GEOS-Chem Newsletter June-July 2010

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Dear GEOS-Chem Users,

We have decided to combine the June and July 2010 Newsletters into one issue...just in time for the Independence Day holiday!

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 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 approximately three months from now (possible dates September 21, October 5, or October 12). We will announce the meeting date as soon as it is established.

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.

Communication within the GEOS-Chem community

Daniel Jacob wrote:

Dear GEOS-Chem user - on behalf of the Steering Committee, I bring to your attention the need to improve communication within the GEOS-Chem community. We need to know the activity of each user group so that we can benefit from each other and avoid duplication of effort. Having up-to-date information on GEOS-Chem use is also essential for impressing upon our sponsors the need for core support of GEOS-Chem. Please attend to the three points below. It won't take much of your time and it can make a world of difference.
  1. Communicate and update your GEOS-Chem activity through the appropriate Working Group(s). It is very important that you sign up with a Working Group and include your activity in the appropriate wiki page. If you have not done so yet please contact the chair of the WG(s) most appropriate for your activity. For more information see
  2. Please let Bob Yantosca know of your submitted papers using GEOS-Chem, and update the references when they get published. Keeping the GEOS-Chem Publications page ( complete and current is important for the GEOS-Chem community and for our sponsors. Support for GEOS-Chem maintenance, users' meetings, etc, hinges on the publication record. Please show your support for GEOS-Chem by doing this.
  3. People and projects - please take a minute to look at your entry in and let Bob Yantosca of any significant updates or if you are not on the map. Again, this is important both for the GEOS-Chem community and for our sponsors. When I pass the hat to get support for general GEOS-Chem maintenance or travel to the users' meeting my main selling point is the size (and publication activity) of the GEOS-Chem community.
Best wishes with your GEOS-Chem modeling!

GEOS-Chem Working Groups

New Working Group: Hg and POPs

Daniel Jacob wrote:

It was brought to my attention that Hg and POPs don't have a home in the current GEOS-Chem WG structure. Considering that these activities are expanding and in consultation with the relevant scientists, it is clear that we need such a WG and Lyatt Jaegle has kindly agreed to chair it.

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.

GEOS-Chem wiki

New pages

The following new wiki pages have been added:

  1. Bromine chemistry mechanism
  2. Hg and POPs Working Group

Wiki philosophy

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.

GEOS-Chem update

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.

Downloading and updating GEOS-Chem with Git

The easiest way to download the GEOS-Chem source code is to use the Git source code management (SCM) tool.

1. If you are downloading GEOS-Chem v8-03-01 for the very first time, then you can use the git clone command to generate a complete copy of the GEOS-Chem source code into a local directory named Code.v8-03-01:
   git clone git:// Code.v8-03-01

2. If you have already downloaded GEOS-Chem v8-03-01 with Git, but just want to get the latest patches, you may use the git pull command as follows:
   git pull git:// master
This will synchronize your local copy of GEOS-Chem with all of the patches that are contained in the remote repository.

3. You can also use Git to download the various full-chemistry run directories. Please see our Using Git with GEOS-Chem wiki page for more information.

In the pipeline

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

Item Author(s) Status
Updated mercury simulation with improved soil model (GTMM) Chris Holmes
Nicole Smith-Downey
Code is being optimized for OpenMP parallelization. Will debut in GEOS-Chem v8-03-02.
Updated CO2 simulation Ray Nassar Code has been added to GEOS-Chem v8-03-02. Final shakedown testing is taking place at U. Toronto.
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 into GEOS-Chem v8-03-02.
Use GEOS-5 liquid water content in SO2 chemistry Jenny Fisher Now included in 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 GEOS-Chem v8-03-02 or later.

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

GEOS-Chem Support Team

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.

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.

--Bob Y. 13:28, 1 July 2010 (EDT)