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<big>'''GEOS-Chem Wiki'''</big>
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|<p><font color="#FFFFFF" size="+3">'''GEOS-Chem Wiki'''</font></p>


The [http://acmg.seas.harvard.edu/geos/ GEOS–Chem model] is a global 3-D model of atmospheric composition driven by assimilated meteorological observations from the Goddard Earth Observing System (GEOS) of the [http://www.as.harvard.edu NASA Global Modeling and Assimilation Office]. It is applied by [http://acmg.seas.harvard.edu/geos/geos_people.html research groups around the world] to a wide range of atmospheric composition problems, Central management and support of the model is provided by the [http://acmg.seas.harvard.edu/index.html Atmospheric Chemistry Modeling Group at Harvard University.]
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This wiki is meant to facilitate communication between GEOS-Chem users and developers. If this is '''your first time here''', check out [[Features of the GEOS-Chem public wiki|the features page]]. If you would like to contribute to the wiki, please register as a user by clicking ''create account'' at the top right corner of this page.
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New information is continually being added to the wiki, so please check back here often, or even better, [[Features_of_the_GEOS-Chem_public_wiki#Let_the_GEOS-Chem_wiki_inform_you_of_recent_changes.21|subscribe to the recent changes' RSS feed]]: you will not miss a discussion!
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== General Information about GEOS-Chem ==
----


The links below provide more information about general GEOS-Chem topics.  
<p align="center"><big>'''GEOS-Chem Community Mission: to advance understanding of human and natural influences on the environment<br>through a comprehensive, state-of-the-science, readily accessible global model of atmospheric composition.'''</big></p>


=== Introduction and Overview ===
The [http://geos-chem.org GEOS–Chem model] is a global 3-D model of atmospheric composition driven by assimilated meteorological observations from the Goddard Earth Observing System (GEOS) of the [http://gmao.gsfc.nasa.gov/ NASA Global Modeling and Assimilation Office]. It is applied by [https://geoschem.github.io/geos-chem-people-projects-map/ research groups around the world] to a wide range of atmospheric composition problems. Central management and support of the model is provided by the [https://acmg.seas.harvard.edu/ Atmospheric Chemistry Modeling Group at Harvard University] and by the [https://sites.wustl.edu/acag/ Atmospheric Composition Analysis Group at Washington University].
* [[Features of the GEOS-Chem public wiki]]
* [[GEOS-Chem welcome letter for new users]]
* [http://acmg.seas.harvard.edu/geos/geos_overview.html GEOS-Chem Overview]
* [http://acmg.seas.harvard.edu/geos/geos_people.html GEOS-Chem People & Projects]
* [http://acmg.seas.harvard.edu/geos/word_pdf_docs/resources_guidelines_tips.pdf User Resources, Code Development Guidelines, and Debugging Tips]
* [[GEOS-Chem programming staff]]
* [[GEOS-Chem newsletters]]


=== Steering Committee and Working Groups ===
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* [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee]
** [[GEOS-Chem model development priorities]]
* [http://acmg.seas.harvard.edu/geos/geos_working_groups.html GEOS-Chem Working Groups]
** [[GEOS-Chem Adjoint|Adjoint Model and Data Assimilation Working Group]]
** [[Aerosols_overview:_projects_and_developments|Aerosols Working Group]]
** [[Carbon Gases and Organics Working Group]]
** [[Emissions Working Group]]
** [[Chemistry Issues|Oxidants and Chemistry Working Group]]
** [[Regional Air Quality Working Group]]


=== Getting Started with GEOS-Chem ===
{|border="1" width="925px" bordercolor="#000000" cellspacing="0" cellpadding="5"
* [[Minimum system requirements for GEOS-Chem]]
* [[GEOS-Chem supported platforms and compilers]]
* [[Downloading GEOS-Chem source code and data]]
* [[GEOS-Chem code development cycle]]
* [[GEOS-Chem programming resources]] (e.g. tutorials, user guides, etc.)
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_7.html GEOS-Chem Programming Style Guide]
* [[Running GEOS-Chem with TESTRUN]]


=== General Technical Information ===
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* [[Initial conditions for GEOS-Chem]]
|colspan="3" align="center" bgcolor="#CCCCCC"|'''<font size="+2">[[GEOS-Chem overview]]</font>'''
* [[GEOS-Chem Debugging Tips|Tips on how to debug GEOS-Chem effectively]]
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* [[Reporting GEOS-Chem bugs]]
|width="225px" align="center"|<font size="+2">[[GEOS-Chem versions|Past releases]]</font>
* [[Parallelizing GEOS-Chem]] with the OpenMP directives
|width="450px" align="center" bgcolor="#CCFFFF"|<font size="+2">[[GEOS-Chem 14.5.0|'''Current release: GEOS-Chem 14.5.0''']]</font>
* [[Common GEOS-Chem error messages]]
|width="225px" align="center"|<font size="+2">[[GEOS-Chem model development_priorities|Future releases]]</font>
* [http://acmg.seas.harvard.edu/geos/geos_search.html GEOS-Chem Search Engines]


