https://wiki.seas.harvard.edu/geos-chem/api.php?action=feedcontributions&user=Linzhang&feedformat=atomGeos-chem - User contributions [en]2024-03-19T10:52:50ZUser contributionsMediaWiki 1.24.2https://wiki.seas.harvard.edu/geos-chem/index.php?title=Steps_to_setup_new_nested_domains&diff=27845Steps to setup new nested domains2016-11-01T18:10:35Z<p>Linzhang: First version of setup new nested domains (2016.10.31)</p>
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<div>It’s not difficult to set up new nested-grid domains in the model, but the process can be tedious.<br />
<br />
* First, prepare for the meteorological data for the new nested domain. Obtain the native-resolution global met fields (not sure if Harvard or Dalhousie still keep those files on their disks; if not, they can be downloaded from NASA) and trim them to save out those over the domain of interest. The GC support team may have scripts to do this step.<br />
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* Second, change all the domain-specific parameters in the code to match with the new nested domain. I don’t have a complete list of those parameters. The easiest thing is to find all the places in the code that have the ‘if nested-grid’ statement. A couple of parameters are defined in CMN_SIZE and make sure to change these. If you use one of the existing nested-grid resolutions (0.5x0.667 or 0.25x0.3125), no change is necessary for the advection code. Only need to change the domain-specific parameters in input.geos.<br />
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* Third, make sure the input data for offline emissions and emission-related files are ready for HEMCO. My understanding is that HEMCO should be ready to take care of emissions in the nested-grid runs on the fly, but you should test if this is the case. <br />
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* Fourth, test-run and debug the model. You will need to archive boundary conditions from the global runs in this step. This step can be long, and we often find missing data or wrong parameters in this step, but nothing major since the code’s already set up to deal with nested-grid simulations. My experience is to do the testing in two steps. First, test the transport processes only by turning off emissions, chemistry, and deposition. After the first step passes the quality control (more on this below), turn on emissions/chemistry/deposition to test the full chemistry runs. <br />
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* Fifth, test if tuning factors for dust emissions are needed for your nested domain because these emissions are resolution-dependent due to how they’re parameterized in the code. To get the tuning factors, run the nested-grid model for a full year, archive those emissions (no tuning applied), and compare the domain-wide total emissions with those from the coarser-resolution global run (i.e., 2x2.5) to derive the tuning factors. We did the same for lightning NOx and soil NOx a few years ago, but now that the model treats these emissions in a different way. <br />
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I think that’s all. For quality control of the new nested model, I use two criteria: <br />
* (1) the spatial distribution of all species needs to be consistent with the 2x2.5 runs – I always regrid the finer-resolution outputs onto the coarser-resolution for the purpose of direct comparison. Make sure to check all model levels. <br />
* (2) do a tracer mass calculation for the nested domain and compare it with the mass from the global run. The difference in mass should be less than a few percent and not enlarge as the simulation period gets longer. There won’t be a 100% match in tracer masses because the finer grids do not completely align with the coarser grids.<br />
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Well, we hope you won’t be discouraged by this long to-do-list. This has been done many times before and it’s definitely doable. If you have questions, feel free to contact us. <br />
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-- Yuxuan Wang, Lin Zhang, Jun Wang; 10/21/16</div>Linzhanghttps://wiki.seas.harvard.edu/geos-chem/index.php?title=Main_Page&diff=27844Main Page2016-11-01T18:04:28Z<p>Linzhang: Add a link to the steps to setup new nested domains page</p>
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<td bgcolor="#CCFFFF"><p align="center"><big><strong>Current public release:</strong></big></p></td><br />
<td bgcolor="#CCFFFF"><p align="center"><big><strong>[[GEOS-Chem v10-01]]</strong></big></p></td><br />
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<td><p align="center"><big><strong>[http://acmg.seas.harvard.edu/geos/geos_pub.html Refer to this page]</strong></big><br />
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** [[GEOS-Chem model development priorities]]<br />
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* [[Frequently asked questions about GEOS-Chem]]<br />
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* [[Common GEOS-Chem error messages]]<br />
* [[Adding tracers to GEOS-Chem|Adding advected tracers and chemical species to GEOS-Chem]]<br />
* [[Adding Passive Tracers|Adding passive (CO-like) tracers to GEOS-Chem]]<br />
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* [[GEOS-Chem versions under development]]<br />
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* [[Floating point math issues]]<br />
* [[Version control with Git]]<br />
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* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_5.html Overview of diagnostics characteristics]<br />
* [[Diagnostic time step]]<br />
* [[Mass Flux (ND24/25/26)]]<br />
* [[Additional diagnostics]]<br />
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<!-- ===== CODE DEVELOPER'S FORUMS : SECOND ROW ===== --><br />
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<th width="50%"scope="col"><big>Emissions</big></th><br />
<th width="50%"scope="col"><big>Chemistry</big></th><br />
</tr><br />
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<tr><br />
<br />
<!-- Emissions: Links --><br />
<td width="50%" valign="top"><br />
* [[HEMCO|HEMCO emissions component]]<br />
* [[HEMCO data directories]]<br />
* [[Aerosol emissions]]<br />
* [[Aircraft emissions]]<br />
* [[Anthropogenic emissions]]<br />
* [[Scale factors for anthropogenic emissions]]<br />
* [[Biofuel emissions]]<br />
* [[Biogenic emissions]]<br />
* [[Biomass burning emissions]]<br />
* [[Lightning NOx emissions]]<br />
* [[Ship emissions]]<br />
* [[Soil NOx emissions]]<br />
* [[Volcanic SO2 emissions from Aerocom|Volcanic emissions]]<br />
* [[Historical and Future Emissions|Historical and future emissions]]<br />
</td><br />
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<!-- Chemistry Links --><br />
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* [[GEOS-Chem chemistry mechanisms]]<br />
* [[GEOS-Chem chemistry mechanisms#Stratospheric chemistry|Stratopsheric chemistry options]]<br />
* [[GEOS-Chem chemistry mechanisms#Specialty simulations|Specialty simulations (aka "offline simulations")]]<br />
* Other resources<br />
** [[Chemistry Issues]]<br />
** [[Process Analysis Diagnostics]]<br />
** [[Photolysis mechanism|Photolysis mechanisms used in GEOS-Chem]]<br />
** [[DSMACC chemical box model]]<br />
** [[Isoprene|List of recent papers about isoprene]]<br />
** [[Linking GEOS-Chem to CMAQ]]<br />
** [[Coupling GEOS-Chem with RRTMG]] <br />
*[[GEOS-Chem species database]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span><br />
