GEOS-Chem Newsletter March 2009

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Dear GEOS-Chem Users,

A belated Happy St. Patrick's Day to one and all! Here is the March 2009 edition of the GEOS-Chem newsletter.

Bob Yantosca, Philippe Le Sager, and Claire Carouge

GEOS-Chem update

Requests for help

Just a reminder: all GEOS-Chem questions should be sent to the email address This will ensure that Bob, Philippe, and Claire will all receive your email question at the same time. This will allow us to serve you better. If one of us is unavailable then the others will be able to respond to you.

Reporting Bugs

Another friendly reminder: if you should find and fix a bug in GEOS-Chem, please report it to Bob, Philippe, and Claire at as soon as possible. This will make sure that the bug fix gets included in the mainline GEOS-Chem code. Other GEOS-Chem users will surely benefit from your discovery!

Emissions release v8-01-04 "beta"

GEOS-Chem v8-01-04 "beta", our emissions release, is now ready for public use. This version contains several updated emissions inventories. You may obtain the code from:

cd pub/geos-chem/beta_releases
get GEOS-Chem.v8-01-04-beta.stdrun.tar.gz 

Please see the following resources for more information about this version:

Chemistry release v8-02-01

GEOS-Chem v8-02-01, our chemistry release, is undergoing final testing at this point. A few technical problems with the GLYX chemistry mechanism are being ironed out by May Fu and Claire Carouge.

Also, we would like to acknowledge Jingqiu Mao (Harvard), the Palmer group (U. Edinburgh), and Dylan Millet (UMN), who have been reviewing the GEOS-Chem chemistry mechanism file to make sure that we have the most up-to-date list of reactions. The updated mechanism will be included in v8-02-01.

GEOS-Chem v8-02-01 will be a "public" release (i.e. the manual page and other documentation will be rewritten). However, due to time concerns, it will probably not be ready before the GEOS-Chem meeting. We hope to have this version ready soon thereafter.

GEOS-Chem email lists

The following email lists:

  • GEOS-Chem users
  • GEOS-Chem aerosols
  • GEOS-Chem adjoint

were recently switched over from the server to the server. Therefore, to send email to the entire list, you must now use the following addresses:


Also note, during the transition, some email addresses may have not been copied over correctly. If you feel that you have been deleted from the list, you can resubscribe via this web interface.

FLAMBE data has been reprocessed

This will be of interest to those of you who are doing ARCTAS-related work. The FLAMBE hourly biomass product has been reprocessed by Ed Hyer after several problems were discovered with the data.

Data files (binary punch format) have been created for GEOS-Chem, and may be downloaded from the following site:

cd pub/geos-chem/NRT-ARCTAS/flambe/2008/

there are subdirectories 01, 02 .. 12 which contain the data from Jan thru Dec 2008. Please discard the old data for 2008 and re-download the new data.

PLEASE NOTE! According to Ed Hyer, there are a few days which have one or more hours of missing data. Therefore, it is recommended to check in flambe_arctas_mod.f if each file exists before it is read.

Also note: FLAMBE is not an option in the standard mainline GEOS-Chem code; at present it is only used in certain ARCTAS-related research versions of GEOS-Chem.

GEOS-Chem advection running slower than before?

A couple of users have pointed out that the new TPCORE advection code implemented into GEOS-Chem v8-01-03 seems to run slower than in previous versions. We are investigating, but cannot say if there is a definite "fix" for this at this point.

ESMF update

Development of the GEOS-Chem column chemistry module is proceeding swiftly. Several of the sub-processes in the chemistry (e.g. inputs, photolysis, carbon & sea salt aerosol chemistry, aerosol thermodynamical equilibrium) have been columnized. Much of the remaining code lends itself to columnization; however, in many cases legacy code must be removed or updated.

Bob and Philippe have provided GSFC with a list of input and output arguments that the GEOS-Chem column chemistry module will use. This list is being refined with the assistance of Max Suarez and Arlindo da Silva from GSFC. Once the list is finalized, GSFC will create an interface to the GEOS-5 GCM to which the GEOS-Chem column chemistry module will be attached.

Development of the ESMF component for the GEOS-Chem emissions has been temporarily suspended, as the priority now is to prepare the GEOS-Chem column chemistry component for inclusion into the GEOS-5 GCM. However, the emissions component will more than likely be adapted to become the GEOS-Chem "emissions" driver within the GEOS-5 GCM. Also, the emmissions component will be an important part of an eventual standalone ESMF GEOS-Chem model.

GEOS-5 met field reprocessing


As described in the February 2009 newsletter, we are reprocessing the entire archive of GEOS-5 met field data. As of March 18th, 2009 the following fields have been completed:

  • 2008: entire year
  • 2004: July - December
  • 2003: December only (NOTE: these have not been TAR'ed yet)
  • 2005: January - March (NOTE: these have not yet been TAR'ed yet)

for each of the following geographic domains:

  • China nested 0.5 x 0.667
  • Global 2 x 2.5
  • Global 4 x 5

The files have been TAR'd and Gzip'd for your convienience (as this dramatically reduces the size of the data). In each directory there are files 01.tar.gz, 02.tar.gz .. 12.tar.gz, each of which contains a single month of met field data. GEOS-Chem users outside Harvard may obtain these data files via anonymous FTP:

 cd pub/geos-chem/data/GEOS_0.5x0.666_CH.d/GEOS_5/2008
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/2008
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/2008
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_0.5x0.666_CH.d/GEOS_5/2004
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/2004
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/2004
 mget *.tar.gz

However, to simplify the FTP process you might want to use a 3rd party FTP software program with a GUI interface, such as Mozilla FireFTP.

At present, the throughput rate is approximately 28 days of model data per day. Therefore it will still be a couple of months before the entire GEOS-5 dataset has been reprocessed.

GEOS-Chem Meeting: April 7-10, 2009

The 4th Annual GEOS-Chem Scientific & Users' Meeting is rapidly approaching. Daniel has provided revised draft of the meeting agenda (click here for PDF format). Please direct your questions about the agenda to Daniel Jacob (

On the last day of the GEOS–Chem meeting there will be a model clinic. During the model clinic, we would like to focus on topics that are the most relevant to GEOS-Chem users. Therefore, we invite you to suggest potential discussion topics/questions to the GEOS–Chem support team ( ahead of time. That will help us to prepare accordingly.

Registration for the meeting is now closed.

--Bob Y. 14:00, 18 March 2009 (EDT)