Difference between revisions of "Sandbox"

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== feel free to experiment here ==
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== Instructions for adding tracers to GEOS-Chem ==
  
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== AQAST Newsletter, July 2014==
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'''''By [mailto:mpayer@seas.harvard.edu Melissa Payer]'''''
  
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== AQAST Semiannual Meetings ==
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These instructions describe how to add advected tracers to GEOS-Chem.  Advected tracers are carried in the <tt>STT</tt> array (which is declared in <tt>GeosCore/tracer_mod.F</tt>), and are transported by the winds. 
  
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AQAST meetings are held on a semiannual schedule and bring together team members, air quality managers, and research and applications partners. Our last meeting was held on June 17-19, 2014 at Harvard University. Access the agenda and presentations from that meeting [http://acmg.seas.harvard.edu/aqast/meetings/2014_jun/program.html here].
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NOTE: Some advected tracers are also chemical species, which comprise GEOS-Chem's NOx-Ox-HC-aerosol chemistry mechanism.
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[http://acmg.seas.harvard.edu/aqast/rotating/AQAST7.jpg Group photo is here]
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=== 8th AQAST Meeting (AQAST8): Dec 2-4, 2014 at the Georgia Institute of Technology ===
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#<p>Add tracers to input.geos under Tracer Menu</p>
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##<p>Increase “Number of tracers” accordingly</p>
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##<p>Add tracer number, name, molecular weight, and emitted species to end of tracer list</p>
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#<p>Add tracer(s) to restart file – see separate instructions</p>
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#<p>Modify the following source code routines:</p>
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##<p><tt>Headers/CMN_SIZE_mod.F</tt></p>
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###<p>Increase <tt>NNPAR</tt> by number of tracers being added</p>
 +
###<p>If the species have anthropogenic emissions, increase NEMPARA accordingly</p>
 +
###<p>If the species have biogenic emissions, increase NEMPARB accordingly</p>
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###<p>If the species have biomass burning emissions, increase NBIOMAX accordingly</p>
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##<p><tt>GeosCore/tracerid_mod.F</tt></p>
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###<p>Increase <tt>NNNTRID</tt> by the number of tracers being added NOTE: <tt>NNNTRID</tt> must be equal to <tt>NNPAR</tt> in <tt>CMN_SIZE_mod.F</tt></p>
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###<p>Define tracer IDs as needed:</p>
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####<p>IDxxxx – ID for SMVGEAR species</p>
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####<p>IDTxxxx – GEOS-Chem tracer ID</p>
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####<p>IDExxxx – GEOS-Chem emission ID</p>
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####<p>IDBFxxxx – GEOS-Chem biofuel ID</p>
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####<p>IDBxxxx – GEOS-Chem biomass ID</p>
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###<p>In subroutine <tt>TRACERID</tt>,</p>
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####<p>Under “Assign tracer, biomass, biofuel, and anthro emission ID’s,” add case for added tracers to initialize IDTxxxx, IDBFxxxx, IDBxxxx</p>
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####<p>Under “Initialize the IDExxx flags,” add IF statement for added tracer IDs and initialize IDExxxx</p>
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####<p>Under “Fill IDEMS with appropriate tracer ID #’s,” add IF statement for added tracers</p>
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####<p>Under “Print additional information,” add WRITE statements for added tracers</p>
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###<p>In subroutine SETTRACE  (NOTE: Only do the following if species is included in SMVGEAR chemical mechanism<p>
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####<p>Add IF statement, to initialize IDxxxx</p>
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####<p>In subroutine INIT_TRACERID,</p>
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####<p>Zero all IDs added (IDxxxx, IDTxxxx, IDExxxx, etc.)</p>
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##<p>Other modules that may need to be updated include:</p>
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###<p>wetscav_mod.F</p>
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###<p>drydep_mod.F</p>
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###<p>emissions_mod.F</p>
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###<p>biomass_mod.F</p>
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###<p>biofuel_mod.F</p> etc.
  
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The next AQAST meeting (AQAST8) will be held on December 2-4(Tuesday-Thursday) at Georgia Tech in Atlanta. Our hosts will be Ted Russell (Georgia Tech) and Yang Liu (Emory U.). The meeting is free and open to all. Air quality managers are especially encouraged to participate. Go to the [http://acmg.seas.harvard.edu/aqast/meetings/2014_jun/index.html meeting website] for more information and to register. Indicate when you register if you would like to give a presentation. We look forward to seeing you in Atlanta in December!
 
