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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"
|'''Oxidants and Chemistry Working Group Chair'''
+
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs
|[http://www.env.leeds.ac.uk/~lecmje/lecmje Mat Evans]
+
|width="600px"|
[http://www.gfdl.noaa.gov/jingqiu-mao Jingqiu Mao]
+
*[http://www.barronh.com Barron Henderson] (GitHub: [https://github.com/barronh @barronh])
|-
+
*[http://hs.umt.edu/luhu/people.php Lu Hu] (GitHub: [https://github.com/luhu0 @luhu0])
|'''Oxidants and Chemistry Working Group email list'''
+
*[https://www.uaf.edu/chem/faculty/mao/ Jingqiu Mao] (Github: [https://github.com/jingqiumao @jingqiumao])
|<tt>geos-chem-oxidants@seas.harvard.edu</tt>
+
|-
+
|'''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>]
+
|-
+
|'''To unsubscribe from email list'''
+
|Send email to [mailto:geos-chem-oxidants-leave@seas.harvard.edu <tt>geos-chem-oxidants-leave@seas.harvard.edu</tt>]
+
|}
+
  
== Current GEOS-Chem Chemistry Projects (please add yours!) ==
+
|-valign="top"
{| border=1 cellspacing=0 cellpadding=5
+
!bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group email list
|- bgcolor="#cccccc"
+
|<tt>geos-chem-oxidants [at] g.harvard.edu</tt>
!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
+
|[mailto:paulot@caltech.edu Fabien Paulot] <br>[mailto:jmao@seas.harvard.edu Jingqiu Mao]
+
|April 28, 2009
+
|-
+
|Caltech/Harvard
+
|Examining the HCHO yield, OH recycling and ozone production with INTEX-A observations from new isoprene chemistry
+
|[mailto:jmao@seas.harvard.edu Jingqiu Mao ] <br>[mailto:paulot@caltech.edu Fabien Paulot]
+
|April 28, 2009
+
|-
+
|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]
+
|June 29, 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 ]
+
|May 19, 2011
+
|}
+
  
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
+
|-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'''
  
=== Isoprene chemistry ===
+
|-valign="top"
I've created a page with some of the recent literature on isoprene chemistry. Please add more papers as they come along! ([[User:mje| MJE Leeds]])
+
!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'''
  
[[isoprene]]
+
|}
  
=== Centralizing chemistry time step===
+
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:29, 21 August 2015 (UTC)
Current set up:
+
<pre>
+
2x2.5:
+
timestep 1 : transport (15min) + Chemistry (60min)
+
timestep 2: transport (15 min)
+
timestep 3 : transport (15min)
+
timestep 4: transport (15 min)--------------------------->output
+
timestep 5 : transport (15min) + Chemistry (60min)
+
timestep 6: transport (15 min)
+
timestep 7 : transport (15min)
+
timestep 8: transport (15 min)--------------------------->output
+
</pre>
+
  
Fix: (provided by Lin Zhang)
+
== Current GEOS-Chem Chemistry Projects (please add yours!) ==
In time_mod.f, change this line
+
{| border=1 cellspacing=0 cellpadding=5
<pre>
+
|- bgcolor="#cccccc"
FLAG = ( MOD( ELAPSED_MIN, TS_CHEM ) == 0 )
+
!width="200px"|User Group
</pre>
+
!width="600px"|Description
 +
!width="150px"|Contact Person
 +
!width="100px"|Date Added
  
to
+
|-valign="top"
<pre>
+
|NASA LARC
      ! changes for proper chemistry time (lzh, ccc, 03/20/2010)
+
|Scheme for higher PN production from aromatics, MEK, monoterpenes, glycolaldehyde, and 1,3-butadiene
      INTEGER :: M
+
|[mailto:katherine.travis@nasa.gov Katherine R. Travis]
 +
|19 Sep 2023
  
      !=================================================================
 
      ! ITS_TIME_FOR_CHEM begins here!
 
      !=================================================================
 
  
      ! Get multiplier between transport and chemistry:
+
|-valign="top"
      M = TS_CHEM/TS_DYN
+
|Columbia University
 +
|Automated model reduction isoprene oxidation mechanism
 +
|[mailto:benjamin.yang@columbia.edu Benjamin Yang]<br>
 +
[mailto:danielmw@ldeo.columbia.edu Dan Westervelt]
 +
|12 Sep 2023
  
      ! Divide by 2 (get middle). KEEP INTEGERS!!!!
+
|-valign="top"
      M = MAX( M/2, 1 )
+
|NOAA CSL
 +
|JPL Kinetic Review Update/C-N balance/stoichiometry update
 +
|[mailto:khbates@ucdavis.edu Kelvin Bates]
 +
|01 Jul 2023
  
