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<big>'''GEOS-Chem Wiki'''</big>
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|<p><font color="#FFFFFF" size="+3">'''GEOS&#150;Chem Wiki'''</font></p>
  
The [http://www.as.harvard.edu/ctm/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://www.as.harvard.edu/ctm/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://www.as.harvard.edu/ctm/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 ==
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----
  
The links below provide more information about general GEOS-Chem topics.  
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<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 ===
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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 [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] and by the [https://sites.wustl.edu/acag/ Atmospheric Composition Analysis Group at Washington University].
* [[Features of the GEOS-Chem public wiki]]
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* [http://www.as.harvard.edu/ctm/geos/geos_overview.html GEOS-Chem Overview]
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* [http://www.as.harvard.edu/ctm/geos/geos_vision.html GEOS-Chem Vision]
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* [http://www.as.harvard.edu/ctm/geos/geos_charter.html GEOS-Chem Management Charter]
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* [http://www.as.harvard.edu/ctm/geos/geos_people GEOS-Chem People & Projects]
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* [[GEOS-Chem Working Groups and Steering Committee]]
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* [[GEOS-Chem welcome letter for new users]]
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* [[GEOS-Chem programming staff]]
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* [[GEOS-Chem newsletters]]
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=== Getting Started with GEOS-Chem ===
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|}
* [[Minimum system requirements for GEOS-Chem]]
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* [[GEOS-Chem supported platforms and compilers]]
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* [[Downloading GEOS-Chem source code and data]]
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* [[GEOS-Chem code development cycle]]
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* [[GEOS-Chem programming resources]] (e.g. tutorials, user guides, etc.)
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* [http://www.as.harvard.edu/ctm/geos/doc/man/appendix_7.html GEOS-Chem Programming Style Guide]
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* [[Running GEOS-Chem with TESTRUN]]
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=== General Technical Information ===
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{|border="1" width="925px" bordercolor="#000000" cellspacing="0" cellpadding="5"
* [[Initial conditions for GEOS-Chem]]
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* [[GEOS-Chem Debugging Tips|Tips on how to debug GEOS-Chem effectively]]
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* [[Reporting GEOS-Chem bugs]]
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* [[Parallelizing GEOS-Chem]] with the OpenMP directives
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* [[Common GEOS-Chem error messages]]
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== Code Developers' Forums ==
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|colspan="3" align="center" bgcolor="#CCCCCC"|'''<font size="+2">[[GEOS-Chem overview]]</font>'''
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|-valign="top"
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|width="225px" align="center"|<font size="+2">[[GEOS-Chem versions|Past releases]]</font>
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|width="450px" align="center" bgcolor="#CCFFFF"|<font size="+2">[[GEOS-Chem 13.4.1|'''Current release: GEOS-Chem 13.4.1''']]</font>
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|width="225px" align="center"|<font size="+2">[[GEOS-Chem model development_priorities|Future releases]]</font>
  
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.
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|}
  
