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== feel free to experiment here ==
== feel free to experiment here ==
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|<p><font color="#FFFFFF" size="+3">'''GEOS&#150;Chem Wiki'''</font></p>
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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://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.]
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.
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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{|border="1" width="1000px" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"
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|width="334px"|'''Getting started w/ GEOS-Chem:'''
|width="333px"|'''[[GEOS-Chem welcome letter for new users|Welcome letter for new users]]'''
|width="333px"|'''[[GEOS-Chem basics]]'''
|-valign="top" bgcolor="#CCFFFF" align="center"
|'''Current public release:'''
|'''[[GEOS-Chem v10-01]]'''
|'''[[GEOS-Chem v10-01 benchmark history|v10-01 benchmark history]]'''
|-valign="top" align="center"
|'''Version in development:'''
|'''[[GEOS-Chem v11-01]]'''
|'''[[GEOS-Chem v11-01 benchmark history|v11-01 benchmark history]]'''
|-valign="top" align="center"
|'''Version for high-performance<br>computing (HPC) environments:'''
|'''[[GEOS-Chem HP]]'''
|'''[[GEOS-Chem HP Dev Kit]]'''
|-valign="top" align="center"
|'''List of publications:'''
|'''[http://acmg.seas.harvard.edu/geos/geos_pub.html Refer to this page]'''
|
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<br>
{|border="1" width="1000px" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"
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|colspan="2"|<p><font color="#FFFFFF" size="+2">'''General information about GEOS-Chem'''</font></p>
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Introduction and overview</big>
!width="500px"|<big>Steering Committee and working groups</big>
|-valign="top"
| <!-- Intro and overview -->
* [[GEOS-Chem welcome letter for new users]]
* [[GEOS-Chem basics]]
* [[Features of the GEOS-Chem public wiki]]
* [[Customizing your GEOS-Chem Wiki Settings]]
* [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 Support Team]]
* [[GEOS-Chem newsletters]]
* [http://acmg.seas.harvard.edu/geos/geos_search.html GEOS-Chem Search Engines]
* [http://acmg.seas.harvard.edu/geos/geos_new_developments.html Recommendations for offering co-authorships to GEOS-Chem developers]
* [http://acmg.seas.harvard.edu/geos/geos_dev_history.html GEOS-Chem code development history]
| <!-- Steering committee etc -->
* [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 Working Group]]
** [[Carbon Cycle Working Group]]
** [[Chemistry-Climate Working Group]]
** [[GEOS-Chem High Performance Working Group]]
** [[Hg and POPs Working Group]]
** [[Organics Working Group]]
** [[Chemistry Issues|Oxidants and Chemistry Working Group]]
** [[Nested Model Working Group]]
** [[Sources and Sinks Working Group|Sources and Surface Uptake Working Group]]
** [[Transport Working Group]]
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!width="500px"|<big>Getting started with GEOS-Chem</big>
!width="500px"|<big>General technical information</big>
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* [[Frequently asked questions about GEOS-Chem]]
* [[Minimum system requirements for GEOS-Chem]]
* [[GEOS-Chem supported platforms and compilers]]
* [[Downloading GEOS-Chem source code and data]]
* [[Creating GEOS-Chem run directories]]
* [[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]
|
* [[Initial conditions for GEOS-Chem]]
