Difference between revisions of "NOx-Ox-HC-aerosol"

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On this page we discuss various aspects of GEOS-Chem's NOx-Ox-hydrocarbon-aerosol simulation (aka the "full-chemistry" simulation).
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#REDIRECT [[Tropospheric chemistry mechanism]]
 
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== Recent chemistry updates ==
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Please follow the links below for more information about recent chemistry updates in GEOS-Chem:
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#[[GEOS-Chem v8-03-01#Photolysis now computed at midpoint of chemistry timestep|v8-03-01: Photolysis now computed at midpoint of chemistry timestep]]
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#[[Secondary organic aerosols#SOA formation from aromatics|v8-03-01: SOA formation from aromatics]]
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#[[Secondary organic aerosols#Modification_to_SOA_formulation|v8-03-01: Modification to SOA formulation]]
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#[[Photolysis mechanism#Updated aerosol optical properties|v8-03-01: Updated aerosol optical properties for photolysis]]
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#[[New isoprene scheme|v8-03-01: Option for updated isoprene chemistry scheme]]
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#[[ISORROPIA II|v8-03-01: ISORROPIA II]]
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#[[MEGAN biogenic emissions#MEGAN in GEOS-Chem v8-02-04 and later versions|v8-02-04: MEGAN v2.1 biogenic emissions]]
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#[[Linoz stratospheric ozone chemistry|v8-02-04: Linoz stratospheric ozone chemistry]]
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#[[Chemistry Issues#near-IR photolysis of HNO4|v8-02-04: Fix for near-IR photolysis of HNO4]]
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#[[KPP solvers FAQ|v8-02-03: KPP chemical solver]]
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#[[#HO2_uptake|v8-02-01: HO2 uptake]]
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#[http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v5.pdf v8-02-01: Updated reaction rates and photolysis rates]
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--[[User:Bmy|Bob Y.]] 14:19, 17 March 2010 (EDT)
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== Evolution of mean OH ==
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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].
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--[[User:Bmy|Bob Y.]] 12:56, 16 February 2010 (EST)
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== Isoprene papers ==
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'''''[mailto:m.j.evans@leeds.ac.uk Mat Evans] wrote:'''''
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:I thought it would be useful to put together all the [[Isoprene|isoprene papers]] that are coming out at the moment.
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== New papers ==
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'''''[mailto:m.j.evans@leeds.ac.uk Mat Evans] wrote:'''''
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:[[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.
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== Acetone treatment in GEOS-Chem ==
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'''''[mailto:Bryan.N.Duncan@nasa.gov Bryan Duncan]wrote:'''''
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: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? 
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'''''[mailto:djacob@fas.harvard.edu Daniel Jacob] replied:'''''
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: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.
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--[[User:Bmy|Bob Y.]] 09:09, 2 December 2008 (EST)
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== Updates to chemistry mechanism ==
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'''''[mailto:Pinder.Rob@epamail.epa.gov Rob Pinder] wrote:'''''
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: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 ?
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'''''[mailto:jmao@seas.harvard.edu Jingqiu Mao] replied:'''''
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: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].
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'''''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.'''''
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--[[User:Bmy|Bob Y.]] 16:52, 16 February 2010 (EST)
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== HO2 uptake ==
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'''''[mailto:h.macintyre@see.leeds.ac.uk Helen MacIntyre] wrote:'''''
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: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.
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'''''[mailto:djacob@fas.harvard.edu Daniel Jacob] replied:'''''
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:Here's the history of HO2 uptake in GC:
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:# Old versions of the model had an HO2 reactive uptake coefficient of 0.1 as per Jacob (AE 2000)
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:# 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.
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:# 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.
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'''''[mailto:bastien.sauvage@aero.obs-mip.fr Bastien Sauvage] replied:'''''
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: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).
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'''''NOTE: This update from Lyatt Jaegle was released in [[GEOS-Chem v8-02-01]].'''''
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--[[User:Bmy|Bob Y.]] 16:51, 16 February 2010 (EST)
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== Methyl chloroform lifetime ==
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'''''[mailto:cklee79@gmail.com Chulkyu Lee] wrote:'''''
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:I'm trying to compare the methyl-chloroform (CH3CCl3) lifetime in two GEOS-Chem simulations. 
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:I've been going through the GEOS-Chem diagnostics listed on the GEOS-Chem website (Appendix 5) and noticed that there is a diagnostic for the lifetime of Methyl-chloroform: ND23.  It doesn't appear in the input.geos file, and from looking at the code itself, I'm not certain if it is still active. I was wondering if this diagnostic is functional for Methyl-chloroform.
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'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] wrote:'''''
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:We have since removed the CH3CCl3 lifetime from the code as a diagnostic of how "hot" the chemistry is.  That has since been replaced with the mean OH concentration diagnostic (which is automatic when you run the code).
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:I also discovered that the CH3CCl3 diagnostic was mislabled in the Appendix 5 -- that should have been "Mean OH".  Sorry for the confusion.
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'''''[mailto:jmao@seas.harvard.edu Jingqiu Mao] wrote:'''''
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:The CH3CCl3 lifetime is supposed to be the destruction rate of CH3CCl3 by OH. For the reaction OH+CH3CCl3, you can get the reaction rate from JPL2006:
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    k = 1.64e-12 * exp( -1520 / T ).
