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| − | == feel free to experiment here == | + | == Instructions for adding tracers to GEOS-Chem == |
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| − | == AQAST Newsletter, October 2013 ==
| + | '''''By [mailto:mpayer@seas.harvard.edu Melissa Payer]''''' |
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| − | Welcome to the October 2013 Newsletter of the NASA Air Quality Applied Sciences Team (AQAST). AQAST is a team of atmospheric scientists serving air quality management needs through the use of Earth Science data and tools. We conduct a wide range of projects in partnership with air quality agencies at the local, state, regional, and national levels.
| + | 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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| − | This newsletter keeps you up to date on AQAST activities. The [http://acmg.seas.harvard.edu/aqast AQAST website] has more comprehensive information. Also follow us on Twitter at [https://twitter.com/NASA_AQAST @NASA_AQAST]. To inquire about specific projects or request assistance please contact any [http://acmg.seas.harvard.edu/aqast/members.html AQAST member], team leader [mailto:djacob@fas.harvard.edu Daniel Jacob], or team deputy leader [mailto:taholloway@wisc.edu Tracey Holloway].
| + | NOTE: Some advected tracers are also chemical species, which comprise GEOS-Chem's NOx-Ox-HC-aerosol chemistry mechanism. |
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| − | <i>This newsletter was produced by [http://acmg.seas.harvard.edu/people/faculty/djj/index.html Daniel Jacob] (AQAST leader) and [http://people.seas.harvard.edu/~yantosca/ Bob Yantosca] (AQAST webmaster). Subscribe/unsubscribe by email to Bob Yantosca.</i>. [http://acmg.seas.harvard.edu/aqast/newsletter.html Access previous newsletters here]. | + | #<p>Add tracers to input.geos under Tracer Menu</p> |
| | + | ##<p>Increase “Number of tracers” accordingly</p> |
| | + | ##<p>Add tracer number, name, molecular weight, and emitted species to end of tracer list</p> |
| | + | #<p>Add tracer(s) to restart file – see separate instructions</p> |
| | + | #<p>Modify the following source code routines:</p> |
| | + | ##<p><tt>Headers/CMN_SIZE_mod.F</tt></p> |
| | + | ###<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> |
| | + | ###<p>If the species have biomass burning emissions, increase NBIOMAX accordingly</p> |
| | + | ##<p><tt>GeosCore/tracerid_mod.F</tt></p> |
| | + | ###<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> |
| | + | ###<p>Define tracer IDs as needed:</p> |
| | + | ####<p>IDxxxx – ID for SMVGEAR species</p> |
| | + | ####<p>IDTxxxx – GEOS-Chem tracer ID</p> |
| | + | ####<p>IDExxxx – GEOS-Chem emission ID</p> |
| | + | ####<p>IDBFxxxx – GEOS-Chem biofuel ID</p> |
| | + | ####<p>IDBxxxx – GEOS-Chem biomass ID</p> |
| | + | ###<p>In subroutine <tt>TRACERID</tt>,</p> |
| | + | ####<p>Under “Assign tracer, biomass, biofuel, and anthro emission ID’s,” add case for added tracers to initialize IDTxxxx, IDBFxxxx, IDBxxxx</p> |
| | + | ####<p>Under “Initialize the IDExxx flags,” add IF statement for added tracer IDs and initialize IDExxxx</p> |
| | + | ####<p>Under “Fill IDEMS with appropriate tracer ID #’s,” add IF statement for added tracers</p> |
| | + | ####<p>Under “Print additional information,” add WRITE statements for added tracers</p> |
| | + | ###<p>In subroutine SETTRACE (NOTE: Only do the following if species is included in SMVGEAR chemical mechanism<p> |
| | + | ####<p>Add IF statement, to initialize IDxxxx</p> |
| | + | ####<p>In subroutine INIT_TRACERID,</p> |
| | + | ####<p>Zero all IDs added (IDxxxx, IDTxxxx, IDExxxx, etc.)</p> |
| | + | ##<p>Other modules that may need to be updated include:</p> |
| | + | ###<p>wetscav_mod.F</p> |
| | + | ###<p>drydep_mod.F</p> |
| | + | ###<p>emissions_mod.F</p> |
| | + | ###<p>biomass_mod.F</p> |
| | + | ###<p>biofuel_mod.F</p> etc. |
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| − | == AQAST Semiannual Meetings ==
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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 4-6 at the University of Maryland and you can access the agenda and presentations from that meeting [http://acmg.seas.harvard.edu/aqast/meetings/2013_jun/program.html here].