*[[Physical properties of GEOS-Chem species]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span><br />
*[[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><br />
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<th width="50%"scope="col"><big>Dynamics</big></th><br />
<th width="50%"scope="col"><big>Deposition</big></th><br />
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<!-- Dynamics: Links --><br />
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* [[Advection scheme TPCORE]]<br />
* [[Boundary layer mixing]]<br />
* [[Cloud convection]]<br />
* [[Dynamic tropopause]]<br />
</td><br />
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<!-- Deposition: Links --><br />
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* [[Dry deposition]]<br />
**[[Leaf area indices in GEOS-Chem]]<br />
* [[Wet deposition]]<br />
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<!-- ===== CODE DEVELOPER'S FORUMS : FOURTH ROW ===== --><br />
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<th width="50%"scope="col"><big>Aerosols</big></th><br />
<th width="50%"scope="col"><big>Met Fields</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Aerosols: Links --><br />
<td width="50%" valign="top"><br />
* [[Aerosols overview: projects and developments|Aerosols working group]]<br />
* [[Aerosol-only simulation]]<br />
* [[Aerosol optical properties]]<br />
* [[Aerosol thermodynamical equilibrium]]<br />
* [[Carbonaceous aerosols]]<br />
* [[Mineral dust aerosols]]<br />
* [[Secondary organic aerosols]]<br />
* [[Sea salt aerosols]]<br />
* [[Sulfate aerosols]]<br />
* Aerosol Microphysics<br />
** [[APM aerosol microphysics|APM]]<br />
** [[TOMAS aerosol microphysics|TOMAS]]<br />
</td><br />
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<!-- Met Fields: Links --><br />
<td width="50%" valign="top"><br />
* [[GCAP]] <br />
** [[List of GCAP met fields|List of GCAP met fields used by GEOS-Chem]]<br />
* [[Overview of GMAO met data products]]<br />
* [[Version history of GMAO met data products]]<br />
* [[GMAO GEOS-4]]<br />
** [[List of GEOS-4 met fields|List of GEOS-4 met fields used by GEOS-Chem]]<br />
* [[GEOS-5|GMAO GEOS-5.2.0]]<br />
** [[List of GEOS-5 met fields|List of GEOS-5.2.0 met fields used by GEOS-Chem]]<br />
** [[GEOS-5 issues|Issues with GEOS-5.2.0 met data]]<br />
* [[MERRA|GMAO MERRA "reanalysis"]]<br />
** [[List of MERRA met fields|List of MERRA met fields used by GEOS-Chem]]<br />
** [[MERRA implementation details|Implementing MERRA into GEOS-Chem]]<br />
* [[GEOS-FP|GMAO GEOS-FP]]<br />
** [[List of GEOS-FP met fields|List of GEOS-FP met fields used by GEOS-Chem]]<br />
** [[GEOS-FP implementation details|Implementing GEOS-FP into GEOS-Chem]]<br />
* [[MERRA-2|GMAO MERRA-2]]<br />
** [[List of MERRA-2 met fields|List of MERRA-2 met fields used by GEOS-Chem]]<br />
** [[MERRA-2 implementation details|Implementing MERRA-2 into GEOS-Chem]]<br />
* [[Notes regarding GEOS vertical grids]]<br />
* [[Available met data for nested grid simulations]]<br />
* [[List of reprocessed met fields]]<br />
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<!-- ===== CODE DEVELOPER'S FORUMS : FIFTH ROW ===== --><br />
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<th width="50%"scope="col"><big>Nested Grid Simulations</big></th><br />
<th width="50%"scope="col"><big>Earth System Model Framework</big></th><br />
</tr><br />
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<tr><br />
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<!-- Nested Grid Simulations: Links --><br />
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* [[GEOS-Chem nested grid simulations]]<br />
* [[Setting up GEOS-Chem nested grid simulations]]<br />
* [[Available met data for nested grid simulations]]<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf Protocol for nested-grid data downloads]<br />
* [[Steps to setup new nested domains]]<br />
* [[GEOS-Chem nested model publications]]<br />
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* [[Installing ESMF and other required libraries]]<br />
* [[Code development with the Earth System Model Framework]]<br />
* [[Automatic documentation with protex|Generating automatic LaTeX documentation with protex]]<br />
** [http://frodo.elon.edu/tutorial/tutorial/tutorial.html Web-based LaTeX tutorial]<br />
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<!-- ===== CODE DEVELOPER'S FORUMS : SIXTH ROW ===== --><br />
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<th width="50%"scope="col"><big>Benchmarking and Evaluation</big></th><br />
<th width="50%"scope="col"><big>Related Projects</big></th><br />
</tr><br />
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<tr><br />
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<!-- Diagnostics: Links --><br />
<td width="50%" valign="top"><br />
* [http://acmg.seas.harvard.edu/geos/geos_benchmark.html General info about GEOS-Chem benchmark simulations]<br />
* [http://acmg.seas.harvard.edu/geos/geos_1yr_plots.html List of GEOS-Chem 1-year benchmark simulations]<br />
* [[Mean OH lifetime in GEOS-Chem]]<br />
* [ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/ FTP site with output from 1-year GEOS-Chem benchmark simulations]<br />
* [[GEOS-Chem participation in community intercomparisons]]<br />
* [[Satellite_Specifications_Table|Satellite Instrument Specifications Table]]<br />
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<!-- Related Projects: Links --><br />
<td width="50%" valign="top"><br />
* [[Grid-independent GEOS-Chem]]<br />
* [[GEOS-Chem Adjoint]]<br />
* [[GEOS-Chem Near-Real-Time Simulations]]<br />
* [[FlexAOD]]<br />
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<!-- ===== REFERENCE: TITLE ===== --><br />
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<p>&nbsp;</p><br />
<table width="100%" border="1" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"><br />
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<tr bgcolor="#00AAAA"><br />
<th colspan="2" height="50" valign="middle"><p><font color="#FFFFFF" size="+2">Reference Section</font></p></th><br />
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<th width="50%"scope="col"><big>IDL</big></th><br />
<th width="50%"scope="col"><big>GAMAP</big></th><br />
</tr><br />
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<tr><br />
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<!-- IDL: Links --><br />
<td width="50%" valign="top"><br />
* [http://www.exelisvis.com/ Exelis Visual Information Solutions (vendor)] <br />
* [http://www.exelisvis.com/docs/routines-1.html Online IDL Reference Manual @ Exelis website]<br />
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Structures.html Structures in IDL]<br />
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Pointers.html Pointers in IDL]<br />
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Overview_of_Mathematics_in_IDL.html Overview of Mathematics in IDL]<br />
* [http://www.dfanning.com/ Coyote's Guide to IDL Programming (David Fanning's Web Site)] - Lots of tips on how to accomplish programming tasks <br />
* [http://www.mpimet.mpg.de/en/misc/software/idl IDL Page at Max Planck Institute for Meteorology] <br />
* [http://www.mpimet.mpg.de/en/misc/software/idl/doc/mgs_script.pdf Martin Schultz's IDL Tutorial (PDF Format)] <br />
* [http://idlastro.gsfc.nasa.gov/homepage.html IDL Astronomy User's Library]<br />
* [http://fermi.jhuapl.edu/s1r/idl/idl.html JHU/APL/S1R IDL routines page]<br />