=== Coding ===
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== News ==
* [[GEOS-Chem versions under development]]
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*'''19 May 2022:''' [[GEOS-Chem 13.4.1]] is now available!
** [[GEOS-Chem v8-02-01|v8-02-01 "public"]]
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*'''24 Feb 2022:''' Read the [[Media:GEOS-Chem_Newsletter_2022_Issue_1.pdf|GEOS-Chem Newsletter 2022, Issue #1]]
** [[GEOS-Chem v8-01-04|v8-01-04 "beta"]]
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*'''11 Dec 2020:''' A [https://scholar.google.com/citations?user=ho-sNj4AAAAJ GEOS-Chem Google Scholar page] is now available!
** [[GEOS-Chem v8-01-03|v8-01-03 "beta]]
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**Click 'Follow' to be notified of new publications.
** [[GEOS-Chem v8-01-02|v8-01-02 "beta"]]
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**Contact [mailto:gxl642@student.bham.ac.uk Gongda Lu] with issues or questions.
** [[GEOS-Chem v8-01-01|v8-01-01 "public"]]
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*'''02 Apr 2020:''' The GEOS-Chem Youtube Channel has 100+ subscribers and a new URL: <tt>'''https://youtube.com/c/geoschem'''</tt>
** [[GEOS-Chem v7-04-13|v7-04-13 "beta"]]
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*'''03 Feb 2020:''' View our GEOS-Chem "dry-run" tutorial at our [http://youtube.geos-chem.org GEOS-Chem Youtube channel]
** [[GEOS-Chem v7-04-12|v7-04-12 "beta"]]
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*'''17 Sep 2019:''' 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
* [[Machine issues & portability]]
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* [[Floating point math issues]]
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* [[Bugs and fixes]]
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* [[Outstanding issues yet to be resolved]]
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=== Diagnostics ===
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For access to all past GEOS-Chem newsletters, visit [[GEOS-Chem newsletters|this page]].
* [http://www-as.harvard.edu/chemistry/trop/geos/doc/man/appendix_5.html Overview of diagnostics characteristics]
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* [[Mass Flux (ND24/25/26)]]
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* [[Additional diagnostics]]
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=== Emissions ===
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== Documentation ==
* [[Overview]]
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* [[Aircraft emissions]]
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* [[Anthropogenic emissions]]
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** [http://www.as.harvard.edu/ctm/geos/word_pdf_docs/INVENTORY_GC_public.pdf Table of available anthropogenic emissions inventories for use w/ GEOS-Chem]
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* [[Biofuel emissions]]
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* [[Biogenic emissions]]
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* [[Biomass burning emissions]]
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* [[Lightning NOx emissions]]
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=== Chemistry ===
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=== GEOS-Chem manuals and tutorials ===
* [[Chemistry Issues]]
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* [[NOx-Ox-HC-aerosol|NOx-Ox-hydrocarbon-aerosol (aka "full-chemistry") simulation]]
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* [[Photolysis mechanism]]
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* [[Mercury|Mercury simulation]]
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* [[Tagged CO simulation]]
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=== Aerosols ===
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The table below lists the various manual pages for GEOS-Chem and its related software packages.
* [[Aerosols overview: projects and developments]]
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* [[Aerosol thermodynamical equilibrium]]
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* [[Secondary organic aerosols]]
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* [[Sea salt aerosols]]
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* [[Sulfate aerosols]]
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=== Met Fields ===
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{| border=1 cellpadding=5 cellspacing=0
* [[GCAP]]
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* GMAO GEOS-5
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** [[List of GEOS-5 met fields]]
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** [[GEOS-5 issues]]
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** [[GEOS-5 met field reprocessing]]
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* [http://www.as.harvard.edu/ctm/geos/doc/man/appendix_4.html GEOS-Chem Met Fields (from website)]
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=== Earth System Model Framework ===
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|-valign="top"
* [[Installing ESMF and other required libraries]]
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!width="200px" bgcolor="#CCCCCC"|Item
* [[Code development with the Earth System Model Framework]]
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!width="360px" bgcolor="#CCCCCC"|Link
* [[Automatic documentation with protex|Generating automatic LaTeX documentation with protex]]
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!width="375px" bgcolor="#CCCCCC"|Description
** [http://frodo.elon.edu/tutorial/tutorial/tutorial.html Web-based LaTeX tutorial]
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=== Related Projects ===
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|-valign="top"
* [[GEOS-Chem Adjoint]]
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|'''GEOS-Chem Classic'''
* [[GEOS-Chem nested grid simulations]]
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|[[Getting Started with GEOS-Chem]] (wiki page)
* [[GEOS-Chem Near-Real-Time Simulations]]
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*NOTE: In the process of being ported to<br>[https://geos-chem.readthedocs.io geos-chem.readthedocs.io]
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|GEOS-Chem single-node implementation<br>(using 1-64 computational cores)
  
== Data Visualization and Analysis ==
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|-valign="top"
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|'''GCHP'''
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|[https://gchp.readthedocs.io gchp.readthedocs.io]
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|GEOS-Chem multi-node "high performance" implementation<br>(using 100's - 1000's of computational cores)
  