* [[Centralized chemistry time step]]
* [[GEOS-Chem coding and debugging#GEOS-Chem debugging tips|Tips on how to debug GEOS-Chem effectively]]
* [[Reporting GEOS-Chem bugs]]
* [[Debugging with the GEOS-Chem unit tester]]
* [[Parallelizing GEOS-Chem]] with the OpenMP directives
* [[Common GEOS-Chem error messages]]
* [[Adding tracers to GEOS-Chem|Adding advected tracers and chemical species to GEOS-Chem]]
* [[Adding Passive Tracers|Adding passive (CO-like) tracers to GEOS-Chem]]
|}
<br>
{|border="1" width="1000px" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"
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|colspan="2"|<p><font color="#FFFFFF" size="+2">'''GEOS-Chem Code Developers' Forums'''</font></p>
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Coding</big>
!width="500px"|<big>Diagnostics</big>
|-valign="top"
| <!-- Coding -->
* [[GEOS-Chem versions under development]]
* [[Bugs and fixes|List of GEOS-Chem bugs and in which version they were resolved]]
* [[Currently unresolved issues in GEOS-Chem]]
* [[Common GEOS-Chem error messages]]
* [[Known issues caused by compiler bugs|Known GEOS-Chem issues caused by compiler bugs]]
* [[GEOS-Chem performance]]
* [[Machine issues and portability]]
* [[Passing array arguments efficiently in GEOS-Chem]]
* [[Floating point math issues]]
* [[Version control with Git]]
| <!-- Diagnostics -->
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_5.html Overview of diagnostics characteristics]
* [[Diagnostic time step]]
* [[Mass Flux (ND24/25/26)]]
* [[Additional diagnostics]]
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Emissions</big>
!width="500px"|<big>Chemistry</big>
|-valign="top"
|<!-- Emissions -->
* [[HEMCO|HEMCO emissions component]]
* [[HEMCO data directories]]
* [[Aerosol emissions]]
* [[Aircraft emissions]]
* [[Anthropogenic emissions]]
* [[Scale factors for anthropogenic emissions]]
* [[Biofuel emissions]]
* [[Biogenic emissions]]
* [[Biomass burning emissions]]
* [[Lightning NOx emissions]]
* [[Ship emissions]]
* [[Soil NOx emissions]]
* [[Volcanic SO2 emissions from Aerocom|Volcanic emissions]]
* [[Historical and Future Emissions|Historical and future emissions]]
|<!-- Chemistry -->
* [[GEOS-Chem chemistry mechanisms]]
* [[GEOS-Chem chemistry mechanisms#Stratospheric chemistry|Stratopsheric chemistry options]]
* [[GEOS-Chem chemistry mechanisms#Specialty simulations|Specialty simulations (aka "offline simulations")]]
* Other resources
** [[Chemistry Issues]]
** [[Process Analysis Diagnostics]]
** [[Photolysis mechanism|Photolysis mechanisms used in GEOS-Chem]]
** [[DSMACC chemical box model]]
** [[Isoprene|List of recent papers about isoprene]]
** [[Linking GEOS-Chem to CMAQ]]
** [[Coupling GEOS-Chem with RRTMG]]
*[[GEOS-Chem species database]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span>
*[[Physical properties of GEOS-Chem species]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span>
*[[Species_indexing_in_GEOS-Chem|Species and tracer indexing in GEOS-Chem]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span>
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!width="500px"|<big>Dynamics</big>
!width="500px"|<big>Deposition</big>
|-valign="top"
| <!-- Dynamics -->
* [[Advection scheme TPCORE]]
* [[Boundary layer mixing]]
* [[Cloud convection]]
* [[Dynamic tropopause]]
| <!-- Deposition -->
* [[Dry deposition]]
**[[Leaf area indices in GEOS-Chem]]
* [[Wet deposition]]
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Aerosols</big>
!width="500px"|<big>Met fields</big>
|-valign="top"
| <!-- Aerosols -->
* [[Aerosols overview: projects and developments|Aerosols working group]]
* [[Aerosol-only simulation]]
