NOx-Ox-HC-aerosol: Difference between revisions

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On this page we discuss various aspects of GEOS-Chem's standard NOx-Ox-hydrocarbon-aerosol simulation (aka the "full-chemistry" simulation).
#REDIRECT [[Tropospheric chemistry mechanism]]
 
== Recent chemistry updates ==
 
The following table lists notable updates to the GEOS-Chem "full-chemistry" mechanism.  For more information about a particular feature, click on the appropriate link below.
 
{| border="1" cellspacing="0" cellpadding="5"
|-bgcolor="#cccccc"
!width="150px"|Version
!width="650px"|Features
 
|-valign="top"
|[[GEOS-Chem v9-02]]
|
*[[Updating_standard_chemistry_with_JPL_10-6|Inorganic chemistry updates]]
*[[Methyl peroxy nitrate chemistry|Methyl peroxy nitrate (MPN) chemistry]]
*[[New_isoprene_scheme|Adopt Paulot isoprene scheme as standard]]
*[[New_isoprene_scheme#Update_One_-_RO2.2BHO2_Reaction_Rate|Fix RO2+HO2 rate constant]]
*[[New_isoprene_scheme#NO3_aerosol_reactive_uptake_coefficient|Increase NO3 uptake by aerosol]]
*[[NOx-Ox-HC-aerosol#Removal of NOx and Ox partitioning|Removal of NOx-Ox partitioning]]
*[[ChemTelecon20111202|Inhibition of N2O5 uptake by nitrate aerosol]]
*[[NOx-Ox-HC-aerosol#Improved_HO2_uptake|Improved HO2 uptake by aerosol]]
 
|-valign="top"
|[[GEOS-Chem v9-01-03]]
|
*[[Bromine chemistry mechanism]]
 
|-valign="top"
|[[GEOS-Chem v8-03-01]]
|
*[[GEOS-Chem v8-03-01#Photolysis now computed at midpoint of chemistry timestep|Photolysis now computed at midpoint of chemistry timestep]]
*[[Secondary organic aerosols#SOA formation from aromatics|SOA formation from aromatics]]
*[[Secondary organic aerosols#Modification_to_SOA_formulation|Modification to SOA formulation]]
*[[Photolysis mechanism#Updated aerosol optical properties|Updated aerosol optical properties for photolysis]]
*[[New isoprene scheme|Option for updated isoprene chemistry scheme]]
*[[ISORROPIA II]]
 
|-valign="top"
|[[GEOS-Chem v8-02-04]]
|
*[[MEGAN biogenic emissions#MEGAN in GEOS-Chem v8-02-04 and later versions|MEGAN v2.1 biogenic emissions]]
*[[Linoz stratospheric ozone chemistry|Linoz stratospheric ozone chemistry]]
*[[Chemistry Issues#near-IR photolysis of HNO4|Fix for near-IR photolysis of HNO4]]
 
|-valign="top"
|[[GEOS-Chem v8-02-03]]
|
*[[KPP solvers FAQ|KPP chemical solver]]
 
|-valign="top"
|[[GEOS-Chem v8-02-01]]
|
*[[#HO2_uptake|HO2 uptake]]
*[http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v5.pdf Updated reaction rates and photolysis rates]
|}
 
--[[User:Bmy|Bob Y.]] 16:30, 30 September 2013 (EDT)
 
== Evolution of mean OH ==
 
Please see our [[Mean OH lifetime in GEOS-Chem|wiki page which tracks the evolution of the mean OH lifetime]] taken from the [http://acmg.seas.harvard.edu/geos/geos_1yr_plots.html GEOS-Chem 1-year benchmark simulations].
 
--[[User:Bmy|Bob Y.]] 12:56, 16 February 2010 (EST)
 
== Isoprene papers ==
'''''[mailto:m.j.evans@leeds.ac.uk Mat Evans] wrote:'''''
 
:I thought it would be useful to put together all the [[Isoprene|isoprene papers]] that are coming out at the moment.
 
== New papers ==
 
'''''[mailto:m.j.evans@leeds.ac.uk Mat Evans] wrote:'''''
 
:[[New papers|This page]] is somewhere to put comments about new papers that have a relevance to the chemistry scheme in GEOS-Chem and assocated parameters.
 
