GEOS-Chem Newsletter March 2010

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Dear GEOS-Chem Users,

Here is your March 2010 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 March 9, 2010. Minutes of this meeting (and past meetings) are available HERE.

Next meeting

The next Steering Committee Telecon shall take place on Tuesday, June 29, 2010 at 10:30 EST. 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 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

Daniel Jacob wrote:

Dear GEOS-Chem user,

I ask for your attention on a few items pertaining to the GEOS-Chem website:

  1. New URL: GEOS-Chem has a new web site address and a new Wiki site address This is part of our effort to identify GEOS-Chem as an international community model. The old Harvard addresses will still work indefinitely. Next is to remove the Harvard logo from the web site and replace it with a GEOS-Chem logo.
  2. Publications: Please let the GEOS-Chem Support Team 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. Credits: Please pay attention to the credits page regarding co-authorships on your papers. While credits are voluntary and we try not to overburden users with them, they are good practice for recent developments as listed on the credits page and a way for you to recognize developers' efforts and give back to the GEOS-Chem community. Keeping track of credits through the publications page also allows the Steering Committee to determine when a development has earned enough credit and can meld into the code mainstream. Please see our blurb on good practices on top of the credits page.
  4. People and projects: Please take a minute to look at your entry in and let the GEOS-Chem Support Team 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.

GEOS-Chem wiki

The GEOS-Chem wiki may now be accessed with the URL This significantly shortens the URL paths to individual wiki pages.

New and improved pages

In the last month, several new pages have been added to the GEOS-Chem wiki. Many other existing wiki pages have also received a "face-lift" in order to make them easier to navigate. In particular:

  1. The Emissions Overview wiki page has been updated with links to the various emissions inventories in GEOS-Chem.
  2. The Anthropogenic Emissions wiki page has been reorganized. Inventories are categorized as "Global" or "Regional". The list of references has been updated and there are also links to other relevant wiki pages.
  3. A separate Intel Fortran Compiler wiki page has been created.
  4. New information has been added to the Biofuel Emissions wiki page.
  5. Wiki pages which document how to use the Git version control system have been added.
  6. The Secondary organic aerosols and Carbonaceous aerosols wiki pages have been updated with the most recent information.
  7. A new page has been added for the GEOS-Chem CO2 simulation.

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.

Wiki logistics

The best way to find information on the GEOS-Chem wiki is to type in your topic to the search box at the left of your browser window. The Main Page has links to several topics on the wiki but it does not link to every single page.

In general, it is better to create smaller wiki pages that are cross-referenced rather than large wiki pages with a lot of text. This ensures that individual pages can be more easily navigated and searched. Also, the MediaWiki system will display a warning message if you try to save a wiki page that contains more than 32 KB of text. If that happens, you can just simply break up your page into smaller pages.

All GEOS-Chem wiki posts can be read by anyone. However, to add or modify wiki pages, you will need to register for a wiki account. Simply click on the "Log In/Create Account" link at the top right of your browser window. The GEOS-Chem support team will confirm your account request (this is an anti-spamming measure).

Each wiki page also has a corresponding discussion page. This is designed as the place to post information (e.g. a long email exchange, user comments, etc.) that would be too cumbersome to post on the front page.

Lastly, we invite all GEOS-Chem users to read our post about wiki user culture.

GEOS-Chem update

GEOS-Chem v8-02-04

GEOS-Chem v8-02-04 was released on 24 Feb 2010. At the moment, this is the most up-to-date version of GEOS-Chem. We encourage all GEOS-Chem users to switch to v8-02-04 whenever possible.

Nomenclature change: v8-02-05 is now v8-03-01!

The version we have previously dubbed GEOS-Chem v8-02-05 "beta" will henceforth be known as GEOS-Chem v8-03-01 "public". The updates going into this version (e.g. new SOA tracers, Caltech isoprene scheme, TOMAS, migration from CVS to Git repository, etc.) require a more thorough explanation in the G-C user's manual than just a brief mention on the Addenda page.

Therefore, the GEOS-Chem Support Team has decided to make this release a "public" version and to rewrite the G-C user's manual accordingly. The version # will be changed from GEOS-Chem v8-02-05 to GEOS-Chem v8-03-01 (recall that the middle digits change for each public version). We will also make the appropriate references on the G-C wiki.

Status of GEOS-Chem v8-03-01

GEOS-Chem v8-03-01 is currently in development. This version will contain everything in GEOS-Chem v8-02-04, plus:

  1. Option to use Caltech isoprene chemistry (F. Paulot)
  2. ISORROPIA II (H. Pye, T. Nenes)
  3. Updated aerosol optical properties for FAST-J photolysis (R. Martin, C. Heald)
  4. Modifications to SOA formation (Aerosols Working Group)
  5. SOA formation from aromatics (D. Henze)
  6. Speciated biogenic emissions from MEGAN v2.1 now used in SOA code (H. O. T. Pye)
  7. Global 1 x 1.25 simulation capability (L. Lamsal)
  8. Modifications to / Creation of the GEOS-5 0.5 x 0.667 N. American and European Nested Grid simulation (A. van Donkelaar)
  9. TOMAS aerosol microphysics option (W. Trivitayanurak, D. Westervelt, J. Pierce)
  10. Extension of annual anthropogenic scale factors to 2006 (A. van Donkelaar)
  11. EMEP emissions extended to 2007 and Seasonality extended to SOx, CO, and NH3 (A. van Donkelaar)

As of this writing, the implementation of the Caltech isoprene chemistry scheme into GEOS-Chem is undergoing testing and validation. Once this has been completed, we will be able to start the benchmarking process.

Linking GEOS-Chem with CMAQ

Tao Zeng has created a code which links the GEOS-Chem chemistry mechanism to the CMAQ regional air quality model. This will be of use to those of you who are using GEOS-Chem boundary conditions as input to CMAQ.

For more information, please see our Linking GEOS-Chem to CMAQ wiki page. This page contains a brief description of the code and instructions for downloading.

Version control with Git

Starting with GEOS-Chem v8-03-01, the GEOS-Chem source code repository will use the Git source code management system instead of CVS. We are doing this for the following reasons:

  • Git is free, open-source software which can be installed on any Unix system.
  • Git avoids some of the limitations of CVS (which is by now 20-year-old software).
  • Git is in general much simpler to use than CVS. It provides useful gui tools:
    1. gitk: GUI tool for examining version history
    2. git gui: GUI tool for merging, branching, committing.
  • With Git, GEOS-Chem developers will be able to:
    1. Download the most current GEOS-Chem source code online. (This will obviate the need for having to download the *.tar.gz files.)
    2. Develop and test their source code additions to GEOS-Chem in their own local repository, and
    3. Submit their mature source code updates back to the GEOS-Chem Support Team for inclusion in the standard mainline code

Please see our Version control with Git wiki page for more information. We have also posted some links to tutorials and videos which explain how Git works.

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; Currently slated for inclusion into v8-03-02.
Updated CO2 simulation Ray Nassar Code delivery to G-C support team is imminent. Slated for inclusion into v8-03-02.
Updated mercury simulation with improved soil model (GTMM) Chris Holmes
Nicole Smith-Downey
Code has been delivered to G-C support team; Slated for inclusion into v8-03-02 or later.

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.

Bob and Arlindo have set up a software testbed suite at Harvard which emulates the NASA/GSFC machine environment. This will be used to ensure that the GEOS-Chem column code routines are correctly "wired up" in the proper order. Once this testing has been done, the GEOS-Chem column code routines should function properly within the GEOS-5 GCM. The testing is ongoing.

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. 13:03, 29 March 2010 (EDT)