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 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])
|'''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])
|'''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>]
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|'''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>]
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== 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'''


=== GLCO3, GLPAN bug in standard mechanism ===
|-valign="top"
!bgcolor="#CCCCCC"|To unsubscribe from email list
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*Send an email to <tt>geos-chem-oxidants+unsubscribe [at] g.harvard.edu</tt>
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*Click on the '''My Settings''' button
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This fix is slated for inclusion into [[GEOS-Chem v9-01-03]]
|}


'''''[mailto:fabienpaulot@gmail.com Fabien Paulot]'''''
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:29, 21 August 2015 (UTC)


: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.
== Current GEOS-Chem Chemistry Projects (please add yours!) ==
{| border=1 cellspacing=0 cellpadding=5
|- bgcolor="#cccccc"
!width="200px"|User Group
!width="600px"|Description
!width="150px"|Contact Person
!width="100px"|Date Added


: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.
|-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


: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.
|-valign="top"
:#I have physically removed GLCO3, GLP, GPAN, MNO3, ISNO3, MNO3, O2CH2OH, MVN2 and their associated reactions.
|Columbia University
:#I have made GLYX active. Not sure why it's not active by default.
|Automated model reduction isoprene oxidation mechanism
|[mailto:benjamin.yang@columbia.edu Benjamin Yang]<br>
[mailto:danielmw@ldeo.columbia.edu Dan Westervelt]
|12 Sep 2023


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


:# I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in <tt>globchem.dat</tt>
|-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


--[[User:Bmy|Bob Y.]] 14:51, 10 November 2011 (EST)
|-valign="top"
|University of York
|Halogen reverse reactions
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
[mailto:hansen.cao@york.ac.ul Hansen Cao]
|01 Jun 2022


=== 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]])
|University of York
|Chlorine chemistry
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
[mailto:al1916@york.ac.uk Amy Lees]
|01 Oct 2022


=== HO2 + CH2O ===
|-valign="top"
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
|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


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
Journal of Physical Chemistry A, 109(19), 4303-4311.
|Adding an adaptive solver capability into [https://kpp.readthedocs.io KPP]
|[mailto:hplin@seas.harvard.edu Haipeng Lin]
|03 Jun 2022


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


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


== Previous issues that have now been resolved ==
|-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 ([[GEOS-Chem 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]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
      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)<br>
|-valign="top"
--[[User:Bmy|Bob Y.]] 16:12, 4 November 2011 (EDT)
|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


=== near-IR photolysis of HNO4 ===
|-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


'''''This update was added to [[GEOS-Chem v8-02-04]].'''''
|-valign="top"
|University of California, Riverside
|Updates to DMS oxidation scheme
|[mailto:wporter@ucr.edu William Porter]
|26 August 2020


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"
|Harvard University
        !---------------------------------------------------------------------
|Overhaul of cloud pH code including: use of Newton's method and addition of crustal cations and organic acids
        ! Prior to 10/27/09:
|[mailto:vshah@g.harvard.edu Viral Shah]<br>[mailto:jmoch@g.harvard.edu Jonathan Moch]
        ! FastJX has taken near-IR photolysis into account with
|5 May 2019
        ! 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"
|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


2. We need to change the branch ratio of HNO4 photolysis in <tt>ratj.d</tt>. Change these lines from:
|-valign="top"
| FSU
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry
|[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
|Methane and methyl chloroform lifetimes
|[mailto:cdholmes@fsu.edu Chris Holmes]
|May 2017


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


13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00      5.0  HO2NO2
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
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].
 
--[[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.
=== 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

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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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