GEOS-Chem Newsletter August 2010

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Dear GEOS-Chem Users,

Here is your August 2010 GEOS-Chem Newsletter...just in time for the dog days of summer!

Thank you for your continued support of GEOS-Chem. Stay cool!

Bob Yantosca and Claire Carouge

News from the GEOS-Chem Steering Committee

Previous meeting

The last GEOS-Chem Steering Committee telecon took place on June 29, 2010. We invite you to read the meeting documents listed below:

  1. June 29th Steering Committee Meeting Minutes
  2. The Status of GISS-Driven GEOS-Chem Simulations (by Lee Murray and Loretta Mickley)

Next meeting

The next GEOS-Chem Steering Committee meeting shall take place on Tuesday September 21 at 10:30 ET (14:30 GMT). Mark your calendars!

If you would like to bring any items to the attention of the Steering Committee before the next telecon, please contact your Working Group Chairperson(s).

GEOS-Chem developer credit

The GEOS-Chem Developer Credit and GEOS-Chem Code Development History web pages have been updated to reflect the latest information from the release of GEOS-Chem v8-03-01. Please visit these pages at your convenience.

Development of the GEOS–Chem model and its adjoint is a grass-roots activity by individual scientists pursuing their own research interests and sharing their work for the benefit of all. Good functioning of the GEOS–Chem community and faster sharing of new model features is promoted by users offering co-authorship for recent developments.

News from the GEOS-Chem Working Groups

Working Groups Overview

We encourage each GEOS-Chem user to join the GEOS-Chem Working Group that is most relevant to his/her area of research. Please see the following working group wiki pages for more information:

  1. Adjoint and Data Assimilation Working Group
  2. Aerosols Working Group
  3. Carbon Gases and Organics Working Group
  4. Emissions Working Group
  5. Hg and POPs Working Group
  6. Oxidants and Chemistry Working Group
  7. Regional Air Quality Working Group

Each GEOS-chem user should also post a short description of their project(s) on the relevant Working Group wiki page. Please remove any obsolete projects, add new ones, and review the work planned by other groups. This will allow the Working Group Chairpersons to be informed about the type of research that is being conducted by individual GEOS-Chem users while avoiding duplication of effort.

News from the GEOS-Chem Support Team

Opening for scientific programmer position

Daniel Jacob wrote:

Dear GEOS-Chem user -
Claire Carouge, valued member of the GEOS-Chem support team, is moving to Australia. She will fortunately be able to continue support GC operations for a while remotely but we need to replace her. So -
I am looking to hire a top-notch scientific programmer to support the GEOS-Chem model for the worldwide user community (50%) and operations at Harvard (50%). The ideal candidate for the job would be a PhD scientist with modeling experience and who would like to work in this support position for a while or long-term. Career growth opportunities are excellent.
Please bring this job opportunity to the attention of whoever you think may be interested. Interested candidates, please contact me.
Best wishes with your GEOS-Chem modeling!
Daniel J. Jacob
GEOS-Chem Model Scientist

Vacation schedule

The GEOS-Chem support team has announced the following vacation schedule:

  1. Claire Carouge will be away from August 11 thru August 27, 2010. In Claire's absence, Bob will be available for GEOS-Chem support tasks.
  2. Both Claire Carouge AND Bob Yantosca will be away on August 23, 2010. On this day there will be no GEOS-Chem support.

Please plan accordingly.

GEOS-Chem Communications


The GEOS-Chem People and Projects and GEOS-Chem Publications pages have recently been updated.

If you have new paper submissions, please send them to Bob and Claire at


We encourage all GEOS-Chem code developers and users to check the wiki frequently, as this is the place where the latest information about GEOS-Chem will be posted. The wiki is designed to be a two-way street of communication. Users should feel free to add content to the wiki pages that are most closely related to their research.

In particular, the GEOS-Chem Support Team has started a new effort to make sure that all 3rd-party code and data that is submitted into GEOS-Chem has a corresponding wiki page. This will ensure that all information can be shared transparently.

Email lists

All GEOS-Chem users should sign up for the GEOS-Chem Users email list, as well as one or more of the following Working Group email lists:

  1. GEOS-Chem Adjoint
  2. GEOS-Chem Aerosols
  3. GEOS-Chem Carbon Gases & Organics
  4. GEOS-Chem Emissions
  5. GEOS-Chem Hg & POPs
  6. GEOS-Chem Oxidants & Chemistry
  7. GEOS-Chem Regional Air Quality

GEOS-Chem development

GEOS-Chem v8-03-02

GEOS-Chem v8-03-02 is in the final valdiation phase before release. We hope to have this version released within the next couple of weeks.