=== IDL ===
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|-valign="top"
* [http://www.ittvis.com/ ITT Visualization (vendor)]
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|'''GEOS-Chem on the cloud'''
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Structures.html Structures in IDL]
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|[http://cloud.geos-chem.org cloud.geos-chem.org]
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Pointers.html Pointers in IDL]
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|Instructions for running GEOS-Chem on the Amazon Web Services EC2 cloud-computing platform
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Overview_of_Mathematics_in_IDL.html Overview of Mathematics in IDL]
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* [http://www.dfanning.com/ Coyote's Guide to IDL Programming (David Fanning's Web Site)] - Lots of tips on how to accomplish programming tasks
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* [http://www.mpimet.mpg.de/en/misc/software/idl IDL Page at Max Planck Institute for Meteorology]
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* [http://www.mpimet.mpg.de/en/misc/software/idl/doc/mgs_script.pdf Martin Schultz's IDL Tutorial (PDF Format)]
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* [http://idlastro.gsfc.nasa.gov/homepage.html IDL Astronomy User's Library]
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* [http://fermi.jhuapl.edu/s1r/idl/idl.html JHU/APL/S1R IDL routines page]
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* [http://cow.physics.wisc.edu/~craigm/idl/idl.html Craig Markwardt's IDL library]
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* [http://cimss.ssec.wisc.edu/~gumley/doc/idltips.pdf The Underground Guide to IDL by Liam Gumley (PDF)]
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* [[Reading binary files in IDL]]
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=== GAMAP ===
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|-valign="top"
* [http://www.as.harvard.edu/ctm/gamap/ GAMAP web page]
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|'''WRF-GC'''
* [http://www.as.harvard.edu/ctm/gamap/doc/ GAMAP on-line users' guide]
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|[http://wrf.geos-chem.org wrf.geos-chem.org]
* [[GAMAP bugs and fixes]]
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[https://wrfgc.readthedocs.io wrfgc.readthedocs.io]
* [[GAMAP tips and tricks]]
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|GEOS-Chem coupled to the WRF weather model
**[[General GAMAP usage]]
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**[[File I/O with GAMAP]]
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***[http://www-as.harvard.edu/chemistry/trop/gamap/doc/timeseries_brief_tutorial.pdf Working with timeseries output in GAMAP]
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**[[Color and graphics with GAMAP]]
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*** [http://www.as.harvard.edu/ctm/geos/wiki_docs/gamap/gamap_color_table_file.pdf Loading Color Tables in GAMAP v2.12]
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*** [http://www.as.harvard.edu/chemistry/trop/forum_files/cdh_ColorInIDL.pdf Working with color in IDL by Chris Holmes]
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**[[Regridding with GAMAP]]
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**[[Date and time computations with GAMAP]]
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**[[Text manipulation with GAMAP]]
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== Wiki Documentation ==
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|-valign="top"
* [[Sandbox]]
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|'''HEMCO'''
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
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|[https://hemco.readthedocs.io hemco.readthedocs.io]
* [http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide]
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|The Harmonized Emissions Component
* [http://meta.wikimedia.org/wiki/Help:Wikitext Examples of Wiki markup text]
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* [http://meta.wikimedia.org/wiki/Help:Reference_card One-page editing reference card]
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|-valign="top"
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration Settings list]
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|'''GCPy'''
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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|[https://gcpy.readthedocs.io gcpy.readthedocs.io]
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|The GEOS-Chem Python Toolkit
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|-valign="top"
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|'''KPP-for-GEOS-Chem'''
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|[https://kpp.readthedocs.io kpp.readthedocs.io]
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|The Kinetic PreProcessor (KPP), customized for GEOS-Chem
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|-valign="top"
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|'''GEOS-Chem Adjoint'''
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|[[GEOS-Chem Adjoint]] (wiki page)
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|The GEOS-Chem adjoint model<br> (NOTE: maintained separately from GEOS-Chem)
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|-valign="top"
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|'''GEOS-Chem Videos'''
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|[https://youtube.com/c/geos-chem youtube.com/c/geos-chem]
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|Tutorial videos for GEOS-Chem, GCHP, HEMCO, GCPy, etc., and recordings of GEOS-Chem meeting sessions
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|-valign="top"
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|'''GEOS-Chem Guides'''
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|[[GEOS-Chem overview#GEOS-Chem Guides|GEOS-Chem Guides]] (wiki page)
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|Short manuals giving a deeper dive into various GEOS-Chem topics (such as compilers, netCDF, diagnostics, etc.)
 +
 
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|}
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 +
=== General information about GEOS-Chem ===
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 +
The table below lists where you can find general information about GEOS-Chem.
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 +
{| border=1 cellpadding=5 cellspacing=0
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|-valign="top"
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!width="200px" bgcolor="#CCCCCC"|Item
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!width="360px" bgcolor="#CCCCCC"|Link
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!width="365px" bgcolor="#CCCCCC"|Description
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|-valign="top"
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|'''GEOS-Chem website'''
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|[http://www.geos-chem.org geos-chem.org]
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|Website that links to GEOS-Chem information and resources
 +
 
 +
|-valign="top"
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|'''Welcome Letter'''
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|[[GEOS-Chem welcome letter for new users]] (wiki page)
 +
|A welcome letter for new users of GEOS-Chem
 +
 
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|-valign="top"
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|'''GEOS-Chem Overview'''
 +
|[[GEOS-Chem overview]] (wiki page)
 +
|A page with linking to many GEOS-Chem topics.
 +
 