* [http://cow.physics.wisc.edu/~craigm/idl/idl.html Craig Markwardt's IDL library]<br />
* [http://cimss.ssec.wisc.edu/~gumley/doc/idltips.pdf The Underground Guide to IDL by Liam Gumley (PDF)]<br />
* [[Reading binary files in IDL]]<br />
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* [http://acmg.seas.harvard.edu/gamap/ GAMAP web page]<br />
* [http://acmg.seas.harvard.edu/gamap/doc/ GAMAP on-line users' guide]<br />
* [[GAMAP bugs and fixes]]<br />
* [[GAMAP tips and tricks]]<br />
**[[General GAMAP usage]]<br />
**[[TVMAP cheat sheet]]<br />
**[[File I/O with GAMAP]]<br />
***[http://acmg.seas.harvard.edu/gamap/doc/timeseries_brief_tutorial.pdf Working with timeseries output in GAMAP]<br />
**[[Color and graphics with GAMAP]]<br />
*** [http://acmg.seas.harvard.edu/geos/wiki_docs/gamap/gamap_color_table_file.pdf Loading Color Tables in GAMAP v2.12]<br />
*** [http://acmg.seas.harvard.edu/forum_files/cdh_ColorInIDL.pdf Working with color in IDL by Chris Holmes]<br />
**[[Regridding with GAMAP]]<br />
**[[Date and time computations with GAMAP]]<br />
**[[Text manipulation with GAMAP]]<br />
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<th width="50%"scope="col"><big>Fortran</big></th><br />
<th width="50%"scope="col"><big>Perl</big></th><br />
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* [[Intel Fortran Compiler]]<br />
** [http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/main_for_lin_v11.pdf Version 11.1]<br />
** [http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/main_for_lin_v12.pdf Version 12.1]<br />
** [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]<br />
** [https://software.intel.com/en-us/compiler_15.0_ug_f Version 15.0]<br />
* [[PGI Fortran compiler]]<br />
**[http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/pgiug.pdf User Guide]<br />
**[http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/pgifortref.pdf Reference Guide]<br />
* [[GNU Fortran compiler]]<br />
* [http://www-01.ibm.com/software/awdtools/fortran/xlfortran/ IBM XL Fortran]<br />
* [http://docs.sun.com/app/docs/doc/819-3686 Sun Studio 11 Fortran Compiler]<br />
* [http://www.liv.ac.uk/HPC/HTMLF90Course/HTMLF90CourseSlides.html Modular Programming w/ Fortran 90 (U. Liverpool)]<br />
* [http://www.liv.ac.uk/HPC/F90page.html Other University of Liverpool F90 tutorials and courses]<br />
* [http://sunsite.unc.edu/pub/languages/fortran/index.html User Notes on FORTRAN Programming]<br />
* [http://www.nsc.liu.se/~boein/f77to90/f77to90.html Fortran 90 for the FORTRAN 77 Programmer] <br />
* [http://www.kcl.ac.uk/kis/support/cc/fortran/f90home.html#1.0 Fortran 90 Home Page at King's College, London]<br />
* [http://www.cs.rpi.edu/~szymansk/oof90.html Object Oriented Fortran 90 Programming]<br />
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* [http://www.perl.com Perl.com]<br />
* [http://www.perl.org/books/beginning-perl/ ''Beginning Perl'' by Simon Cozens (free online book)]<br />
* [http://backpan.perl.org/authors/id/Q/QU/QUONG/perlin20.html Perl in 20 pages]<br />
* [http://www.enginsite.com/Library-Robert%27s-Perl-Tutorial.htm MediaWiki User's Guide]<br />
* [http://www.cpan.org/ Comprehensive Perl Archive Network (CPAN.org)]<br />
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<th width="50%"scope="col"><big>R</big></th><br />
<th width="50%"scope="col"><big>Python</big></th><br />
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*[http://www.r-project.org/ The R project for statistical computing]<br />
*[http://journal.r-project.org/ The R journal]<br />
*[http://www.mayin.org/ajayshah/KB/R/index.html R by example]<br />
*[[Using R to analyze GEOS-Chem data]]<br />
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*[[Python code for GEOS-Chem]]<br />
*[http://www.python.org Python.org]: Main site for all things Python<br />
*[http://docs.python.org/2/tutorial/ Python.org Tutorial]<br />
*[http://wiki.python.org/moin/BeginnersGuide/Programmers PythonWiki.org: List of tutorials and resources]<br />
*[https://developers.google.com/edu/python/ Google's Python tutorial]<br />
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<th width="50%"scope="col"><big>NCAR Command Language (NCL)</big></th><br />
<th width="50%"scope="col"><big>Wiki Documentation</big></th><br />
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* [http://www.ncl.ucar.edu/ NCL main page]<br />
* [http://www.ncl.ucar.edu/Applications/ NCL applications]<br />
* [http://www.ncl.ucar.edu/Document/ NCL documentation]<br />
* [http://www.ncl.ucar.edu/Support/email_lists.shtml Sign up for NCL-Talk email list]<br />
* [[NCL_tools_for_GEOS-Chem|NCL4GC: NCL tools for GEOS-Chem]]<br />
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* [[Sandbox]]<br />
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide]<br />
* [http://meta.wikimedia.org/wiki/Help:Wikitext Examples of Wiki markup text]<br />
* [http://meta.wikimedia.org/wiki/Help:Reference_card One-page editing reference card]<br />
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration Settings list]<br />
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]<br />
</td><br />
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</table></div>Linzhanghttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_nested_model_publications&diff=27843GEOS-Chem nested model publications2016-11-01T17:57:44Z<p>Linzhang: First version of GEOS-Chem nested model publications (2016.10.30)</p>
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<div>== Asian nested-grid ==<br />
* Wang, Y. X., Mcelroy, M. B., Jacob, D. J., and Yantosca, R. M.: A nested grid formulation for chemical transport over Asia: Applications to CO, J. Geophys. Res. Atmos., 109, D22307, 10.1029/2004JD005237, 2004.<br />
* Wang, Y. X., McElroy, M. B., Wang, T., and Palmer, P. I.: Asian emissions of CO and NOx: Constraints from aircraft and Chinese station data, J. Geophys. Res. Atmos., 109, 10--1029, 2004.<br />
* Chen, D., Wang, Y., McElroy, M. B., He, K., Yantosca, R. M., and Le Sager, P.: Regional CO pollution and export in China simulated by the high-resolution nested-grid GEOS-Chem model, Atmos. Chem. Phys., 9, 3825-3839, 10.5194/acp-9-3825-2009, 2009.<br />
* Wang, Y., Hao, J., McElroy, M. B., Munger, J. W., Ma, H., Chen, D., and Nielsen, C. P.: Ozone air quality during the 2008 Beijing Olympics: effectiveness of emission restrictions, Atmos. Chem. Phys., 9, 5237-5251, 10.5194/acp-9-5237-2009, 2009.<br />
* Jeong, J. I., Park, R. J., Woo, J. H., Han, Y. J., and Yi, S. M.: Source contributions to carbonaceous aerosol concentrations in Korea, Atmos. Environ., 45, 1116-1125, 2011.<br />
* Lin, J. T.: Satellite constraint for emissions of nitrogen oxides from anthropogenic, lightning and soil sources over East China on a high-resolution grid, Atmos. Chem. Phys., 12, 2881-2898, 2012.<br />
* Trivitayanurak, W., Palmer, P. I., Barkley, M. P., and Robinson, N. H.: The composition and variability of atmospheric aerosol over Southeast Asia during 2008, Atmos. Chem. Phys., 11, 22033-22073, 2011.<br />
* Fu, T. M., Cao, J. J., Zhang, X. Y., Lee, S. C., Zhang, Q., Han, Y. M., Qu, W. J., Han, Z., Zhang, R., Wang, Y. X., Chen, D., and Henze, D. K.: Carbonaceous aerosols in China: top-down constraints on primary sources and estimation of secondary contribution, Atmos. Chem. Phys., 12, 2725-2746, 10.5194/acp-12-2725-2012, 2012.<br />
* Lin, J. T., Liu, Z., Zhang, Q., and Liu, H.: Modeling uncertainties for tropospheric nitrogen dioxide columns affecting satellite-based inverse modeling of nitrogen oxides emissions, Atmos. Chem. Phys., 12, 12255-12275, 2012.<br />
