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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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|-valign="top"
 
|-valign="top"
 
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs
 
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs
|width="600px"|
+
|width="600px"|  
*[http://www.york.ac.uk/chemistry/staff/academic/d-g/evansm/ Mat Evans] and
+
*[http://www.barronh.com Barron Henderson] (GitHub: [https://github.com/barronh @barronh])
*[http://www.barronh.com Barron Henderson]
+
*[http://hs.umt.edu/luhu/people.php Lu Hu] (GitHub: [https://github.com/luhu0 @luhu0])
 +
*[https://www.uaf.edu/chem/faculty/mao/ Jingqiu Mao] (Github: [https://github.com/jingqiumao @jingquimao])
  
 
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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:hyl@nianet.org Hongyu Liu]
 
|5 May 2015
 
|-
 
|MIT
 
|Exploring the impact of monoterpene and aromatic chemistry on ozone and OH reactivity
 
|[mailto:wporter@mit.edu Will Porter]
 
|12 April 2017
 
|-
 
|MIT
 
|Exploring the global reactive carbon budget
 
|[mailto:sarahsaf@mit.edu Sarah Safieddine]
 
|12 April 2017
 
|-
 
|University of York
 
|Halogen chemistry
 
|[mailto:ts551@york.ac.uk Tomas Sherwen]
 
|12 April 2017
 
|-
 
|University of York
 
|Isoprene over Borneo
 
|[mailto:sag527@york.ac.uk Shani Garraway]
 
|12 April 2017
 
|-
 
|University of York
 
|Impacts of uncertainty in chemical kinetics
 
|[mailto:bn506@york.ac.uk Ben Newsome]
 
|12 April 2017
 
|-
 
|University of York
 
|Impacts of resolution in GEOS-Chem
 
|[mailto:bn506@york.ac.uk Ben Newsome]
 
|12 April 2017
 
|-
 
|University of York
 
|Updates to the kinetics of Criegee chemistry based on new chamber experiments
 
|[mailto:mat.evans@york.ac.uk Mat Evans]
 
|12 April 2017
 
|-
 
|University of Wollongong
 
|Simulation of small (methyl, ethyl, propyl) alkyl nitrates in GEOS-Chem
 
|[mailto:jennyf@uow.edu.au Jenny Fisher]
 
|12 April 2017
 
|-
 
|Harvard University
 
|Halogen extension to include explicit phase partitioning and mass transfer
 
|[mailto:seastham@fas.harvard.edu Sebastian D. Eastham]
 
|12 April 2017
 
|}
 
  
--[[User:Bmy|Bob Y.]] 15:08, 25 April 2014 (EDT)
+
|-valign="top"
 +
|University of York
 +
|Nitrate Photolysis
 +
|[mailto:mat.evans@york.ac.ul Mat Evans]
 +
|08 Jun 2022
  
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
+
|-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
  
=== Fixes to correct ALK4 lumping issue ===
+
|-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
  
<span style="color:darkorange">'''''NOTE: This update is currently slated for [[GEOS-Chem v11-02#v11-02a|v11-02a]].'''''</span>
+
|-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:Barronh|Barron Henderson]] wrote:'''''
+
|-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
  
<blockquote>I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).
+
|-valign="top"
 +
|U Montana
 +
|Formic acid and acetic acid formation in fire smoke
 +
|[mailto:wade.permar@umontana.edu Wade Permar]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]
 +
|21 May 2022
  
Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy.  When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.
+
|-valign="top"
 +
|U Montana
 +
|Formic acid and acetic acid formation in fire smoke
 +
|[mailto:wade.permar@umontana.edu Wade Permar]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]
 +
|21 May 2022
  
If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.
+
|-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
  
I have [https://www.evernote.com/shard/s315/sh/f2ec9589-d827-4ee1-afcb-96ee5a2d2914/d84318450f729cd414e4a6653c03a296 extensive notes] on what I interpret as happening.  To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.
+
|-valign="top"
 +
|U Wollongong
 +
|Evaluation of aromatic oxidation products using new observational constraints
 +
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]
 +
|9 June 2022
  