GEOS-Chem v8-03-02 will contain the following updates:

  1. Terrestrial and deep ocean mercury (N. Smith-Downey, E. Sunderland)
  2. Updated CO2 simulation (R. Nassar)
  3. Liquid water content taken from GEOS-5 met fields (J. Fisher)

Bug fixes

GEOS-Chem v8-03-02 will contain the following bug fixes:

  1. Fix for EPA/NEI 2005 emissions
  2. Minor fixes in gamap_mod.f
  3. Bug fix for ND42 diagnostic and ISORROPIA II
  4. Minor fix for AOD calculation
  5. Avoid using unallocated arrays in edgar_mod.f
  6. All of the post-release patches from v8-03-01

GEOS-Chem v8-03-01


GEOS-Chem v8-03-01 was released on 04 May 2010. We recommend all GEOS-Chem users to migrate to v8-03-01 when feasible.

NOTE: At present the Caltech isoprene scheme should not be used, as there are still some unresolved issues to be worked out. We will let you know when it is ready.

Post-release patches

The following updates were not included into GEOS-Chem v8-03-01 at the time of its release. These were subsequently released as patches. All have been added to the GEOS-Chem Git repository as of 01 Jul 2010:

  1. Patch to enable call to SOA_PARA_INIT
  2. Patch to fix declaration of IONIC in ISORROPIA_II
  3. Patch to fix SCHEM data input
  4. Patch to fix bug in Aromatic SOA
  5. Patch to scale AOD diagnostic output to other wavelengths

Please make sure that you have these patches in your version of GEOS-Chem v8-03-01. An easy way to view the version history of your GEOS-Chem source code is to use the gitk viewer. This will allow you to view at a glance all of the log messages that describe each "commit" to the repository, as well as the individual lines of source code that were changed.

Also see our Using Git with GEOS-Chem wiki page for more information about how to download and manage the GEOS-Chem source code.

In the pipeline

The following updates will be added into GEOS-Chem following the v8-03-01 release.

Item Author(s) Status
APM aerosol microphysics Fangqun Yu APM code is ready. Work is currently being done at SUNY/Albany to interface APM into GEOS-Chem. Currently slated for inclusion after the release of GEOS-Chem v8-03-02.
Bromine chemistry mechanism Justin Parella We have begun the process to bring this into the standard code. Will be included after the release of GEOS-Chem v8-03-02.
Add scavenging by snow Qiaoqiao Wang Slated for inclusion after the release of GEOS-Chem v8-03-02.

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

MERRA reanalysis met fields

The GEOS-Chem Support Team has started the process of modifying GEOS-Chem for use with the MERRA met field product. MERRA is a 30-year reanalysis done with GMAO's GEOS-5.2.0 GCM.

While many aspects of MERRA are similar to the GEOS-5 data product, there are significant differences in certain data fields that require special handling before GEOS-Chem be driven by the MERRA product.

For the latest information, please the following wiki pages:

  1. MERRA
  2. List of MERRA met fields used by GEOS-Chem
  3. MERRA implementation details

Information may be subject to change. Please contact Bob Yantosca if you have any questions about the MERRA data.

GAMAP v2-14 release

Version 2-14 of the GAMAP visualization package is now available for download! This version now standardizes several minor fixes and improvements that have been submitted to us since the previous version (Oct 2009). The highlights of GAMAP v2-14 are:

  1. Updates to read in MERRA met fields
  2. Minor fixes in routine CTM_OVERLAY (i.e. plot data or points atop a world map)
  3. Minor fixes in routines that read timeseries data from disk
  4. User-submitted bug fixes for plotting routines

GAMAP v2-14 has now been migrated to Git. For downloading instructions, please see Chapter 2.2 of the GAMAP User's Guide.

Also please see the following references for more information about GAMAP:

  1. Online GAMAP manual
  2. GAMAP tips & tricks
  3. Using Git with GAMAP

Column code update

An ESMF Gridded Component has been created which calls the GEOS-Chem column chemistry routines. Some key bugs have now been fixed and work to finalize the interface has begun. Bob is currently testing to make sure that the column chemistry code running within the ESMF environment returns the same output as when driven in a GEOS-Chem test environment. The work is ongoing.

At present, column code development is on the back burner due to the pressing need to modify GEOS-Chem to be driven by the MERRA reanalysis product from GMAO.

--Bob Y. 16:45, 18 August 2010 (EDT)