== Acetone treatment in GEOS-Chem ==
 
'''''[mailto:Bryan.N.Duncan@nasa.gov Bryan Duncan]wrote:'''''
 
:I've asked you before about how you treat acetone in GEOS-Chem, but I thought to ask you again since Eric Nielson is implementing the GMI Combo chemistry package into the NASA GEOS-5 Chemistry Climate Model (Steven Pawson/Rich Stolarski = PIs).  In the Combo CTM, we simply read in static acetone fields, instead of having acetone emissions.  We did this a while back following Harvard's lead.  So, I'd like to know if there has been any change to the treatment of acetone that we should adopt? 
 
'''''[mailto:djacob@fas.harvard.edu Daniel Jacob] replied:'''''
 
:We still read the same static acetone fields (from [http://acmg.seas.harvard.edu/publications/jacob2001/paper.new.pdf Jacob et al. 2002]) in the standard full-chemistry version of GEOS-Chem and I recommend that you still do that too in GMI.  The reason is that there's a 300 ppt acetone background in the atmosphere that we don't understand and can't model. In my 2002 paper I tried to simulate it with an ocean source but subsequent work showed that the ocean is more often a sink (so much for that). At least the 2002 paper has a good simulation of observed concentrations, even if it's for the wrong reason.
 
--[[User:Bmy|Bob Y.]] 09:09, 2 December 2008 (EST)
 
== Updates to chemistry mechanism ==
 
'''''[mailto:Pinder.Rob@epamail.epa.gov Rob Pinder] wrote:'''''
 
:We downloaded the code from [[GEOS-Chem versions under development#v8-01-01|the latest version of GEOS-Chem (v8-01-01)]], but the [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/geoschem_mech.pdf documentation that we found is from version 5-07-08].  Do you know if these rate constants have been overhauled recently, especially to reflect guidance from JPL 2006 ?
 
'''''[mailto:jmao@seas.harvard.edu Jingqiu Mao] replied:'''''
 
:I updated most of the reactions according to JPL06 and IUPAC06.  Please find  [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/updated_rxns_jingqiu_mao.pdf a document with the revised reaction rates].
 
'''''NOTE: These [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v5.pdf updated reaction rates] were released in [[GEOS-Chem v8-02-01]] in May 2009.'''''
 
--[[User:Bmy|Bob Y.]] 16:52, 16 February 2010 (EST)
 
== HO2 uptake ==
 
=== Original implementation ===
 
'''''[mailto:h.macintyre@see.leeds.ac.uk Helen MacIntyre] wrote:'''''
 
:I noticed that in the new version of the model, HO2 uptake has been switched off to 'give better results over the tropics'. I would be very grateful if you could give me some more information regarding this issue, or point me in the direction of some.
 
'''''[mailto:djacob@fas.harvard.edu Daniel Jacob] replied:'''''
 
:Here's the history of HO2 uptake in GC:
 
:# Old versions of the model had an HO2 reactive uptake coefficient of 0.1 as per Jacob (AE 2000)
:# Then results started coming out of Jon Abbatt's lab showing that HO2 uptake was much slower than that. At the same time, Randall Martin  and Bastien told me that they were getting better results with HO2 uptake shut off. So that's what we did.
:# Most recently, Lyatt Jaegle worked with Joel Thornton on inclusion of HO2 uptake in GC by the aqueous-phase recombination mechanism. That paper is now published in JGR (Thornton et al., 2008) and Lyatt was going to give us the code for including it in GC.
 
'''''[mailto:bastien.sauvage@aero.obs-mip.fr Bastien Sauvage] replied:'''''
 
:I confirm the history version concerning the reason why we turned off the HO2 uptake, as decribed in Sauvage et al. ACP, 2007. It was based on simulations over the Tropics and comparison of GC ozone simulation versus observations (SHADOZ and MOZAIC).
 
'''''NOTE: This update from Lyatt Jaegle was released in [[GEOS-Chem v8-02-01]].'''''
 
--[[User:Bmy|Bob Y.]] 16:51, 16 February 2010 (EST)
 
=== Improved HO2 uptake ===
 
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02j|v9-02j]] and approved on 28 May 2013.'''''
 
'''''[mailto:djacob@fas.harvard.edu Daniel Jacob] replied:'''''
 
:I have conferred with Jingqiu and Mat on this latest update and we agreed that using gamma_HO2 = 1 in the standard model is too high since it is given in [http://www.atmos-chem-phys.net/13/509/2013/acp-13-509-2013.pdf Mao et al. 2013] as an upper limit (and obviously is). We will use instead gamma_HO2 = 0.2 giving H2O, which can be citable as Jacob [2000] (for the gamma) and Mao et al. [2013] (for the yield).
 