#Increase MO2 stoichiometry from 0.18 to 0.19
+
|-valign="top"
#Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).
+
|UNSW, Sydney
#Modify the carbon count for ALK4 (i.e. the <tt>MolecRatio</tt> field in the [[GEOS-Chem species database]]) from 4 to 4.3.
+
|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
  
Fixes 1 and 2&mdash;which can be applied to the KPP <tt>globchem.eqn</tt> file&mdash;will make the carbon conservation consistent with Lurmann's.    Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.</blockquote>
+
|-valign="top"
 +
|University of California, Riverside
 +
|Updates to DMS oxidation scheme
 +
|[mailto:wporter@ucr.edu William Porter]
 +
|26 August 2020
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:21, 31 January 2017 (UTC)
+
|-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
  
=== JPL Released 18th Rate Coefficient Evaluation ===
+
|-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
  
<span style="color:darkorange">'''''NOTE: This update is currently slated for [[GEOS-Chem v11-02|v11-02a]].'''''</span>
+
|-valign="top"
 +
|NIA / LaRC
 +
|Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis
 +
|[mailto:hyl@nianet.org Hongyu Liu]
 +
|5 May 2015
  
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page ([[Updates in JPL Publication 15-10]]) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10.
+
|-valign="top"
 +
|MIT
 +
|Simulating the global reactive carbon budget
 +
|[mailto:sarahsaf@mit.edu Sarah Safieddine]
 +
|12 April 2017
  
:J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.
+
|-valign="top"
 +
|University of York
 +
|Halogen chemistry
 +
|[mailto:ts551@york.ac.uk Tomas Sherwen]
 +
|12 April 2017
  
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)
+
|-valign="top"
 +
|Harvard University
 +
|Halogen extension to include explicit phase partitioning and mass transfer
 +
|[mailto:seastham@fas.harvard.edu Sebastian D. Eastham]
 +
|12 April 2017
  
=== Working Group Tele-con on the 2nd December 2011 ===
+
|-valign="top"
[[ChemTelecon20111202]]
+
| US EPA
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''
+
|Alkane chemistry and product yields as a function of temperature/pressure.
 +
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
 +
|4 May 2017
  
=== 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]])
+
| US EPA
 +
|Carbon and Nitrogen Balance and checking software.
 +
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
 +
|4 May 2017
  
=== HO2 + CH2O ===
+
|-valign="top"
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
+
| US EPA
 +
|Update DSMACC for v11 GEOS-Chem Chemistry and Emissions to facilitate chemical experiments
 +
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
 +
|4 May 2017
  
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,
+
| FSU
Journal of Physical Chemistry A, 109(19), 4303-4311.
+
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
  
According to this paper, this reaction is significant when Temperature is below 220K.
+
|-valign="top"
 +
|FSU
 +
|Methane and methyl chloroform lifetimes
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
  
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
+
|-valign="top"
 +
|FSU
 +
|Arctic halogen & ozone chemistry
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
 +
|}
  
== Previous issues that have now been resolved ==
+
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
  
=== Centralizing chemistry time step===
+
=== Working group telecom on the 13/3/2019 ===
 +
There was a telecon to discuss issues with the chemistry. The notes from the meeting are here  [[Media:Chemistry_WG_March_2019..pdf ]] .  '''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''
  
<span style="color:green">'''''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.'''''</span>
+
=== Carbon balance ===
  
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.
+
==== Script for evaluating carbon balance ====
  
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)
+
'''''[http://www.barronh.com/ Barron Henderson] wrote:'''''
  
=== Acetone photolysis ===
+
<blockquote>[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 [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.
  