  
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== AQAST AQtivities ==
 
  
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=== AQAST Special Issue of <I>Environmental Manager ===
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Instructions for adding species to GEOS-Chem
  
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<I>Environmental Manager</I>, the monthly magazine of the Air & Waste Management Association, devoted its February 2014 issue to a presentation of AQAST activities in service of air quality management. The issue features an AQAST overview and six feature articles written by AQAST members. [http://acmg.seas.harvard.edu/aqast/highlight_em_2014.html Access the full issue here].
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Modify run directory files
  
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=== Q&A Session with Johnson County (Iowa) AQ managers ===
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1) Add tracers to input.geos under Tracer Menu
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c) Increase “Number of tracers” accordingly
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d) Add tracer number, name, molecular weight, and emitted species to end of tracer list
  
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AQAST member Scott Spak led a Q&A session on Johnson County air quality, recent trends, and regulatory updates with the Joint Meeting of the Johnson County Boards of Directors and Public Health, Iowa City, October 23, 2013.
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2) Add tracer(s) to restart file – see separate instructions
  
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=== AQAST Oil & Gas Tiger Team ===
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3) Modify globchem.dat to include additional species, kinetic reactions (including emissions and drydep), or photolysis reactions
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NOTE: If you modify globchem.dat and plan to run GEOS-Chem using the KPP chemical solver, you will need to generate new gckpp*.F90 files. For more information see the following wiki pages:
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http://wiki.seas.harvard.edu/geos-chem/index.php/KPP_solvers_FAQ#What_are_the_cons_of_using_KPP.3F
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http://wiki.seas.harvard.edu/geos-chem/index.php/Interfacing_GEOS-Chem_with_KPP#Generating_KPP_input_files_from_GEOS-Chem_globchem.dat
  
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Early results from the new AQAST Tiger Team project on emissions from US oil & gas recovery activities (PI Anne Thompson) will be presented at the [http://www.ladco.org/about/general/2014%20Midwest%20Air%20Quality%20Workshop/Announcement.html 2014 Midwest and Central States Air Quality Workshop] in St. Louis on April 22-24,sponsored jointly by LADCO and CenSARA.
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4) If necessary, modify:
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a) ratj.d – contains species names and branching ratios for FAST–JX photolysis species
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== New AQAST publications (with links) ==
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For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.1
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b) jv_spec.dat – contains cross-sections and quantum yields for FAST–JX photolysis species
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=== [http://acmg.seas.harvard.edu/publications/aqast/articles/February_2014_EM.pdf AQAST special issue of <I>Environmental Manager</I>] ===
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For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.3
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=== AQ User's Guide to Satellite Data ===
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Duncan, B.N., et al., Satellite Data for U.S. Air Quality Applications: Examples of Applications, Summary of Data End-User Resources, Answers to FAQs, and Common Mistakes to Avoid,, submitted to Atmospheric Environment, February 2014.
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[http://acdb-ext.gsfc.nasa.gov/People/Duncan/Duncan_2014a.pdf Article]
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=== Effect of climate change on wildfires ===
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Yue, X., L.J. Mickley, and J.A. Logan, Projection of wildfire activity in
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southern California in the mid-21st century, in press, Clim. Dyn., 2014.
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[http://acmg.seas.harvard.edu/publications/Yue_cd_accepted_2014.pdf Article]
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=== Interstate Pollution Transport in the Northeast ===
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He, H., et al., An elevated reservoir of air pollutants over the Mid-Atlantic States during the 2011 DISCOVER-AQ campaign: Airborne measurements and numerical simulations, Atmos. Environ., 85, 18-30, 2014. [http://acmg.seas.harvard.edu/publications/aqast/articles/He_2014AE_ElevatedReservoirDISOCVERAQ.pdf Article]
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=== NAQFC Evaluation ===
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Chai, T., Kim, H.-C., Lee, P., Tong, D., Pan, L., Tang, Y., Huang, J., McQueen, J., Tsidulko, M., and Stajner, I.: Evaluation of the United States National Air Quality Forecast Capability experimental real-time predictions in 2010 using Air Quality System ozone and NO2 measurements, Geosci. Model Dev., 6, 1831-1850, doi:10.5194/gmd-6-1831-2013, 2013.
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[http://www.geosci-model-dev.net/6/1831/2013/gmd-6-1831-2013.html Article]
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=== Ozone inflow to California ===
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Pfister, G., S. Walters, L.K. Emmons, and D.P. Edwards (2013), Quantifying the contribution of inflow on surface ozone over California, J. Geophys. Res., 118, doi:10.1002/2013JD020336, 2013 [http://onlinelibrary.wiley.com/doi/10.1002/2013JD020336/abstract Abstract]
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=== Secondary standard for ozone ===
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Lapina, K., D. K. Henze, J. B. Milford, M. Huang, M. Lin, A. M. Fiore, G. Carmichael, G. G. Pfister, and K. Bowman, Assessment of source contributions to seasonal vegetative exposure to ozone in the U.S., J. Geophys. Res. Atmos., 119, doi:10.1002/2013JD020905, 2014. [http://acmg.seas.harvard.edu/publications/aqast/articles/jgrd51032.pdf Article]
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=== GLIMPSE decision tool for climate and air quality ===
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Akhtar, F. H., R. W. Pinder, D. H. Loughlin, and D. K. Henze, GLIMPSE: a rapid decision framework for energy and environmental policy, Environ. Sci. Technol., 47, 12011--12019, doi:10.1021/es402283j, 2013. [http://acmg.seas.harvard.edu/publications/aqast/articles/es402283j.pdf Article]
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=== US ammonia emissions ===
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Paulot F., Jacob, D.J., Pinder R.W., Bash J.O., Travis, K., Henze D.K., Ammonia emissions in the United States, Europe, and China derived by high-resolution inversion of ammonium wet deposition data: Interpretation with a new agricultural emissions inventory (MASAGE_NH3), submitted to J. Geophys. Res., 2014. [http://acmg.seas.harvard.edu/publications/paulot_2013b.pdf Article]
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=== Older publications ===
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See the [http://acmg.seas.harvard.edu/aqast/publications.html AQAST publications webpage] for the full list of AQAST publications.
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== New AQAST presentations (with links) ==
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=== [http://acmg.seas.harvard.edu/aqast/meetings/2014_jan/program.html Presentations from the 6th AQAST Meeting, Houston, January 2014] ===
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=== Beyond the Stability Index—Fire management & forecasting tools for air quality, weather & climate impacts of prescribed fires ===
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Webinar presented by Scott Spak at the Tallgrass Prairie & Oak Savanna Regional Fire Science Consortium Webinar, 15 October 2013[http://vimeo.com/77241318]
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Latest revision as of 21:25, 10 May 2023

