Tropospheric chemistry mechanism

On this page we discuss various aspects of GEOS-Chem's standard NOx-Ox-hydrocarbon-aerosol simulation (aka "tropchem", and formerly known as "fullchem".

Recent chemistry updates

The following table lists notable updates to the GEOS-Chem "tropchem" mechanism. For more information about a particular feature, click on the appropriate link below.

Version	Features
GEOS-Chem v10-01	UCX stratospheric-tropopsheric chemistry mechanism Incorporation of FAST-JX v7.0 photolysis mechanism; replaces older FAST-J photolysis mechanism Updated stratospheric Bry concentrations from CCM
GEOS-Chem v9-02	Inorganic chemistry updates Methyl peroxy nitrate (MPN) chemistry Adopt Paulot isoprene scheme as standard Fix RO2+HO2 rate constant Increase NO3 uptake by aerosol Removal of NOx-Ox partitioning Inhibition of N2O5 uptake by nitrate aerosol Improved HO2 uptake by aerosol
GEOS-Chem v9-01-03	Bromine chemistry mechanism
GEOS-Chem v8-03-01	Photolysis now computed at midpoint of chemistry timestep SOA formation from aromatics Modification to SOA formulation Updated aerosol optical properties for photolysis Option for updated isoprene chemistry scheme ISORROPIA II
GEOS-Chem v8-02-04	MEGAN v2.1 biogenic emissions Linoz stratospheric ozone chemistry Fix for near-IR photolysis of HNO4
GEOS-Chem v8-02-03	KPP chemical solver
GEOS-Chem v8-02-01	HO2 uptake Updated reaction rates and photolysis rates

--Bob Y. (talk) 21:07, 27 May 2015 (UTC)

Photolysis

GEOS-Chem v10-01 and newer versions now use the FAST-JX v7.0 photolysis mechanism. Prior versions used the older FAST-J photolysis mechanism.

--Bob Y. (talk) 21:03, 27 May 2015 (UTC)

CH4 concentrations

Latitude bands

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?

Bob Yantosca wrote:

Yes, in the full chemistry mechanism, CH4 is a constant. The values for years and latitude bands are set by routine get_global_ch4.f.

--Bob Y. 09:52, 14 July 2008 (EDT)

Lee Murray wrote:

The methane concentrations used for non-UCX full chemistry runs in GEOS-Chem (fixed throughout the troposphere to annual zonal mean values in four bands) have not have their values updated since 2008, which was the tail end of the hiatus in the growth rate. I can provide updated values through the present. This is something we should flag as necessary for every public model release — it's trivial to do, I'm happy to be point person.

This update is slated for inclusion in the GEOS-Chem v10-01 public release.

--Melissa Sulprizio (talk) 18:06, 20 May 2015 (UTC)

Monthly mean surface distributions

The following update has been proposed for GEOS-Chem v11-01.

Lee Murray wrote:

I have prepared spatially kriged (interpolated) monthly mean surface methane distributions from the NOAA GMD flask observations from the early 1980s through the present in a NetCDF file. This allows for seasonality in the methane concentrations and local maxima (e.g., south central US; western Russia) and minima. It is not appropriate to use these surface distributions fixed throughout the entire column (spatial heterogeneity will be reduced in the free troposphere), but I use them in all my current simulations to fix surface concentrations and advect methane at the cost of an additional transported tracer. Since the surface concentration is fixed, tropospheric chemistry equilibrates much faster than if we were to have online methane emissions, on the time-scale of tropospheric mixing. UCX does the same thing for its treatment of methane by default, but with a single mean surface value. Fixing surface concentrations and allowing advection is common treatment in other atmospheric chemistry models. If the steering committee wants to transition toward this style of treating methane, then I will be happy to provide these maps.

--Melissa Sulprizio (talk) 18:06, 20 May 2015 (UTC)

Bromine chemistry

Please see our Bromine chemistry mechanism wiki page for complete information about the bromine species used in this mechanism.

--Bob Y. (talk) 21:07, 27 May 2015 (UTC)

Removal of NOx and Ox partitioning

This update was tested in the 1-month benchmark simulation 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:

1. 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.
2. Dry deposition of NOx is now dry deposition of NO2.
3. Routine OHSAVE has been updated to remove FRACO3, FRACNO, FRACNO2, SAVENO, SAVENO2, and SAVENO3. These are no longer needed because O3, NO, NO2, and NO3 are now tracers.
4. Routine PARTITION has been updated to remove partitioning of NOx and Ox.

--Melissa Payer 15:21, 1 April 2013 (EDT)

Evolution of mean OH

Please see our wiki page which tracks the evolution of the mean OH lifetime taken from the GEOS-Chem 1-year benchmark simulations.

--Bob Y. 12:56, 16 February 2010 (EST)

Isoprene papers

Mat Evans wrote:

I thought it would be useful to put together all the isoprene papers that are coming out at the moment.

New papers

Mat Evans wrote:

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

Bryan Duncanwrote:

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?

Daniel Jacob replied:

We still read the same static acetone fields (from 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.

--Bob Y. 09:09, 2 December 2008 (EST)

Updates to chemistry mechanism

Rob Pinder wrote:

We downloaded the code from the latest version of GEOS-Chem (v8-01-01), but the 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 ?

Jingqiu Mao replied:

I updated most of the reactions according to JPL06 and IUPAC06. Please find a document with the revised reaction rates.

NOTE: These updated reaction rates were released in GEOS-Chem v8-02-01 in May 2009.

--Bob Y. 16:52, 16 February 2010 (EST)

HO2 uptake

Original implementation

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.

Daniel Jacob replied:

Here's the history of HO2 uptake in GC:

1. Old versions of the model had an HO2 reactive uptake coefficient of 0.1 as per Jacob (AE 2000)
2. 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.
3. 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.

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.

--Bob Y. 16:51, 16 February 2010 (EST)

Improved HO2 uptake

This update was tested in the 1-month benchmark simulation v9-02j and approved on 28 May 2013.

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 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).

--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 our paper). This remains largely uncertain.

--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 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 Taketani et al. 2012 paper).

--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.

--Bob Y. 15:30, 8 June 2011 (EDT)

Previous issues that are now resolved

NOTE: Please also see our list of 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.

1. Buggy implementation in v7-04-12
2. Polar cap @ 200 hPa is now applied

Other errors in SMVGEAR

1. May Fu and Philippe Le Sager fixed 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.
2. Lok Lamsal reported a bug with NaN's in SMVGEAR. Bob Yantosca recommended a fix for this error. Visit the discussion here.

--Bob Y. 12:52, 13 September 2010 (EDT)