GEOS-Chem Newsletter December 2010

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Dear GEOS-Chem Users,

Just in time for Christmas...the December 2010 GEOS-Chem Newsletter!

Warmest wishes for a Happy Holiday Season and a Wonderful New Year 2011!

Bob Yantosca and Claire Carouge

What's new in the GEOS-Chem community

The 5th International GEOS-Chem Meeting

Harvard University will host the 5th International GEOS-Chem Meeting from May 2-5, 2011. Please mark your calendars!

Please see the official meeting web page,, for:

  1. Registration instructions
  2. Information about hotels near Harvard University
  3. Contact information

Be sure to check back here for the latest information!

We invite you to read the preliminary meeting agenda (subject to change). To help with your travel plans, please note that:

  1. An icebreaker social for young scientists will be organized on the evening of Sunday May 1. This will be an opportunity for graduate students and postdocs to meet in a relaxed atmosphere prior to the meeting.
  2. The first two-and-a-half days of the meeting (Monday May 2 at 8:30 am to Wednesday May 4 at 12 pm) will be devoted to general scientific sessions and should be of broad interest to the atmospheric composition research community.
  3. The final day of the meeting (Wednesday afternoon to Thursday May 5 at 12:30 pm) will be devoted to working groups and GEOS-Chem community business. This should be of most interest to GEOS-Chem users.
  4. Thursday afternoon events will include the GEOS-Chem steering committee meeting (open to all) and a GEOS-Chem model clinic. The model clinic will be led by the GEOS-Chem Support Team to initiate new users as well as answer questions from experienced users.

The scientific sessions will include a mix of oral and poster presentations. All sessions will be plenary. Due to the nature of the meeting, priority for oral presentations will have to be given to GEOS-Chem users. Poster presentations are open to all and will be scheduled to receive a lot of attention.

We look forward to seeing you in May!

New and updated wiki pages

For your convenience, we have updated the following wiki pages. We ask that you take a moment and peruse these pages. You may find the exact answer to your question!

  1. Implementation of RETRO Anthropogenic Emissions (New page!)
  2. Notes regarding vertical grids
  3. MERRA met fields
  4. Machine issues and portability
  5. Secondary organic aerosols
  6. Common GEOS-Chem error messages
  7. Setting up GEOS-Chem nested grid simulations
  8. Dynamic tropopause
  9. Mass Flux (ND24/25/26)
  10. GEOS-Chem supported platforms and compilers

GEOS-Chem Support Team

Claire Carouge continues to provide support for GEOS-Chem from her location in Canberra. We ask that you continue to send your requests for GEOS-Chem support to the email address. This will forward your request to both Claire and Bob.

Winter recess schedule

Bob Yantosca and Claire Carouge will be unavailable during Harvard's winter recess (Dec 23, 2010 thru Jan 2, 2011). Therefore, you should not expect a quick turnaround for support requests during the Christmas-New Year's week.

Bob will also be unavailable on Jan 6, 2011 (personal day) and Jan 13, 2011 (jury duty). Please plan accordingly.

GEOS-Chem Steering Committee

The next GEOS-Chem Steering Committee telecon date is Tuesday, January 25th, 2011 @ 10:30 ET (15:30 GMT). Contact your Working Group chairpersons if you have any items that you would address to the Steering Committee.

We invite you to read the minutes from the September 21st Steering Committee Meeting.

GEOS-Chem Working Groups

We invite all GEOS-Chem users (especially new users) to join a Working Group and sign up for the relevant email list. Working Groups are designed to foster discussion between GEOS-Chem users who are doing research in similar areas.

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 model development update

GEOS-Chem v9-01-01

GEOS-Chem v9-01-01 will be the next version to be released. It will contain the following updates:

  1. Compatibility with MERRA met fields (GEOS-Chem Support Team)
  2. Modified algorithms for convective updraft scavenging and wet deposition (H. Amos, B. Corbitt, Q. Wang et al)
  3. Bug fix: Restore capability to start GEOS-Chem from times other than 0 GMT (GEOS-Chem Support Team)
  4. Minor fixes for timeseries diagnostics
  5. Bug fixes for ship emissions (Geert Vinken)
  6. Updated SO2 emissions from volcanoes (Jenny Fisher)
  7. Improved automatic code documentation with ProTeX. (GEOS-Chem Support Team)
  8. Other minor bug fixes

We are currently resolving a parallelization/segmentation fault issue with the non-local PBL scheme. This should be fixed imminently. Once this issue has been resolved, we will start the benchmarking process.