[[FAST-J_photolysis_mechanism#v9-02_post-release_patch_to_fix_bug_in_acetone_photolysis_pressure_dependency|This discussion has been moved to our ''FAST-J photolysis mechanism'' wiki page]].
+
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>
  
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)
+
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
  
== Issues that have been since rendered obsolete by newer code updates ==
+
==== Fixes for carbon creating reactions ====
  
Most of the issues described below pertained to the SMVGEAR chemical solver (which was replaced by FlexChem in [[GEOS-Chem v11-01|v11-01]]) and/or the FAST-J photolysis mechanism (which was replaced by FAST-JX in [[GEOS-Chem v10-01|v10-01]]).
+
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span>
  
=== NIT should be converted to molec/cm3 in calcrate.F ===
+
'''''Sarah Safieddine wrote:'''''
  
[[Image:Obsolete.jpg]]
+
<blockquote>Colette, Barron, Mat and myself modified 13 previous "carbon creating" reactions to preserve carbon. The [table below] lists all the corrections for the reactions in globchem.dat V902 that we corrected, with all the details.</blockquote>
  
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The code in <tt>calcrate.F</tt> will be replaced by the KPP master equation file.'''''</span>
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!Reaction # in globchem.dat v9-02
 +
!Unbalanced Reaction
 +
!Rate constant
 +
!Issue<br>(R=Reactants, P=Products)
 +
!Fix and corrected reaction (in <span style="color:green">green</span>)
  
In <tt>calcrate.F</tt>, we have:
+
|-valign="top
 +
|453
 +
|R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2
 +
|K* (1-YN) where YN is returned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.5)
 +
|Creates carbon: R=4C P=4.26C
 +
|Replace 0.18B3O2 by 0.093B3O2 to achieve carbon closure (as suggested by Barron).<br>
 +
<span style="color:green">R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + '''0.093B3O2''' + 0.32ETO2</span><br>
 +
<span style="color:darkorange">'''Use Barron's [[Chemistry_Issues#Fixes_to_correct_ALK4_lumping_issue|fix to correct ALK4 lumping issue]] instead.'''</span>
  
                    ! Nitrate effect; reduce the gamma on nitrate by a
+
|-valign="top
                    ! factor of 10 (lzh, 10/25/2011)
+
|453
                    IF ( N == 8 ) THEN
+
|R4N1 + NO → 2NO2 + 0.39CH2O + 0.75ALD2 + 0.57RCHO + 0.3R4O2
                        TMP1 = State_Chm%Tracers(IX,IY,IZ,IDTSO4) +
+
|2.7E-12 exp(350/T)
    &                        State_Chm%Tracers(IX,IY,IZ,IDTNIT)
+
|Creates carbon: R=4C, P=4.8C
                        TMP2 = State_Chm%tracers(IX,IY,IZ,IDTNIT)
+
|Fix, as suggested by Matt:<br>
                        IF ( TMP1 .GT. 0.0 ) THEN
+
<span style="color:green">R4N1 + NO → 2NO2 + 0.570RCHO + '''0.86ALD2''' + '''0.57CH2O'''</span>
                          XSTKCF = XSTKCF * ( 1.0e+0_fp - 0.9e+0_fp
+
    &                            *TMP2/TMP1 )
+
                        ENDIF
+
                    ENDIF
+
  
Here NIT is added to SO4 but NIT is in different units than SO4. This unit difference can be traced to the definition of IDTRMB, which is only nonzero for species that are in the SMVGEAR mechanism. Since NIT is not a SMVGEAR species, IDTRMB = 0 for NIT and it is therefore skipped in the unit conversion from kg --> molec/cm3 in <tt>partition.F</tt>.
+
|-valign="top
 +
|453
 +
|ATO2 + NO → 0.96NO2 + 0.96CH2O + 0.96MCO3 + 0.04R4N2
 +
|2.8E-12 exp(300/T)
 +
|Creates carbon: R=3C, P=3.04
 +
|Fix as suggested by Mat: ditch the R4N2 channel<br>
 +
<span style="color:green">ATO2 + NO → NO2 + CH2O + MCO3
  
