Difference between revisions of "Chemistry Working Group"
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'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03a|v9-01-03a]] and approved on 08 Dec 2011.''''' | '''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03a|v9-01-03a]] and approved on 08 Dec 2011.''''' | ||
| − | '''''[mailto:fabienpaulot@gmail.com Fabien Paulot]''''' | + | '''''[mailto:fabienpaulot@gmail.com 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. | :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. | ||
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:#I set GLPAN and GLCO3 rxns from active to dead. These rxns were causing an artificial loss of NOx. | :#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, | + | :#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. | :#I have made GLYX active. I'm not sure why it's not active by default. | ||
| Line 75: | Line 75: | ||
:# I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in <tt>globchem.dat</tt> | :# I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in <tt>globchem.dat</tt> | ||
| − | --[[User:Bmy|Bob Y.]] 14:51, 10 November 2011 (EST) | + | --[[User:Bmy|Bob Y.]] 14:51, 10 November 2011 (EST)<br> |
| + | --[[User:Melissa Payer|Melissa Payer]] 10:49, 15 December 2011 (EST) | ||
=== Isoprene chemistry === | === Isoprene chemistry === | ||
Revision as of 15:49, 15 December 2011
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).
Contents
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 |
| To unsubscribe from email list | Send email to geos-chem-oxidants-leave@seas.harvard.edu |
Current GEOS-Chem Chemistry Projects (please add yours!)
| User Group | Description | Contact Person | Date Added |
|---|---|---|---|
| Caltech/Harvard | Examining the effects of isoprene nitrates and epoxide on tropical ozone and OH using SHADOZ and OMI measurements | Fabien Paulot Jingqiu Mao |
April 28, 2009 |
| Caltech/Harvard | Examining the HCHO yield, OH recycling and ozone production with INTEX-A observations from new isoprene chemistry | Jingqiu Mao Fabien Paulot |
April 28, 2009 |
| NIA / LaRC | Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis | Yiqiang Zhang Hongyu Liu |
June 29, 2010 |
| U. Wollongong | Tropospheric ozone precursors over Australasia: Using GEOS-Chem to interpret FTIR measurements of CO, NO2 and HCHO | Rebecca Buchholz | May 19, 2011 |
Current GEOS-Chem Chemistry Issues (please add yours!)
Working Group Tele-con on the 2nd December 2011
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
--Bob Y. 14:51, 10 November 2011 (EST)
--Melissa Payer 10:49, 15 December 2011 (EST)
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
! 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
to:
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)
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)
