Chemistry Working Group: Difference between revisions
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|Automated model reduction isoprene oxidation mechanism | |||
|[mailto:benjamin.yang@columbia.edu Benjamin Yang]<br> | |||
[mailto:danielmw@ldeo.columbia.edu Dan Westervelt] | |||
|12 Sep 2023 | |||
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Revision as of 18:29, 12 September 2023
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 |
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|---|---|
| Oxidants and Chemistry Working Group email list | geos-chem-oxidants [at] g.harvard.edu |
| To subscribe to email list | Either
Or
|
| To unsubscribe from email list | Either
Or
|
--Bob Y. (talk) 18:29, 21 August 2015 (UTC)
Current GEOS-Chem Chemistry Projects (please add yours!)
| User Group | Description | Contact Person | Date Added |
|---|---|---|---|
| Columbia University | Automated model reduction isoprene oxidation mechanism | Benjamin Yang |
12 Sep 2023 |
| NOAA CSL | JPL Kinetic Review Update/C-N balance/stoichiometry update | Kelvin Bates | 01 Jul 2023 |
| University of York | Nitrate Photolysis | Mat Evans |
08 Jun 2022 |
| University of York | Halogen reverse reactions | Mat Evans |
01 Jun 2022 |
| University of York | Chlorine chemistry | Mat Evans |
01 Oct 2022 |
| Harvard University and MPIC-Mainz |
Further development of The Kinetic PreProcessor (KPP) | Bob Yantosca (GCST) | 03 Jun 2022 |
| Harvard University | Adding an adaptive solver capability into KPP | Haipeng Lin | 03 Jun 2022 |
| GCST | Migrating the Hg chemistry mechanism to KPP | Bob Yantosca (GCST) | 03 Jun 2022 |
| GCST | Adding a CO-CO2-CH4-OCS chemistry mechanism with KPP | Bob Yantosca (GCST) | 03 Jun 2022 |
| U Montana | Formic acid and acetic acid formation in fire smoke | Wade Permar Lu Hu |
21 May 2022 |
| U Montana | Furans chemistry in MCM and in GEOS-Chem | Lixu Jin Lu Hu |
21 May 2022 |
| U Wollongong | Evaluation of aromatic oxidation products using new observational constraints | Stephen MacFarlane | 9 June 2022 |
| UNSW, Sydney | Contribution of the unexplored photochemistry of aldehydes to the tropospheric levels of hydrogen | Maria Paula Perez-Pena | 25 June 2021 |
| University of California, Riverside | Updates to DMS oxidation scheme | William Porter | 26 August 2020 |
| Harvard University | Overhaul of cloud pH code including: use of Newton's method and addition of crustal cations and organic acids | Viral Shah Jonathan Moch |
5 May 2019 |
| U Alaska Fairbanks | Monoterpene oxidation and its impact on SOA formation | Yiqi Zheng Jingqiu Mao |
21 April 2019 |
| MIT | Simulating the global reactive carbon budget | Sarah Safieddine | 12 April 2017 |
| FSU | Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry | Chris Holmes | May 2017 |
| FSU | Methane and methyl chloroform lifetimes | Chris Holmes | May 2017 |
| FSU | Arctic halogen & ozone chemistry | Chris Holmes | May 2017 |
Current GEOS-Chem Chemistry Issues (please add yours!)
Working group telecom on the 13/3/2019
There was a telecon to discuss issues with the chemistry. The notes from the meeting are here Media:Chemistry_WG_March_2019..pdf . Mat Evans
Carbon balance
Script for evaluating carbon balance
Barron Henderson wrote:
[I created] an evaluation script to preserve balances going forward as the mechanism evolves (e.g., as isoprene gets updated).
Currently, this done using an off-line script described in a linked note. The approach is pretty straight-forward, but could be expanded to check conservation of functional groups as suggested by Mat.
Longer term, the same technique would ideally be built-in to the standard KPP as an optional report. I discussed it with Michael Long and we both think that KPP has most of the capability for atom conservation (if not all). It may simply be a matter of defining the chemical formulas in the *.spc file.
--Melissa Sulprizio (talk) 21:06, 22 May 2017 (UTC)
Fixes for carbon creating reactions
This update was included in v11-02c and approved on 21 Sep 2017.