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| − | === 6th AQAST Meeting (AQAST6): January 15-17, 2014 at Rice University ===
| + | Instructions for adding species to GEOS-Chem |
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| − | The next AQAST meeting (AQAST6) will be held January 15-17, 2014 (Wednesday-Friday) at Rice University in Houston, hosted by AQAST member [http://acmg.seas.harvard.edu/aqast/members.html Dan Cohan]. The meeting is free and open to the public. Air quality managers are especially encouraged to participate. Go to the [http://acmg.seas.harvard.edu/aqast/meetings/2014_jan/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 Houston!
| + | Modify run directory files |
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| − | == AQAST Highlights ==
| + | 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 |
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| − | === AQAST in the news ===
| + | 2) Add tracer(s) to restart file – see separate instructions |
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| − | The recently published [http://acmg.seas.harvard.edu/publications/ellis2013.pdf Ellis et al.] AQAST paper on excessive nitrogen deposition in US national parks received a lot of media attention including [http://www.latimes.com/science/sciencenow/la-sci-sn-national-park-fertilize-nitrogen-air-pollution-20131014,0,6264129.story) this piece in the Los Angeles Times]. Read the
| + | 3) Modify globchem.dat to include additional species, kinetic reactions (including emissions and drydep), or photolysis reactions |
| − | [http://www.seas.harvard.edu/news/2013/10/unregulated-agricultural-ammonia-threatens-national-parks-ecology press release].
| + | 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 |
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| − | === NASA training course ===
| + | 4) If necessary, modify: |
| − | | + | a) ratj.d – contains species names and branching ratios for FAST–JX photolysis species |
| − | [http://acmg.seas.harvard.edu/aqast/members.html AQAST member Yang Liu] co-taught a NASA training course for the Bay Area Air Quality Management District in Santa Clara, CA (September 10-12, 2013). Topics included NASA aerosol products, and NASA / NOAA smoke/fire and products and their applications to air quality monitoring.
| + | 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 |
| − | === Effect of climate change on fires and air quality ===
| + | For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.3 |
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| − | [http://www.people.fas.harvard.edu/~mickley/ AQAST member Loretta Mickley] has received a lot of media attention for her recent work on how future climate change will affect wildfires in the US with implications for air quality. Read [http://www.people.fas.harvard.edu/~mickley/wildf2013.html Mickley's blog on the topic] with links to publications, media stories, graphics, and more.
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| − | === AQAST Team Members Participate in Air Quality Conference ===
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| − | [http://acmg.seas.harvard.edu/aqast/members.html AQAST Team Member Dick McNider] of the University of Alabama in Huntsville gave a keynote speech on the role of the physical atmosphere in air quality decision making at the [https://sites.google.com/site/meteorologyandairquality/home Traversing New Terrain Meteorology and Air Quality Conference] held at the University Of California Davis Sept -10-12, 2013. The purpose of the conference was to bring physical atmosphere modelers both from the air quality community and other areas such as weather forecasting, fire forecasting and climate to examine issues and possible improvements to the physical atmosphere related to air quality.
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| − | One new area examined by McNider in his opening talk was the evidence of too much mixing in nighttime stable boundary layers is reducing the decoupling and strength of associated inertial low level jets and shear in the residual layer between the surface and the previous day’s boundary layer height. Using long range dispersion results it was shown that such under-prediction of the decoupling can dramatically change the transport and spread of urban and power plant plumes into rural areas. It was hypothesized that part of the under-prediction in modeled rural NO2 columns compared to satellite column NO2 may be due to model under-estimates of NOy export from urban areas because of the under-estimate of the nighttime decoupling.
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| − | Another AQAST Team member, Brad Pierce of NOAA, served on the Program Committee and organized the “Data Assimilation, Adjoints, and Inverse Modeling “ session, which focused on techniques of bring satellite and ground based air quality observations into models and to decision making by air quality agencies.
