Chemistry Working Group: Difference between revisions

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<big><big><strong>Oxidants and Chemistry Working Group</strong></big></big>
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|contact information section]] below).
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|contact information section]] below).


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{| border=1 cellspacing=0 cellpadding=5
{| border=1 cellspacing=0 cellpadding=5
|-
|-valign="top"
|bgcolor="#CCCCCC"|'''Oxidants and Chemistry Working Group Co-Chairs'''
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs
|[http://www.env.leeds.ac.uk/~lecmje/lecmje Mat Evans] and [http://www.gfdl.noaa.gov/jingqiu-mao Jingqiu Mao]
|width="600px"|
|-
*[http://www.barronh.com Barron Henderson] (GitHub: [https://github.com/barronh @barronh])
|bgcolor="#CCCCCC"|'''Oxidants and Chemistry Working Group email list'''
*[http://hs.umt.edu/luhu/people.php Lu Hu] (GitHub: [https://github.com/luhu0 @luhu0])
|<tt>geos-chem-oxidants@seas.harvard.edu</tt>
*[https://www.jessicahaskinsphd.com/ Jessica Haskins] (Github: [https://github.com/jhaskinsPhD jhaskinsPhD])
|-
*[https://www.kelvinbates.com/ Kelvin Bates] (Github: [https://github.com/kelvinhb @kelvinb])
|bgcolor="#CCCCCC"|'''To subscribe to email list'''
 
|Send email to [mailto:geos-chem-oxidants-join@seas.harvard.edu <tt>geos-chem-oxidants-join@seas.harvard.edu</tt>]
|-valign="top"
|-
!bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group email list
|bgcolor="#CCCCCC"|'''To unsubscribe from email list'''
|<tt>geos-chem-oxidants [at] g.harvard.edu</tt>
|Send email to [mailto:geos-chem-oxidants-leave@seas.harvard.edu <tt>geos-chem-oxidants-leave@seas.harvard.edu</tt>]
 
|-valign="top"
!bgcolor="#CCCCCC"|To subscribe to email list
|Either
*Send an email to <tt>geos-chem-oxidants+subscribe [at] g.harvard.edu</tt>
Or
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]
*Click on '''Subscribe to this group'''
 
|-valign="top"
!bgcolor="#CCCCCC"|To unsubscribe from email list
|Either
*Send an email to <tt>geos-chem-oxidants+unsubscribe [at] g.harvard.edu</tt>
Or
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]
*Click on the '''My Settings''' button
*Click on '''Leave this group'''
 
|}
|}
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:29, 21 August 2015 (UTC)


== Current GEOS-Chem Chemistry Projects (please add yours!) ==
== Current GEOS-Chem Chemistry Projects (please add yours!) ==
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!width="150px"|Contact Person
!width="150px"|Contact Person
!width="100px"|Date Added
!width="100px"|Date Added
|-
|NIA / LaRC
|Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis
|[mailto:yiqiang.zhang@nianet.org Yiqiang Zhang ] <br>[mailto:hyl@nianet.org Hongyu Liu]
|29 Jun 2010
|-
|U. Wollongong
|Tropospheric ozone precursors over Australasia: Using GEOS-Chem to interpret FTIR measurements of CO, NO2 and HCHO
|[mailto:rb864@uowmail.edu.au Rebecca Buchholz ]
|19 May 2011
|-
|University of York
|Role of iodine chemistry in the troposphere
|[mailto:mat.evans@york.ac.uk Mat Evans]<br>[mailto:lucy.carpenter@york.ac.uk Lucy Carpenter]
|12 Apr 2012
|-
|University of Florida
|[[Process_Analysis_Diagnostics|Process Analysis Diagnostics]]
|[mailto:barronh@ufl.edu Barron Henderson ]
|12 Sep 2013
|-
|Harvard University
|Implementation of recent updates to isoprene low-NOx chemistry (includes irreversible uptake of isoprene SOA)
|[mailto:emarais@seas.harvard.edu Eloise Marais ]
|27 April 2014
|}


