Difference between revisions of "Chemistry Working Group"

From Geos-chem
Jump to: navigation, search
(Current GEOS-Chem Chemistry Issues (please add yours!))
(Contact information)
 
(184 intermediate revisions by 17 users not shown)
Line 1: Line 1:
<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).
  
 
== Contact information ==
 
== Contact information ==
  
* Chair: [http://www.env.leeds.ac.uk/people/m.evans Mat Evans]
+
{| border=1 cellspacing=0 cellpadding=5
* Mailing List Address: <tt>geos-chem-oxidants@seas.harvard.edu</tt>
+
|-valign="top"
* Mailing List Subscribe/Unsubscribe: https://lists.seas.harvard.edu/mailman/listinfo/geos-chem-oxidants
+
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs
 +
|width="600px"|
 +
*[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])
 +
*[https://www.uaf.edu/chem/faculty/mao/ Jingqiu Mao] (Github: [https://github.com/jingqiumao @jingquimao])
 +
 
 +
|-valign="top"
 +
!bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group email list
 +
|<tt>geos-chem-oxidants [at] g.harvard.edu</tt>
 +
 
 +
|-valign="top"
 +
!bgcolor="#CCCCCC"|To subscribe to email list
 +
|Either
 +
*Send an email to <tt>geos-chem-oxidants+subscribe [at] g.harvard.edu</tt>
 +
Or
 +
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]
 +
*Click on '''Subscribe to this group'''
 +
 
 +
|-valign="top"
 +
!bgcolor="#CCCCCC"|To unsubscribe from email list
 +
|Either
 +
*Send an email to <tt>geos-chem-oxidants+unsubscribe [at] g.harvard.edu</tt>
 +
Or
 +
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]
 +
*Click on the '''My Settings''' button
 +
*Click on '''Leave this group'''
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:29, 21 August 2015 (UTC)
  
 
== Current GEOS-Chem Chemistry Projects (please add yours!) ==
 
== Current GEOS-Chem Chemistry Projects (please add yours!) ==
 
{| 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
+
|-valign="top"
|Examining the effects of isoprene nitrates and epoxide on tropical ozone and OH using SHADOZ and OMI measurements
+
|University of York
|[mailto:paulot@caltech.edu Fabien Paulot] <br>[mailto:jmao@seas.harvard.edu Jingqiu Mao]
+
|Nitrate Photolysis
|April 28, 2009
+
|[mailto:mat.evans@york.ac.ul Mat Evans]
|-
+
|08 Jun 2022
|Caltech/Harvard
+
 
|Examining the HCHO yield, OH recycling and ozone production with INTEX-A observations from new isoprene chemistry
+
|-valign="top"
|[mailto:jmao@seas.harvard.edu Jingqiu Mao ] <br>[mailto:paulot@caltech.edu Fabien Paulot]
+
|Harvard University and<br>MPIC-Mainz
|April 28, 2009
+
|Further development of [https://kpp.readthedocs.io The Kinetic PreProcessor (KPP)]
|-
+
|[mailto:yantosca@seas.harvard.edu Bob Yantosca] (GCST)
 +
|03 Jun 2022
 +
 
 +
|-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
 +
 
 +
|-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
 +
|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
 +
 
 +
|-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
 +
 
 +
|-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
 +
 
 +
|-valign="top"
 +
|U Wollongong
 +
|Evaluation of aromatic oxidation products using new observational constraints
 +
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]
 +
|9 June 2022
 +
 
 +
|-valign="top"
 +
|UNSW, Sydney
 +
|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
 +
 
 +
|-valign="top"
 +
|University of California, Riverside
 +
|Updates to DMS oxidation scheme
 +
|[mailto:wporter@ucr.edu William Porter]
 +
|26 August 2020
 +
 
 +
|-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
 +
 
 +
|-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
 +
 
 +
|-valign="top"
 
|NIA / LaRC
 
|NIA / LaRC
 
|Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis
 
|Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis
|[mailto:yiqiang.zhang@nianet.org Yiqiang Zhang ] <br>[mailto:hyl@nianet.org Hongyu Liu]
+
|[mailto:hyl@nianet.org Hongyu Liu]
|June 29, 2010
+
|5 May 2015
 +
 
 +
|-valign="top"
 +
|MIT
 +
|Simulating the global reactive carbon budget
 +
|[mailto:sarahsaf@mit.edu Sarah Safieddine]
 +
|12 April 2017
 +
 
 +
|-valign="top"
 +
|University of York
 +
|Halogen chemistry
 +
|[mailto:ts551@york.ac.uk Tomas Sherwen]
 +
|12 April 2017
 +
 
 +
|-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
 +
 
 +
|-valign="top"
 +
| US EPA
 +
|Alkane chemistry and product yields as a function of temperature/pressure.
 +
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
 +
|4 May 2017
 +
 
 +
|-valign="top"
 +
| US EPA
 +
|Carbon and Nitrogen Balance and checking software.
 +
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
 +
|4 May 2017
 +
 
 +
|-valign="top"
 +
| 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
 +
 
 +
|-valign="top"
 +
| FSU
 +
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
 +
 
 +
|-valign="top"
 +
|FSU
 +
|Methane and methyl chloroform lifetimes
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
 +
 