This issue was discovered during the implementation of [[FlexChem]]. In [[GEOS-Chem v11-01#v11-01g|GEOS-Chem v11-01g]] and later versions, units of NIT are properly accounted for in routine <tt>HETN2O5</tt> (found in <tt>gckpp_HetRates.F90</tt>).
+
|-valign="top
 +
|803
 +
|RIO2 → 2HO2 + CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.5HAC + OH
 +
|4.07E+08 exp(-7694/T)
 +
|Creates carbon: R=5C, P=7C<br>There was a [[Caltech_isoprene_scheme#Remove_duplicate_GLYX_product_from_RIO2_reaction|fix proposed on the isoprene scheme wiki page]] but still not enough
 +
|Fix as suggested by Sarah: remove CH2O<br>
 +
<span style="color:green">RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH</span><br>
 +
<span style="color:darkorange">This reaction was replaced with '''RIO2 → 0.5HPALD + 0.5DHPCARP''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span>
  
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 20:25, 12 September 2016 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:27, 31 January 2017 (UTC)
+
|-valign="top
 +
|453
 +
|ISNOOB + NO3 → R4N2 + GLYX + 2NO2
 +
|2.3E-12
 +
|Creates carbon: R=5C, P=6C
 +
|Fix as suggested by Barron: Replace R4N2 by PROPNN<br>
 +
<span style="color:green">ISNOOB + NO3 → '''PROPNN''' + GLYX + 2NO2</span><br>
 +
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO3 → 0.94PROPNN + GLYX + 2NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span>
  
=== rate of HNO4 ===
+
|-valign="top
 +
|453
 +
|ISNOOB+NO → 0.94R4N2 +0.94GLYX +1.88NO2
 +
|2.6E-12 exp(380/T)
 +
|Creates carbon: R=5C, P=5.64C
 +
|Same as above<br>
 +
<span style="color:green">ISNOOB + NO → '''0.06R4N2''' + ''''0.94PROPNN'''' + 0.94GLYX + 1.88NO2</span><br>
 +
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO → 0.9PROPNN + 0.94GLYX + 1.88NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span>
  
[[Image:Obsolete.jpg]]
+
|-valign="top
 +
|453
 +
|ISNOHOO + NO → 0.934R4N2 + 0.934HO2 + 0.919GLYX
 +
|2.6E-12 exp(380/T)
 +
|Creates carbon: R=5C, P=5.574C
 +
|Fix by Barron:<br>
 +
<span style="color:green">ISNOHOO + NO → '''0.081R4N2''' + '''0.919PROPNN''' + 0.934HO2 + 0.919GLYX</span><br>
 +
<span style="color:darkorange">This reaction was replaced with '''ISNOHOO + NO3 → 0.894PROPNN + 0.934HO2 + 0.919GLYX + 0.4ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span>
  
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions. The <tt>globchem.dat</tt> file is now replaced by the KPP master equation file.'''''</span>
+
|-valign="top
 +
|472
 +
|MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85ISNP
 +
|2.91E-13*exp(1300/T)[1-exp(-0.245*n)],n=4
 +
|Creates carbon: R=4C, P=4.85C
 +
|Fix by both Mat and Barron: Replace ISNP with 0.85MAOP + 0.85NO2<br>
 +
<span style="color:green">MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + '''0.85MAOP + 0.85NO2'''</span>
  
[mailto:ecbrow@berkeley.edu Ellie Browne] found a typo in the globchem.dat ([[GEOS-Chem v8-02-01]] and beyond)
+
|-valign="top
<pre>
+
|719
A  73 9.52E-05  3.2E+00 -10900 1 P  0.60    0.    0.       
+
|ATO2 + MCO3 → MEK + ACTA
      1.38E+15  1.4E+00 -10900 0    0.00    0.    0.       
+
|1.87E-13 exp(500/T)
      HNO4          +                        M                               
+
|Creates carbon: R=5C, P=6C
=1.000HO2          +1.000NO2          +                  +
+
|From the WIKI: replace MEK with MGLY<br>
</pre>
+
<span style="color:green">ATO2 + MCO3 → '''MGLY''' + ACTA</span>
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 Yantosca]] ([[User talk:Bmy|talk]]) 20:29, 31 January 2017 (UTC)
+
|817
 +
|Br + ALD2 → HBr + MCO3 + CO
 +
|1.3E-11 exp(-360/T)
 +
|Creates carbon: R=2C, P=3C
 +
|Remove CO Following Parrella et al., Table 2a, reactions R7 to R10 (also for the 3 reactions below)<br>
 +
<span style="color:green">Br + ALD2 → HBr + MCO3</span>
  