* Wang, S. W., Zhang, Q., Streets, D. G., and He, K. B.: Growth in NOx emissions from power plants in China: bottom-up estimates and satellite observations, Atmos. Chem. Phys., 12, 45-91, 2012.<br />
* Kharol, S. K., Martin, R. V., Philip, S., Vogel, S., Henze, D. K., Chen, D., Wang, Y., Zhang, Q., and Heald, C. L.: Persistent sensitivity of Asian aerosol to emissions of nitrogen oxides, Geophys. Res. Lett., 40, 1021-1026, 10.1002/grl.50234, 2013.<br />
* Li, M., Wang, Y., and Ju, W.: Effects of a Remotely Sensed Land Cover Dataset with High Spatial Resolution on the Simulation of Secondary Air Pollutants over China Using the Nested-grid GEOS-Chem Chemical Transport Model, Advances in Atmospheric Sciences, 31, 179-187, 2013.<br />
* Shim, C., Lee, J., and Wang, Y.: Effect of continental sources and sinks on the seasonal and latitudinal gradient of atmospheric carbon dioxide over East Asia, Atmos. Environ., 79, 853-860, 2013.<br />
* Wang, Y., Zhang, Q. Q., He, K., Zhang, Q., and Chai, L.: Sulfate-nitrate-ammonium aerosols over China: response to 2000–2015 emission changes of sulfur dioxide, nitrogen oxides, and ammonia, Atmos. Chem. Phys., 13, 2635-2652, 10.5194/acp-13-2635-2013, 2013.<br />
* Zhang, Y., and Jaeglé, L.: Decreases in Mercury Wet Deposition over the United States during 2004–2010: Roles of Domestic and Global Background Emission Reductions, Atmosphere, 4, 113-131, 2013.<br />
* He, C., Li, Q. B., Liou, K. N., Zhang, J., Qi, L., Mao, Y., Gao, M., Lu, Z., Streets, D. G., and Zhang, Q.: A global 3-D CTM evaluation of black carbon in the Tibetan Plateau, Atmos. Chem. Phys., 14, 7091-7112, 2014.<br />
* Lin, J., Xin, J., Che, H., Wang, Y., and Donkelaar, A. V.: Clear-sky aerosol optical depth over East China estimated from visibility measurements and chemical transport modeling, Atmos. Environ., 95, 258-267, 2014.<br />
* Lin, J. T., Martin, R. V., Boersma, K. F., Sneep, M., Stammes, P., Spurr, R., Wang, P., Van Roozendael, M., Clémer, K., and Irie, H.: Retrieving tropospheric nitrogen dioxide over China from the Ozone Monitoring Instrument: effects of aerosols, surface reflectance anisotropy and vertical profile of nitrogen dioxide, Atmos. Chem. Phys., 14, 1441-1461, 2014.<br />
* Mu, Q., and Liao, H.: Simulation of the interannual variations of aerosols in China: role of variations in meteorological parameters, Atmos. Chem. Phys., 14, 11177-11219, 2014.<br />
* Wai, K. M., and Tanner, P. A.: Recent Springtime Regional CO Variability in Southern China and the Adjacent Ocean: Anthropogenic and Biomass Burning Contribution, Aerosol & Air Quality Research, 14, 21-32, 2014.<br />
* Wang, L., Wang, S., Zhang, L., Wang, Y., Zhang, Y., Nielsen, C., Mcelroy, M. B., and Hao, J.: Source apportionment of atmospheric mercury pollution in China using the GEOS-Chem model, Environ. Pollut., 190, 166-175, 2014.<br />
* Wang, Y., Zhang, Q., Jiang, J., Wei, Z., Wang, B., He, K., Duan, F., Qian, Z., Sajeev, P., and Xie, Y.: Enhanced sulfate formation during China's severe winter haze episode in Jan 2013 missing from current models, J. Geophys. Res. Atmos., 119, 10,425-410,440, 2014.<br />
* Geng, G. N., Zhang, Q., Martin, R. V., van Donkelaar, A., Huo, H., Che, H. Z., Lin, J. T., and He, K. B.: Estimating long-term PM2.5 concentrations in China using satellite-based aerosol optical depth and a chemical transport model, Remote Sensing Of Environment, 166, 262-270, 10.1016/j.rse.2015.05.016, 2015.<br />
* Lou, S. J., Liao, H., Yang, Y., and Mu, Q.: Simulation of the interannual variations of tropospheric ozone over China: Roles of variations in meteorological parameters and anthropogenic emissions, Atmos. Environ., 122, 839-851, 10.1016/j.atmosenv.2015.08.081, 2015.<br />
* Zhang, L., Liu, L., Zhao, Y., Gong, S., Zhang, X., Henze, D. K., Capps, S. L., Fu, T.-M., Zhang, Q., and Wang, Y.: Source attribution of particulate matter pollution over North China with the adjoint method, Environmental Research Letters, 10, 084011, 10.1088/1748-9326/10/8/084011, 2015.<br />
* Zhao, Y., Zhang, L., Pan, Y., Wang, Y., Paulot, F., and Henze, D. K.: Atmospheric nitrogen deposition to the northwestern Pacific: seasonal variation and source attribution, Atmos. Chem. Phys., 15, 10905-10924, 10.5194/acp-15-10905-2015, 2015.<br />
* Zhang, Q.Q., Y. Wang, Q. Ma, Y. Xie, K. He, Regional differences in Chinese SO2 emission control efficiency and policy implications, Atmos. Chem. Phys., 15, 6521-6533, 2015<br />
* Cui, Y. Z., Lin, J. T., Song, C. Q., Liu, M. Y., Yan, Y. Y., Xu, Y., and Huang, B.: Rapid growth in nitrogen dioxide pollution over Western China, 2005-2013, Atmos. Chem. Phys., 16, 6207-6221, 10.5194/acp-16-6207-2016, 2016.<br />
* Li, K., Liao, H., Mao, Y. H., and Ridley, D. A.: Source sector and region contributions to concentration and direct radiative forcing of black carbon in China, Atmos. Environ., 124, 351-366, 10.1016/j.atmosenv.2015.06.014, 2016.<br />
* Zhu, J., and Liao, H.: Future ozone air quality and radiative forcing over China owing to future changes in emissions under the Representative Concentration Pathways (RCPs), J. Geophys. Res.-Atmos., 121, 1978-2001, 10.1002/2015jd023926, 2016.<br />
<br />
== North America nested-grid ==<br />
* Li, Q., Jacob, D. J., Park, R., Wang, Y., Heald, C. L., Hudman, R., Yantosca, R. M., Martin, R. V., and Evans, M.: North American pollution outflow and the trapping of convectively lifted pollution by upper‐level anticyclone, J. Geophys. Res. Atmos., 110, 257-266, 2005.<br />
* Wang, H., Jacob, D. J., Sager, P. L., Streets, D. G., Park, R. J., Gilliland, A. B., and Donkelaar, A. V.: Surface ozone background in the United States: Canadian and Mexican pollution influences, Atmos. Environ., 43, 1310-1319, 2009.<br />
* Zhang, L., Jacob, D. J., Downey, N. V., Wood, D. A., Blewitt, D., Carouge, C. C., van Donkelaar, A., Jones, D. B. A., Murray, L. T., and Wang, Y.: Improved estimate of the policy-relevant background ozone in the United States using the GEOS-Chem global model with 1/2° × 2/3° horizontal resolution over North America, Atmos. Environ., 45, 6769-6776, 10.1016/j.atmosenv.2011.07.054, 2011.<br />
* Zoogman, P., Jacob, D. J., Chance, K., Zhang, L., Le Sager, P., Fiore, A. M., Eldering, A., Liu, X., Natraj, V., and Kulawik, S. S.: Ozone air quality measurement requirements for a geostationary satellite mission, Atmos. Environ., 45, 7143-7150, 10.1016/j.atmosenv.2011.05.058, 2011.<br />
* van Donkelaar, A., Martin, R. V., Pasch, A. N., Szykman, J. J., Zhang, L., Wang, Y. X., and Chen, D.: Improving the Accuracy of Daily Satellite-Derived Ground-Level Fine Aerosol Concentration Estimates for North America, Environ. Sci. Technol., 46, 11971-11978, 10.1021/es3025319, 2012.<br />
* Heald, C. L., J. L. Collett, J., Lee, T., Benedict, K. B., Schwandner, F. M., Li, Y., Clarisse, L., Hurtmans, D. R., Van Damme, M., Clerbaux, C., Coheur, P. F., Philip, S., Martin, R. V., and Pye, H. O. T.: Atmospheric ammonia and particulate inorganic nitrogen over the United States, Atmos. Chem. Phys., 12, 10295-10312, 10.5194/acp-12-10295-2012, 2012.<br />
* Hu, L., Millet, D. B., Kim, S. Y., Wells, K. C., Griffis, T. J., Fischer, E. V., Helmig, D., Hueber, J., and Curtis, A. J.: North American acetone sources determined from tall tower measurements and inverse modeling, Atmos. Chem. Phys., 12, 30869-30908, 2012.<br />