 +
|-valign="top"
 +
|FSU
 +
|Arctic halogen & ozone chemistry
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
 
|}
 
|}
  
 
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
 
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
  
=== Isoprene chemistry ===
+
=== Working group telecom on the 13/3/2019 ===
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]])
+
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]'''''
  
[[isoprene]]
+
=== Carbon balance ===
  
=== yield of isoprene nitrates ===
+
==== Script for evaluating carbon balance ====
[mailto:paulot@caltech.edu Fabien Paulot] found a problem in current chemistry scheme.In 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%.
+
<pre>
+
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          +                  +                  +           
+
</pre>
+
So it should be corrected as (no channel A):
+
<pre>
+
A  453 2.70E-12  0.0E+00    350 1 0  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          +                  +     
+
  
D  453 2.70E-12  0.0E+00    350 1 A  0.00    0.    0.       
+
'''''[http://www.barronh.com/ Barron Henderson] wrote:'''''
      5.00E+00  0.0E+00      0 0    0.00    0.    0.       
+
      RIO2          +    NO                                             
+
=1.000HNO3          +                  +                  + 
+
</pre>
+
--[[User:Jmao|J Mao.]] 18:04, 30 Aug 2010 (EDT)
+
  
=== rate of HNO4 ===
+
<blockquote>[I created] an evaluation script to preserve balances going forward as the mechanism evolves (e.g., as isoprene gets updated).
[mailto:ecbrow@berkeley.edu Ellie Browne] found a typo in the globchem.dat (v8-02-01 and beyond)
+
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.
<pre>
+
 
A  73 9.52E-05  3.2E+00 -10900 1 P   0.60    0.     0.        
+
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>
      1.38E+15  1.4E+00 -10900 0     0.00    0.     0.        
+
 
      HNO4          +                         M                               
+
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
=1.000HO2          +1.000NO2          +                   +
+
 
</pre>
+
==== Fixes for carbon creating reactions ====
This should be corrected as:
+
 
<pre>
+
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span>
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.        
+
'''''Sarah Safieddine wrote:'''''
      HNO4          +                         M                               
+
 
=1.000HO2          +1.000NO2          +                   +  
+
<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>
</pre>
+
 
The difference is within 2%.
+
{| 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>)
 +
 
 +
|-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>
 +
 
 +
|-valign="top
 +
|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:<br>
 +
<span style="color:green">R4N1 + NO → 2NO2 + 0.570RCHO + '''0.86ALD2''' + '''0.57CH2O'''</span>
 +
 
 +
|-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
 +
 
 +
|-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>
 +
 
 +
|-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>
 +
 
 +
|-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>
 +
 
 +
|-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>
 +
 
 +
|-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>
 +
 
 +
|-valign="top
 +
|719
 +
|ATO2 + MCO3 → MEK + ACTA
 +
|1.87E-13 exp(500/T)
 +
|Creates carbon: R=5C, P=6C
 +
|From the WIKI: replace MEK with MGLY<br>
 +
<span style="color:green">ATO2 + MCO3 → '''MGLY''' + ACTA</span>
 +
 
 +
|-valign="top
 +
|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>
 +
 
 +
|-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>
 +
 
 +
|-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>
 +
 
 +
|-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>
 +
 
 +
|}
 +
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:59, 27 July 2017 (UTC)
 +
 
 +
==== Identification of carbon leaking reactions ====
 +
 
 +
'''''Sarah Safieddine wrote:'''''
 +
 
 +
<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>
 +
 
 +
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
 +
 
 +
==== Fixes to correct ALK4 lumping issue ====
 +
 
 +
<span style="color:green">'''''These fixes were included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span>
 +
 
 +
'''''[[User:Barronh|Barron Henderson]] wrote:'''''
 +
 
 +
<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).
 +
 
 +
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 [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.
 +
 
 +
#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.
 +
 
 +
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>
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:21, 31 January 2017 (UTC)
 +
 
 +
=== JPL Released 18th Rate Coefficient Evaluation ===
 +
 
 +
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span>
 +
 
 +
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.
 +
 
 +
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)
 +
 
 +
=== Working Group Tele-con on the 2nd December 2011 ===
 +
[[ChemTelecon20111202]]
 +
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''
 +
 
 +
=== 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]])
  
--[[User:Jmao|J Mao.]] 19:04, 30 Aug 2010 (EDT)
 
 
=== HO2 + CH2O ===
 
=== HO2 + CH2O ===
 
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
 
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
Line 98: Line 387:
 
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
 
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
  
=== near-IR photolysis of HNO4 ===
+
== Previous issues that have now been resolved ==
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:
+
+
        !---------------------------------------------------------------------
+
        ! 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
+
        !---------------------------------------------------------------------
+
  
 +
=== Centralizing chemistry time step===
  
2. We need to change the branch ratio of HNO4 photolysis in <tt>ratj.d</tt>.  Change these lines from:
+
<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>
  
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00    33.3  HO2NO2
+
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.
14 HNO4      PHOTON    HO2        NO2                  0.00E+00  0.00    66.7  HO2NO2
+
  
to:
+
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)
  
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00      5.0  HO2NO2
+
=== Acetone photolysis ===
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.
+
[[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]].
  
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).
+
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)
  
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].
+
== Documentation ==
  
--[[User:Jmao|J Mao.]] 11:00, 26 Oct 2009 (EDT)
+
[[Image:Obsolete.jpg]]
 
+
== Documentation ==
+
  
 
*[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.
 
*[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.

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
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
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)