== Code Developers' Forums ==
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These pages contain more specific information about coding issues, emissions, chemistry, met fields, version history, and other aspects of GEOS-Chem. GEOS-Chem users and developers should feel free to contribute to these pages and to initiate discussion on the various topics listed here.
== News ==
*02 Feb 2024: Read the [https://drive.google.com/file/d/1lUsMZkO0prJGc2eAR1hSxAlYlRooDwK5/view?usp=sharing GEOS-Chem Newsletter 2024, Issue #1]
*13 Aug 2024: [[GEOS-Chem 14.4.3]] is now available!
*03 Jul 2024: We have started migrating older content to the [[GEOS-Chem Wiki archives]].
*A [https://scholar.google.com/citations?user=ho-sNj4AAAAJ GEOS-Chem Google Scholar page] is now available!
**Click 'Follow' to be notified of new publications.
**Contact [mailto:rebekah.horner.20@ucl.ac.uk Bex Horner] with issues or questions.
*The GEOS-Chem Youtube Channel has 350+ subscribers and a new URL: <tt>'''https://www.youtube.com/~geoschem'''</tt>
*NASA/GMAO is now producing [https://gmao.gsfc.nasa.gov/weather_prediction/GEOS-CF/ GEOS chemical forecasts (GEOS-CF)] using GEOS-Chem coupled to the NASA/GEOS ESM


=== Coding ===
For access to all past GEOS-Chem newsletters, visit [[GEOS-Chem newsletters|this page]].
* [[GEOS-Chem versions under development]]
** [[GEOS-Chem v8-02-03|v8-02-03 "beta"]]
** [[GEOS-Chem v8-02-02|v8-02-02 "beta"]]
** [[GEOS-Chem v8-02-01|v8-02-01 "public"]]
** [[GEOS-Chem v8-01-04|v8-01-04 "beta"]]
** [[GEOS-Chem v8-01-03|v8-01-03 "beta"]]
** [[GEOS-Chem v8-01-02|v8-01-02 "beta"]]
** [[GEOS-Chem v8-01-01|v8-01-01 "public"]]
* [[Machine issues & portability]]
* [[Floating point math issues]]
* [[Bugs and fixes]]
* [[Outstanding issues yet to be resolved]]


=== Diagnostics ===
== Documentation ==
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_5.html Overview of diagnostics characteristics]
* [[Mass Flux (ND24/25/26)]]
* [[Additional diagnostics]]


=== Emissions ===
=== Archives ===
* [[Overview]]
* [[Aircraft emissions]]
* [[Anthropogenic emissions]]
** [http://wiki.seas.harvard.edu/geos-chem/images/Anth_gc_emiss_v8_02_03.pdf Description of anthropogenic emissions inventories in GEOS-Chem v8-02-03]
** [http://wiki.seas.harvard.edu/geos-chem/images/Anth_emiss_gc_v8-01-04.pdf Description of anthropogenic emissions inventories in GEOS-Chem v8-01-04]
** [http://acmg.seas.harvard.edu/geos/word_pdf_docs/INVENTORY_GC_public-pre_v8.pdf Table of available anthropogenic emissions inventories for use w/ GEOS-Chem (pre-v8)]
* [[Biofuel emissions]]
* [[Biogenic emissions]]
* [[Biomass burning emissions]]
* [[Lightning NOx emissions]]


=== Chemistry ===
In order to prepare for a migration of the wiki platform, we have archived many of the oldest wiki pages to PDF format.  Please see our '''[[GEOS-Chem Wiki archives]]''' to view these pages.
* [[Chemistry Issues]]
* [[NOx-Ox-HC-aerosol|NOx-Ox-hydrocarbon-aerosol (aka "full-chemistry") simulation]]
* [[Photolysis mechanism]]
* [[Mercury|Mercury simulation]]
* [[Tagged CO simulation]]
* [[KPP solvers FAQ]]
* [[Isoprene}}


=== Aerosols ===
=== GEOS-Chem manuals and guides ===
* [[Aerosols overview: projects and developments]]
* [[Aerosol-only simulation]]
* [[Aerosol thermodynamical equilibrium]]
* [[Secondary organic aerosols]]
* [[Sea salt aerosols]]
* [[Sulfate aerosols]]


