Dicarbonyls simulation

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This page describes the optional dicarbonyls chemistry mechanism as implemented in GEOS-Chem.


Brief description

From Fu et al [2008]:

We use the Master Chemistry Mechanism version 3.1 (MCMv3.1) [Saunders et al., 2003; Bloss et al., 2005] as principal guide for the VOC chemistry leading to glyoxal and methylglyoxal formation. Primary VOC precursors include isoalkanes, alkenes, acetylene, aromatics, isoprene, monoterpenes, acetone, methylbutenol (2-methyl-3-buten-2-ol), glycolaldehyde, and hydroxyacetone. The latter two are secondary products of VOC oxidation but are also emitted directly by biofuel use and open biomass burning. Glyoxal and methylglyoxal are themselves also emitted directly from these two sources [McDonald et al., 2000; Hays et al., 2002]. Primary anthropogenic emissions of glyoxal and methylglyoxal are small [Environmental Protection Agency, 2004; Volkamer et al., 2005b] and are not considered here.
GEOS-Chem includes a detailed O3-NOx-VOC-aerosol chemical mechanism [Horowitz et al., 1998; Bey et al., 2001; Martin et al., 2003; Park et al., 2006]. ... Fu et al. [2007] added to the model the chemistry of ethylene and xylenes For this work, we further updated the photochemical mechanisms of isoprene, propene, acetylene, glyoxal, methylglyoxal, glycolaldehyde, and hydroxyacetone based on MCMv3.1 and Jet Propulsion Laboratory (JPL) [2006]. The quantum yield for acetone photolysis is updated to be dependent on both temperature and pressure, based on Blitz et al. [2004]. We also added parameterized dicarbonyl production from benzene, toluene, xylenes, monoterpenes, and methylbutenol.

Authors and collaborators

Dicarbonyls simulation user groups

User Group Personnel Projects
Peking University Tzung-May Fu ...
Univeristy of Minnesoata Dylan Millet ...
Colorado State University Colette Heald ...

--Bob Y. 16:10, 26 February 2010 (EST)

Input files

For this simulation, you need different input files for the chemistry:

You will also need a restart file with additional tracers. You can create your own (see GAMAP manual) or download one from the ftp:

 ftp ftp.as.harvard.edu
 cd pub/geos-chem/public_releases/
 get GEOS-Chem.v8-02-01-public-dicarb.rundir.4x5.tar.gz


 get GEOS-Chem.v8-02-01-public-dicarb.rundir.2x25.tar.gz

You'll also need a specific restart file for the SOA tracers. You can find one in the same archive file on the ftp.