--[[User:Bmy|Bob Y.]] 15:08, 25 April 2014 (EDT)
|-valign="top"
|NASA LARC
|Scheme for higher PN production from aromatics, MEK, monoterpenes, glycolaldehyde, and 1,3-butadiene
|[mailto:katherine.travis@nasa.gov Katherine R. Travis]
|19 Sep 2023


== Current GEOS-Chem Chemistry Issues (please add yours!) ==


=== Working Group Tele-con on the 2nd December 2011 ===
|-valign="top"
[[ChemTelecon20111202]]
|Columbia University
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''
|Automated model reduction isoprene oxidation mechanism
|[mailto:benjamin.yang@columbia.edu Benjamin Yang]<br>
[mailto:danielmw@ldeo.columbia.edu Dan Westervelt]
|12 Sep 2023


=== Isoprene chemistry ===
|-valign="top"
I've created a page with some of the recent literature on [[Isoprene|isoprene chemistry]]. Please add more papers as they come along! ([[User:mje| MJE Leeds]])
|NOAA CSL
|JPL Kinetic Review Update/C-N balance/stoichiometry update
|[mailto:khbates@ucdavis.edu Kelvin Bates]
|01 Jul 2023


=== HO2 + CH2O ===
|-valign="top"
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
|University of York
|Nitrate Photolysis
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
[mailto:matthew.rowlinson@york.ac.ul Matthew Rowlinson]
|08 Jun 2022


Hermans, I., et al. (2005), Kinetics of alpha-hydroxy-alkylperoxyl radicals in oxidation
|-valign="top"
processes. HO2 center dot-initiated oxidation of ketones/aldehydes near the tropopause,
|University of York
Journal of Physical Chemistry A, 109(19), 4303-4311.
|Halogen reverse reactions
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
[mailto:hansen.cao@york.ac.ul Hansen Cao]
|01 Jun 2022


According to this paper, this reaction is significant when Temperature is below 220K.
|-valign="top"
|University of York
|Chlorine chemistry
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
[mailto:al1916@york.ac.uk Amy Lees]
|01 Oct 2022


--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
|-valign="top"
|Harvard University and<br>MPIC-Mainz
|Further development of [https://kpp.readthedocs.io The Kinetic PreProcessor (KPP)]
|[mailto:yantosca@seas.harvard.edu Bob Yantosca] (GCST)
|03 Jun 2022


== Previous issues that have now been resolved ==
|-valign="top"
|Harvard University
|Adding an adaptive solver capability into [https://kpp.readthedocs.io KPP]
|[mailto:hplin@seas.harvard.edu Haipeng Lin]
|03 Jun 2022


=== rate of HNO4 ===
|-valign="top"
[mailto:ecbrow@berkeley.edu Ellie Browne] found a typo in the globchem.dat ([[GEOS-Chem v8-02-01]] and beyond)
|GCST
<pre>
|Migrating the Hg chemistry mechanism to [https://kpp.readthedocs.io KPP]
A  73 9.52E-05  3.2E+00 -10900 1 P  0.60    0.    0.       
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)
      1.38E+15  1.4E+00 -10900 0    0.00    0.    0.       
|03 Jun 2022
      HNO4          +                        M                               
=1.000HO2          +1.000NO2          +                  +
</pre>
This should be corrected as:
<pre>
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          +                  +
</pre>
The difference is within 2%.