* Zhang, L., Jacob, D. J., Knipping, E. M., Kumar, N., Munger, J. W., Carouge, C. C., van Donkelaar, A., Wang, Y. X., and Chen, D.: Nitrogen deposition to the United States: distribution, sources, and processes, Atmos. Chem. Phys., 12, 4539-4554, 10.5194/acp-12-4539-2012, 2012.<br />
* Zhang, Y., Jaeglé, L., Donkelaar, A. V., Martin, R. V., Holmes, C. D., Amos, H. M., Wang, Q., Talbot, R., Artz, R., and Brooks, S.: Nested-grid simulation of mercury over North America, Atmos. Chem. Phys., 12, 2603-2646, 2012.<br />
* Ellis, R. A., Jacob, D. J., Sulprizio, M. P., Zhang, L., Holmes, C. D., Schichtel, B. A., Blett, T., Porter, E., Pardo, L. H., and Lynch, J. A.: Present and future nitrogen deposition to national parks in the United States: critical load exceedances, Atmos. Chem. Phys., 13, 9083-9095, 10.5194/acp-13-9083-2013, 2013.<br />
* Zhang, L., Jacob, D. J., Yue, X., Downey, N. V., Wood, D. A., and Blewitt, D.: Sources contributing to background surface ozone in the US Intermountain West, Atmos. Chem. Phys., 14, 5295-5309, 10.5194/acp-14-5295-2014, 2014.<br />
* Hu, L., Millet, D. B., Baasandorj, M., Griffis, T. J., Travis, K. R., Tessum, C. W., Marshall, J. D., Reinhart, W. F., Mikoviny, T., Muller, M., Wisthaler, A., Graus, M., Warneke, C., and de Gouw, J.: Emissions of C6-C8 aromatic compounds in the United States: Constraints from tall tower and aircraft measurements, J. Geophys. Res.-Atmos., 120, 826-842, 10.1002/2014jd022627, 2015.<br />
* Jiang, Z., Jones, D. B. A., Worden, J., Worden, H. M., Henze, D. K., and Wang, Y. X.: Regional data assimilation of multi-spectral MOPITT observations of CO over North America, Atmos. Chem. Phys., 15, 5327-5358, 2015.<br />
* Kim, P. S., Jacob, D. J., Fisher, J. A., Travis, K., Yu, K., Zhu, L., Yantosca, R. M., Sulprizio, M. P., Jimenez, J. L., and Campuzano-Jost, P.: Sources, seasonality, and trends of Southeast US aerosol: an integrated analysis of surface, aircraft, and satellite observations with the GEOS-Chem chemical transport model, Atmos. Chem. Phys., 15, 17651-17709, 2015.<br />
* Kim, P. S., Jacob, D. J., Mickley, L. J., Koplitz, S. N., Marlier, M. E., DeFries, R. S., Myers, S. S., Chew, B. N., and Mao, Y. H.: Sensitivity of population smoke exposure to fire locations in Equatorial Asia, Atmos. Environ., 102, 11-17, 10.1016/j.atmosenv.2014.09.045, 2015.<br />
* Wang, Y., Xie, Y., Cai, L., Dong, W., Zhang, Q., and Zhang, L.: Impact of the 2011 Southern U.S. Drought on Ground-Level Fine Aerosol Concentration in Summertime, Journal of the Atmospheric Sciences, 72, 1075-1093, 10.1175/jas-d-14-0197.1, 2015.<br />
* D'Andrea, S. D., Ng, J. Y., Kodros, J. K., Atwood, S. A., Wheeler, M. J., Macdonald, A. M., Leaitch, W. R., and Pierce, J. R.: Source attribution of aerosol size distributions and model evaluation using Whistler Mountain measurements and GEOS-Chem-TOMAS simulations, Atmos. Chem. Phys., 16, 383-396, 10.5194/acp-16-383-2016, 2016.<br />
* Yu, K., Jacob, D. J., Fisher, J. A., Kim, P. S., Marais, E. A., Miller, C. C., Travis, K. R., Zhu, L., Yantosca, R. M., and Sulprizio, M. P.: Sensitivity to grid resolution in the ability of a chemical transport model to simulate observed oxidant chemistry under high-isoprene conditions, Atmos. Chem. Phys., 16, 1-16, 2016.<br />
* Fisher, J. A., Jacob, D. J., Travis, K. R., Kim, P. S., Marais, E. A., Miller, C. C., Yu, K., Zhu, L., Yantosca, R. M., and Sulprizio, M. P.: Organic nitrate chemistry and its implications for nitrogen budgets in an isoprene- and monoterpene-rich atmosphere: constraints from aircraft (SEAC4RS) and ground-based (SOAS) observations in the Southeast US, Atmos. Chem. Phys., 16, 1-38, 2016.<br />
* Travis, K. R., D. J. Jacob, J. A. Fisher, P. S. Kim, E. A. Marais, L. Zhu, K. Yu, C. C. Miller, R. M. Yantosca, M. P. Sulprizio, A. M. Thompson, P. O. Wennberg, J. D. Crounse, J. M. St. Clair, R. C. Cohen, J. L. Laughner, J. E. Dibb, S. R. Hall, K. Ullmann, G. M. Wolfe, J. A. Neuman, and X. Zhou, NOx emissions, isoprene oxidation pathways, vertical mixing, and implications for surface ozone in the Southeast United States, submitted to Atmos. Chem. Phys. Discuss., 2016.<br />
<br />
== Other nested-grid domains ==<br />
* Tombrou, M., Bossioli, E., Protonotariou, A. P., Flocas, H., Giannakopoulos, C., and Dandou, A.: Coupling GEOS-CHEM with a regional air pollution model for Greece, Atmos. Environ., 43, 4793-4804, 2009.<br />
* Protonotariou, A. P., Tombrou, M., Giannakopoulos, C., Kostopoulou, E., and Sager, P. L.: Study of CO surface pollution in Europe based on observations and nested-grid applications of GEOS-CHEM global chemical transport model, Tellus Series B-chemical & Physical Meteorology, 62, 209-227, 2010.<br />
* Barkley, M. P., Palmer, P. I., Ganzeveld, L., Arneth, A., Hagberg, D., Karl, T., Guenther, A., Paulot, F., Wennberg, P. O., and Mao, J.: Can a “state of the art” chemistry transport model simulate Amazonian tropospheric chemistry?, J. Geophys. Res. Atmos., 116, 2011.<br />
* Barkley, M. P., Smedt, I. D., Van Roozendael, M., Kurosu, T. P., Chance, K., Arneth, A., Hagberg, D., Guenther, A., Paulot, F., and Marais, E.: Top-down isoprene emissions over tropical South America inferred from SCIAMACHY and OMI formaldehyde columns, J. Geophys. Res. Atmos., 118, 6849–6868, 2013.<br />
* Vinken, G. C. M., Boersma, K. F., van Donkelaar, A., and Zhang, L.: Constraints on ship NOx emissions in Europe using GEOS-Chem and OMI satellite NO2 observations, Atmos. Chem. Phys., 14, 1353-1369, 10.5194/acp-14-1353-2014, 2014.<br />
* Dunmore, R. E., Whalley, L. K., Sherwen, T., Evans, M. J., Heard, D. E., Hopkins, J. R., Lee, J. D., Lewis, A. C., Lidster, R. T., Rickard, A. R., and Hamilton, J. F.: Atmospheric ethanol in London and the potential impacts of future fuel formulations, Faraday Discussions, 189, 105-120, 10.1039/c5fd00190k, 2016.<br />
<br />
== Nested-grid Adjoint ==<br />
* Zhang, L., Liu, L., Zhao, Y., Gong, S., Zhang, X., Henze, D. K., Capps, S. L., Fu, T.-M., Zhang, Q., and Wang, Y.: Source attribution of particulate matter pollution over North China with the adjoint method, Environmental Research Letters, 10, 084011, 10.1088/1748-9326/10/8/084011, 2015.<br />
* Zhang, L., Shao, J., Lu, X., Zhao, Y., Hu, Y., Henze, D. K., Liao, H., Gong, S., and Zhang, Q.: Sources and Processes Affecting Fine Particulate Matter Pollution over North China: An Adjoint Analysis of the Beijing APEC Period, Environmental science & technology, 50, 8731-8740, 10.1021/acs.est.6b03010, 2016.<br />
<br />
== Two-way nested-grid ==<br />
* Yan, Y. Y., Lin, J. T., Kuang, Y., Yang, D., and Zhang, L.: Tropospheric carbon monoxide over the Pacific during HIPPO: two-way coupled simulation of GEOS-Chem and its multiple nested models, Atmos. Chem. Phys., 14, 12649-12663, 2014.<br />
* Yan, Y. Y., Lin, J. T., Chen, J. X., and Hu, L.: Improved simulation of tropospheric ozone by a global-multi-regional two-way coupling model system, Atmos. Chem. Phys., 16, 2381-2400, 10.5194/acp-16-2381-2016, 2016.</div>Linzhanghttps://wiki.seas.harvard.edu/geos-chem/index.php?title=Main_Page&diff=27842Main Page2016-11-01T17:33:29Z<p>Linzhang: Adding a link to the nested model publication page</p>
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</table><br />
<br />
<blockquote><p align="justify">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.]</p></blockquote><br />
<br />
<blockquote><p align="justify">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.</p></blockquote><br />
<br />
<blockquote><p align="justify">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!</p></blockquote><br />
<br />
<blockquote><br />