=== near-IR photolysis of HNO4 ===
+
|-valign="top
 +
|818
 +
|Br + ACET → HBr + ATO2 + CO
 +
|1.66E-10exp(-7000/T)
 +
|Creates carbon: R=3C, P=4C
 +
|Remove CO, same as above<br>
 +
<span style="color:green">Br + ACET → HBr + ATO2</span>
  
<span style="color:green">'''''This update was added to [[GEOS-Chem v8-02-04]].'''''</span>
+
|-valign="top
 +
|819
 +
|Br + C2H6 → HBr + ETO2 + CO
 +
|2.36E-10 exp(-6411/T)
 +
|Creates carbon: R=2C, P=3C
 +
|Remove CO, same as above<br>
 +
<span style="color:green">Br + C2H6 → HBr + ETO2</span>
  
[[Image:Obsolete.jpg]]
+
|-valign="top
 +
|820
 +
|Br + C3H8 → HBr + A3O2 + CO
 +
|8.77E-11 exp(-4330/T)
 +
|Creates carbon: R=3C, P=4C
 +
|Remove CO, same as above<br>
 +
<span style="color:green">Br + C3H8 → HBr + A3O2</span>
  
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The <tt>globchem.dat</tt> file is now replaced by the KPP master equation file.  Also, FAST-JX has now replaced FAST-J photolysis.'''''</span>
+
|}
 +
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:59, 27 July 2017 (UTC)
  
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:
+
==== Identification of carbon leaking reactions ====
+
        !---------------------------------------------------------------------
+
        ! 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
+
        !---------------------------------------------------------------------
+
  
 +
'''''Sarah Safieddine wrote:'''''
  
2. We need to change the branch ratio of HNO4 photolysis in <tt>ratj.d</tt>. Change these lines from:
+
<blockquote>76 other reactions leaked carbon, we enforced carbon conservation by tracking the lost carbon as CO2 (labeled as <tt>{CO2}</tt> in the document [http://onlinelibrary.wiley.com/store/10.1002/2017GL072602/asset/supinfo/grl55781-sup-0001-Supplementary.docx?v=1&s=21c96c26c411290d72b64fc4f9ecdc5e806af2c5 ROC_SI.docx], Table 2). This is the supplementary material for Safieddine, Heald and Henderson, 2017. It contains the corrections for both the carbon leaking and carbon creating reactions and all other information. The paper for reference can be found here: http://onlinelibrary.wiley.com/doi/10.1002/2017GL072602/abstract.</blockquote>
  
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00    33.3  HO2NO2
+
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
14 HNO4      PHOTON    HO2        NO2                  0.00E+00  0.00    66.7  HO2NO2
+
  
to:
+
==== Fixes to correct ALK4 lumping issue ====
  
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00      5.0  HO2NO2
+
<span style="color:green">'''''These fixes were included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span>
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.
+
'''''[[User:Barronh|Barron Henderson]] wrote:'''''
  
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).
+
<blockquote>I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).
  
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].
+
Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy. When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.
  
--[[User:Jmao|J Mao.]] 11:00, 26 Oct 2009 (EDT)<br>
+
If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.
--[[User:Bmy|Bob Y.]] 16:08, 4 November 2011 (EDT)
+
  
=== yield of isoprene nitrates ===
+
I have [https://www.evernote.com/shard/s315/sh/f2ec9589-d827-4ee1-afcb-96ee5a2d2914/d84318450f729cd414e4a6653c03a296 extensive notes] on what I interpret as happening.  To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.
  