--[[User:Jmao|J Mao.]] 19:04, 30 Aug 2010 (EDT)<br>
|-valign="top"
--[[User:Bmy|Bob Y.]] 16:12, 4 November 2011 (EDT)
|GCST
|Adding a CO-CO2-CH4-OCS chemistry mechanism with [https://kpp.readthedocs.io KPP]
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)
|03 Jun 2022


=== near-IR photolysis of HNO4 ===
|-valign="top"
|U Montana
|Furans chemistry in MCM and in GEOS-Chem
|[mailto:lixu.jin@umontana.edu Lixu Jin]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]
|21 May 2022


'''''This update was added to [[GEOS-Chem v8-02-04]].'''''
|-valign="top"
|U Wollongong
|Evaluation of aromatic oxidation products using new observational constraints
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
|9 June 2022


1. Since FastJX already takes this into account with cross section data at 574nm, we do not need to redo this in <tt>calcrate.f</tt>.  We can therefore comment out this entire IF block:
|-valign="top"
|U Wollongong, U Sydney, UNSW
        !---------------------------------------------------------------------
|Impacts of photophysical oxidation of aldehydes
        ! Prior to 10/27/09:
|[mailto:paolos@uow.edu.au Paolo Sebastianelli]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
        ! FastJX has taken near-IR photolysis into account with
|10 June 2024
        ! 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
        !---------------------------------------------------------------------


|-valign="top"
|UNSW, U Wollongong
|GEOS-Chem simulation of HFO and CF3CHO chemistry
|[mailto:b.killen@unsw.edu.au Beth Killen]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
|10 June 2024


2. We need to change the branch ratio of HNO4 photolysis in <tt>ratj.d</tt>.  Change these lines from:
|-valign="top"
|University of California, Riverside
|Updates to DMS oxidation scheme
|[mailto:wporter@ucr.edu William Porter]
|26 August 2020


13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00    33.3  HO2NO2
|-valign="top"
14 HNO4      PHOTON    HO2        NO2                  0.00E+00  0.00    66.7  HO2NO2
|Harvard University
|Overhaul of cloud pH code including: use of Newton's method and addition of crustal cations and organic acids
|[mailto:vshah@g.harvard.edu Viral Shah]<br>[mailto:jmoch@g.harvard.edu Jonathan Moch]
|5 May 2019


to:
|-valign="top"
|U Alaska Fairbanks
|Monoterpene oxidation and its impact on SOA formation
|[mailto:yzheng4@alaska.edu Yiqi Zheng]<br>[mailto:jmao2@alaska.edu Jingqiu Mao]
|21 April 2019


13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00      5.0  HO2NO2
|-valign="top"
14 HNO4      PHOTON    HO2        NO2                  0.00E+00  0.00    95.0  HO2NO2
| FSU
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry
|[mailto:cdholmes@fsu.edu Chris Holmes]
|May 2017


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.
|-valign="top"
|FSU
|Methane and methyl chloroform lifetimes
|[mailto:cdholmes@fsu.edu Chris Holmes]
|May 2017


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).
|-valign="top"
|FSU
|Arctic halogen & ozone chemistry
|[mailto:cdholmes@fsu.edu Chris Holmes]
|May 2017
|}


This update has now been added to the [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf chemistry mechanism documentation file].
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
 
--[[User:Jmao|J Mao.]] 11:00, 26 Oct 2009 (EDT)<br>
--[[User:Bmy|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]].'''''
 
[mailto:paulot@caltech.edu 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          +                  +                  + 
 
--[[User:Jmao|J Mao.]] 18:04, 30 Aug 2010 (EDT)<br>
--[[User:Bmy|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 [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02c|v9-01-02c]] and approved on 21 Jul 2011.'''''
 
Jingqiu Mao discovered a mis-indexing problem when using the <tt>restart.cspec.YYYYMMDDhh</tt> file.  Please see [[Restart files#Potential issue with reading restart.cspec_file|this wiki post]] for more information.
 
--[[User:Bmy|Bob Y.]] 16:02, 4 November 2011 (EDT)
 
=== Centralizing chemistry time step===
 
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02q|v9-01-02q]] and approved on 18 Oct 2011.'''''
 
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.
 
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)
 
=== GLCO3, GLPAN bug in standard mechanism ===
 
'''''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] 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 <tt>globchem.dat</tt>:
 
:#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 <tt>ratj.d</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)<br>
--[[User:Melissa Payer|Melissa Payer]] 10:49, 15 December 2011 (EST)
 
=== Bug in routine ARSL1K ===
 
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem v9-01-03 benchmark history#v9-01-03m|v9-01-03m]] and approved on 06 Jun 2012.'''''
 
