GEOS-Chem Newsletter March 2011

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Dear GEOS-Chem Users,

Here is your March 2011 GEOS-Chem newsletter!

Bob Yantosca and Matthew Cooper

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!

NOTE: Registration is now closed.

We have posted a revised meeting agenda (as of 23 Mar 2011). For those of you who are attending, please check the agenda to see in which session your talk or poster is scheduled. (NOTE: agenda is subject to change.)

Other highlights of the meeting include:

  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 midday Wednesday May 4) 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
    1. The GEOS-Chem steering committee meeting
    2. A GEOS-Chem model clinic. This will be led by the GEOS-Chem Support Team to initiate new users as well as answer questions from experienced users.
    3. A GEOS-Chem Adjoint model clinic. This will be led by the GEOS-Chem Adjoint and Data Assimilation Working Group 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!

GEOS-Chem Steering Committee

The previous GEOS-Chem Steering Committee meeting took place on January 25th, 2011. We invite you to read the minutes from the Jan 25th GCSC meeting.

The next GEOS-Chem Steering Committee meeting will take place at Harvard University on May 5, 2011 at 12:30 PM, as part of the 5th International GEOS-Chem Meeting. Elections for Steering Committee positions will be held at this time. Please see the GEOS-Chem Steering Committee web page for a list of the Steering Committee members and when their terms expire.

Also, please join us in welcoming Hong Liao and Loretta Mickley to the GEOS-Chem Steering Committee! They are the co-chairs of the new Chemistry-Climate Working Group.

Climate-Chemistry Working Group

We are proud to announce the creation of the Chemistry-Climate Working Group!

Hong Liao wrote:

Dear GEOS-Chem users,
This email is to let you know that the GEOS-Chem steering committee has decided to form a new "Chemistry-Climate" working group for studying chemistry-climate interactions using the GEOS-Chem model. This new working group will be co-chaired by Hong Liao and Loretta Mickley .
We have set up a Chemistry-Climate Working Group wiki page. What we would like from all of you who are interested in Chemistry-Climate:
  1. Join the Chemistry-Climate mailing list by sending an email (Subject & body can be blank) to this address:
    You can unsubscribe by sending an email to this address:
  2. Consider adding information to the wiki Chemistry-Climate Working Group, to let us know your projects on Chemistry-Climate.
Thank you for your attention and see you all at the upcoming GEOS-Chem meeting,
-- Loretta Mickley & Hong Liao

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

GEOS-Chem Support Team

The GEOS-Chem Support Team presently consists of Bob Yantosca and Matthew Cooper. Please send all of your GEOS-Chem-related requests to them via the email address.

Michael Long, a new Harvard hire, will join the GEOS-Chem Support Team in June 2011. Michael has recently finished his PhD at the University of Virginia and has extensive expertise with atmospheric models and the KPP chemical solver. Michael will attend the 5th International GEOS-Chem Meeting in May, so you will have the opportunity to meet him then.

Daniel Jacob wrote:

I'm looking to hire a scientific programmer at the Bachelor's/Master's level to support GEOS-Chem. Below is the ad that I'm putting out. If you know anyone who might be interested please have them contact me.
Scientific Programmer/School of Engineering and Applied Sciences/ Harvard University. Maintains and develops the GEOS-Chem global model of atmospheric transport and chemistry, conducts simulations, prepares graphical output, supports users, writes documentation. Bachelor's or Master's degree in atmospheric science, physics, applied mathematics, mechanical engineering, or chemical engineering. Experience in scientific programming. Knowledge of FORTRAN and UNIX.

