem community.
Chapter 2: Installation gives installation instructions for required software, including how to download the GEOS-Chem source code directory, run directories, shared data directories, and netCDF libraries.
Chapter 3: Compilation describes the makefile structure of GEOS-Chem and covers how to compile the GEOS-Chem source code into an executable.
Chapter 4: Data Directories provides resources for data input files, such as the met fields and emissions inventories, contained in the shared data directories.
Chapter 5: Run Directories details the contents of GEOS-Chem run directories required for running a GEOS-Chem simulation.
Chapter 6: Running GEOS-Chem gives instruction on how to set up and run a GEOS-Chem simulation and provides resources for trouble-shooting issues.
Chapter 7: Coding and Debugging describes Fortran coding best practices, parallelization, debugging, and Git verson control software.
Chapter 8: GEOS-Chem Reference Guides contains links to software-generated GEOS-Chem reference guides and gives instruction on how to generate your own GEOS-Chem documentation.
GEOS-Chem began as a merging of Mian Chin's GEOS-CTM code with the emissions, dry deposition, and chemistry routines from the old Harvard-GISS 9-layer model. Since then, we have added many updates and improvements to GEOS-Chem. The model now uses detailed inventories for fossil fuel, biomass burning, biofuel burning, biogenic, and aerosol emissions. GEOS-Chem includes state-of-the-art transport (TPCORE) and photolysis (FAST-JX) routines, as well as the SMVGEAR II and KPP chemistry solver packages. Detailed aerosol microphysical simulations using GEOS-Chem may performed with the TOMAS aerosol microphysics code or the APM aerosol microphysics code.
GEOS-Chem has been parallelized using the OpenMP compiler directives, and it scales well when running across multiple CPU's on shared-memory machines. We are currently building a High-Performance Computing version of GEOS-Chem in order to take advantage of distributed memory architectures and MPI parallelization.
GEOS-Chem has kept pace with changes in the meteorological data products being produced by GMAO. You can perform GEOS-Chem simulations with GMAO's GEOS-4, GEOS-5, MERRA, and GEOS-FP data products on 1° x 1.25°, 2° x 2.5° or 4° x 5° global grids. GEOS-Chem has become a popular tool for regional-scale modeling and you can perform nested-grid simulations (one-way nesting) using GEOS-5 at 0.5° x 0.666° horizontal resolution for the following regions: China, North America, and Europe. Nested-grid simuations may now also be performed using GEOS-FP at 0.25° x 0.3125° horizontal resolution over the following regions: China, North America, Europe, and SE Asia.
Those of you who are part of the GCAP project can use GEOS-Chem to perform simulations using meteorology from the GISS-II GCM (23 layers, 4° x 5° horizontal grid). You can select from several IPCC future-climate scenarios.
See Appendix 10 of this User's Guide for a complete list of features that were introduced into GEOS-Chem v10-01. Detailed information about this version can also be found on the GEOS-Chem v10-01 wiki page.
Starting with version GEOS-Chem v9-01-02, we have updated our benchmarking procedure. For details on the 1-month and 1-year benchmarks, please see the GEOS-Chem Benchmark Simulations wiki page.
Minimum system requirements for GEOS-Chem are outlined on the Minimum system requirements for GEOS-Chem wiki page. Below are quick links to subsections of that wiki page for easy reference:
If you are not sure what hardware or software is available to you, then please check with your local IT department. For the most up-to-date information regarding GEOS-Chem performance on specific platforms and operating systems, please see the GEOS-Chem supported platforms and compilers wiki page.
In order to use GEOS-Chem, it is helpful to have general experience with the following:
For resources about these topics, including tutorials, please see the GEOS-Chem programming resources wiki page and Version control with Git wiki page.
1.3 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.
Please send an email to geos-chem-support[at]g.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 our GEOS-Chem People and Projects web page. Registering your group helps us to accurately track how many research groups are using GEOS-Chem.
Please subscribe to the general GEOS-Chem email list and to an email list of one or more Working Groups. The general GEOS-Chem listserv 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 listserv where group members can discuss various aspects of model development and validation among themselves. Please see our Subscribing to the GEOS-Chem email lists wiki page for instructions.
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.
Please adhere to our 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!
We encourage you to send us your timing results from a 1-month benchmark simulation. 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 supported platforms and compilers wiki page.
Please read our GEOS-Chem Credits and References wiki 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.