<table width="1000px" border="1" bordercolor="#000000" cellspacing="0" cellpadding=10"> <br />
<tr><br />
<td bgcolor="#CCFFFF"><p align="center"><big><strong>Current public release:</strong></big></p></td><br />
<td bgcolor="#CCFFFF"><p align="center"><big><strong>[[GEOS-Chem v10-01]]</strong></big></p></td><br />
<td bgcolor="#CCFFFF"><p align="center"><big><strong>[[GEOS-Chem v10-01 benchmark history|v10-01 benchmark history]]</strong></big></p></td><br />
</tr><br />
<tr><br />
<td width="300px"><p align="center"><big><strong>Version in development:</strong></big></p></td><br />
<td width="250px"><p align="center"><big><strong>[[GEOS-Chem v11-01]]</strong></big></p></td><br />
<td width="250px"><p align="center"><big><strong>[[GEOS-Chem v11-01 benchmark history|v11-01 benchmark history]]</strong></big></p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><big><strong>Version for high-performance computing (HPC) environments:</strong></big></p></td><br />
<td><p align="center"><big><strong>[[GEOS-Chem HP]]</strong></big><br />
</p></td><br />
<td>&nbsp;</td><br />
<tr><br />
<tr><br />
<td><p align="center"><big><strong>Supported meteorological fields:</strong></big></p></td><br />
<td><p align="center"><big><strong>[[Overview_of_GMAO_met_data_products#GMAO_met_field_comparison_chart|Refer to this table]]</strong></big><br />
</p></td><br />
<td>&nbsp;</td><br />
<tr><br />
<td><p align="center"><big><strong>List of publications:</strong></big></p></td><br />
<td><p align="center"><big><strong>[http://acmg.seas.harvard.edu/geos/geos_pub.html Refer to this page]</strong></big><br />
</p></td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
</blockquote><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== GENERAL INFO ABOUT GEOS-CHEM ===== --><br />
<!-- ======================================================== --><br />
<p>&nbsp;</p><br />
<table width="100%" border="1" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"><br />
<br />
<tr bgcolor="#00AAAA"><br />
<th colspan="2" height="50" valign="middle"><p><font color="#FFFFFF" size="+2">General information about GEOS&#150;Chem</font></p></th><br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== GENERAL INFO : FIRST ROW ===== --><br />
<!-- ======================================================== --><br />
<br />
<!-- Header title --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>Introduction and overview</big></th><br />
<th width="50%"scope="col"><big>Steering Committee And Working Groups</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Introduction & Overview: Links --><br />
<td width="50%" valign="top"><br />
* [[GEOS-Chem welcome letter for new users]]<br />
* [[Features of the GEOS-Chem public wiki]]<br />
* [[Customizing your GEOS-Chem Wiki Settings]]<br />
* [http://acmg.seas.harvard.edu/geos/geos_overview.html GEOS-Chem Overview]<br />
* [http://acmg.seas.harvard.edu/geos/geos_people.html GEOS-Chem People & Projects]<br />
* [http://acmg.seas.harvard.edu/geos/word_pdf_docs/resources_guidelines_tips.pdf User Resources, Code Development Guidelines, and Debugging Tips]<br />
* [[GEOS-Chem Support Team]]<br />
* [[GEOS-Chem newsletters]]<br />
* [http://acmg.seas.harvard.edu/geos/geos_search.html GEOS-Chem Search Engines]<br />
* [http://acmg.seas.harvard.edu/geos/geos_new_developments.html Recommendations for offering co-authorships to GEOS-Chem developers]<br />
* [http://acmg.seas.harvard.edu/geos/geos_dev_history.html GEOS-Chem code development history]<br />
<br />
</td><br />
<br />
<!-- Steering Committee and Working Groups: Links --><br />
<td width="50%" valign="top"><br />
* [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee]<br />
** [[GEOS-Chem model development priorities]]<br />
* [http://acmg.seas.harvard.edu/geos/geos_working_groups.html GEOS-Chem Working Groups]<br />
** [[GEOS-Chem Adjoint|Adjoint Model and Data Assimilation Working Group]]<br />
** [[Aerosols Working Group]]<br />
** [[Carbon Cycle Working Group]]<br />
** [[Chemistry-Climate Working Group]]<br />
** [[GEOS-Chem High Performance Working Group]]<br />
** [[Hg and POPs Working Group]]<br />
** [[Organics Working Group]]<br />
** [[Chemistry Issues|Oxidants and Chemistry Working Group]]<br />
** [[Nested Model Working Group]]<br />
** [[Sources and Sinks Working Group|Sources and Surface Uptake Working Group]]<br />
** [[Transport Working Group]]<br />
</td><br />
<br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== GENERAL INFO : SECOND ROW ===== --><br />
<!-- ======================================================== --><br />
<br />
<!-- Header title --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>Getting Started With GEOS-Chem</big></th><br />
<th width="50%"scope="col"><big>General Technical Information</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Getting Started With GEOS-Chem: Links --><br />
<td width="50%" valign="top"><br />
* [[Frequently asked questions about GEOS-Chem]]<br />
* [[Minimum system requirements for GEOS-Chem]]<br />
* [[GEOS-Chem supported platforms and compilers]]<br />
* [[Downloading GEOS-Chem source code and data]]<br />
* [[Creating GEOS-Chem run directories]]<br />
* [[GEOS-Chem programming resources]] (e.g. tutorials, user guides, etc.)<br />
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_7.html GEOS-Chem Programming Style Guide]<br />
</td><br />
<br />
<!-- General Technical Information: Links --><br />
<td width="50%" valign="top"><br />
* [[Initial conditions for GEOS-Chem]]<br />
* [[Centralized chemistry time step]]<br />
* [[GEOS-Chem Debugging Tips|Tips on how to debug GEOS-Chem effectively]]<br />
* [[Reporting GEOS-Chem bugs]]<br />
* [[Debugging with the GEOS-Chem unit tester]]<br />
* [[Parallelizing GEOS-Chem]] with the OpenMP directives<br />
* [[Common GEOS-Chem error messages]]<br />
* [[Adding tracers to GEOS-Chem|Adding advected tracers and chemical species to GEOS-Chem]]<br />
* [[Adding Passive Tracers|Adding passive (CO-like) tracers to GEOS-Chem]]<br />
</td><br />
<br />
</tr><br />
</table><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== CODE DEVELOPER'S FORUMS: TITLE ===== --><br />
<!-- ======================================================== --><br />
<p>&nbsp;</p><br />
<table width="100%" border="1" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"><br />
<br />
<tr bgcolor="#00AAAA"><br />
<th colspan="2" height="50" valign="middle"><p><font color="#FFFFFF" size="+2">GEOS&#150;Chem Code Developers' Forums</font></p></th><br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== CODE DEVELOPER'S FORUMS : FIRST ROW ===== --><br />
<!-- ======================================================== --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>Coding</big></th><br />
<th width="50%"scope="col"><big>Diagnostics</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Coding: Links --><br />
<td width="50%" valign="top"><br />
* [[GEOS-Chem versions under development]]<br />
* [[Bugs and fixes|List of GEOS-Chem bugs and in which version they were resolved]]<br />
* [[Currently unresolved issues in GEOS-Chem]]<br />
* [[Common GEOS-Chem error messages]]<br />
* [[Known issues caused by compiler bugs|Known GEOS-Chem issues caused by compiler bugs]]<br />
* [[GEOS-Chem performance]]<br />
* [[Machine issues and portability]]<br />
* [[Passing array arguments efficiently in GEOS-Chem]]<br />
* [[Floating point math issues]]<br />
* [[Version control with Git]]<br />
</td><br />
<br />
<!-- Diagnostics: Links --><br />
<td width="50%" valign="top"><br />