* [[Aerosol optical properties]]
* [[Aerosol thermodynamical equilibrium]]
* [[Carbonaceous aerosols]]
* [[Mineral dust aerosols]]
* [[Secondary organic aerosols]]
* [[Sea salt aerosols]]
* [[Sulfate aerosols]]
* Aerosol Microphysics
** [[APM aerosol microphysics|APM]]
** [[TOMAS aerosol microphysics|TOMAS]]
| <!-- Met fields -->
* [[GCAP]]
** [[List of GCAP met fields|List of GCAP met fields used by GEOS-Chem]]
* [[Overview of GMAO met data products]]
* [[Version history of GMAO met data products]]
* [[GMAO GEOS-4]]
** [[List of GEOS-4 met fields|List of GEOS-4 met fields used by GEOS-Chem]]
* [[GEOS-5|GMAO GEOS-5.2.0]]
** [[List of GEOS-5 met fields|List of GEOS-5.2.0 met fields used by GEOS-Chem]]
** [[GEOS-5 issues|Issues with GEOS-5.2.0 met data]]
* [[MERRA|GMAO MERRA "reanalysis"]]
** [[List of MERRA met fields|List of MERRA met fields used by GEOS-Chem]]
** [[MERRA implementation details|Implementing MERRA into GEOS-Chem]]
* [[GEOS-FP|GMAO GEOS-FP]]
** [[List of GEOS-FP met fields|List of GEOS-FP met fields used by GEOS-Chem]]
** [[GEOS-FP implementation details|Implementing GEOS-FP into GEOS-Chem]]
* [[MERRA-2|GMAO MERRA-2]]
** [[List of MERRA-2 met fields|List of MERRA-2 met fields used by GEOS-Chem]]
** [[MERRA-2 implementation details|Implementing MERRA-2 into GEOS-Chem]]
* [[Notes regarding GEOS vertical grids]]
* [[Available met data for nested grid simulations]]
* [[List of reprocessed met fields]]
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Nested grid simulations</big>
!width="500px"|<big>Earth System Modeling Framework</big>
|-valign="top"
| <!-- Nested grid -->
* [[GEOS-Chem nested grid simulations]]
* [[Setting up 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]
* [[Steps to setup new nested domains]]
* [[GEOS-Chem nested model publications]]
| <!-- ESMF -->
* [[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]
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Benchmarking and Evaluation</big>
!width="500px"|<big>Related projects</big>
|-valign="top"
| <!-- Benchmarks -->
* [http://acmg.seas.harvard.edu/geos/geos_benchmark.html General info about GEOS-Chem benchmark simulations]
* [http://acmg.seas.harvard.edu/geos/geos_1yr_plots.html List of GEOS-Chem 1-year benchmark simulations]
* [[Mean OH lifetime in GEOS-Chem]]
* [ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/ FTP site with output from 1-year GEOS-Chem benchmark simulations]
* [[GEOS-Chem participation in community intercomparisons]]
* [[Satellite_Specifications_Table|Satellite Instrument Specifications Table]]
| <!-- Projects -->
* [[Grid-independent GEOS-Chem]]
* [[GEOS-Chem Adjoint]]
* [[GEOS-Chem Near-Real-Time Simulations]]
* [[FlexAOD]]
|}
<br>
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|-height="50" bgcolor="#00AAAA" align="center"
|colspan="2"|<p><font color="#FFFFFF" size="+2">'''Reference Section'''</font></p>
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>IDL</big>
!width="500px"|<big>GAMAP</big>
|-valign="top"
| <!-- IDL -->
* [http://www.exelisvis.com/ Exelis Visual Information Solutions (vendor)]
* [http://www.exelisvis.com/docs/routines-1.html Online IDL Reference Manual @ Exelis website]
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Structures.html Structures in IDL]
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Pointers.html Pointers in IDL]
* [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 -->
* [http://acmg.seas.harvard.edu/gamap/ GAMAP web page]
* [http://acmg.seas.harvard.edu/gamap/doc/ GAMAP on-line users' guide]
* [[GAMAP bugs and fixes]]
* [[GAMAP tips and tricks]]
