Difference between revisions of "Chemistry Working Group"

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(Acetone photolysis)
(Acetone photolysis)
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[http://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v10-01c_UCX/v10-01c_UCX.jvalue_maps.pdf Fast-JX v6.4] vs.  
[http://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v10-01c_UCX/v10-01c_UCX.jvalue_maps.pdf Fast-JX v6.4] vs.  
[http://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v10-01c_UCX/v10-01c_UCX.jvalue_maps.pdf Fast-JX v7.0]
[http://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v10-01c_UCX/v10-01c_UCX.jvalue_maps.pdf Fast-JX v7.0]
'''Recommendation: update to Fast-JX v7.0'''
====Remaining issues====
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.
== Documentation ==
== Documentation ==

Revision as of 19:51, 9 May 2014

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 Mat Evans and Jingqiu Mao
Oxidants and Chemistry Working Group email list geos-chem-oxidants@seas.harvard.edu
To subscribe to email list Send email to geos-chem-oxidants-join@seas.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 Yiqiang Zhang
Hongyu Liu
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
Lucy Carpenter
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

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

rate of HNO4

Ellie Browne found a typo in the globchem.dat (GEOS-Chem v8-02-01 and beyond)

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%.

--J Mao. 19:04, 30 Aug 2010 (EDT)
--Bob Y. 16:12, 4 November 2011 (EDT)

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
        !   NKN     = NKNPHOTRT(PHOTVAL,NCS)
        !   DO KLOOP=1,KTLOOP
        !      RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) + 1d-5
        !   ENDDO

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.

--J Mao. 11:00, 26 Oct 2009 (EDT)
--Bob Y. 16:08, 4 November 2011 (EDT)

yield of isoprene nitrates

This update was added to GEOS-Chem v8-03-02 as a post-release patch, and standardized in GEOS-Chem v9-01-01.

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          +                   +                   +  

--J Mao. 18:04, 30 Aug 2010 (EDT)
--Bob Y. 16:05, 4 November 2011 (EDT)

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:
  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.

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

Current GC (v9-02) includes two channels of acetone photolysis:

AcetA: CH3COCH3 = CH3CO3 + CH3O2
AcetB: CH3COCH3 = CH3O2 + CH3O2 + CO

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.

'Note that in FastJX v6.4, AcetA shows very little difference between 220 K and 300 K for 294 nm, 303 nm and 310 nm. This is inconsistent with JPL 10-6, which suggests a very strong pressure dependence when wavelengths> 300 nm.

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.

Sebastian D. Eastham showed that J-acetone is significantly higher in Fast-JX v7.0. Comparison Fast-JX v6.4 vs. Fast-JX v7.0

Recommendation: update to Fast-JX v7.0

Remaining issues

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.


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