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|-valign="top"
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|'''GEOS-Chem Narrative'''
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|[https://geos-chem.seas.harvard.edu/geos-chem-narrative geos-chem.seas.harvard.edu/geos-chem-narrative]
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|A narrative descrption of GEOS-Chem that you can include in scientific papers (plus instructions for citing GEOS-Chem)
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|-valign="top"
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|'''GEOS-Chem New Developments'''
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|[https://geos-chem.seas.harvard.edu/geos-new-developments geos-chem.seas.harvard.edu/geos-new-developments]
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|A list of significant GEOS-Chem updates and the developers who worked on them
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|-valign="top"
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|'''GEOS-Chem Steering Committee (GCSC)'''
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|[http://geos-chem.seas.harvard.edu/geos-steering-cmte geos-chem.seas.harvard.edu/geos-steering-cmte]  
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|A listing of current GCSC members and minutes from GCSC meetings
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|-valign="top"
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|'''GEOS-Chem Working Groups'''
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|[https://geos-chem.seas.harvard.edu/geos-working-groups geos-chem.seas.harvard.edu/geos-working-groups]  
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|A listing of GEOS-Chem Working Groups and Working Group Co-Chairs
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|-valign="top"
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|'''GEOS-Chem Versions'''
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|[[GEOS-Chem versions]] (wiki page)
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|A listing of GEOS-Chem versions (with links for more information)
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|-valign="top"
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|'''GEOS-Chem Species List'''
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|[[Guide to species in GEOS-Chem]] (wiki page)
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|A listing of the species used in the GEOS-Chem chemistry mechanisms
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|-valign="top"
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|'''Requesting Support'''
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|[[Submitting GEOS-Chem support requests]] (wiki page)
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|Instructions for creating GEOS-Chem support requests using the Github issue trackers
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|-valign="top"
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|'''Submitting code or data'''
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|[[Submitting updates for inclusion in GEOS-Chem]] (wiki page)
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|Instructions for submitting new source code or data updates to be included into GEOS-Chem.
 +
 
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|}

Latest revision as of 17:15, 21 June 2022

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 13.4.1 Future releases

News

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

Documentation

GEOS-Chem manuals and tutorials

The table below lists the various manual pages for GEOS-Chem and its related software packages.

Item Link Description
GEOS-Chem Classic Getting Started with GEOS-Chem (wiki page) GEOS-Chem single-node implementation
(using 1-64 computational cores)
GCHP gchp.readthedocs.io GEOS-Chem multi-node "high performance" implementation
(using 100's - 1000's of computational cores)
GEOS-Chem on the cloud cloud.geos-chem.org Instructions for running GEOS-Chem on the Amazon Web Services EC2 cloud-computing platform
WRF-GC wrf.geos-chem.org

wrfgc.readthedocs.io

GEOS-Chem coupled to the WRF weather model
HEMCO hemco.readthedocs.io The Harmonized Emissions Component
GCPy gcpy.readthedocs.io The GEOS-Chem Python Toolkit
KPP-for-GEOS-Chem kpp.readthedocs.io The Kinetic PreProcessor (KPP), customized for GEOS-Chem
GEOS-Chem Adjoint GEOS-Chem Adjoint (wiki page) The GEOS-Chem adjoint model
(NOTE: maintained separately from GEOS-Chem)
GEOS-Chem Videos youtube.com/c/geos-chem Tutorial videos for GEOS-Chem, GCHP, HEMCO, GCPy, etc., and recordings of GEOS-Chem meeting sessions
GEOS-Chem Guides GEOS-Chem Guides (wiki page) Short manuals giving a deeper dive into various GEOS-Chem topics (such as compilers, netCDF, diagnostics, etc.)

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 welcome letter for new users (wiki page) 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.seas.harvard.edu/geos-chem-narrative 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.seas.harvard.edu/geos-new-developments A list of significant GEOS-Chem updates and the developers who worked on them
GEOS-Chem Steering Committee (GCSC) geos-chem.seas.harvard.edu/geos-steering-cmte A listing of current GCSC members and minutes from GCSC meetings
GEOS-Chem Working Groups geos-chem.seas.harvard.edu/geos-working-groups 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 Guide to species in GEOS-Chem (wiki page) A listing of the species used in the GEOS-Chem chemistry mechanisms
Requesting Support Submitting GEOS-Chem support requests (wiki page) Instructions for creating GEOS-Chem support requests using the Github issue trackers
Submitting code or data Submitting updates for inclusion in GEOS-Chem (wiki page) Instructions for submitting new source code or data updates to be included into GEOS-Chem.