<span style="color:green">'''''This update was added to [[GEOS-Chem v8-03-02]] as a post-release patch, and standardized in [[GEOS-Chem v9-01-01]].'''''</span>
+
#Increase MO2 stoichiometry from 0.18 to 0.19
 +
#Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).
 +
#Modify the carbon count for ALK4 (i.e. the <tt>MolecRatio</tt> field in the [[GEOS-Chem species database]]) from 4 to 4.3.
  
[[Image:Obsolete.jpg]]
+
Fixes 1 and 2&mdash;which can be applied to the KPP <tt>globchem.eqn</tt> file&mdash;will make the carbon conservation consistent with Lurmann's.    Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.</blockquote>
  
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The <tt>globchem.dat</tt> file is now replaced by the KPP master equation file.'''''</span>
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:21, 31 January 2017 (UTC)
  
[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%.
+
=== JPL Released 18th Rate Coefficient Evaluation ===
  
A  453 2.70E-12  0.0E+00    350 1 B  0.00    0.    0.       
+
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span>
        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):
+
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page ([[Updates in JPL Publication 15-10]]) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10.
  
A  453 2.70E-12  0.0E+00    350 0 0  0.00    0.     0.        
+
:J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.
      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:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:31, 31 January 2017 (UTC)
+
  
=== Potential issue with reading restart.cspec file ===
+
=== Working Group Tele-con on the 2nd December 2011 ===
 +
[[ChemTelecon20111202]]
 +
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''
  
<span style="color:green">'''''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.'''''</span>
+
=== Isoprene chemistry ===
 +
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]])
  
[[Image:Obsolete.jpg]]
+
=== HO2 + CH2O ===
 +
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
  
<span style="color:red">'''''The binary-punch format <tt>restart.cspec.YYYYMMDDhh</tt> file is slated to be replaced by a netCDF-format restart file, starting in [[GEOS-Chem v11-01]] and higher versions. But during a transition period, you can still request binary-punch format output.'''''</span>
+
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.
  
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.
+
According to this paper, this reaction is significant when Temperature is below 220K.
  
--[[User:Bmy|Bob Y.]] 16:02, 4 November 2011 (EDT)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:33, 31 January 2017 (UTC)
+
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
  
=== GLCO3, GLPAN bug in standard mechanism ===
+
== Previous issues that have now been resolved ==
  
<span style="color:green">'''''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.'''''</span>
+
=== Centralizing chemistry time step===
  
[[Image:Obsolete.jpg]]
+
<span style="color:green">'''''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.'''''</span>
  
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The <tt>globchem.dat</tt> file is now replaced by the KPP master equation file.'''''</span>
+
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.
  
'''''[mailto:fabienpaulot@gmail.com Fabien Paulot] wrote:'''''
+
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)
  
: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.
+
=== Acetone photolysis ===
  
: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.
+
[[FAST-J_photolysis_mechanism#v9-02_post-release_patch_to_fix_bug_in_acetone_photolysis_pressure_dependency|This discussion has been moved to our ''FAST-J photolysis mechanism'' wiki page]].
  
:To fix the error, I made the following modifications in <tt>globchem.dat</tt>:
+
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)
 
+
:#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)<br>
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:35, 31 January 2017 (UTC)
+
 
+
=== Bug in routine ARSL1K ===
+
 
+
<span style="color:green">'''''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.'''''</span>
+
 
+
[[Image:Obsolete.jpg]]
+
 
+
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The <tt>ARSL1K</tt> routine was replaced by an equivalent function in KPP's rate law library.'''''</span>
+
 
+
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)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:35, 31 January 2017 (UTC)
+
  