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_5.html Overview of diagnostics characteristics]<br />
* [[Diagnostic time step]]<br />
* [[Mass Flux (ND24/25/26)]]<br />
* [[Additional diagnostics]]<br />
</td><br />
<br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== CODE DEVELOPER'S FORUMS : SECOND ROW ===== --><br />
<!-- ======================================================== --><br />
<br />
<!-- Header title --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>Emissions</big></th><br />
<th width="50%"scope="col"><big>Chemistry</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Emissions: Links --><br />
<td width="50%" valign="top"><br />
* [[HEMCO|HEMCO emissions component]]<br />
* [[HEMCO data directories]]<br />
* [[Aerosol emissions]]<br />
* [[Aircraft emissions]]<br />
* [[Anthropogenic emissions]]<br />
* [[Scale factors for anthropogenic emissions]]<br />
* [[Biofuel emissions]]<br />
* [[Biogenic emissions]]<br />
* [[Biomass burning emissions]]<br />
* [[Lightning NOx emissions]]<br />
* [[Ship emissions]]<br />
* [[Soil NOx emissions]]<br />
* [[Volcanic SO2 emissions from Aerocom|Volcanic emissions]]<br />
* [[Historical and Future Emissions|Historical and future emissions]]<br />
</td><br />
<br />
<!-- Chemistry Links --><br />
<td width="50%" valign="top"><br />
* [[GEOS-Chem chemistry mechanisms]]<br />
* [[GEOS-Chem chemistry mechanisms#Stratospheric chemistry|Stratopsheric chemistry options]]<br />
* [[GEOS-Chem chemistry mechanisms#Specialty simulations|Specialty simulations (aka "offline simulations")]]<br />
* Other resources<br />
** [[Chemistry Issues]]<br />
** [[Process Analysis Diagnostics]]<br />
** [[Photolysis mechanism|Photolysis mechanisms used in GEOS-Chem]]<br />
** [[DSMACC chemical box model]]<br />
** [[Isoprene|List of recent papers about isoprene]]<br />
** [[Linking GEOS-Chem to CMAQ]]<br />
** [[Coupling GEOS-Chem with RRTMG]] <br />
*[[GEOS-Chem species database]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span><br />
*[[Physical properties of GEOS-Chem species]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span><br />
*[[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><br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== CODE DEVELOPER'S FORUMS : THIRD ROW ===== --><br />
<!-- ======================================================== --><br />
<br />
<!-- Header title --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>Dynamics</big></th><br />
<th width="50%"scope="col"><big>Deposition</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Dynamics: Links --><br />
<td width="50%" valign="top"><br />
* [[Advection scheme TPCORE]]<br />
* [[Boundary layer mixing]]<br />
* [[Cloud convection]]<br />
* [[Dynamic tropopause]]<br />
</td><br />
<br />
<!-- Deposition: Links --><br />
<td width="50%" valign="top"><br />
* [[Dry deposition]]<br />
**[[Leaf area indices in GEOS-Chem]]<br />
* [[Wet deposition]]<br />
</td><br />
<br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== CODE DEVELOPER'S FORUMS : FOURTH ROW ===== --><br />
<!-- ======================================================== --><br />
<br />
<!-- Header title --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>Aerosols</big></th><br />
<th width="50%"scope="col"><big>Met Fields</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Aerosols: Links --><br />
<td width="50%" valign="top"><br />
* [[Aerosols overview: projects and developments|Aerosols working group]]<br />
* [[Aerosol-only simulation]]<br />
* [[Aerosol optical properties]]<br />
* [[Aerosol thermodynamical equilibrium]]<br />
* [[Carbonaceous aerosols]]<br />
* [[Mineral dust aerosols]]<br />
* [[Secondary organic aerosols]]<br />
* [[Sea salt aerosols]]<br />
* [[Sulfate aerosols]]<br />
* Aerosol Microphysics<br />
** [[APM aerosol microphysics|APM]]<br />
** [[TOMAS aerosol microphysics|TOMAS]]<br />
</td><br />
<br />
<!-- Met Fields: Links --><br />
<td width="50%" valign="top"><br />
* [[GCAP]] <br />
** [[List of GCAP met fields|List of GCAP met fields used by GEOS-Chem]]<br />
* [[Overview of GMAO met data products]]<br />
* [[Version history of GMAO met data products]]<br />
* [[GMAO GEOS-4]]<br />
** [[List of GEOS-4 met fields|List of GEOS-4 met fields used by GEOS-Chem]]<br />
* [[GEOS-5|GMAO GEOS-5.2.0]]<br />
** [[List of GEOS-5 met fields|List of GEOS-5.2.0 met fields used by GEOS-Chem]]<br />
** [[GEOS-5 issues|Issues with GEOS-5.2.0 met data]]<br />
* [[MERRA|GMAO MERRA "reanalysis"]]<br />
** [[List of MERRA met fields|List of MERRA met fields used by GEOS-Chem]]<br />
** [[MERRA implementation details|Implementing MERRA into GEOS-Chem]]<br />
* [[GEOS-FP|GMAO GEOS-FP]]<br />
** [[List of GEOS-FP met fields|List of GEOS-FP met fields used by GEOS-Chem]]<br />
** [[GEOS-FP implementation details|Implementing GEOS-FP into GEOS-Chem]]<br />
* [[MERRA-2|GMAO MERRA-2]]<br />
** [[List of MERRA-2 met fields|List of MERRA-2 met fields used by GEOS-Chem]]<br />
** [[MERRA-2 implementation details|Implementing MERRA-2 into GEOS-Chem]]<br />
* [[Notes regarding GEOS vertical grids]]<br />
* [[Available met data for nested grid simulations]]<br />
* [[List of reprocessed met fields]]<br />
</td><br />
<br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== CODE DEVELOPER'S FORUMS : FIFTH ROW ===== --><br />
<!-- ======================================================== --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>Nested Grid Simulations</big></th><br />
<th width="50%"scope="col"><big>Earth System Model Framework</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Nested Grid Simulations: Links --><br />
<td width="50%" valign="top"><br />
* [[GEOS-Chem nested grid simulations]]<br />
* [[Setting up GEOS-Chem nested grid simulations]]<br />
* [[Available met data for nested grid simulations]]<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf Protocol for nested-grid data downloads]<br />
* [[GEOS-Chem nested model publications]]<br />
</td><br />
<br />
<!-- Libraries --><br />
<td width="50%" valign="top"><br />
* [[Installing ESMF and other required libraries]]<br />
* [[Code development with the Earth System Model Framework]]<br />
* [[Automatic documentation with protex|Generating automatic LaTeX documentation with protex]]<br />
** [http://frodo.elon.edu/tutorial/tutorial/tutorial.html Web-based LaTeX tutorial]<br />
</td><br />
<br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== CODE DEVELOPER'S FORUMS : SIXTH ROW ===== --><br />
<!-- ======================================================== --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>Benchmarking and Evaluation</big></th><br />
<th width="50%"scope="col"><big>Related Projects</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Diagnostics: Links --><br />
<td width="50%" valign="top"><br />
* [http://acmg.seas.harvard.edu/geos/geos_benchmark.html General info about GEOS-Chem benchmark simulations]<br />
* [http://acmg.seas.harvard.edu/geos/geos_1yr_plots.html List of GEOS-Chem 1-year benchmark simulations]<br />
* [[Mean OH lifetime in GEOS-Chem]]<br />
* [ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/ FTP site with output from 1-year GEOS-Chem benchmark simulations]<br />
* [[GEOS-Chem participation in community intercomparisons]]<br />
* [[Satellite_Specifications_Table|Satellite Instrument Specifications Table]]<br />
</td><br />
<br />
<!-- Related Projects: Links --><br />
<td width="50%" valign="top"><br />
* [[Grid-independent GEOS-Chem]]<br />
* [[GEOS-Chem Adjoint]]<br />
* [[GEOS-Chem Near-Real-Time Simulations]]<br />
