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 Documentation
|Oxidants and Chemistry Working Group Co-Chairs||Mat Evans and Jingqiu Mao|
|Oxidants and Chemistry Working Group email firstname.lastname@example.org|
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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||Yiqiang Zhang
|29 Jun 2010|
|U. Wollongong||Tropospheric ozone precursors over Australasia: Using GEOS-Chem to interpret FTIR measurements of CO, NO2 and HCHO||Rebecca Buchholz||19 May 2011|
|University of York||Role of iodine chemistry in the troposphere||Mat Evans
|12 Apr 2012|
|University of Florida||Process Analysis Diagnostics||Barron Henderson||12 Sep 2013|
|Harvard University||Implementation of recent updates to isoprene low-NOx chemistry (includes irreversible uptake of isoprene SOA)||Eloise Marais||27 April 2014|
--Bob Y. 15:08, 25 April 2014 (EDT)
Current GEOS-Chem Chemistry Issues (please add yours!)
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
rate of HNO4
A 73 9.52E-05 3.2E+00 -10900 1 P 0.60 0. 0. 1.38E+15 1.4E+00 -10900 0 0.00 0. 0. HNO4 + M =1.000HO2 +1.000NO2 + +
This should be corrected as:
A 73 9.52E-05 3.4E+00 -10900 1 P 0.60 0. 0. 1.38E+15 1.1E+00 -10900 0 0.00 0. 0. HNO4 + M =1.000HO2 +1.000NO2 + +
The difference is within 2%.
near-IR photolysis of HNO4
This update was added to GEOS-Chem v8-02-04.
1. Since FastJX already takes this into account with cross section data at 574nm, we do not need to redo this in calcrate.f. We can therefore comment out this entire IF block:
!--------------------------------------------------------------------- ! Prior to 10/27/09: ! FastJX has taken near-IR photolysis into account with ! cross section at 574nm, so we don't need to add 1e-5 anymore. ! According to Jimenez et al., "Quantum yields of OH, HO2 and ! NO3 in the UV photolysis of HO2NO2", PCCP, 2005, we also ! changed the branch ratio from 0.67(HO2)/0.33(OH) to 0.95/0.05 ! This will put most weight of near-IR photolysis on HO2 channel. ! (jmao, bmy, 10/27/09) ! !!============================================================== !! HARDWIRE addition of 1e-5 s-1 photolysis rate to !! HNO4 -> HO2+NO2 to account for HNO4 photolysis in near-IR -- !! see Roehl et al. 'Photodissociation of peroxynitric acid in !! the near-IR', 2002. (amf, bmy, 1/7/02) !! !! Add NCS index to NKHNO4 for SMVGEAR II (gcc, bmy, 4/1/03) !!============================================================== !IF ( NKHNO4(NCS) > 0 ) THEN ! ! ! Put J(HNO4) in correct spot for SMVGEAR II ! PHOTVAL = NKHNO4(NCS) - NRATES(NCS) ! NKN = NKNPHOTRT(PHOTVAL,NCS) ! ! DO KLOOP=1,KTLOOP ! RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) + 1d-5 ! ENDDO !ENDIF !---------------------------------------------------------------------
2. We need to change the branch ratio of HNO4 photolysis in ratj.d. Change these lines from:
13 HNO4 PHOTON OH NO3 0.00E+00 0.00 33.3 HO2NO2 14 HNO4 PHOTON HO2 NO2 0.00E+00 0.00 66.7 HO2NO2
13 HNO4 PHOTON OH NO3 0.00E+00 0.00 5.0 HO2NO2 14 HNO4 PHOTON HO2 NO2 0.00E+00 0.00 95.0 HO2NO2
This is based on Jimenez et al. (Quantum yields of OH, HO2 and NO3 in the UV photolysis of HO2NO2, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2005) shows that HO2 yield should be 0.95 and OH yield should be 0.05 for wavelength above 290nm.
This way all the near-IR photolysis will have most weight on HO2 channel(Stark et al., Overtone dissociation of peroxynitric acid (HO2NO2): Absorption cross sections and photolysis products, JOURNAL OF PHYSICAL CHEMISTRY A, 2008).
This update has now been added to the chemistry mechanism documentation file.
yield of isoprene nitrates
Fabien Paulot found a problem in current chemistry scheme. In GEOS-Chem v8-02-01 and beyond, isoprene nitrates are produced twice: one through channel A and one through 10% loss in channel B. This makes the loss of NOx larger than it should be (18.7% vs. 10%) and also reduces the yield of MVK/MACR/CH2O by about 13%.
