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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!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.jessicahaskinsphd.com/ Jessica Haskins] (Github: [https://github.com/jhaskinsPhD jhaskinsPhD])
*[https://www.kelvinbates.com/ Kelvin Bates] (Github: [https://github.com/kelvinhb @kelvinb])


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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
|Simulating 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
|-
| US EPA
|Alkane chemistry and product yields as a function of temperature/pressure.
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
|4 May 2017
|-
| US EPA
|Carbon and Nitrogen Balance and checking software.
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
|4 May 2017
|-
| 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
|}


--[[User:Bmy|Bob Y.]] 15:08, 25 April 2014 (EDT)
|-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


== Current GEOS-Chem Chemistry Issues (please add yours!) ==


=== Carbon balance ===
|-valign="top"
|Columbia University
|Automated model reduction isoprene oxidation mechanism
|[mailto:benjamin.yang@columbia.edu Benjamin Yang]<br>
[mailto:danielmw@ldeo.columbia.edu Dan Westervelt]
|12 Sep 2023


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


'''''Barron Henderson wrote:'''''
|-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


<blockquote>[I created] an evaluation script to preserve balances going forward as the mechanism evolves (e.g., as isoprene gets updated).  
|-valign="top"
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.
|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


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


--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
|-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 for carbon creating reactions ====
|-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">'''''These fixes will be included in [[GEOS-Chem v11-02#v11-02acv11-02c]].'''''</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


'''''Sarah Safieddine 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>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>
|-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


{| border=1 cellspacing=0 cellpadding=5
|-valign="top"
|-bgcolor="#CCCCCC"
|U Wollongong
!Reaction # in globchem.dat v9-02
|Evaluation of aromatic oxidation products using new observational constraints
!Unbalanced Reaction
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
!Rate constant
|9 June 2022
!Issue<br>(R=Reactants, P=Products)
!Fix and corrected reaction (in <span style="color:green">green</span>)


|-valign="top
|-valign="top"
|453
|U Wollongong, U Sydney, UNSW
|R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2
|Impacts of photophysical oxidation of aldehydes
|K* (1-YN) where YN is returned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.5)
|[mailto:paolos@uow.edu.au Paolo Sebastianelli]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
|Creates carbon: R=4C P=4.26C
|10 June 2024
|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>


|-valign="top
|-valign="top"
|453
|UNSW, U Wollongong
|R4N1 + NO → 2NO2 + 0.39CH2O + 0.75ALD2 + 0.57RCHO + 0.3R4O2
|GEOS-Chem simulation of HFO and CF3CHO chemistry
|2.7E-12 exp(350/T)
|[mailto:b.killen@unsw.edu.au Beth Killen]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
|Creates carbon: R=4C, P=4.8C
|10 June 2024
|Fix, as suggested by Matt:<br>
<span style="color:green">R4N1 + NO → 2NO2 + 0.570RCHO + '''0.86ALD2''' + '''0.57CH2O'''</span>


|-valign="top
|-valign="top"
|453
|University of California, Riverside
|ATO2 + NO → 0.96NO2 + 0.96CH2O + 0.96MCO3 + 0.04R4N2
|Updates to DMS oxidation scheme
|2.8E-12 exp(300/T)
|[mailto:wporter@ucr.edu William Porter]
|Creates carbon: R=3C, P=3.04
|26 August 2020
|Fix as suggested by Mat: ditch the R4N2 channel<br>
<span style="color:green">ATO2 + NO → NO2 + CH2O + MCO3


|-valign="top
|-valign="top"
|803
|Harvard University
|RIO2 → 2HO2 + CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.5HAC + OH
|Overhaul of cloud pH code including: use of Newton's method and addition of crustal cations and organic acids
|4.07E+08 exp(-7694/T)
|[mailto:vshah@g.harvard.edu Viral Shah]<br>[mailto:jmoch@g.harvard.edu Jonathan Moch]
|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
|5 May 2019
|Fix as suggested by Sarah: remove CH2O<br>
<span style="color:green">RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH</span>


|-valign="top
|-valign="top"
|453
|U Alaska Fairbanks
|ISNOOB + NO3 → R4N2 + GLYX + 2NO2
|Monoterpene oxidation and its impact on SOA formation
|2.3E-12
|[mailto:yzheng4@alaska.edu Yiqi Zheng]<br>[mailto:jmao2@alaska.edu Jingqiu Mao]
|Creates carbon: R=5C, P=6C
|21 April 2019
|Fix as suggested by Barron: Replace R4N2 by PROPNN<br>
<span style="color:green">ISNOOB + NO3 → '''PROPNN''' + GLYX + 2NO2</span>


|-valign="top
|-valign="top"
|453
| FSU
|ISNOOB+NO→0.94R4N2 +0.94GLYX +1.88NO2
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry
|2.6E-12 exp(380/T)
|[mailto:cdholmes@fsu.edu Chris Holmes]
|Creates carbon: R=5C, P=5.64C
|May 2017
|Same as above<br>
<span style="color:green">ISNOOB + NO → '''0.06R4N2''' + ''''0.94PROPNN'''' + 0.94GLYX + 1.88NO2</span>


