Chemistry Working Group
Oxidants and Chemistry Working Group
All users interested in the GEOS-Chem chemistry scheme and associated processes (photolysis, heterogeneous, deposition) are encouraged to subscribe to the chemistry email list (click on the link in the contact information section below).
- 1 Contact information
- 2 Current GEOS-Chem Chemistry Projects (please add yours!)
- 3 Current GEOS-Chem Chemistry Issues (please add yours!)
- 4 Previous issues that have now been resolved
- 5 Issues that have been since rendered obsolete by newer code updates
- 6 Documentation
|Oxidants and Chemistry Working Group Co-Chairs|
|Oxidants and Chemistry Working Group email list||geos-chem-oxidants [at] g.harvard.edu|
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Current GEOS-Chem Chemistry Projects (please add yours!)
|User Group||Description||Contact Person||Date Added|
|NIA / LaRC||Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis||Hongyu Liu||5 May 2015|
|University of York||Iodine chemistry||Tomas Sherwen||24 June 2015|
|University of York||Low NOx isoprene chemistry||Shani Garraway||24 June 2015|
|University of York||Impacts of uncertainty in chemical kinetics||Ben Newsome||24 June 2015|
|University of York||New spin-based formulation of ozone production||Pete Edwards||24 June 2015|
|University of York||New surface ozone dataset for model evaluation||Eric Sofen||24 June 2015|
|University of York||Spectral methodology for model evaluation||Dene Bowdalo||24 June 2015|
|University of York||Updates to the kinetics of Criegee chemistry based on new chamber experiments||Mat Evans||24 June 2015|
|University of York||Impact of ClNO2 chemistry on UK marine composition||Mat Evans||24 June 2015|
--Bob Y. 15:08, 25 April 2014 (EDT)
Current GEOS-Chem Chemistry Issues (please add yours!)
Fixes to correct ALK4 lumping issue
NOTE: This update is currently slated for v11-02a.
Barron Henderson wrote:
I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).
Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy. When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.
If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.
I have extensive notes on what I interpret as happening. To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.
Fixes 1 and 2—which can be applied to the KPP globchem.eqn file—will make the carbon conservation consistent with Lurmann's. Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.
- Increase MO2 stoichiometry from 0.18 to 0.19
- Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).
- Modify the carbon count (i.e. the MolecRatio field in the GEOS-Chem species database) from 4 to 4.3.
JPL Released 18th Rate Coefficient Evaluation
NOTE: This update is currently slated for v11-02a.
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page (Updates in JPL Publication 15-10) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10.
- J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.
---B. Henderson 2016-05-03 15:25 (EDT)
Working Group Tele-con on the 2nd December 2011
HO2 + CH2O
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
Hermans, I., et al. (2005), Kinetics of alpha-hydroxy-alkylperoxyl radicals in oxidation processes. HO2 center dot-initiated oxidation of ketones/aldehydes near the tropopause, Journal of Physical Chemistry A, 109(19), 4303-4311.
According to this paper, this reaction is significant when Temperature is below 220K.
--J Mao. 15:00, 10 Aug 2009 (EDT)
Previous issues that have now been resolved
Centralizing chemistry time step
This update was tested in the 1-month benchmark simulation v9-01-02q and approved on 18 Oct 2011.
Please see the full discussion on the Centralized chemistry time step wiki page.
--Bob Y. 16:01, 4 November 2011 (EDT)
GLCO3, GLPAN bug in standard mechanism
This update was tested in the 1-month benchmark simulation v9-01-03a and approved on 08 Dec 2011.
SMVGEAR will be removed from GEOS-Chem v11-01 and higher versions. The globchem.dat file will be replaced by the KPP master equation file.
Fabien Paulot wrote:
- I think there is a relatively serious bug in the standard chemistry. GLPAN and GLCO3 are set to inactive but their production and loss reactions are active. As a result they never reach equilibrium and this results in an artificial loss of NOx.
- If this is the only cause of the imbalance between sources and sinks of NOx in my simulations, this would account for ~5% of NOy losses. I don't see that problem in a simulation with a different chemistry that among other changes does not feature those reactions. So hopefully that's it.
- To fix the error, I made the following modifications in globchem.dat:
- I set GLPAN and GLCO3 rxns from active to dead. These rxns were causing an artificial loss of NOx.
- I have physically removed GLCO3, GLP, GLPAN, GPAN, ISNO3, MNO3, O2CH2OH, MVN2 and their associated reactions.
- I have made GLYX active. I'm not sure why it's not active by default.
- and to ratj.d:
- I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in globchem.dat
Bug in routine ARSL1K
This update was tested in the 1-month benchmark simulation v9-01-03m and approved on 06 Jun 2012.
SMVGEAR will be removed from GEOS-Chem v11-01 and higher versions. The ARSL1K routine will be replaced by an equivalent function in KPP's rate law library.
A bug in routine ARSL1K became problematic in the implementation of Justin Parrella's tropospheric bromine chemistry mechanism for GEOS-Chem v9-01-03. In the bromine chemistry mechanism, a sticking coefficient of 0.0 is passed to the routine ARSL1K for non-sulfate, non-sea salt aerosol. The IF statement modified in GEOS-Chem v8-02-04 resulted in the reaction rate being set to the default value of 1.0d-3. A 1-month benchmark for July 2005 indicated that the simulated BrO was a little more than twice the expected zonal mean. Modifying the default value from 1.0d-3 to 1.0d-30 resulted in reasonable simulated BrO values.
Mat Evans wrote:
- I've re-run two 2 month simulation [using GEOS-Chem v9-01-02]. One with the error handling value of 1e-3 (standard) and one with it being 1e-30. There are 5127 time and space points where the model traps the problem and invokes the 1e-3 or 1e-30 value. There are 30*24*2*37*72*46 (roughly 200 million) time and space points when the error could have occurred so we are looking at a relatively infrequent event.
- The simulations show virtually no difference between the two simulations.
- mean and stddev ratio of all grid boxes with and without the fix are shown below
NOx 0.999996 0.000409291 Ox 1.00000 1.27233e-05 O3 1.00000 1.52284e-05 PAN 0.997849 0.0111997 CO 1.00000 4.21768e-06 ALK4 0.990514 0.0351941 ISOP 0.999979 0.0108033 H2O2 0.992067 0.0264659 DST1 1.00000 0.00000 HO2 0.999996 0.00309464 OH 1.00003 0.00767954
- So although there are some differences they are very minor. For completeness we should put this in as a bug fix (make the error value 1d-30 rather than 1d-3). But it is not a major problem.
--Melissa Payer 17:52, 14 May 2012 (EDT)
--Bob Y. 15:20, 20 May 2014 (EDT)
Issues that have been since rendered obsolete by newer code updates
- Updated chemical reactions that will be used in GEOS-Chem v8-02-04 and higher.
- Updated chemical reactions now used in GEOS-Chem v8-02-01 through GEOS-Chem v8-02-03.
- All typos have now been corrected in the present file.
- Format of FAST-J input file jv_spec.dat
--Bob Y. 15:41, 27 October 2009 (EDT)