  1. Bey I., D. J. Jacob, R. M. Yantosca, J. A. Logan, B. Field, A. M. Fiore, Q. Li, H. Liu, L. J. Mickley, and M. Schultz, Global modeling of tropospheric chemistry with assimilated meteorology: Model description and evaluation, J. Geophys. Res., 106, 23,073-23,096, 2001. PDF
  2. Blitz, M. A., D. E. Heard, M. J. Pilling, S. R. Arnold, and M. P. Chipperfield, Pressure and temperature-dependent quantum yields for the photodissociation of acetone between 279 and 327.5 nm, Geophys. Res. Lett., 31, L06111, doi:10.1029/2003GL018793, 2004.
  3. Bloss, C., et al., Development of detailed chemical mechanism (MCMv3.1) for the atmospheric oxidation of aromatic hydrocarbons, Atmos. Chem. Phys., 5, 641–664, 2005.
  4. Environmental Protection Agency, 1999 National emissions inventory version 3.0, Environmental Protection Agency, Washington, D.C., 2004. Link
  5. Horowitz, L.W., J. Liang, G.M. Gardner, and D.J. Jacob, Export of reactive nitrogen from North America during summertime, J. Geophys. Res., 103, 13,451-13,476, 1998. PDF
  6. Fu, T.-M., D. J. Jacob, P. I. Palmer, K. Chance, Y. X. Wang, B. Barletta, D. R. Blake, J. C. Stanton, M. J. Pilling, Space-based formaldehyde measurements as constraints on volatile organic compound emissions in East and South Asia, J. Geophys. Res., 112, D06312, doi:10.1029/2006JD007853, 2007. PDF
  7. Fu, T.-M., D.J. Jacob, and C.L. Heald, Aqueous-phase reactive uptake of dicarbonyls as a source of organic aerosol over eastern North America, Atmos. Environ., 43, 1,814-1,822, 2009.PDF
  8. Hays, M. D., C. D. Geron, K. J. Linna, N. D. Smith, and J. J. Schauer, Speciation of gas-phase and fine particle emissions from burning of foliar fuels, Environ. Sci. Technol., 36(11), 2281–2295, doi:10.1021/es0111683, 2002.
  9. Jet Propulsion Laboratory (JPL), Chemical Kinetics and PhotochemicalData for Use in Atmospheric Studies, Evaluation Number 15, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, 2006.
  10. Martin, R.V., D.J. Jacob, R.M. Yantosca, M. Chin, and P. Ginoux, Global and Regional Decreases in Tropospheric Oxidants from Photochemical Effects of Aerosols, J. Geophys. Res., 108(D3), 4097, doi:10.1029/2002JD002622. PDF
  11. McDonald, J. D., B. Zielinska, E. M. Fujita, J. C. Sagebiel, J. C. Chow, and J. G. Watson, Fine particle and gaseous emission rates from residential wood combustion, Environ. Sci. Technol., 34(11), 2080–2091, doi:10.1021/es9909632, 2000.
  12. Park, R. J., D. J. Jacob, N. Kumar, and R. M. Yantosca, Regional visibility statistics in the United States: Natural and transboundary pollution influences, and implications for the Regional Haze Rule, Atmos. Environ., 40(28), 5405-5423, 2006. PDF
  13. Saunders, S. M., M. E. Jenkin, R. G. Derwen, and M. J. Pilling, Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): Tropospheric degradation of non-aromatic volatile organic compounds, Atmos. Chem. Phys., 3, 161–180, 2003.
  14. Volkamer, R., L. T. Molina, M. J. Molina, T. Shirley, and W. H. Brune, DOAS measurement of glyoxal as an indicator for fast VOC chemistry in urban air,Geophys. Res. Lett., 32, L08806, doi:10.1029/2005GL022616, 2005.

--Bob Y. 15:57, 26 February 2010 (EST)

Known issues

KPP is not compatible with the dicarbonyls simulation

As of Feb 2010, the files needed to use the KPP solver were not generated for the dicarbonyls chemistry. You can not run the dicarbonyls chemistry with the KPP solver. You have to use SMVGEAR.

If someone is so motivated, one can build the KPP solver files with the dicarbonyls chemistry mechanism on their own.

--Bob Y. 16:20, 26 February 2010 (EST)

Input file issues

Dylan Millet wrote:

I found some problems with the standard v8-2-1 code and specific run directories for running dicarbonyl simulations, which lead to mysterious and cryptic run death. globchem.dat has an extra line under the HNO3 emission and before the NO2 drydep (line 2170 needs to be deleted). I also ran into other problems which I traced to read-in errors with jv_spec.dat (...).
--Dbm 00:00, 12 October 2009 (EDT)

As explained above, Dylan Millet had some problems with the input files for dicarbonyl simulation. There were some problems in the format of globchem.dat and jv_spec.dat for dicarbonyls. The files had been updated. If you want to use the dicarbonyl simulation, please redownload the run directories from the ftp:

  ftp ftp.as.harvard.edu
  cp pub/geos-chem/public_releases
  get GEOS-Chem.v8-02-01-public-dicarb.rundir.4x5.tar.gz


  get GEOS-Chem.v8-02-01-public-dicarb.rundir.2x25.tar.gz

--Ccarouge 12:54, 16 October 2009 (EDT)

Out-of-bounds error in SOAG_LIGGIO_DIFF

There was an out-of-bounds error in SOAG_LIGGIO_DIFF. Here is the solution:

Claire Carouge wrote:

In fact, in SOAG_LIGGIO_DIFF (carbon_mod.f), there is a loop over LLTROP. It's the maximum number of levels for the tropopause. But in the loop we use JLOP indexes which are 0 outside the actual tropopause.
So the fix is to add the line:
           ! JLOP equal 0 if we're not in the tropopause. (ccc,10/16/09)
           IF ( JLOOP == 0 ) CYCLE
after line 1224:
           ! Get 1-D index
           JLOOP   = JLOP( I, J, L )
There is the same kind of loop in SOAM_LIGGIO_DIFF just after. You should add the same fix.

--Ccarouge 12:54, 16 October 2009 (EDT)