|-valign="top
|-valign="top"
|453
|FSU
|ISNOHOO + NO → 0.934R4N2 + 0.934HO2 + 0.919GLYX
|Methane and methyl chloroform lifetimes
|2.6E-12 exp(380/T)
|[mailto:cdholmes@fsu.edu Chris Holmes]
|Creates carbon: R=5C, P=5.574C
|May 2017
|Fix by Barron:<br>
<span style="color:green">ISNOHOO + NO → '''0.081R4N2''' + '''0.919PROPNN''' + 0.934HO2 + 0.919GLYX</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>


|-valign="top"
|FSU
|Arctic halogen & ozone chemistry
|[mailto:cdholmes@fsu.edu Chris Holmes]
|May 2017
|}
|}
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 20:51, 22 May 2017 (UTC)


==== Identification of carbon leaking reactions ====
== Current GEOS-Chem Chemistry Issues (please add yours!) ==


'''''Sarah Safieddine wrote:'''''
=== Carbon balance ===


<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 phttp://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>
==== Script for evaluating carbon balance ====


--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
'''''[http://www.barronh.com/ Barron Henderson] wrote:'''''


==== Fixes to correct ALK4 lumping issue ====
<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.
<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]])
 
=== 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.
 
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
 
== Previous issues that have now been resolved ==
 
=== Centralizing chemistry time step===
 
<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>
 
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.
 
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)
 
=== Acetone photolysis ===
 
[[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]].
 
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)
 
== Issues that have been since rendered obsolete by newer code updates ==
 
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]]).
 
=== NIT should be converted to molec/cm3 in calcrate.F ===
 
[[Image:Obsolete.jpg]]
 
<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>
 
In <tt>calcrate.F</tt>, we have:
 
                    ! Nitrate effect; reduce the gamma on nitrate by a
                    ! factor of 10 (lzh, 10/25/2011)
                    IF ( N == 8 ) THEN
                        TMP1 = State_Chm%Tracers(IX,IY,IZ,IDTSO4) +
    &                        State_Chm%Tracers(IX,IY,IZ,IDTNIT)
                        TMP2 = State_Chm%tracers(IX,IY,IZ,IDTNIT)
                        IF ( TMP1 .GT. 0.0 ) THEN
                          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>.
 
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>).
 
--[[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)
 
=== rate of HNO4 ===
 
[[Image:Obsolete.jpg]]
 
<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>
 
[mailto:ecbrow@berkeley.edu Ellie Browne] found a typo in the globchem.dat ([[GEOS-Chem v8-02-01]] and beyond)
<pre>
A  73 9.52E-05  3.2E+00 -10900 1 P  0.60    0.    0.       
      1.38E+15  1.4E+00 -10900 0    0.00    0.    0.       
      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>
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:29, 31 January 2017 (UTC)
 
=== near-IR photolysis of HNO4 ===
 
<span style="color:green">'''''This update was added to [[GEOS-Chem v8-02-04]].'''''</span>
 
[[Image:Obsolete.jpg]]
 
<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>
 
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
        !---------------------------------------------------------------------
 
 
2. We need to change the branch ratio of HNO4 photolysis in <tt>ratj.d</tt>.  Change these lines from:
 
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00    33.3  HO2NO2
14 HNO4      PHOTON    HO2        NO2                  0.00E+00  0.00    66.7  HO2NO2
 
to:
 
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00      5.0  HO2NO2
14 HNO4      PHOTON    HO2        NO2                  0.00E+00  0.00    95.0  HO2NO2
 
This is based on Jimenez et al. (Quantum yields of OH, HO2 and NO3 in the UV photolysis of HO2NO2, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2005) shows that HO2 yield should be 0.95 and OH yield should be 0.05 for wavelength above 290nm.
 
This way all the near-IR photolysis will have most weight on HO2 channel(Stark et al., Overtone dissociation of peroxynitric acid (HO2NO2): Absorption cross sections and photolysis products, JOURNAL OF PHYSICAL CHEMISTRY A, 2008).
 
This update has now been added to the [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf chemistry mechanism documentation file].
 
--[[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 ===
 
<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>
 
[[Image:Obsolete.jpg]]
 
<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>
 
[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 Yantosca]] ([[User talk:Bmy|talk]]) 20:31, 31 January 2017 (UTC)
 
=== Potential issue with reading restart.cspec file ===
 
<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>
 
[[Image:Obsolete.jpg]]
 
<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>
 
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)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:33, 31 January 2017 (UTC)
 
=== GLCO3, GLPAN bug in standard mechanism ===
 
<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>
 
[[Image:Obsolete.jpg]]
 
<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>
 
'''''[mailto:fabienpaulot@gmail.com Fabien Paulot] wrote:'''''
 
: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.
 
: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.
 
: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.
:#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 ==
 
[[Image:Obsolete.jpg]]
 
*[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_v5.pdf Updated chemical reactions] now used in [[GEOS-Chem v8-02-01]] through [[GEOS-Chem v8-02-03]].
**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

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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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