Chemistry Working Group

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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).

Contact information

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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--Bob Y. (talk) 18:29, 21 August 2015 (UTC)

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.

  1. Increase MO2 stoichiometry from 0.18 to 0.19
  2. 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).
  3. Modify the carbon count (i.e. the MolecRatio field in the GEOS-Chem species database) from 4 to 4.3.

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.

--Bob Yantosca (talk) 20:21, 31 January 2017 (UTC)

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

ChemTelecon20111202 Mat Evans

Isoprene chemistry

I've created a page with some of the recent literature on isoprene chemistry. Please add more papers as they come along! ( MJE Leeds)

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:
  1. I set GLPAN and GLCO3 rxns from active to dead. These rxns were causing an artificial loss of NOx.
  2. I have physically removed GLCO3, GLP, GLPAN, GPAN, ISNO3, MNO3, O2CH2OH, MVN2 and their associated reactions.
  3. I have made GLYX active. I'm not sure why it's not active by default.
and to ratj.d:
  1. I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in globchem.dat

--Bob Y. 14:51, 10 November 2011 (EST)
--Melissa Payer 10:49, 15 December 2011 (EST)

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)

Acetone photolysis

This discussion has been moved to our FAST-J photolysis mechanism wiki page.

--Bob Y. 15:20, 20 May 2014 (EDT)

Issues that have been since rendered obsolete by newer code updates

Documentation

--Bob Y. 15:41, 27 October 2009 (EDT)

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