Difference between revisions of "Sandbox"

Latest revision as of 21:25, 10 May 2023

Instructions for adding tracers to GEOS-Chem

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.

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

@@ Line 1: / Line 1: @@
-== feel free to experiment here ==
+== Instructions for adding tracers to GEOS-Chem ==
-== AQAST Newsletter, February 2014==
+'''''By [mailto:mpayer@seas.harvard.edu Melissa Payer]'''''
-== AQAST Semiannual Meetings ==
+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.
-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 January 15-17, 2014 at Rice University in Houston. You can access the agenda and presentations from that meeting [http://acmg.seas.harvard.edu/aqast/meetings/2014_jan/program.html here].
+NOTE: Some advected tracers are also chemical species, which comprise GEOS-Chem's NOx-Ox-HC-aerosol chemistry mechanism.
-=== 7th AQAST Meeting (AQAST7): June 17-19, 2014 at Harvard University ===
+#<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.
-The next AQAST meeting (AQAST7) will be held June 17-19, 2014 (Wednesday-Friday) at Harvard University in Cambridge, MA, hosted by [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_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 Cambridge in June!
-== AQAST Highlights ==
-=== AQAST Special Issue of <I>Environmental Manager ===
+Instructions for adding species to GEOS-Chem
-<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].
+Modify run directory files
-== New AQAST publications (with links) ==
+)	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
-=== PM trends seen from space ===
+)	Add tracer(s) to restart file – see separate instructions
-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]
+)	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
-=== NOx emission trends seen from space ===
+)	If necessary, modify:
+a)	ratj.d – contains species names and branching ratios for FAST–JX photolysis species
-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]
+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
-=== GLIMPSE decision tool for energy and air quality policy ===
+For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.3
-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]
-=== Aerosol optical depths over the US ===
-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]
-=== Nitrogen deposition in national parks ===
-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]
-=== Background influences on western US air quality ===
-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]
-=== Fire emissions from MODIS ===
-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]
-=== Emission trends in India ===
-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]
-=== Ammonia pollution from food export ===
-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]
-=== Future fires and PM in the western US ===
-Yue, X., L.J. Mickley, and J.A. Logan, Projection of wildfire activity in
-southern California in the mid-21st century, submitted to Clim. Dyn., 2013.
-[http://acmg.seas.harvard.edu/publications/Yue_submitted_2013b.pdf Full paper]
-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]
-=== Effect of rising CO<sub>2</sub> on isoprene emission and air quality implications ===
-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]
-=== Detecting emissions from space: a review ===
-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]
-=== Use of satellite observations for PM forecasts ===
-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.
-[http://www.atmos-chem-phys-discuss.net/13/12213/2013/acpd-13-12213-2013.html Full paper]
-=== Air quality modeling with coupled meteorology-chemistry models ===
-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]
-=== High ozone on hot days ===
-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]
-=== Improved ammonia emission inventory for the US ===
-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]
-=== Older publications ===
-See the [http://acmg.seas.harvard.edu/aqast/publications.html AQAST publications webpage] for the full list of AQAST publications.
-== New AQAST presentations (with links) ==
-=== [http://acmg.seas.harvard.edu/aqast/meetings/2014_jan/program.html Presentations from the 6th AQAST Meeting, Houston, January 2014 ===
-=== Beyond the Stability Index—Fire management & forecasting tools for air quality, weather & climate impacts of prescribed fires ===
-Webinar presented by Scott Spak at the Tallgrass Prairie & Oak Savanna Regional Fire Science Consortium Webinar, 15 October 2013[http://vimeo.com/77241318]
-=== Review of the Air Quality Applied Sciences Team (AQAST) and Year 2 Highlights ===
-presented by Daniel J. Jacob at the NASA Applied Science Program Review, Washington, DC, July 18, 2013.
-[http://acmg.seas.harvard.edu/presentations/powerpoints/djj2013/aqast_overview_asp.ppt Powerpoint]

Difference between revisions of "Sandbox"

Latest revision as of 21:25, 10 May 2023

Instructions for adding tracers to GEOS-Chem

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