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| − | == New AQAST publications (with links) ==
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| − | === PM trends seen from space ===
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| − | Hu, X., L. A. Waller, A. Lyapustin, Y. Wang, and Y. Liu (2013), 10 yr spatial and temporal trends of PM2.5 concentrations in the southeastern US estimated using high-resolution satellite data, Atmos. Chem. Phys. Discuss., 13(10), 25617-25648, doi:10.5194/acpd-13-25617-2013. [http://www.atmos-chem-phys-discuss.net/13/25617/2013/acpd-13-25617-2013.html Article]
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| − | === NOx emission trends seen from space ===
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| − | Duncan, B., Y. Yoshida, B. de Foy, L. Lamsal, D. Streets, Z. Lu, K. Pickering, and N. Krotkov, The observed response of Ozone Monitoring Instrument (OMI) NO2 columns to NOx emission controls on power plants in the United States: 2005-2011, Atmos. Environ., 81, p. 102-111, doi:10.1016/jatmosenv.2013.08.068, 2013. [http://acmg.seas.harvard.edu/publications/aqast/articles/Duncan2013.pdf Article]
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| − | === GLIMPSE decision tool for energy and air quality policy ===
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| − | Akhtar, F., R. W. Pinder, D. H. Loughlin, and D. K. Henze, GLIMPSE: a rapid decision framework for energy and environmental policy, Environ. Sci Tech, doi:10.1021/es402283j, in press. [http://acmg.seas.harvard.edu/publications/aqast/articles/Akhtar2013.pdf Article]
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| − | === Aerosol optical depths over the US ===
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| − | Li, S., L. Chen, M. Garay, and Y. Liu (2014), Comparison of GEOS-Chem aerosol optical depth with AERONET and MISR data over the contiguous United States, JGR-Atmosphere, 118, 1-14. [http://acmg.seas.harvard.edu/publications/aqast/articles/Li2013.pdf Article]
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| − | === Nitrogen deposition in national parks ===
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| − | Ellis, R.A., D.J. Jacob, M.P. Sulprizio, L. Zhang, C.D. Holmes, B.A. Schichtel, T. Blett, E. Porter, L.H. Pardo, and J.A. Lynch, Present and future nitrogen deposition to national parks in the United States: critical load exceedances, Atmos. Chem. Phys., 13, 9083-9095, 2013. [http://acmg.seas.harvard.edu/publications/ellis2013.pdf Article]
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| − | === Background influences on western US air quality ===
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| − | Huang, M. , G. R. Carmichael, T. Chai, R. B. Pierce, S. J. Oltmans, D. A. Jaffe, K. W. Bowman, A. Kaduwela, C. Cai, S. N. Spak, A. J. Weinheimer, L. G. Huey, and G. S. Diskin, Impacts of transported background pollutants on summertime western US air quality: model evaluation, sensitivity analysis and data assimilation, Atmos. Chem. Phys., 13, 359-391, 2013. [http://www.atmos-chem-phys.net/13/359/2013/acp-13-359-2013.html Article]
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| − | === Fire emissions from MODIS ===
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| − | Peterson, D., J. Wang, C. Ichoku, E. Hyer, and V. Ambrosia, A sub-pixel-based calculation of fire radiative power from MODIS observations: 1: Algorithm development and initial assessment, Remote Sensing of Environment, 129, 262-279, 15 Feb 2013. [http://www.sciencedirect.com/science/article/pii/S0034425712004300 Article]
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| − | === Emission trends in India ===
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| − | Lu, Zifeng. David G. Streets, Benjamin de Foy, and Nikolay. A. Krotkov, OMI Observations of Interannual Increase in SO2 Emissions from Indian Coal-Fired Power Plants during 2005−2012, Env. Sci. Tech, submitted, 2013. [http://acmg.seas.harvard.edu/publications/aqast/articles/Indian_Power_SO2_submitted_to_EST.pdf Article]
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| − | === Ammonia pollution from food export ===
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| − | Paulot F, D.J. Jacob, Hidden cost of U.S. agricultural exports: particulate matter from ammonia emissions, submitted to Environ. Sci. Technol., 2013. [http://acmg.seas.harvard.edu/publications/paulot2013c.pdf Article]
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| − | === Future fires and PM in the western US ===
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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, submitted to Clim. Dyn., 2013.