* [[FlexAOD]]<br />
</td><br />
<br />
</tr><br />
</table><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== REFERENCE: TITLE ===== --><br />
<!-- ======================================================== --><br />
<p>&nbsp;</p><br />
<table width="100%" border="1" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"><br />
<br />
<tr bgcolor="#00AAAA"><br />
<th colspan="2" height="50" valign="middle"><p><font color="#FFFFFF" size="+2">Reference Section</font></p></th><br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== REFERENCE: FIRST ROW ===== --><br />
<!-- ======================================================== --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>IDL</big></th><br />
<th width="50%"scope="col"><big>GAMAP</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- IDL: Links --><br />
<td width="50%" valign="top"><br />
* [http://www.exelisvis.com/ Exelis Visual Information Solutions (vendor)] <br />
* [http://www.exelisvis.com/docs/routines-1.html Online IDL Reference Manual @ Exelis website]<br />
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Structures.html Structures in IDL]<br />
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Pointers.html Pointers in IDL]<br />
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Overview_of_Mathematics_in_IDL.html Overview of Mathematics in IDL]<br />
* [http://www.dfanning.com/ Coyote's Guide to IDL Programming (David Fanning's Web Site)] - Lots of tips on how to accomplish programming tasks <br />
* [http://www.mpimet.mpg.de/en/misc/software/idl IDL Page at Max Planck Institute for Meteorology] <br />
* [http://www.mpimet.mpg.de/en/misc/software/idl/doc/mgs_script.pdf Martin Schultz's IDL Tutorial (PDF Format)] <br />
* [http://idlastro.gsfc.nasa.gov/homepage.html IDL Astronomy User's Library]<br />
* [http://fermi.jhuapl.edu/s1r/idl/idl.html JHU/APL/S1R IDL routines page]<br />
* [http://cow.physics.wisc.edu/~craigm/idl/idl.html Craig Markwardt's IDL library]<br />
* [http://cimss.ssec.wisc.edu/~gumley/doc/idltips.pdf The Underground Guide to IDL by Liam Gumley (PDF)]<br />
* [[Reading binary files in IDL]]<br />
</td><br />
<br />
<!-- Diagnostics: Links --><br />
<td width="50%" valign="top"><br />
* [http://acmg.seas.harvard.edu/gamap/ GAMAP web page]<br />
* [http://acmg.seas.harvard.edu/gamap/doc/ GAMAP on-line users' guide]<br />
* [[GAMAP bugs and fixes]]<br />
* [[GAMAP tips and tricks]]<br />
**[[General GAMAP usage]]<br />
**[[TVMAP cheat sheet]]<br />
**[[File I/O with GAMAP]]<br />
***[http://acmg.seas.harvard.edu/gamap/doc/timeseries_brief_tutorial.pdf Working with timeseries output in GAMAP]<br />
**[[Color and graphics with GAMAP]]<br />
*** [http://acmg.seas.harvard.edu/geos/wiki_docs/gamap/gamap_color_table_file.pdf Loading Color Tables in GAMAP v2.12]<br />
*** [http://acmg.seas.harvard.edu/forum_files/cdh_ColorInIDL.pdf Working with color in IDL by Chris Holmes]<br />
**[[Regridding with GAMAP]]<br />
**[[Date and time computations with GAMAP]]<br />
**[[Text manipulation with GAMAP]]<br />
</td><br />
<br />
</tr><br />
<br />
<!-- ======================================================== --><br />
<!-- ===== REFERENCE: SECOND ROW ===== --><br />
<!-- ======================================================== --><br />
<br />
<!-- Header title --><br />
<tr bgcolor="#cccccc"><br />
<th width="50%"scope="col"><big>Fortran</big></th><br />
<th width="50%"scope="col"><big>Perl</big></th><br />
</tr><br />
<br />
<tr><br />
<br />
<!-- Fortran: Links --><br />
<td width="50%" valign="top"><br />
* [[Intel Fortran Compiler]]<br />
** [http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/main_for_lin_v11.pdf Version 11.1]<br />
** [http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/main_for_lin_v12.pdf Version 12.1]<br />
** [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]<br />
** [https://software.intel.com/en-us/compiler_15.0_ug_f Version 15.0]<br />
* [[PGI Fortran compiler]]<br />
**[http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/pgiug.pdf User Guide]<br />
**[http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/pgifortref.pdf Reference Guide]<br />
* [[GNU Fortran compiler]]<br />
* [http://www-01.ibm.com/software/awdtools/fortran/xlfortran/ IBM XL Fortran]<br />
* [http://docs.sun.com/app/docs/doc/819-3686 Sun Studio 11 Fortran Compiler]<br />
* [http://www.liv.ac.uk/HPC/HTMLF90Course/HTMLF90CourseSlides.html Modular Programming w/ Fortran 90 (U. Liverpool)]<br />
* [http://www.liv.ac.uk/HPC/F90page.html Other University of Liverpool F90 tutorials and courses]<br />
* [http://sunsite.unc.edu/pub/languages/fortran/index.html User Notes on FORTRAN Programming]<br />
* [http://www.nsc.liu.se/~boein/f77to90/f77to90.html Fortran 90 for the FORTRAN 77 Programmer] <br />
* [http://www.kcl.ac.uk/kis/support/cc/fortran/f90home.html#1.0 Fortran 90 Home Page at King's College, London]<br />
* [http://www.cs.rpi.edu/~szymansk/oof90.html Object Oriented Fortran 90 Programming]<br />
</td><br />
<br />
<!-- Perl: Links --><br />
<td width="50%" valign="top"><br />
* [http://www.perl.com Perl.com]<br />
* [http://www.perl.org/books/beginning-perl/ ''Beginning Perl'' by Simon Cozens (free online book)]<br />
* [http://backpan.perl.org/authors/id/Q/QU/QUONG/perlin20.html Perl in 20 pages]<br />
* [http://www.enginsite.com/Library-Robert%27s-Perl-Tutorial.htm MediaWiki User's Guide]<br />
* [http://www.cpan.org/ Comprehensive Perl Archive Network (CPAN.org)]<br />
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<th width="50%"scope="col"><big>R</big></th><br />
<th width="50%"scope="col"><big>Python</big></th><br />
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*[http://www.r-project.org/ The R project for statistical computing]<br />
*[http://journal.r-project.org/ The R journal]<br />
*[http://www.mayin.org/ajayshah/KB/R/index.html R by example]<br />
*[[Using R to analyze GEOS-Chem data]]<br />
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<!-- Python: links --><br />
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*[[Python code for GEOS-Chem]]<br />
*[http://www.python.org Python.org]: Main site for all things Python<br />
*[http://docs.python.org/2/tutorial/ Python.org Tutorial]<br />
*[http://wiki.python.org/moin/BeginnersGuide/Programmers PythonWiki.org: List of tutorials and resources]<br />
*[https://developers.google.com/edu/python/ Google's Python tutorial]<br />
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<th width="50%"scope="col"><big>NCAR Command Language (NCL)</big></th><br />
<th width="50%"scope="col"><big>Wiki Documentation</big></th><br />
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* [http://www.ncl.ucar.edu/ NCL main page]<br />
* [http://www.ncl.ucar.edu/Applications/ NCL applications]<br />
* [http://www.ncl.ucar.edu/Document/ NCL documentation]<br />
* [http://www.ncl.ucar.edu/Support/email_lists.shtml Sign up for NCL-Talk email list]<br />
* [[NCL_tools_for_GEOS-Chem|NCL4GC: NCL tools for GEOS-Chem]]<br />
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* [[Sandbox]]<br />
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide]<br />
* [http://meta.wikimedia.org/wiki/Help:Wikitext Examples of Wiki markup text]<br />
* [http://meta.wikimedia.org/wiki/Help:Reference_card One-page editing reference card]<br />
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration Settings list]<br />
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]<br />
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</table></div>Linzhang