Instructions for adding tracers to GEOS-Chem

By Melissa Payer

These instructions describe how to add advected tracers to GEOS-Chem. Advected tracers are carried in the STT array (which is declared in GeosCore/tracer_mod.F), and are transported by the winds.

NOTE: Some advected tracers are also chemical species, which comprise GEOS-Chem's NOx-Ox-HC-aerosol chemistry mechanism.

  1. Add tracers to input.geos under Tracer Menu

    1. Increase “Number of tracers” accordingly

    2. Add tracer number, name, molecular weight, and emitted species to end of tracer list

  2. Add tracer(s) to restart file – see separate instructions

  3. Modify the following source code routines:

    1. Headers/CMN_SIZE_mod.F

      1. Increase NNPAR by number of tracers being added

      2. If the species have anthropogenic emissions, increase NEMPARA accordingly

      3. If the species have biogenic emissions, increase NEMPARB accordingly

      4. If the species have biomass burning emissions, increase NBIOMAX accordingly

    2. GeosCore/tracerid_mod.F

      1. Increase NNNTRID by the number of tracers being added NOTE: NNNTRID must be equal to NNPAR in CMN_SIZE_mod.F

      2. Define tracer IDs as needed:

        1. IDxxxx – ID for SMVGEAR species

        2. IDTxxxx – GEOS-Chem tracer ID

        3. IDExxxx – GEOS-Chem emission ID

        4. IDBFxxxx – GEOS-Chem biofuel ID

        5. IDBxxxx – GEOS-Chem biomass ID

      3. In subroutine TRACERID,

        1. Under “Assign tracer, biomass, biofuel, and anthro emission ID’s,” add case for added tracers to initialize IDTxxxx, IDBFxxxx, IDBxxxx

        2. Under “Initialize the IDExxx flags,” add IF statement for added tracer IDs and initialize IDExxxx

        3. Under “Fill IDEMS with appropriate tracer ID #’s,” add IF statement for added tracers

        4. Under “Print additional information,” add WRITE statements for added tracers

      4. In subroutine SETTRACE (NOTE: Only do the following if species is included in SMVGEAR chemical mechanism<p>

        1. <p>Add IF statement, to initialize IDxxxx

        2. In subroutine INIT_TRACERID,

        3. Zero all IDs added (IDxxxx, IDTxxxx, IDExxxx, etc.)

    3. Other modules that may need to be updated include:

      1. wetscav_mod.F

      2. drydep_mod.F

      3. emissions_mod.F

      4. biomass_mod.F

      5. biofuel_mod.F

        etc.


Instructions for adding species to GEOS-Chem

Modify run directory files

1) Add tracers to input.geos under Tracer Menu c) Increase “Number of tracers” accordingly d) Add tracer number, name, molecular weight, and emitted species to end of tracer list

2) Add tracer(s) to restart file – see separate instructions

3) Modify globchem.dat to include additional species, kinetic reactions (including emissions and drydep), or photolysis reactions NOTE: If you modify globchem.dat and plan to run GEOS-Chem using the KPP chemical solver, you will need to generate new gckpp*.F90 files. For more information see the following wiki pages: http://wiki.seas.harvard.edu/geos-chem/index.php/KPP_solvers_FAQ#What_are_the_cons_of_using_KPP.3F http://wiki.seas.harvard.edu/geos-chem/index.php/Interfacing_GEOS-Chem_with_KPP#Generating_KPP_input_files_from_GEOS-Chem_globchem.dat

4) If necessary, modify: a) ratj.d – contains species names and branching ratios for FAST–JX photolysis species For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.1 b) jv_spec.dat – contains cross-sections and quantum yields for FAST–JX photolysis species For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.3

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