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| − | [http://acmg.seas.harvard.edu/publications/Yue_submitted_2013b.pdf Full paper]
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| − | Yue, X., L. J. Mickley, J. A. Logan, and J. O. Kaplan, Ensemble projections of wildfire activity and carbonaceous aerosol concentrations over the western United States in the mid-21st century, Atmos. Env., 77, 767-780, 2013. [http://acmg.seas.harvard.edu/publications/Yue_ae_2013.pdf Article]
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| − | === Effect of rising CO<sub>2</sub> on isoprene emission and air quality implications ===
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| − | Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use, Geophys. Res. Let., 40, 3479-3483, 2013. [http://acmg.seas.harvard.edu/publications/Tai_grl_2013.pdf Article]
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| − | === Detecting emissions from space: a review ===
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| − | Streets, D., T. Canty, G. Carmichael, B. de Foy, R. Dickerson,, B. Duncan, D. Edwards, J. Haynes, D. Henze, M. Houyoux, D. Jacob, N. Krotkov, L. Lamsal, Y. Liu, Z. Lu, R. Martin, Pfister, R. Pinder, R. Salawitch, and K. Wecht, Emissions estimation from satellite retrievals: A review of current capability, Atmos. Environ., 77, 1011-1042, 2013.[http://www.sciencedirect.com/science/article/pii/S1352231013004007 Article]
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| − | === Use of satellite observations for PM forecasts ===
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| − | Saide, P. E., Carmichael, G. R., Liu, Z., Schwartz, C. S., Lin, H. C., da Silva, A. M., and Hyer, E.: Aerosol optical depth assimilation for a size-resolved sectional model: impacts of observationally constrained, multi-wavelength and fine mode retrievals on regional scale forecasts, Atmos. Chem. Phys. Discuss., 13, 12213-12261, doi:10.5194/acpd-13-12213-2013, 2013.
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| − | [http://www.atmos-chem-phys-discuss.net/13/12213/2013/acpd-13-12213-2013.html Full paper]
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| − | === Air quality modeling with coupled meteorology-chemistry models ===
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| − | Baklanov, A. Schluenzen, P. Suppan, J. Baldasano, D. Brunner, S. Aksoyoglu, G. Carmichael, et al., Online coupled regional meteorology-chemistry models in Europe: current status and prospects, Atmos. Chem. Phys. Discuss., 13, 12541–12724, , 2013. [ http://www.atmos-chem-phys-discuss.net/13/12541/2013/acpd-13-12541-2013.html Article]
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| − | === High ozone on hot days ===
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| − | H. He, L. Hembeck, R. J. Salawitch, K. M. Hosley, and R. R. Dickerson, High ozone concentrations on hot days: The role of electric power demand and NOx emissions, Geophys. Res. Lett, 40, 1–4, doi:10.1002/grl.50967, 2013. [http://acmg.seas.harvard.edu/publications/aqast/articles/he_etal_GRLproof_2013.pdf Article]
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| − | === Improved ammonia emission inventory for the US ===
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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., 2013. [http://acmg.seas.harvard.edu/publications/paulot_2013b.pdf Full paper]
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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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| − | === NASA Air Quality Applied Sciences Team (AQAST): recent work on ammonia and methane emissions relevant to CenSARA ===
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| − | Webinar presented by Daniel J. Jacob at the CenSARA Technical Committee, August 6, 2013. [http://acmg.seas.harvard.edu/presentations/powerpoints/djj2013/censara.ppt Powerpoint]
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| − | === Review of the Air Quality Applied Sciences Team (AQAST) and Year 2 Highlights ===
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| − | presented by Daniel J. Jacob at the NASA Applied Science Program Review, Washington, DC, July 18, 2013.
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| − | [http://acmg.seas.harvard.edu/presentations/powerpoints/djj2013/aqast_overview_asp.ppt Powerpoint]
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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
c) Increase “Number of tracers” accordingly
d) Add tracer number, name, molecular weight, and emitted species to end of tracer list