A 453 2.70E-12 0.0E+00 350 1 B 0.00 0. 0. 5.00E+00 0.0E+00 0 0 0.00 0. 0. RIO2 + NO =0.900NO2 +0.900HO2 +0.340IALD +0.340MVK +0.220MACR +0.560CH2O + + A 453 2.70E-12 0.0E+00 350 1 A 0.00 0. 0. 5.00E+00 0.0E+00 0 0 0.00 0. 0. RIO2 + NO =1.000HNO3 + + +
So it should be corrected as (no channel A):
A 453 2.70E-12 0.0E+00 350 0 0 0.00 0. 0. RIO2 + NO =0.900NO2 +0.900HO2 +0.340IALD +0.340MVK +0.220MACR +0.560CH2O + + D 453 2.70E-12 0.0E+00 350 1 A 0.00 0. 0. 5.00E+00 0.0E+00 0 0 0.00 0. 0. RIO2 + NO =1.000HNO3 + + +
Potential issue with reading restart.cspec file
This update was tested in the 1-month benchmark simulation v9-01-02c and approved on 21 Jul 2011.
Jingqiu Mao discovered a mis-indexing problem when using the restart.cspec.YYYYMMDDhh file. Please see this wiki post for more information.
--Bob Y. 16:02, 4 November 2011 (EDT)
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.
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.
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)
Current GC (v9-02) includes two channels of acetone photolysis:
AcetA: CH3COCH3 = CH3CO3 + CH3O2 AcetB: CH3COCH3 = CH3O2 + CH3O2 + CO AcetA is the dominant channel under tropospheric conditions with strong pressure dependence.
Current cross section in jv_spec.dat (obtained from FastJX v6.4): Cross section
w-eff(nm) 294. 303. 310. 316. 333. 380. 574. AcetA 220 3.100E-20 1.944E-20 1.088E-20 5.532E-21 4.637E-22 3.425E-25 0.000E+00 AcetA 300 3.439E-20 2.255E-20 1.356E-20 7.273E-21 8.481E-22 6.682E-25 0.000E+00 AcetB 240 5.156E-03 1.931E-03 8.022E-04 4.144E-04 4.156E-05 0.000E+00 0.000E+00 AcetB 300 8.564E-02 5.100E-02 3.298E-02 2.214E-02 3.533E-03 0.000E+00 0.000E+00
and quantum yield
Q1A-Ac 240 1.000E+00 1.207E+00 4.133E+00 2.498E+01 9.452E+01 1.000E+02 1.000E+02 Q1A-Ac 300 1.006E+00 1.223E+00 2.411E+00 6.656E+00 1.969E+01 2.100E+01 2.100E+01 Q1B-Ac 240 1.028E+00 1.066E+01 5.202E+01 2.632E+02 2.760E+03 3.210E+03 3.210E+03 Q1B-Ac 300 8.792E-01 4.897E+00 1.617E+01 5.268E+01 3.023E+02 3.420E+02 3.420E+02
And the pressure dependence is described here as in FastJX v6.4 (JRATET.F in our code):
VALJ(NJVAL-1) = VALJ(NJVAL-1) & + FFF(K,L)*QQQA*(1.d0-QQ2)/(QQ1A + QQ1B*DD)
where DD = 7.24e18*Pressure/Temperature in the code.
'The problem here is that the pressure dependence of J-acetone seems wrong (see the comparison below). This is inconsistent with JPL 10-6, which suggests a very strong pressure dependence of J when wavelengths> 300 nm.'
This is also confirmed by Michael Prather, who mentioned that the implementation of J-acetone in FastJX v6.4 was different from JPL 10-6 recommendation. But the most recent one (v7.1) is consistent with JPL 10-6.
Katie Travis used SEAC4RS data to examine the J-acetone in v9-02, and indeed J-acetone was way off in upper trop, see the validation here.
Recommendation: use the pressure dependence calculation in Fast-JX v7.0
Seb also found large difference on J-acetone between UCX simulation and tropospheric only UCX simulations (J-acetone is a lot higher in version). This needs further investigation. This is due to some bug in the source code when switching from 18 bins to 12 bins, and the bug is now fixed.
- 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)