=== Met Fields ===
* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/related-docs.html User manuals for GEOS-Chem starting in version 13]
* [[GCAP]]
*[https://geoschem.github.io/gcclassic-manpage-archive/ User manuals for GEOS-Chem 12 and prior versions]
* GMAO GEOS-5
*Guide to running [[GEOS-Chem in CESM]]
** [[List of GEOS-5 met fields]]
*[[Software_maintained_by_GEOS-Chem_community_members|List of software tools maintained by GEOS-Chem users]]
** [[GEOS-5 issues]]
** [[GEOS-5 met field reprocessing]]
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_4.html GEOS-Chem Met Fields (from website)]
** [[Notes regarding GEOS vertical grids]]


=== Nested Grid Simulations ===
=== General information about GEOS-Chem ===
* [[GEOS-Chem nested grid simulations]]
* [[Available met data for nested grid simulations]]
** [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf Protocol for nested-grid data downloads]


=== Earth System Model Framework ===
The table below lists where you can find general information about GEOS-Chem.
* [[Installing ESMF and other required libraries]]
* [[Code development with the Earth System Model Framework]]
* [[Automatic documentation with protex|Generating automatic LaTeX documentation with protex]]
** [http://frodo.elon.edu/tutorial/tutorial/tutorial.html Web-based LaTeX tutorial]


=== Related Projects ===
{| border=1 cellpadding=5 cellspacing=0
* [[GEOS-Chem column code]]
* [[GEOS-Chem Adjoint]]
* [[GEOS-Chem Near-Real-Time Simulations]]


== Data Visualization and Analysis ==
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!width="200px" bgcolor="#CCCCCC"|Item
!width="360px" bgcolor="#CCCCCC"|Link
!width="365px" bgcolor="#CCCCCC"|Description


=== IDL ===
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* [http://www.ittvis.com/ ITT Visualization (vendor)]
|'''GEOS-Chem website'''
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Structures.html Structures in IDL]
|[http://www.geos-chem.org geos-chem.org]
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Pointers.html Pointers in IDL]
|Website that links to GEOS-Chem information and resources
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Overview_of_Mathematics_in_IDL.html Overview of Mathematics in IDL]
* [http://www.dfanning.com/ Coyote's Guide to IDL Programming (David Fanning's Web Site)] - Lots of tips on how to accomplish programming tasks
* [http://www.mpimet.mpg.de/en/misc/software/idl IDL Page at Max Planck Institute for Meteorology]
* [http://www.mpimet.mpg.de/en/misc/software/idl/doc/mgs_script.pdf Martin Schultz's IDL Tutorial (PDF Format)]
* [http://idlastro.gsfc.nasa.gov/homepage.html IDL Astronomy User's Library]
* [http://fermi.jhuapl.edu/s1r/idl/idl.html JHU/APL/S1R IDL routines page]
* [http://cow.physics.wisc.edu/~craigm/idl/idl.html Craig Markwardt's IDL library]
* [http://cimss.ssec.wisc.edu/~gumley/doc/idltips.pdf The Underground Guide to IDL by Liam Gumley (PDF)]
* [[Reading binary files in IDL]]


=== GAMAP ===
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* [http://acmg.seas.harvard.edu/gamap/ GAMAP web page]
|'''Welcome Letter'''
* [http://acmg.seas.harvard.edu/gamap/doc/ GAMAP on-line users' guide]
|[http://geos-chem.org/welcome.html geos-chem.org/welcome.html]
* [[GAMAP bugs and fixes]]
|A welcome letter for new users of GEOS-Chem
* [[GAMAP tips and tricks]]
**[[General GAMAP usage]]
**[[File I/O with GAMAP]]
***[http://acmg.seas.harvard.edu/gamap/doc/timeseries_brief_tutorial.pdf Working with timeseries output in GAMAP]
**[[Color and graphics with GAMAP]]
*** [http://acmg.seas.harvard.edu/geos/wiki_docs/gamap/gamap_color_table_file.pdf Loading Color Tables in GAMAP v2.12]
*** [http://acmg.seas.harvard.edu/forum_files/cdh_ColorInIDL.pdf Working with color in IDL by Chris Holmes]
**[[Regridding with GAMAP]]
**[[Date and time computations with GAMAP]]
**[[Text manipulation with GAMAP]]


== Wiki Documentation ==
|-valign="top"
* [[Sandbox]]
|'''GEOS-Chem Overview'''
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
|[[GEOS-Chem overview]] (wiki page)
* [http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide]
|A page with linking to many GEOS-Chem topics.
* [http://meta.wikimedia.org/wiki/Help:Wikitext Examples of Wiki markup text]
 