 
== Documentation ==
 
== Documentation ==

Latest revision as of 15:16, 22 July 2022

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
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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
University of York Nitrate Photolysis Mat Evans 08 Jun 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 Formic acid and acetic acid formation in fire smoke Wade Permar
Lu Hu
21 May 2022
U Montana Formic acid and acetic acid formation in fire smoke Wade Permar
Lu Hu
21 May 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
NIA / LaRC Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis Hongyu Liu 5 May 2015
MIT Simulating the global reactive carbon budget Sarah Safieddine 12 April 2017
University of York Halogen chemistry Tomas Sherwen 12 April 2017
Harvard University Halogen extension to include explicit phase partitioning and mass transfer Sebastian D. Eastham 12 April 2017
US EPA Alkane chemistry and product yields as a function of temperature/pressure. Barron H. Henderson 4 May 2017
US EPA Carbon and Nitrogen Balance and checking software. Barron H. Henderson 4 May 2017
US EPA Update DSMACC for v11 GEOS-Chem Chemistry and Emissions to facilitate chemical experiments Barron H. Henderson 4 May 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!)

Working group telecom on the 13/3/2019

There was a telecon to discuss issues with the chemistry. The notes from the meeting are here Media:Chemistry_WG_March_2019..pdf . Mat Evans

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.

--Melissa Sulprizio (talk) 21:06, 22 May 2017 (UTC)

Fixes for carbon creating reactions

This update was included in v11-02c and approved on 21 Sep 2017.

Sarah Safieddine wrote:

Colette, Barron, Mat and myself modified 13 previous "carbon creating" reactions to preserve carbon. The [table below] lists all the corrections for the reactions in globchem.dat V902 that we corrected, with all the details.
Reaction # in globchem.dat v9-02 Unbalanced Reaction Rate constant Issue
(R=Reactants, P=Products)
Fix and corrected reaction (in green)
453 R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2 K* (1-YN) where YN is returned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.5) Creates carbon: R=4C P=4.26C Replace 0.18B3O2 by 0.093B3O2 to achieve carbon closure (as suggested by Barron).

R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.093B3O2 + 0.32ETO2
Use Barron's fix to correct ALK4 lumping issue instead.

453 R4N1 + NO → 2NO2 + 0.39CH2O + 0.75ALD2 + 0.57RCHO + 0.3R4O2 2.7E-12 exp(350/T) Creates carbon: R=4C, P=4.8C Fix, as suggested by Matt:

R4N1 + NO → 2NO2 + 0.570RCHO + 0.86ALD2 + 0.57CH2O

453 ATO2 + NO → 0.96NO2 + 0.96CH2O + 0.96MCO3 + 0.04R4N2 2.8E-12 exp(300/T) Creates carbon: R=3C, P=3.04 Fix as suggested by Mat: ditch the R4N2 channel

ATO2 + NO → NO2 + CH2O + MCO3

803 RIO2 → 2HO2 + CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.5HAC + OH 4.07E+08 exp(-7694/T) Creates carbon: R=5C, P=7C
There was a fix proposed on the isoprene scheme wiki page but still not enough
Fix as suggested by Sarah: remove CH2O

RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH
This reaction was replaced with RIO2 → 0.5HPALD + 0.5DHPCARP in the isoprene chemistry updates added in v11-02c

453 ISNOOB + NO3 → R4N2 + GLYX + 2NO2 2.3E-12 Creates carbon: R=5C, P=6C Fix as suggested by Barron: Replace R4N2 by PROPNN

ISNOOB + NO3 → PROPNN + GLYX + 2NO2
This reaction was replaced with ISNOOB + NO3 → 0.94PROPNN + GLYX + 2NO2 + 0.04ISN1OG in the isoprene chemistry updates added in v11-02c

453 ISNOOB+NO → 0.94R4N2 +0.94GLYX +1.88NO2 2.6E-12 exp(380/T) Creates carbon: R=5C, P=5.64C Same as above

ISNOOB + NO → 0.06R4N2 + '0.94PROPNN' + 0.94GLYX + 1.88NO2
This reaction was replaced with ISNOOB + NO → 0.9PROPNN + 0.94GLYX + 1.88NO2 + 0.04ISN1OG in the isoprene chemistry updates added in v11-02c

