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 ==
-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.
+'''''By [mailto:mpayer@seas.harvard.edu Melissa Payer]'''''
-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].
+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.
-<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].
+NOTE: Some advected tracers are also chemical species, which comprise GEOS-Chem's NOx-Ox-HC-aerosol chemistry mechanism.
-== AQAST Communications ==
+#<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 has great success stories to tell, but how do we tell them best? We have taken recent actions to improve communications outside the Team:
-=== Tracey Holloway appointed deputy leader ===
-AQAST member [http://www.sage.wisc.edu/people/holloway/holloway.html Tracey Holloway] was appointed deputy leader in December 2012. She assumes specific responsibility for external relations with the public, air quality agencies, and NASA. Tracey has had training in public outreach and engagement as a 2011 Stanford University Leopold Leadership Fellow, media training at the University of Wisconsin--Madison, and outreach experience in her role as research center director at the University of Wisconsin--Madison. Air quality managers are encouraged to contact Tracey if there are stories, data, or images that would be helpful.
+Instructions for adding species to GEOS-Chem
-=== Twitter ===
+Modify run directory files
-AQAST is now on Twitter. You can read our content (e.g. links to AQAST papers, presentations, press coverage, etc.) and read our "re-tweets" (flagging tweets related to AQAST issues) by clicking here: [https://twitter.com/NASA_AQAST https://twitter.com/NASA_AQAST]. Sign up as a "follower" and stay on top of AQAST news! To get started on Twitter yourself, [http://blogs.lse.ac.uk/impactofsocialsciences/files/2011/11/Published-Twitter_Guide_Sept_2011.pdf here is a good getting-started guide].
+)	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
-=== New journalist on staff ===
+)	Add tracer(s) to restart file – see separate instructions
-Sarah Wiltman, a recent journalism graduate from the University of Wisconsin, is now working part-time with Tracey Holloway to write AQAST stories and promote AQAST activities. Sarah and Tracey can help AQAST members work with their home institutions press office, promote press releases, and fill gaps in coverage of new stories or resources. They are planning to build capacity in data visualization as well.
+)	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
-=== New directory of AQAST members ===
+)	If necessary, modify:
+a)	ratj.d – contains species names and branching ratios for FAST–JX photolysis species
-The [http://acmg.seas.harvard.edu/aqast/members.html AQAST members' directory] has received a major upgrade to list areas of expertise, photos, webpage links, and contact information for each member. Use it to find the members with the expertise that you seek!
+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
-== AQAST Project Highlights ==
+For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.3
-=== Air quality and health impacts of June 2012 Colorado wildfires ===
-– A Joined Collaboration between NCAR, CDPHE, and Emory University ([http://acd.ucar.edu/~pfister/ Gabriele Pfister] and [http://acd.ucar.edu/~edwards/ David Edwards])
-Colorado experienced one of its most costly and highest impact fire seasons in June 2012. Much of the State was blanketed in smoke because of large events that included the High Park fire near Ft. Collins and the Waldo Canyon fire near Colorado Springs. Fire plumes transported from wildfires in Wyoming and New Mexico further impacted the Colorado Front Range. NCAR, the Colorado Department of Public Health and Environment (CDPHE) and Emory University are working together to examine the impact that these fires had on local air quality and human health. This will be achieved through an integrated analysis of surface and satellite observations, WRF-Chem modeling including assimilation of meteorological observations, and health data. This work will provide a baseline for evaluating methods to be used for exceedance demonstrations and for establishing predictive tools to support agencies in issuing health advisors during wildfire events. Christine Wiedinmyer (NCAR), supporting the work by providing fire emission estimates, recently discussed this project as well as other aspects of air pollution from wildfires on Colorado Public Radio:
-[http://www.cpr.org/category/colorado_matters#load_article|Fire_Danger_Air_Pollution click here for link].
-=== New MODIS aerosol product available ===
-The new MODIS Level 3 aerosol product from AQAST member [mailto:Edward.Hyer@nrlmry.navy.mil Edward Hyer] has now been transitioned to [http://lance-modis.eosdis.nasa.gov/ NASA LANCE]. [https://earthdata.nasa.gov/about-eosdis/news/nrt-value-added-modis-aerosol-optical-depth-product-available Click here for press release]. Satellite detection of aerosols, or particles in the atmosphere, provides one of the most useful remote sensing products for air quality analysis. This new MODIS product supports a wide range of applications for air quality management. It provides global, gridded aerosol optical depth (AOD) at a resolution of 1/2-degree latitude-longitude in near-real time, for immediate access. In addition to reducing error in the AOD retrievals, the product includes quantitative uncertainty estimates at each data point. Contact [mailto:Edward.Hyer@nrlmry.navy.mil Edward Hyer] for more information.