* [http://meta.wikimedia.org/wiki/Help:Reference_card One-page editing reference card]
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* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration Settings list]
|'''GEOS-Chem Narrative'''
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
|[http://geos-chem.org/narrative.html geos-chem.org/narrative.html]
|A narrative descrption of GEOS-Chem that you can include in scientific papers (plus instructions for citing GEOS-Chem)
 
|-valign="top"
|'''GEOS-Chem New Developments'''
|[http://geos-chem.org/new-developments.html geos-chem.org/new-developments.html]
|A list of significant GEOS-Chem updates and the developers who worked on them
 
|-valign="top"
|'''GEOS-Chem Steering Committee (GCSC)'''
|[http://geos-chem.org/steering-committee.html geos-chem.org/steering-committee.html]
|A listing of current GCSC members and minutes from GCSC meetings
 
|-valign="top"
|'''GEOS-Chem Working Groups'''
|[http://geos-chem.org/working-groups geos-chem.org/working-groups.html]
|A listing of GEOS-Chem Working Groups and Working Group Co-Chairs
 
|-valign="top"
|'''GEOS-Chem Versions'''
|[[GEOS-Chem versions]] (wiki page)
|A listing of GEOS-Chem versions (with links for more information)
 
|-valign="top"
|'''GEOS-Chem Species List'''
|[https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/species-guide.html View GEOS-Chem Species properties] (ReadTheDocs page)
|A listing of the species used in the GEOS-Chem chemistry mechanisms
 
|-valign="top"
|'''GEOS-Chem Guides'''
|[[GEOS-Chem_overview#GEOS-Chem_Guides|GEOS-Chem Guides (wiki page)]]
|List of several user guides explaining topics in-depth
 
|-valign="top"
|'''Requesting Support'''
|[https://geos-chem.readthedocs.io/en/latest/help-and-reference/SUPPORT.html GEOS-Chem support guidelines]
|ReadTheDocs page with instructions for creating GEOS-Chem support requests using the Github issue trackers
 
|-valign="top"
|'''Submitting code or data'''
|[https://geos-chem.readthedocs.io/en/latest/help-and-reference/CONTRIBUTING.html GEOS-Chem contributing guidelines]
|ReadTheDocs page with instructions for submitting new source code or data updates to be included into GEOS-Chem.
 
|}

Latest revision as of 16:12, 12 November 2024

GEOS-Chem Wiki

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.

The GEOS–Chem model is a global 3-D model of atmospheric composition driven by assimilated meteorological observations from the Goddard Earth Observing System (GEOS) of the NASA Global Modeling and Assimilation Office. It is applied by research groups around the world to a wide range of atmospheric composition problems. Central management and support of the model is provided by the Atmospheric Chemistry Modeling Group at Harvard University and by the Atmospheric Composition Analysis Group at Washington University.

GEOS-Chem overview
Past releases Current release: GEOS-Chem 14.5.0 Future releases

News

For access to all past GEOS-Chem newsletters, visit this page.

Documentation

Archives

In order to prepare for a migration of the wiki platform, we have archived many of the oldest wiki pages to PDF format. Please see our GEOS-Chem Wiki archives to view these pages.

GEOS-Chem manuals and guides

General information about GEOS-Chem

The table below lists where you can find general information about GEOS-Chem.

Item Link Description
GEOS-Chem website geos-chem.org Website that links to GEOS-Chem information and resources
Welcome Letter geos-chem.org/welcome.html A welcome letter for new users of GEOS-Chem
GEOS-Chem Overview GEOS-Chem overview (wiki page) A page with linking to many GEOS-Chem topics.
GEOS-Chem Narrative geos-chem.org/narrative.html A narrative descrption of GEOS-Chem that you can include in scientific papers (plus instructions for citing GEOS-Chem)
GEOS-Chem New Developments geos-chem.org/new-developments.html A list of significant GEOS-Chem updates and the developers who worked on them
GEOS-Chem Steering Committee (GCSC) geos-chem.org/steering-committee.html A listing of current GCSC members and minutes from GCSC meetings
GEOS-Chem Working Groups geos-chem.org/working-groups.html A listing of GEOS-Chem Working Groups and Working Group Co-Chairs
GEOS-Chem Versions GEOS-Chem versions (wiki page) A listing of GEOS-Chem versions (with links for more information)
GEOS-Chem Species List View GEOS-Chem Species properties (ReadTheDocs page) A listing of the species used in the GEOS-Chem chemistry mechanisms
GEOS-Chem Guides GEOS-Chem Guides (wiki page) List of several user guides explaining topics in-depth
Requesting Support GEOS-Chem support guidelines ReadTheDocs page with instructions for creating GEOS-Chem support requests using the Github issue trackers
Submitting code or data GEOS-Chem contributing guidelines ReadTheDocs page with instructions for submitting new source code or data updates to be included into GEOS-Chem.
Retrieved from "https://wiki.seas.harvard.edu/geos-chem/index.php?title=Main_Page&oldid=54457"