--[[User:Melissa Payer|Melissa Payer]] 11:08, 22 May 2013 (EDT)
 
One thing I would like to add is, the effective gamma_HO2 could be higher than 1, if one considers the uptake of H2O2 induced by HO2 uptake (shown in [http://www.atmos-chem-phys.net/13/509/2013/acp-13-509-2013.pdf our paper]). This remains largely uncertain.
 
--[[User:Jmao|Jmao]] 09:54, 8 November 2013 (EST)
 
gamma = 0.2 (instead of previous 0.07) is consistent with our independent analysis on Cu and Fe mass fractions in Chinese aerosols (e.g., Cu fraction in China is a factor of 1.6-12 higher than the U.S. mean; shown in [http://www.atmos-chem-phys.net/12/12255/2012/acp-12-12255-2012.html our 2012 ACP paper]). The number is also in line with the campaign measurements over China (0.13-0.34 over Mt. Tai and 0.09-0.40 over Mt. Mang; shown in [http://www.atmos-chem-phys.net/12/11907/2012/acp-12-11907-2012.html Taketani et al. 2012 paper]).
 
--[[User:Jintai Lin|Jintai Lin]] 0:05, 23 Decemeber 2013 (EST)
 
== Methyl chloroform lifetime ==
 
This content has now been moved to the separate [[Methyl chloroform lifetime]] wiki page.
 
--[[User:Bmy|Bob Y.]] 15:30, 8 June 2011 (EDT)
 
== CH4 concentrations ==
 
'''''[mailto:cbuten@pdx.edu Chris Buten] wrote:'''''
 
:When running the NOxOxHC simulation, I presume that CH4 concentration is specified as an input and not determined by emissions and transport (and therefore not a tracer). If so, is there a way to easily visualize or extract these input concentrations?
 
'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] wrote:'''''
 
:Yes, in the full chemistry mechanism, CH4 is a constant.  The values for years and latitude bands are set by routine <tt>get_global_ch4.f</tt>.
 
--[[User:Bmy|Bob Y.]] 09:52, 14 July 2008 (EDT)
 
== FAST-J Photolysis ==
 
NOTE: This discussion has now been moved to the [[Photolysis mechanism]] page.
 
== Removal of NOx and Ox partitioning ==
 
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02h|v9-02h]] and approved on 15 May 2013.'''''
 
Family tracers NOx and Ox have been removed and are now replaced with their individual constituents: NO, NO2, NO3, HNO2, and O3. In order to remove NOx and Ox, the following updates were also made:
   
#NOx emissions are now NO emissions and Ox emissions are now O3 emissions. This is consistent with the previous treatment of NOx and Ox emissions. Previously, in the Tracer Menu of input.geos, NO and O3 were denoted with parentheses, indicating NOx was emitted as NO and Ox was emitted as O3.
#Dry deposition of NOx is now dry deposition of NO2.
#Routine <tt>OHSAVE</tt> has been updated to remove <tt>FRACO3, FRACNO, FRACNO2, SAVENO, SAVENO2,</tt> and <tt>SAVENO3</tt>. These are no longer needed because O3, NO, NO2, and NO3 are now tracers.
#Routine <tt>PARTITION</tt> has been updated to remove partitioning of NOx and Ox.
 
--[[User:Melissa Payer|Melissa Payer]] 15:21, 1 April 2013 (EDT)
 
== Previous issues that are now resolved ==
 
NOTE: Please also see our list of [[Bugs and fixes|GEOS-Chem bugs and the versions in which they were fixed]] for the latest information.
 
=== Variable Tropopause ===
 
Please see the following links for more information about issues with the dynamic tropopause that have since been fixed.
 
# [[Dynamic tropopause#Buggy implementation in v7-04-12|Buggy implementation in v7-04-12]]
# [[Dynamic tropopause#Polar cap|Polar cap @ 200 hPa is now applied]]
 
=== Other errors in SMVGEAR ===
 
# May Fu and Philippe Le Sager fixed [[GEOS-Chem v7-04-13#smvgear.f|a bug in SMVGEAR that caused concentrations of certain tracers in STT to go to zero.]]  This bug was fixed in [[GEOS-Chem v7-04-13]]. 
# Lok Lamsal reported a bug with NaN's in SMVGEAR.  Bob Yantosca recommended a fix for this error.  [[GEOS-Chem v7-04-10#NaN's in smvgear.f|Visit the discussion here]].
 
--[[User:Bmy|Bob Y.]] 12:52, 13 September 2010 (EDT)

Latest revision as of 16:54, 13 June 2019

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