A bug in routine ARSL1K became problematic in the implementation of Justin Parrella's [[Bromine_chemistry_mechanism|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#Div-by-zero_error_encountered_in_arsl1k.f|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.
 
'''''[mailto:mat.evans@york.ac.uk 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.
 
--[[User:Melissa Payer|Melissa Payer]] 17:52, 14 May 2012 (EDT)
 
=== Acetone photolysis ===
Current GC (v9-02) includes two channels of acetone photolysis:
<pre>
AcetA: CH3COCH3 = CH3CO3 + CH3O2
AcetB: CH3COCH3 = CH3O2 + CH3O2 + CO
AcetA is the dominant channel under tropospheric conditions with strong pressure dependence.
</pre>
Current cross section in jv_spec.dat (obtained from FastJX v6.4):
Cross section
<pre>
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
</pre>
and quantum yield
<pre>
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
</pre>
And the pressure dependence is described here as in FastJX v6.4 (JRATET.F in our code):
<pre>
          VALJ(NJVAL-1) = VALJ(NJVAL-1)
    &        + FFF(K,L)*QQQA*(1.d0-QQ2)/(QQ1A + QQ1B*DD)
</pre>
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 [http://wiki.seas.harvard.edu/geos-chem/images/Seac4rs_jvalues50714.pdf here].


Sebastian D. Eastham showed that J-acetone is significantly higher in Fast-JX v7.0.
=== Carbon balance ===
Comparison
[http://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v10-01b/v10-01b.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]


'''Recommendation: use the pressure dependence calculation in Fast-JX v7.0'''
==== Script for evaluating carbon balance ====
====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.
This is due to some bug in the source code when switching from 18 bins to 12 bins, and the bug is now fixed.


== Documentation ==
'''''[http://www.barronh.com/ Barron Henderson] wrote:'''''


*[http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf Updated chemical reactions] that will be used in [[GEOS-Chem v8-02-04]] and higher.
<blockquote>[I created] an evaluation script to preserve balances going forward as the mechanism evolves (e.g., as isoprene gets updated).  
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v5.pdf Updated chemical reactions] now used in [[GEOS-Chem v8-02-01]] through [[GEOS-Chem v8-02-03]].
Currently, this done using an off-line script described in a [http://www.evernote.com/l/ATuCIZsKADFPPKnKQBlk07TFevitHHQ1Q_o/ linked note]. The approach is pretty straight-forward, but could be expanded to check conservation of functional groups as suggested by Mat.
**All typos have now been corrected in the present file.
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jv_spec_format.pdf Format of FAST-J input file <tt>jv_spec.dat</tt>]


--[[User:Bmy|Bob Y.]] 15:41, 27 October 2009 (EDT)
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.</blockquote>

Latest revision as of 14:47, 23 September 2024

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Contact information

Oxidants and Chemistry Working Group Co-Chairs
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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
NASA LARC Scheme for higher PN production from aromatics, MEK, monoterpenes, glycolaldehyde, and 1,3-butadiene Katherine R. Travis 19 Sep 2023


Columbia University Automated model reduction isoprene oxidation mechanism Benjamin Yang

Dan Westervelt

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

Matthew Rowlinson

08 Jun 2022
University of York Halogen reverse reactions Mat Evans

Hansen Cao

01 Jun 2022
University of York Chlorine chemistry Mat Evans

Amy Lees

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 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
Jenny Fisher 		9 June 2022
U Wollongong, U Sydney, UNSW Impacts of photophysical oxidation of aldehydes Paolo Sebastianelli
Jenny Fisher 		10 June 2024
UNSW, U Wollongong GEOS-Chem simulation of HFO and CF3CHO chemistry Beth Killen
Jenny Fisher 		10 June 2024
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
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!)

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.

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