**[[General GAMAP usage]]
**[[TVMAP cheat sheet]]
**[[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]]
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Fortran</big>
!width="500px"|<big>Perl</big>
|-valign="top"
|<!-- Fortran -->
* [[Intel Fortran Compiler]]
** [http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/main_for_lin_v11.pdf Version 11.1]
** [http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/main_for_lin_v12.pdf Version 12.1]
** [https://nf.nci.org.au/facilities/software/intel-ct/13.2.146/Documentation/en_US/compiler_f/main_for/index.htm#GUID-81DC012F-20D6-46B1-A524-BFAC4B6F7747.htm#GUID-81DC012F-20D6-46B1-A524-BFAC4B6F7747 Version XE 13.1]
** [https://software.intel.com/en-us/compiler_15.0_ug_f Version 15.0]
* [[PGI Fortran compiler]]
**[http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/pgiug.pdf User Guide]
**[http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/pgifortref.pdf Reference Guide]
* [[GNU Fortran compiler]]
* [http://www-01.ibm.com/software/awdtools/fortran/xlfortran/ IBM XL Fortran]
* [http://docs.sun.com/app/docs/doc/819-3686 Sun Studio 11 Fortran Compiler]
* [http://www.liv.ac.uk/HPC/HTMLF90Course/HTMLF90CourseSlides.html Modular Programming w/ Fortran 90 (U. Liverpool)]
* [http://www.liv.ac.uk/HPC/F90page.html Other University of Liverpool F90 tutorials and courses]
* [http://sunsite.unc.edu/pub/languages/fortran/index.html User Notes on FORTRAN Programming]
* [http://www.nsc.liu.se/~boein/f77to90/f77to90.html Fortran 90 for the FORTRAN 77 Programmer]
* [http://www.kcl.ac.uk/kis/support/cc/fortran/f90home.html#1.0 Fortran 90 Home Page at King's College, London]
* [http://www.cs.rpi.edu/~szymansk/oof90.html Object Oriented Fortran 90 Programming]
|<!-- Perl -->
* [http://www.perl.com Perl.com]
* [http://www.perl.org/books/beginning-perl/ ''Beginning Perl'' by Simon Cozens (free online book)]
* [http://backpan.perl.org/authors/id/Q/QU/QUONG/perlin20.html Perl in 20 pages]
* [http://www.enginsite.com/Library-Robert%27s-Perl-Tutorial.htm MediaWiki User's Guide]
* [http://www.cpan.org/ Comprehensive Perl Archive Network (CPAN.org)]
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>R</big>
!width="500px"|<big>Python</big>
|-valign="top"
|<!-- R -->
*[http://www.r-project.org/ The R project for statistical computing]
*[http://journal.r-project.org/ The R journal]
*[http://www.mayin.org/ajayshah/KB/R/index.html R by example]
*[[Using R to analyze GEOS-Chem data]]
|<!-- Python -->
*[[Python code for GEOS-Chem]]
*[http://www.python.org Python.org]: Main site for all things Python
*[http://docs.python.org/2/tutorial/ Python.org Tutorial]
*[http://wiki.python.org/moin/BeginnersGuide/Programmers PythonWiki.org: List of tutorials and resources]
*[https://developers.google.com/edu/python/ Google's Python tutorial]
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>NCAR Command Language (NCL)</big>
!width="500px"|<big>Wiki documentation</big>
|-valign="top"
|<!-- MCL -->
* [http://www.ncl.ucar.edu/ NCL main page]
* [http://www.ncl.ucar.edu/Applications/ NCL applications]
* [http://www.ncl.ucar.edu/Document/ NCL documentation]
* [http://www.ncl.ucar.edu/Support/email_lists.shtml Sign up for NCL-Talk email list]
* [[NCL_tools_for_GEOS-Chem|NCL4GC: NCL tools for GEOS-Chem]]
|<!-- Wiki doc -->
* [[Sandbox]]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide]
* [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]
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration Settings list]
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
|}

Revision as of 18:40, 6 December 2016

feel free to experiment here

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