GEOS-Chem Newsletter April 2010

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Dear GEOS-Chem Users,

Here is your April 2010 Newsletter. Better late than never!

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 wiki

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. A new GEOS-Chem performance page has been added.
  2. A page which describes Linking GEOS-Chem to CMAQ has been added.
  3. The GEOS-Chem supported platforms and compilers page has been "pruned"; new info was added and obsolete info removed.
  4. Extra information has been added to the CO2 simulation wiki page.

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.


We would like to update the timing information contained on the GEOS-Chem supported platforms and compilers page. If you have run the 1-month benchmark on your system, please consider updating this page with the following information:

  1. GEOS-Chem model version
  2. Platform/OS combination
  3. Compiler version
  4. Number of CPU's
  5. Wall time
  6. Contact person

We have removed the timing information from some of the more ancient versions of GEOS-Chem, in favor of more recent model releases.

GEOS-Chem update

GEOS-Chem v8-01-status

GEOS-Chem v8-03-01 shall be released shortly, pending completion of the benchmarking phase. This version will contain everything in GEOS-Chem v8-02-04, plus:

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

Aerosol Microphysics

GEOS-Chem v8-03-01 is the first standard version of GEOS-Chem to contain an aerosol microphysics option. The TOMAS aerosol microphysics code from Carnegie-Mellon can be invoked to perform simulations which track both aerosol size and number.

The CMU group will perform aerosol microphysics benchmark simulations in order to ensure the scientific integrity of the TOMAS code. These simulations, however, will not become part of the standard GEOS-Chem benchmark suite (i.e. the 1-yr and 1-month benchmarks). The GEOS-Chem Support Team is not responsible for TOMAS support (other than making sure the latest TOMAS code is added to the GEOS-Chem standard code).

All inquiries about TOMAS should be directed to Dan Westervelt at CMU.

We have plans to include a second aerosol microphysics package, the APM microphysics code from SUNY Albany into GEOS-Chem v8-03-02. Work on this will commence once v8-03-01 is released.

Version control with Git

GEOS-Chem v8-03-01 is now the first version of GEOS-Chem to use the Git source code management system instead of CVS. Git is a powerful, flexible, simple-to-use software package that contains useful GUI tools for managing source code revisions. It is open-source software, and is freely available.

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.

NOTE: Git will be the preferred method for downloading the GEOS-Chem source code and run directories. We will no longer produce the GEOS-Chem*.tar.gz files (which was the previous method of distributing the GEOS-Chem source code). Please install (or ask your IT dept to install) Git on your systems as soon as possible.

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 has been received by G-C support team is imminent. Will be installed in v8-03-02 immediately after v8-03-01 is released.
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 a later version.

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 created an ESMF Gridded Component to which the GEOS-Chem column code is attached. The Gridded Component can initialize, run, and finalize the GEOS-Chem column code without any software errors (such as segmentation faults, bus errors, etc). However, much work remains to ensure that the test simulation is producing proper results. The testing is ongoing.

--Bob Y. 15:24, 28 April 2010 (EDT)