-== AQAST Meetings ==
-=== AQAST4 meeting at California Air Resources Board ===
-The 4th biannual AQAST meeting was held on Nov 29-30 2012 at the California Air Resources Board in Sacramento. It was a highly successful meeting by all accounts and provided AQAST with a better understanding of the air quality issues facing California. [http://acmg.seas.harvard.edu/aqast/meetings/nov2012/program.html Click here to access the presentations from the meeting.]
-=== AQAST sessions at the Fall 2012 AGU meeting ===
-AQAST organized a special session, "Application of satellite data to serve air quality management needs ", at the Fall 2012 meeting of the American Geophysical Union in San Francisco on December 3-7. The session attracted 69 oral presentations spread over a full day as well as a half-day poster session. We also held a Town Hall to share information about AQAST and receive input from air quality managers and Earth Scientists interested in air quality applications.
-=== Next AQAST meeting on June 4-6, 2013 at the University of Maryland ===
-The next biannual AQAST meeting will be held on June 4-6 at the University of Maryland in College Park, hosted by AQAST member [http://www.atmos.umd.edu/~russ/index.html Russ Dickerson].The meeting will be free and open to all. Please mark your calendars. More information will be forthcoming and e-mailed to AQAST Newsletter subscribers.
-== New AQAST publications (with links) ==
-=== How do different source regions contribute to climate warming from ozone? ===
-Bowman, K., and D. K. Henze (2012), Attribution of direct ozone radiative forcing to spatially resolved emissions, Geophys. Res. Lett., 39, L22704, doi:10.1029/2012GL053274.  [http://onlinelibrary.wiley.com/doi/10.1029/2012GL053274/abstract Abstract]
-=== A better way to see fires from space ===
-David Peterson, Jun Wang, Charles Ichoku, Edward Hyer, Vincent Ambrosia, A sub-pixel-based calculation of fire radiative power from MODIS observations: 1: Algorithm development and initial assessment, Remote Sensing of Environment, Available online 11 December 2012, ISSN 0034-4257, 10.1016/j.rse.2012.10.036. ([http://dx.doi.org/10.1016/j.rse.2012.10.036 Link])
-=== Understanding wintertime aerosol nitrate pollution in the Great Lakes Region ===
-C. Stanier, A. Singh, W. Adamski, J. Baek, M. Caughey, G. Carmichael, E. Edgerton, D. Kenski, M. Koerber, J. Oleson, T. Rohlf, S.R. Lee, N. Riemer, S. Shaw, S. Sousan, S.N. Spak (2012). Overview of the LADCO winter nitrate study: Hourly ammonia, nitric acid and PM2.5 composition at an urban and rural site pair during PM2.5 episodes in the U.S. Great Lakes region, Atmospheric Chemistry & Physics, 12, 11037-11056, doi: 10.5194/acp-12-11037-2012. [http://www.atmos-chem-phys.net/12/11037/2012/acp-12-11037-2012.html Link to full article]
-=== 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 November 29-30 AQAST meeting at the California Air Resources Board ===
-[http://acmg.seas.harvard.edu/aqast/meetings/nov2012/program.html Click here] for the meeting agenda with links to all presentations.
-=== Using AIRS observations to predict Asian and stratospheric influences on Western U.S. high surface ozone events ===
-presented by Meiyun Lin at the NASA Sounder Science Team Meeting, Greenbelt, MA, November 2012. [[https://www.gfdl.noaa.gov/cms-filesystem-action/user_files/m1l/nasa_airs_maryland_nov2012_meiyunlin.ppt Download ppt]]
-=== Understanding the spatial resolution of satellite observations of aerosols: the example of MODIS ===
-presented by Edward Hyer at the AWMA Specialty Conference on Air Quality and Visibility, Whitefish, MT, 26 September 2012. ([http://acmg.seas.harvard.edu/presentations/aqast/hyer_awma_talk_final.pdf Download pdf])
-=== Building a next generation public health toolkit for local air pollution events ===
-presented by Scott Spak at the Iowa Environmental Health Association Fall Conference, Marshalltown, IA, October 23, 2012. ([http://dl.dropbox.com/u/8441417/spak_ieha_smokefire.pdf Download pdf])
-== Other AQAST news ==
-=== Tracey Holloway awarded undergraduate research mentor award ===
-[http://www.sage.wisc.edu/people/holloway/holloway.html Tracey Holloway] was awarded the 2012 Undergraduate Research Mentor Award from the Council on Undergraduate Research in the Geosciences (GeoCUR). Holloway accepted the award at the Charlotte, NC, meeting of the Geological Society of America, where she presented a talk on engaging undergraduates in air quality research with satellite data, ground-based measurements, and atmospheric models. [http://www.personal.psu.edu/uxg3/blogs/geocur/geocurresaward.html Click here for more info and podcast online].

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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