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"
|'''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.jessicahaskinsphd.com/ Jessica Haskins] (Github: [https://github.com/jhaskinsPhD jhaskinsPhD])
|<tt>geos-chem-oxidants@seas.harvard.edu</tt>
*[https://www.kelvinbates.com/ Kelvin Bates] (Github: [https://github.com/kelvinhb @kelvinb])
|-
 
|'''To subscribe to email list'''
|-valign="top"
|Send email to [mailto:geos-chem-oxidants-join@seas.harvard.edu <tt>geos-chem-oxidants-join@seas.harvard.edu</tt>]
!bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group email list
|-
|<tt>geos-chem-oxidants [at] g.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>]
|-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
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|}
|}
--[[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!) ==
{| border=1 cellspacing=0 cellpadding=5
{| border=1 cellspacing=0 cellpadding=5
|- bgcolor="#cccccc"
|- bgcolor="#cccccc"
!User Group
!width="200px"|User Group
!Description
!width="600px"|Description
!Contact Person
!width="150px"|Contact Person
!Date Added
!width="100px"|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"
|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


=== Isoprene chemistry ===
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]])


[[isoprene]]
|-valign="top"
|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


|-valign="top"
|NOAA CSL
|JPL Kinetic Review Update/C-N balance/stoichiometry update
|[mailto:khbates@ucdavis.edu Kelvin Bates]
|01 Jul 2023


|-valign="top"
|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


=== rate of HNO4 ===
|-valign="top"
[mailto:ecbrow@berkeley.edu Ellie Browne] found a typo in the globchem.dat (v8-02-01 and beyond)
|University of York
<pre>
|Halogen reverse reactions
A  73 9.52E-05  3.2E+00 -10900 1 P  0.60    0.    0.       
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
      1.38E+15  1.4E+00 -10900 0    0.00    0.    0.       
[mailto:hansen.cao@york.ac.ul Hansen Cao]
      HNO4          +                        M                               
|01 Jun 2022
=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 ===
|University of York
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
|Chlorine chemistry
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
[mailto:al1916@york.ac.uk Amy Lees]
|01 Oct 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,
|Harvard University and<br>MPIC-Mainz
Journal of Physical Chemistry A, 109(19), 4303-4311.
|Further development of [https://kpp.readthedocs.io The Kinetic PreProcessor (KPP)]
|[mailto:yantosca@seas.harvard.edu Bob Yantosca] (GCST)
|03 Jun 2022


According to this paper, this reaction is significant when Temperature is below 220K.
|-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


--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
|-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


|-valign="top"
|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


|-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


== Previous issues that have now been resolved ==
|-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


'''''This update was added to [[GEOS-Chem v8-03-02]] as a post-release patch, and standardized in [[GEOS-Chem v9-01-01]].'''''
|-valign="top"
|U Wollongong, U Sydney, UNSW
|Impacts of photophysical oxidation of aldehydes
|[mailto:paolos@uow.edu.au Paolo Sebastianelli]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
|10 June 2024


=== 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%.
|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


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.       
|University of California, Riverside
      RIO2          +    NO                                             
|Updates to DMS oxidation scheme
=0.900NO2          +0.900HO2          +0.340IALD          +0.340MVK   
|[mailto:wporter@ucr.edu William Porter]
+0.220MACR          +0.560CH2O          +                  + 
|26 August 2020
         
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"
|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


A  453 2.70E-12  0.0E+00    350 0 0  0.00    0.    0.       
|-valign="top"
      RIO2          +    NO                                             
|U Alaska Fairbanks
=0.900NO2          +0.900HO2          +0.340IALD          +0.340MVK   
|Monoterpene oxidation and its impact on SOA formation
+0.220MACR          +0.560CH2O          +                  +     
|[mailto:yzheng4@alaska.edu Yiqi Zheng]<br>[mailto:jmao2@alaska.edu Jingqiu Mao]
|21 April 2019
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>
|-valign="top"
--[[User:Bmy|Bob Y.]] 16:05, 4 November 2011 (EDT)
| FSU
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry
|[mailto:cdholmes@fsu.edu Chris Holmes]
|May 2017


=== Potential issue with reading restart.cspec file ===
|-valign="top"
|FSU
|Methane and methyl chloroform lifetimes
|[mailto:cdholmes@fsu.edu Chris Holmes]
|May 2017


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


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.
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
 
--[[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.
=== Carbon balance ===


--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (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 14:47, 23 September 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

Or

To unsubscribe from email list Either
  • Send an email to geos-chem-oxidants+unsubscribe [at] g.harvard.edu

Or

--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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