GEOS-Chem Newsletter January 2010

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Dear GEOS-Chem Users,

Happy New Year 2010 to one and all! Here is your January Newsletter.

Thank you for your continued support of GEOS-Chem,

Bob Yantosca and Claire Carouge

GEOS-Chem model management and logistics

GEOS-Chem Steering Committee

Previous meeting

The last GEOS-Chem Steering Committee telecon took place on December 8, 2009. Minutes of this meeting (and past meetings) are available HERE.

Next meeting

The next Steering Committee Telecon shall take place on Tuesday, March 9, 2010 at 10:30 EST. Mark your calendars!

GEOS-Chem Working Groups

Please see the GEOS-Chem Working Groups web page for links to each of the Working Groups.

We encourage each GEOS-Chem user to join the Working Group that is most relevant to his/her area of research.

GEOS-Chem website

Please take a moment to review the website. Please inform the GEOS-Chem Support Team of any new developments such as newly submitted or published papers, personnel changes in your user group, updated research blurbs, etc.

GEOS-Chem wiki

The GEOS-Chem wiki has the following updates:

  1. Bugs and fixes are now listed on the individual wiki pages for each GEOS-Chem version. For your convenience, a master list of bug reports is provided for you on the Bugs and fixes wiki page.
  2. The Photolysis mechanism contains some new information about the various updates that will become a part of GEOS-Chem v8-03-01.
  3. A page has been added for the TOMAS aerosol microphysics package, which is currently being implemented into GEOS-Chem v8-03-01.

GEOS-Chem update

Suggested new guidelines for writing code

Bob Yantosca recently gave a presentation for the Jacob Group in which he outlined some of the new coding guidelines that are being used in the development of the GEOS-Chem column code. These include:

  1. Data shall be passed between routines via the argument list, rather than via USE statements or common blocks.
  2. No more common blocks!
    • Except in legacy code routines under certain circumstances
  3. Include files may be used, provided that they only contain PARAMETERs (i.e. constants).
  4. When the code encounters an error, do not simply die with an error message.
    • Instead, immediately exit the routine where the error occurred (and all higher-level routines) with a descriptive error code.
  5. All columnized routines shall use the ProTeX documentation headers.

We hope that you will start using some of these new guidelines when writing GEOS-Chem code. The presentation contains more details and examples.

Status of GEOS-Chem v8-02-04

GEOS-Chem v8-02-04 "beta" is currently undergoing 1-month and 1-year benchmark test simulations. We ran 3 1-year benchmark simulations:

  • Run 0: "Baseline" run (with EPA/NEI05 emissions)
  • Run 1: Same as Run #1, but with updated MEGAN emissions
  • Run 2: Same as Run #2, but with Linoz strat Ox chemistry turned on

For more detailed information about the benchmarking process, click HERE. (NOTE: Due to some problems with the KPP solver (described in the next section), each of the benchmark simulations were done with the SMVGEAR solver.)

Issues with KPP

Claire Carouge ( wrote:

While benchmarking GEOS-Chem v8-02-04, Bob and I found a problem when using KPP in GEOS-Chem. The concentrations output by GEOS_Chem when using KPP are very different than when using SMVGEAR.
It turned out that we obtain the same differences when using v8-02-03.
I've attached some plots showing the differences in monthly means after 2 months of simulation to give you a more precise idea of the differences.
We do not know what the problem is now, and we are working on it. In the mean time, we ask you not to use KPP.
The release of v8-02-04 is therefore delayed until we could fix the KPP problem.
If some of you already performed simulations with KPP with v8-02-03 and got bad or good results, we would like to hear back from you. Comparing the setups may help us to find out where the problem lies.
Sorry for the inconvenience,
Claire and Bob

Claire Carouge ( wrote:

We have found that the loop used to update CSPEC in routine gckpp_driver, actually wrongly updates 3 inactive species concentrations. And this creates cascade events that completely mess up the chemistry.

Update as of Jan 27, 2010: The problem of updating CSPEC is solved and we are now running few tests to make sure there are no other problems. We'll let you know as soon as we are confident in the results from simulations using KPP.

Met field update

GEOS-5 met field data downloading at Harvard was temporarily halted due to a technical issue involving a filesystem disk mount. This issue has now been resolved by our sysadmin Jack Yatteau.

The Harvard University GEOS-Chem archive ( now contains GEOS-5 met data through January 2010. Please view our GEOS-Chem Simulation Years web page for a complete catalog of available data.

As a reminder, Dalhousie University maintains a secondary GEOS-Chem data archive ( This archive is not as comprehensive as the Harvard archive, but contains met data and emissions data for several GEOS-5 high-resolution nested grids.

In the pipeline

The following updates are currently being incorporated into the GEOS-Chem v8-03-01 release.

Item Author(s) Status
Global 1x1.25 model capability Lok Lamsal Code modifications added to GEOS-Chem v8-03-01, awaiting validation & release.
TOMAS aerosol microphysics Peter Adams
Win T.
Dan Westervelt
Jeffrey Pierce
TOMAS code has been merged into GEOS-Chem v8-03-01; awaiting final validation.
Thanos Nenes
Code has been delivered to G-C support team; currently in testing.
Updated aerosol optics Randall Martin, Colette Heald New jv_spec.dat files have been received by the G-C support team; will ship standard w/ GEOS-Chem v8-03-01
Modification to SOA formation Aerosols Working Group Included in GEOS-Chem v8-03-01; awaiting validation.

Note from Colette Heald:

SOA formation should not depend on the mass on inorganics. Specifically, in carbon_mod.f, MPOC in the code should only consist of organic aerosol.
We carry carbon mass only in the STT array and multiply by 2.1 to account for non-carbon mass in the SOA.
Partitioning theory (Pankow, 1994) describes organic phase partitioning assuming absorption into pre-existing organic mass. There is currently no theoretical or laboratory support for absorption of organics into inorganics.
Note that previous versions of the standard code (v7-04-07 through v8-02-04) did include absorption into inorganics. (Colette Heald, 12/3/09)
Updated Isoprene Chemistry Fabien Poulot
P. Le Sager
Jingqiu Mao
In beta testing. The GEOS-Chem KPP source code is currently being recompiled for the new isoprene mechanism.
Updated mercury simulation with improved soil model (GTMM) Chris Holmes, Nicole Smith-Downey Code has been delivered to G-C support team

For a complete list of outstanding code updates, please see our GEOS-Chem model development priorities page.

Column code update

The GEOS-Chem column code continues to progress quickly. Bob Yantosca and Arlindo da Silva from GSFC are working on interfacing the GEOS-Chem column code to the GEOS-5 GCM.

Also, Harvard and GSFC will collaborate on the construction of a common emissions component that can be shared by both the columnized versions the GEOS-Chem and GMI models. This will also allow easy interchange of GEOS-Chem emissions into GMI and vice-versa.

We have listed our guidelines for writing columnized code on the wiki. These are good rules of thumb for any programming project, and we encourage all GEOS-Chem users to follow these guidelines whenever possible.

You can track our progress on the GEOS-Chem column code wiki page. Check back often for the latest developments!

--Bob Y. 11:29, 27 January 2010 (EST)