453 ISNOHOO + NO → 0.934R4N2 + 0.934HO2 + 0.919GLYX 2.6E-12 exp(380/T) Creates carbon: R=5C, P=5.574C Fix by Barron:

ISNOHOO + NO → 0.081R4N2 + 0.919PROPNN + 0.934HO2 + 0.919GLYX
This reaction was replaced with ISNOHOO + NO3 → 0.894PROPNN + 0.934HO2 + 0.919GLYX + 0.4ISN1OG in the isoprene chemistry updates added in v11-02c

472 MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85ISNP 2.91E-13*exp(1300/T)[1-exp(-0.245*n)],n=4 Creates carbon: R=4C, P=4.85C Fix by both Mat and Barron: Replace ISNP with 0.85MAOP + 0.85NO2

MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85MAOP + 0.85NO2

719 ATO2 + MCO3 → MEK + ACTA 1.87E-13 exp(500/T) Creates carbon: R=5C, P=6C From the WIKI: replace MEK with MGLY

ATO2 + MCO3 → MGLY + ACTA

817 Br + ALD2 → HBr + MCO3 + CO 1.3E-11 exp(-360/T) Creates carbon: R=2C, P=3C Remove CO Following Parrella et al., Table 2a, reactions R7 to R10 (also for the 3 reactions below)

Br + ALD2 → HBr + MCO3

818 Br + ACET → HBr + ATO2 + CO 1.66E-10exp(-7000/T) Creates carbon: R=3C, P=4C Remove CO, same as above

Br + ACET → HBr + ATO2

819 Br + C2H6 → HBr + ETO2 + CO 2.36E-10 exp(-6411/T) Creates carbon: R=2C, P=3C Remove CO, same as above

Br + C2H6 → HBr + ETO2

820 Br + C3H8 → HBr + A3O2 + CO 8.77E-11 exp(-4330/T) Creates carbon: R=3C, P=4C Remove CO, same as above

Br + C3H8 → HBr + A3O2

--Melissa Sulprizio (talk) 19:59, 27 July 2017 (UTC)

Identification of carbon leaking reactions

Sarah Safieddine wrote:

76 other reactions leaked carbon, we enforced carbon conservation by tracking the lost carbon as CO2 (labeled as {CO2} in the document ROC_SI.docx, Table 2). This is the supplementary material for Safieddine, Heald and Henderson, 2017. It contains the corrections for both the carbon leaking and carbon creating reactions and all other information. The paper for reference can be found here: http://onlinelibrary.wiley.com/doi/10.1002/2017GL072602/abstract.

--Melissa Sulprizio (talk) 21:06, 22 May 2017 (UTC)

Fixes to correct ALK4 lumping issue

These fixes were included in v11-02a and approved on 12 May 2017.

Barron Henderson wrote:

I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).

Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy. When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.

If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.

I have extensive notes on what I interpret as happening. To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.

  1. Increase MO2 stoichiometry from 0.18 to 0.19
  2. Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).
  3. Modify the carbon count for ALK4 (i.e. the MolecRatio field in the GEOS-Chem species database) from 4 to 4.3.
Fixes 1 and 2—which can be applied to the KPP globchem.eqn file—will make the carbon conservation consistent with Lurmann's. Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.

--Bob Yantosca (talk) 20:21, 31 January 2017 (UTC)

JPL Released 18th Rate Coefficient Evaluation

This update was included in v11-02a and approved on 12 May 2017.

JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page (Updates in JPL Publication 15-10) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10.

J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.

---B. Henderson 2016-05-03 15:25 (EDT)

Working Group Tele-con on the 2nd December 2011

ChemTelecon20111202 Mat Evans

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

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)

Acetone photolysis

This discussion has been moved to our FAST-J photolysis mechanism wiki page.

--Bob Y. 15:20, 20 May 2014 (EDT)

Documentation

Obsolete.jpg

--Bob Y. 15:41, 27 October 2009 (EDT)