      ! Is it time for chemistry?
+
|-valign="top"
      !FLAG = ( MOD( ELAPSED_MIN, TS_CHEM ) == 0 )
+
|University of York
      FLAG = ( MOD( ELAPSED_MIN, TS_CHEM ) == (M-1)*TS_DYN )
+
|Nitrate Photolysis
 +
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
 +
[mailto:matthew.rowlinson@york.ac.ul Matthew Rowlinson]
 +
|08 Jun 2022
  
      ! Might be M+1 or M didn't think it through completely. And we may want
+
|-valign="top"
      ! to calculate M only once, so put it as a module variable
+
|University of York
      ! (and change the name)
+
|Halogen reverse reactions
</pre>
+
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
 +
[mailto:hansen.cao@york.ac.ul Hansen Cao]
 +
|01 Jun 2022
  
In this way, chemistry time step is put in the center of transport time steps.
+
|-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
  
=== yield of isoprene nitrates ===
+
|-valign="top"
[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%.
+
|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
  
A  453 2.70E-12  0.0E+00    350 1 B  0.00    0.    0.       
+
|-valign="top"
        5.00E+00  0.0E+00      0 0    0.00    0.    0.       
+
|Harvard University
      RIO2          +    NO                                             
+
|Adding an adaptive solver capability into [https://kpp.readthedocs.io KPP]
=0.900NO2          +0.900HO2          +0.340IALD          +0.340MVK   
+
|[mailto:hplin@seas.harvard.edu Haipeng Lin]
+0.220MACR          +0.560CH2O          +                  + 
+
|03 Jun 2022
         
+
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):
+
|-valign="top"
 +
|GCST
 +
|Migrating the Hg chemistry mechanism to [https://kpp.readthedocs.io KPP]
 +
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)
 +
|03 Jun 2022
  
A  453 2.70E-12  0.0E+00    350 0 0  0.00    0.    0.       
+
|-valign="top"
      RIO2          +    NO                                             
+
|GCST
=0.900NO2          +0.900HO2          +0.340IALD          +0.340MVK   
+
|Adding a CO-CO2-CH4-OCS chemistry mechanism with [https://kpp.readthedocs.io KPP]
+0.220MACR          +0.560CH2O          +                  +     
+
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)
+
|03 Jun 2022
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)
+
|-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
  
=== rate of HNO4 ===
+
|-valign="top"
[mailto:ecbrow@berkeley.edu Ellie Browne] found a typo in the globchem.dat (v8-02-01 and beyond)
+
|U Wollongong
<pre>
+
|Evaluation of aromatic oxidation products using new observational constraints
A  73 9.52E-05  3.2E+00 -10900 1 P  0.60    0.    0.       
+
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]
      1.38E+15  1.4E+00 -10900 0    0.00    0.    0.       
+
|9 June 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)
+
|-valign="top"
=== HO2 + CH2O ===
+
|UNSW, Sydney
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
+
|Contribution of the unexplored photochemistry of aldehydes to the tropospheric levels of hydrogen
 +
|[mailto:m.perez_pena@unsw.edu.au Maria Paula Perez-Pena]
 +
|25 June 2021
  
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 California, Riverside
Journal of Physical Chemistry A, 109(19), 4303-4311.
+
|Updates to DMS oxidation scheme
 +
|[mailto:wporter@ucr.edu William Porter]
 +
|26 August 2020
  
According to this paper, this reaction is significant when Temperature is below 220K.
+
|-valign="top"
 +
|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
  
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
+
|-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
  
=== near-IR photolysis of HNO4 ===
+
|-valign="top"
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:
+
|MIT
+
|Simulating the global reactive carbon budget
        !---------------------------------------------------------------------
+
|[mailto:sarahsaf@mit.edu Sarah Safieddine]
        ! Prior to 10/27/09:
+
|12 April 2017
        ! 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
+
        !---------------------------------------------------------------------
+
  
 +
|-valign="top"
 +
| FSU
 +
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
  
2. We need to change the branch ratio of HNO4 photolysis in <tt>ratj.d</tt>.  Change these lines from:
+
|-valign="top"
 +
|FSU
 +
|Methane and methyl chloroform lifetimes
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
  
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
+
|FSU
 +
|Arctic halogen & ozone chemistry
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
 +
|}
  
to:
+
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
 
+
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 [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf chemistry mechanism documentation file].
+
=== Carbon balance ===
  
--[[User:Jmao|J Mao.]] 11:00, 26 Oct 2009 (EDT)
+
==== Script for evaluating carbon balance ====
  
== 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 15:50, 30 January 2024

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
Oxidants and Chemistry Working Group email list geos-chem-oxidants [at] g.harvard.edu
To subscribe to email list Either
  • Send an email to geos-chem-oxidants+subscribe [at] g.harvard.edu

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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 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!)

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.