New and updated wiki pages

For your convenience, we have added the following new wiki pages:

  1. Chemistry-Climate Working Group
  2. Subscribing to the GEOS-Chem email lists

and have updated these pages:

  1. APM aerosol microphysics
  2. Carbonaceous aerosols
  3. Date and time computations with GAMAP
  4. Downloading GEOS-Chem source code and data
  5. GAMAP tips and tricks
  6. GEOS-Chem v9-01-01
  7. GEOS-Chem v9-01-02
  8. GEOS-Chem versions under development
  9. Hg and POPs Working Group
  10. Implementation of RETRO Anthropogenic Emissions
  11. List of MERRA met fields
  12. Secondary organic aerosols
  13. Soil NOx emissions
  14. Wet deposition

We ask that you take a moment and peruse these pages. You may find the exact answer to your question!

GEOS-Chem model development update

GEOS-Chem v9-01-01

GEOS-Chem v9-01-01 was released in February 2011. This version is the first version of GEOS-Chem that is compatible with GMAO's MERRA met fields. It also contained many updates and fixes.

A few issues with v9-01-01 were discovered by GEOS-Chem users shortly after the v9-01-01 release. We have since issued post-release patches to fix these issues:

  1. Typos in vdiff_mod.f90
  2. Now use updated CDIAC CO2 emissions for offline CO2 simulation
  3. Double counting of biofuel emissions over Asia

You can use the gitk viewer to tell if you have these patches in your downloaded version of GEOS-Chem v9-01-01. Type gitk at the Unix prompt and look in the upper left-hand window. You should see the yellow tags:

  1. v9-01-01-Patch-VDIFF
  2. v9-01-01-Patch-CO2
  3. v9-01-01-Patch-biofuel

If you are missing any of these patches, you can download them into your code with a Git Pull operation. Type at the Unix prompt:

git pull git://  master

This will update your local copy of GEOS-Chem with the above-mentioned patches.

GEOS-Chem v9-01-02

The current development version is GEOS-Chem v9-01-02. This version will contain the following major updates:

  1. APM aerosol microphysics (F. Yu & G. Luo, SUNY Albany)
  2. GFED3 biomass burning emissions (P. Kasibhatla)
  3. RETRO anthropogenic VOC's (W. Reinhart, D. Millet)
  4. Updated soil NOx emissions algorithm

as well as the following minor improvements or fixes:

  1. Updated dry deposition velocities for aerosols over ice and snow (J. Fisher)
  2. Imposed seasonality on NH3 emissions from David Streets 2000 inventory (J. Fisher)
  3. Corrected inconsistencies in aerosol optical depth diagnostics (S. Kim)
  4. Bug fix for GCAP leap-year problem
  5. Fixes for better compatibility with the PGI compiler
  6. Bug fix to prevent NaN's in mercury simulation diagnostics

At present, the APM microphysics package has been validated and tested in GEOS-Chem v9-01-02 and is working properly. We are currently doing final testing of the GFED3 biomass emissions code, and plan to implement the RETRO and soil NOx emissions packages shortly. We will also look into adding the new stratospheric chemistry (based on GMI/COMBO results) into v9-01-02.

GEOS-5 met fields

GEOS-5 data for 2010

The Harvard archive ( contains GEOS-5 met data through the end of July 2010. If you need GEOS-5 met data for August thru December 2010, you may download it from the Dalhousie archive (

News from GMAO

We received the following news from NASA/GMAO about the GEOS-5 operational met data product, which is what we use to drive GEOS-Chem. The following email describes changes that GMAO will make will be made to the GEOS-5 "raw" data product:

Gi-Kong Kim wrote:

Dear GEOS-5 data users,
The GMAO plans to make a major upgrade to its near real time (NRT) GEOS-5 data production system. Designated as GEOS-5.7.1, the new system includes many scientific improvements to the dynamics, physics, and the analysis. These improvements improve the quality of all GEOS-5 products. Additionally, as advertised some time ago, a few major engineering changes are also present in the new system, including;
  1. the horizontal spatial resolution is increased from 1/2° to 1/4°
  2. file format is changed from the current HDF-4 to netCDF-4/HDF-5;
  3. temporal frequency of 3-D products is changed from 6 hr to 3 hr
  4. temporal frequency of most 2-D products is changed from 3 hr to 1 hr
  5. new variables are added such as ocean and aerosols fields.
  6. The groupings of variables in the GEOS-5.7.1 file collections are considerably different from those of the current GEOS-5.2.0.
All the GEOS-5 variables you have been using are provided in GEOS-5.7.1. If you notice any discrepancy, please let us know.
A few major activities and their target dates required for this system upgrade are proposed as follows. These dates may change depending on your feedback. The system is currently running as a NRT parallel science run and is now being configured into its operational setting. Hence, depending on your requirements for sample data, the test data may be available earlier than the schedule below.
  1. March 29
    • GMAO posts on its home page the draft GEOS-5.7.1 file specification (FS) document for user review.
    • GES DISC starts the implementation of the operational subsetting function and necessary modifications to the data management subsystem at GES DISC.
  2. April 12, or earlier
    • We request that you email me your comments on the FS document, your requirements for test data for both SW and algorithm tests, and requirements for product subsetting. Please send one consolidated response per team.
  3. April 19
    • GMAO posts the final FS.
    • The GEOS-5.7.1 data generated from the NRT parallel test run will be made available. (Information for accessing the data will be provided when the parallel run is ready.)
  4. May 3
    • GMAO provides sample test data for user algorithm and SW tests.
  5. May 17
    • GES DISC/ESDIS conducts end-to-end operations readiness test. (Test includes subscription, subsetting, network, ..)
  6. May 24
    • GMAO starts the GEOS-5.7.1 NRT operations, i.e., starts sending the NRT products to users via GES DISC.
Note that we plan to keep the GEOS-5.2.0 running in parallel for at least 2 months, depending on your requirements.
Your comments on the schedule and of course on the products are very welcome. If you have any questions on the products or on the changes, please don't hesitate to ask. We will have documentation online as to the changes from GEOS-5.2.0 to GEOS-5.7.1 shortly.
With best regards,

To recap, GMAO will send out a new document describing the new GEOS-5 product (this is called the "File Specification") document. Bob Yantosca will review this document and inform the GEOS-Chem community if there are any significant changes.

MERRA reanalysis met fields


The GEOS-Chem Support Team has modified 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 regridded the entire MERRA data period (1979-2010) to 4° x 5° resolution). You may download these data from the Harvard archive (

After a planned storage upgrade we will have the capacity to also store the 2° x 2.5° MERRA data as well.

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
Bromine chemistry mechanism Justin Parella Substantially complete but undergoing further validation.
Updated stratospheric chemistry from GMI prod/loss rates Lee Murray Completed; Awaiting inclusion into v9-01-02
Capability to read data files in netCDF format Lee Murray Completed; Awaiting inclusion into v9-01-02
Add scavenging by snow Qiaoqiao Wang Slated for inclusion into GEOS-Chem v9-01-02 or v9-01-03
Updated aircraft emissions Lee Murray Awaiting handover from MIT; expected ETA late Feb or early Mar 2011

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.

Bob Yantosca has successfully columnized the updated wet deposition routines from v9-01-01 and is working on including them into the mainline GEOS-Chem code. This will allow the columnized wet deposition code to grow with GEOS-Chem, instead of being developed in a separate code repository.

Bob will be spending 50% of his time towards GEOS-Chem Column Code development and 50% towards GEOS-Chem support tasks.

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

  • We send information about new GEOS-Chem releases, bug fixes, and other notices of importance to the the GEOS-Chem "general" email list (
  • Each GEOS-Chem Working Group uses its own email list to exchange information between group members.

We invite you to join the Working Group that is most appropriate to your research, and to subscribe to the relevant email list. Consider joining more than one Working Group (and email list) if your research spans several topics.

For complete instructions on how to subscribe to (or unsubscribe from) the GEOS-Chem email lists, please see our Subscribing to the GEOS-Chem email lists wiki page.

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. 12:16, 28 March 2011 (EDT)