We plan to run the 1-month benchmarks with both GEOS-5 and MERRA met fields. We will also run the 1-year benchmarks with GEOS-5 and MERRA in order to validate GEOS-Chem against observations. We hope to have the benchmarking process completed shortly after the holidays.

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. For the latest information about MERRA, please the following wiki pages:

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

Data availability

The GEOS-Chem Support Team has started to download and regrid the MERRA data for GEOS-Chem. At present we have downloaded the following time periods.

  • 2008: full year 4° x 5°
  • 1982-2005: full year 4° x 5°
  • 1981: December 4° x 5°

We plan to obtain the full 30-year MERRA archive (1979-2010). At present, we are only regridding the data to 4° x 5° due to disk storage limitations at Harvard. After a planned storage upgrade we will have the capacity to also store the 2° x 2.5° MERRA data as well.

At the present pace, we estimate that to complete regridding of the entire 30-year MERRA data archive to 4° x 5° by early January 2011.

MERRA data subsetting

Several of you have asked us about how to obtain the "raw" 0.5° x 0.666° MERRA met field data for your own research projects. NASA's GES-DISC department has created a user interface from which you can request "subsetted" data files (i.e. data files that have been trimmed down to a specific geographic region and/or contain a reduced number of data fields). You can then download the subsetted files via FTP file transfer to your own disk space.

For more information, please see the NASA GES-DISC user interface for requesting subsetted MERRA data.

In the pipeline

The following updates will be added into GEOS-Chem following the v9-01-01 release.

Item Author(s) Status
Add scavenging by snow Qiaoqiao Wang Slated for inclusion into GEOS-Chem v9-01-02.
Bromine chemistry mechanism Justin Parella Substantially complete; Slated for inclusion into GEOS-Chem v9-01-02.
Updated stratospheric chemistry from GMI prod/loss rates Lee Murray Completed; Awaiting inclusion into v9-01-02
Updated vertical emission profiles for lightning NOx Lee Murray Completed; Awaiting inclusion into v9-01-02
Updated aircraft emissions Lee Murray Slated for inclusion into v9-01-02
Implementation of RETRO Anthropogenic Emissions Wes Reinhart Slated for inclusion into v9-01-02 or v9-01-03
APM aerosol microphysics Fangqun Yu Code has been given to the G-C Support Team; Slated for inclusion into v9-01-03

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

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.

GEOS-Chem reference


Please take a moment to review your group's entry on the GEOS-Chem People and Projects web page. Kindly inform the GEOS-Chem Support Team if anyone has recently joined or left your research group.

Be sure to send all new journal article submissions to the GEOS-Chem support team at We will post your papers on the GEOS-Chem Publications page.

We invite you to consult our Guidelines for Offering Co-authorship and GEOS-Chem Code Development History web pages if you are unsure how to give credit to GEOS-Chem developers.


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.

Please see the Recent Changes wiki page to see which wiki pages have been updated.

Finally, if you have not already done so, consider signing up for automatic wiki notification. You will be updated whenever someone modifies the GEOS-Chem'll never miss a discussion!

Subscribing to the GEOS-Chem email lists

We use several GEOS-Chem email lists to share information among the user community:

Email list address Intended audience To subscribe, send an email to: All GEOS-Chem users and developers
NOTE: This is the email list to which information about
new model versions, bugs & fixes, etc. will be sent Adjoint Model and Data Assimilation Working Group Aerosols Working Group Carbon Gases and Organics Working Group Hg and POPs Working Group Oxidants and Chemistry Working Group Regional Air Quality Working Group Sources and Sinks Working Group

To subscribe to any of the GEOS-Chem lists, send an email to:

To unsubscribe from any of the GEOS-Chem lists, send an email to:

where LISTNAME is the name of the intended email list (e.g. geos-chem, geos-chem-adjoint etc.). You can leave the subject and body of the email blank if you wish. You will receive a confirmation email from the system.

NOTE: To prevent spam, the GEOS-Chem email lists will reject mail from unrecognized addresses. When sending an email message to a list, make sure that you send your message from the same email address under which you subscribed to that list. Otherwise your message may not get delivered.

Search engines

We have set up several GEOS-Chem search engines which will let you search for information in the GEOS-Chem website, wiki, and manual pages.

You can also search the GEOS-Chem wiki by means of the search box in the left column. It is often more efficient to search for a topic rather than to follow links down from the main page.

--Bob Y. 16:25, 20 December 2010 (EST)