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:The lifetime of CH3CCl3 is
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    1 / ( k * [OH] ).
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:So if the global mean OH is 1e6 molecule/cm3, and the temperature is 298K, the lifetime of CH3CCl3 would be 1e8 seconds, which equals to 3.2 years.
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:Also you can calculate the lifetime of CH3CCl3 at each grid box, which you need to read the temperature and OH concentration. Then you can average globally to get a mean lifetime of CH3CCl3.
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'''''[mailto:mickley@fas.harvard.edu Loretta Mickley] wrote:'''''
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:Historically, we calculated the lifetime of CH3CCL3 in a different way. In [http://acmg.seas.harvard.edu/publications/bey2001a.pdf Bey et al., 2001], this is the procedure we used.
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:First the value you want to calculate is: the lifetime of global CH3CCl3 against the tropospheric sink of OH, Toh.
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    Toh = sum ( burden CH3CCl3 ) / sum (loss rate due to tropospheric OH),
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:where sum is the sum over all gridboxes, including the stratosphere, and the units are molecules / (molecules/s).  For the stratsopheric gridboxes, the loss rate will be zero by definition. Note you need to do the sums first, then the ratio.
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:Another way to write this is:
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    Toh =  sum ( [CH3CCl3] * air dens * volume)
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        / sum (k * conc OH * [CH3CCl3] * air dens * volume)
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:where the brackets signify mixing ratio, conc OH is OH molecules/cm3, air dens is the density in molecules/cm3, and volume is the volume of each grid box in cm3. Now assume that the mixing ratio of CH3CCl3 is uniform throughout the atmosphere.
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    Toh =  sum ( air dens * volume )
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        / sum (k * conc OH * air dens * volume)
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:To apply this to GEOS-Chem, you need these quantities for each gridbox, either as monthly means or more finely time-resolved:
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:* air density
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:* volume
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:* temperature
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:* OH concentration in molecules /cm3
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:Then calculate this:
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    Toh =  sum ( air dens * volume )
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        / sum (k as a function of temperature * conc OH * air dens * volume)
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:Sum first over all gridboxes and timesteps. Then calculate the ratio.
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:You can see vestiges of this approach in old versions of GEOS-Chem, though that code didn't take into account the stratospheric boxes. I believe there exists IDL code kicking around Harvard that can calculate this in the proper way, once you have saved the necessary inputs. I will ask. Please let me know if you use IDL and would be interested in this.
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:By the way, the global lifetime of CH3CCl3, Ttot, is calculated in this way:
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    1/Ttot = 1/Toh + 1/Tstrat + 1/Tocean
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:In Bey et al., we assumed Tstrat (the lifetime of CH3CCl3 against chemical loss in the stratosphere) was 43 years. We assumed that Tocean (the lifetime against loss to oceans) was 80 years. Since we had already calculated Toh, following the method above, we could calculate Ttot. This number is useful to compare with published values such as Spivakovsky 2000 and some of the Prinn papers.
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:In my view, however you decide to calculate the lifetime, you should make clear in your paper exactly what method you used.
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--[[User:Bmy|Bob Y.]] 10:19, 22 July 2008 (EDT)
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== CH4 concentrations ==
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'''''[mailto:cbuten@pdx.edu Chris Buten] wrote:'''''
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: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?
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'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] wrote:'''''
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: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>.
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--[[User:Bmy|Bob Y.]] 09:52, 14 July 2008 (EDT)
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== FAST-J Photolysis ==
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NOTE: This discussion has now been moved to the [[Photolysis mechanism]] page.
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== Previous issues that are now resolved ==
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=== Variable Tropopause ===
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# Note that the implementation of the variable tropopause is buggy in versions prior to [[GEOS-Chem_versions_under_development#v7-04-12|GEOS-Chem v7-04-12]].  If you are using versions prior to v7-04-12, you should turn the variable tropopause OFF.
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# Jennifer Logan (see correspondence below) suggested that we should cap the variable tropopause at 200hPa in near-polar regions (90-60S and 60-90N), to avoid the problem with anomalously high tropopause heights at high latitudes.  This fix was not in v7-04-12, but will be implemented into [[wiki:geos-chem:development#v7-04-13|GEOS-Chem internal version v7-04-13]].
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:'''''[mailto:jlogan@seas.harvard.edu Jennifer Logan] wrote:'''''
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<blockquote>After looking at the two papers I sent, I think we should restrict the tropopause at latitudes > 60 deg. to pressures greater than 200 mb (about 11 km).  From Fig. 3 in Seidel and Randel, there are tropopause (TP) heights as high as 13.5 km in the Antarctic (median height is ~9.8 km, 250 mb), but I don't think we want to be doing trop. chem there. The median TP pressure at ~80 N is ~300 mb, compared to ~250 mb at 70-85 S.  The extratropical TP heights are higher (lower pressure) in the SH than in the NH according to Fig. 3.</blockquote>
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<blockquote>This approach is also very easy to explain in a paper.</blockquote>
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<blockquote>Jennifer</blockquote>
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=== Other errors in SMVGEAR ===
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# 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]]. 
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# 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]].
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--[[User:Bmy|Bob Y.]] 16:02, 3 March 2010 (EST)
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Latest revision as of 16:54, 13 June 2019