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, July 2013 ==
+'''''By [mailto:mpayer@seas.harvard.edu Melissa Payer]'''''
-Welcome to the January 2013 Newsletter of the NASA Air Quality Applied Sciences Team (AQAST). AQAST is a team of atmospheric scientists serving air quality management needs through creative 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.
-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.
-<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.
-== AQAST Semiannual Meetings ==
-AQAST meetings are held on a semiannual schedule and bring together team members, air quality managers, and research and applications partners.
-=== 5th AQAST Meeting (AQAST5): Jue 4-6, 2013 at the University of Maryland at College Park ===
+Instructions for adding species to GEOS-Chem
-AQAST5 was held on June 4-6, 2013 at the University of Maryland at College Park. Our hosts were AQAST members [http://acmg.seas.harvard.edu/aqast/members.html Russ Dickerson and Bryan Duncan], together with Ana Prados who leads the NASA [http://airquality.gsfc.nasa.gov/ NASA Applied Remote SEnsing Training (ARSET)]. [http://acmg.seas.harvard.edu/aqast/index.html The meeting attracted over 130 attendees] including air quality managers from a number of state, regional, and national agencies. [http://acmg.seas.harvard.edu/aqast/meetings/2013_jun/program.html Click here] for the meeting program and links to the presentations.
+Modify run directory files
-=== 6th AQAST Meeting (AQAST6): January 15-17, 2014 at the University of Texas at Austin ===
+)	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
-The next AQAST meeting (AQAST6) will be held January 15-17 (Wednesday-Friday) at the University of Texas at Austin. Our hosts will be [http://www.che.utexas.edu/faculty-staff/faculty-directory/david-t-allen-phd/ Prof. David Allen] from U. Texas Austin and AQAST member [http://acmg.seas.harvard.edu/aqast/members.html Dan Cohan]. Mark your calendars!
+)	Add tracer(s) to restart file – see separate instructions
-== AQAST Project Highlights ==
+)	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
-=== AQAST supports Wyoming exceptional event demonstration ===
+)	If necessary, modify:
+a)	ratj.d – contains species names and branching ratios for FAST–JX photolysis species
-AQAST member Brad Pierce provided aircraft, satellite, and modeling data to assist the state of Wyoming in an exceptional event demonstration related to a NAAQS ozone exceedance at Thunder Basin on June 5, 2012. [http://acmg.seas.harvard.edu/aqast/highlight_pierce_2013.html Click here for more details]
+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
-=== Saint Louis ozone garden gears up for its second year ===
+For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.3
-AQAST member Jack Fishman is using ozone gardens to educate the public on the harm to vegetation from surface ozone. [http://acmg.seas.harvard.edu/aqast/highlights/2013/St_Louis_Ozone_Garden_Release.pdf Click here to learn more]. A second ozone garden was also recently started by the [http://acmg.seas.harvard.edu/aqast/highlight_harvard_ozone_garden_2013.html AQAST group at Harvard].
-== New AQAST publications (with links) ==
-=== Future fires in Southern California ===
-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]
-=== Future fires and PM in the western US ===
-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, in press, Atmospheric Environment, 2013.
-[http://acmg.seas.harvard.edu/publications/Yue_accepted_2013a.pdf Full paper]
-=== 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, in press, Geophys. Res. Let.,
-. [http://acmg.seas.harvard.edu/publications/Tai_accepted_2013.pdf Full paper]
-=== 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., in press, doi:10.1016/j.atmosenv.2013.05.051. [http://www.sciencedirect.com/science/article/pii/S1352231013004007 Full paper]
-=== 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 in Europe ===
-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, doi:10.5194/acpd-13-12541-2013, 2013.
-[http://www.atmos-chem-phys-discuss.net/13/12541/2013/acpd-13-12541-2013.html Full paper]
-=== Air quality forecasting for Maryland ===
-Garner, G.G., A.M. Thompson, P. Lee, and D.K. Martins, Evaluation of NAQFC model performance in forecasting surface ozone during the 2011 DISCOVER-AQ campaign, J. Atmos. Chem., DOI 10.1007/s10874-013-9251-z, 2013. [http://acmg.seas.harvard.edu/publications/aqast/articles/GARNER-DAQ-JAC13.pdf Full paper]
-=== Nitrogen deposition in US National Parks ===
-Ellis, R.A., D.J. Jacob, M. Payer, 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, submitted to Atmos. Chem. Phys., 2013. [http://acmg.seas.harvard.edu/publications/ellis2013.pdf Full paper]
-=== 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) ==
-=== Presentations from the AQAST5 meeting (June 4-6, 2013) ===
-[http://acmg.seas.harvard.edu/aqast/meetings/2013_jun/program.html Click here] for the meeting agenda with links to all presentations.
-=== DISCOVER-AQ and the uses of remote sensing in air quality and climate studies ===
-presented by Russ Dickerson at Brookhaven National Lab, May 16, 2013.  [http://acmg.seas.harvard.edu/presentations/aqast/BNL_Dickerson2013short1.pdf Download pdf]
-=== What can we learn from observations and modeling to inform inventory estimates? ===
-presented by Russ Dickerson to the Mid-Atlantic Regional Air Management Association, Inc. (MARAMA), February 27, 2013.  [http://acmg.seas.harvard.edu/presentations/aqast/9_MARAMA_Dickerson2013.pdf Download]
-=== Iowa air quality: sources, trends, and new resources for emergency and routine events ===
-presented by Scott Spak at the IPHA Governor’s Conference on Public Health, Ames, IA, 9 April 2013.
-[http://www.iowapha.org/Resources/Documents/23%20Iowa%20Air%20Quality.pdf Workshop handout]
-[http://www.iowapha.org/Resources/Documents/23%20Iowa%20Air%20Quality2.pdf Presentation]
-=== Modeling Ozone Exceptional Events: California, 2008 & Colorado/Wyoming, 2012 ===
-presented by Gabriele Pfister at the WESTAR Wildfire and Exceptional Ozone Events Meeting, California Air Resources Board, Sacramento, March 5-6, 2013 [http://westar.org/O3%20EE%20mtg%203-13/O3%20Wildfire%20EE%20agenda2.htm Meeting agenda and link to presentation]

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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