Sarah Safieddine wrote:
Colette, Barron, Mat and myself modified 13 previous "carbon creating" reactions to preserve carbon. The [table below] lists all the corrections for the reactions in globchem.dat V902 that we corrected, with all the details.
| Reaction # in globchem.dat v9-02 | Unbalanced Reaction | Rate constant | Issue (R=Reactants, P=Products) |
Fix and corrected reaction (in green) |
|---|---|---|---|---|
| 453 | R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2 | K* (1-YN) where YN is returned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.5) | Creates carbon: R=4C P=4.26C | Replace 0.18B3O2 by 0.093B3O2 to achieve carbon closure (as suggested by Barron). R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.093B3O2 + 0.32ETO2 |
| 453 | R4N1 + NO → 2NO2 + 0.39CH2O + 0.75ALD2 + 0.57RCHO + 0.3R4O2 | 2.7E-12 exp(350/T) | Creates carbon: R=4C, P=4.8C | Fix, as suggested by Matt: R4N1 + NO → 2NO2 + 0.570RCHO + 0.86ALD2 + 0.57CH2O |
| 453 | ATO2 + NO → 0.96NO2 + 0.96CH2O + 0.96MCO3 + 0.04R4N2 | 2.8E-12 exp(300/T) | Creates carbon: R=3C, P=3.04 | Fix as suggested by Mat: ditch the R4N2 channel ATO2 + NO → NO2 + CH2O + MCO3 |
| 803 | RIO2 → 2HO2 + CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.5HAC + OH | 4.07E+08 exp(-7694/T) | Creates carbon: R=5C, P=7C There was a fix proposed on the isoprene scheme wiki page but still not enough |
Fix as suggested by Sarah: remove CH2O RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH |
| 453 | ISNOOB + NO3 → R4N2 + GLYX + 2NO2 | 2.3E-12 | Creates carbon: R=5C, P=6C | Fix as suggested by Barron: Replace R4N2 by PROPNN ISNOOB + NO3 → PROPNN + GLYX + 2NO2 |
| 453 | ISNOOB+NO → 0.94R4N2 +0.94GLYX +1.88NO2 | 2.6E-12 exp(380/T) | Creates carbon: R=5C, P=5.64C | Same as above ISNOOB + NO → 0.06R4N2 + '0.94PROPNN' + 0.94GLYX + 1.88NO2 |
| 453 | ISNOHOO + NO → 0.934R4N2 + 0.934HO2 + 0.919GLYX | 2.6E-12 exp(380/T) | Creates carbon: R=5C, P=5.574C | Fix by Barron: ISNOHOO + NO → 0.081R4N2 + 0.919PROPNN + 0.934HO2 + 0.919GLYX |
| 472 | MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85ISNP | 2.91E-13*exp(1300/T)[1-exp(-0.245*n)],n=4 | Creates carbon: R=4C, P=4.85C | Fix by both Mat and Barron: Replace ISNP with 0.85MAOP + 0.85NO2 MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85MAOP + 0.85NO2 |
| 719 | ATO2 + MCO3 → MEK + ACTA | 1.87E-13 exp(500/T) | Creates carbon: R=5C, P=6C | From the WIKI: replace MEK with MGLY ATO2 + MCO3 → MGLY + ACTA |
| 817 | Br + ALD2 → HBr + MCO3 + CO | 1.3E-11 exp(-360/T) | Creates carbon: R=2C, P=3C | Remove CO Following Parrella et al., Table 2a, reactions R7 to R10 (also for the 3 reactions below) Br + ALD2 → HBr + MCO3 |
| 818 | Br + ACET → HBr + ATO2 + CO | 1.66E-10exp(-7000/T) | Creates carbon: R=3C, P=4C | Remove CO, same as above Br + ACET → HBr + ATO2 |
| 819 | Br + C2H6 → HBr + ETO2 + CO | 2.36E-10 exp(-6411/T) | Creates carbon: R=2C, P=3C | Remove CO, same as above Br + C2H6 → HBr + ETO2 |
| 820 | Br + C3H8 → HBr + A3O2 + CO | 8.77E-11 exp(-4330/T) | Creates carbon: R=3C, P=4C | Remove CO, same as above Br + C3H8 → HBr + A3O2 |
--Melissa Sulprizio (talk) 19:59, 27 July 2017 (UTC)
Identification of carbon leaking reactions
Sarah Safieddine wrote:
76 other reactions leaked carbon, we enforced carbon conservation by tracking the lost carbon as CO2 (labeled as {CO2} in the document ROC_SI.docx, Table 2). This is the supplementary material for Safieddine, Heald and Henderson, 2017. It contains the corrections for both the carbon leaking and carbon creating reactions and all other information. The paper for reference can be found here: http://onlinelibrary.wiley.com/doi/10.1002/2017GL072602/abstract.
--Melissa Sulprizio (talk) 21:06, 22 May 2017 (UTC)
Fixes to correct ALK4 lumping issue
These fixes were included in v11-02a and approved on 12 May 2017.
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.
- 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 for ALK4 (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
This update was included in v11-02a and approved on 12 May 2017.
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
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)
Acetone photolysis
This discussion has been moved to our FAST-J photolysis mechanism wiki page.
--Bob Y. 15:20, 20 May 2014 (EDT)
Documentation
- 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)