GEOS-Chem Newsletter May 2010

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Dear GEOS-Chem Users,

Here is your May 2010 Newsletter...just in time for the Memorial Day Weekend!

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 developer credit

The GEOS-Chem developer credit web page has been updated to include the latest information from GEOS-Chem v8-03-01.

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.

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 updates have been made to the GEOS-Chem wiki. In particular:

  1. Information about particle types has been added to the APM aerosol microphysics page
  2. The Aerosols Working Group was updated
  3. The Adjoint working group was updated
  4. The GEOS-Chem Makefile Structure page was updated with info about GEOS-Chem v8-03-01

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 public release


GEOS-Chem v8-03-01 was released on 04 May 2010. This is a public release containing the following updates:

  1. Option to use Caltech isoprene chemistry (F. Paulot)
  2. ISORROPIA II package for aerosol thermodynamical equilibrium (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)
  12. 1st GEOS-Chem version to use the Git version control system

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.

Bug fixes

The following issues were fixed in GEOS-Chem v8-03-01:

  1. Photolysis now computed at midpoint of chemistry timestep
  2. Bug fix in ISORROPIA for offline aerosol
  3. Minor bug fix in SRCSO2
  5. Bug in READ_ANTHRO_NH3
  6. Fix for initialization of EMEP ship emissions
  7. Bug fix in AVGPOLE
  8. Bug fix in EMITHIGH (carbon_mod.f)
  9. Fix to prevent numerical overflow in EXP function

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:

  1. Patch to fix bug in Aromatic SOA
  2. 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.


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

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.

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.

New aerosol optical depth diagnostic capability

Colette Heald and Randall Martin have added a new capability to the GEOS-Chem v8-03-01 diagnostics that will facilitate comparing GEOS-Chem data to satellite observations. This was released as a patch shortly after the release of v8-03-01.

The aerosol optical depth (AOD) output computed by the following diagnostics:

  1. ND21 (output to the ctm.bpch file)
  2. ND48 (timeseries station data)
  3. ND49 (instantaneous timeseries output)
  4. ND50 (24-hr timeseries output)
  5. ND51 (satellite timeseries)
  6. ND51b (satellite timeseries)

can now be scaled from 400nm (i.e. the FAST-J wavelength) to any arbitrary wavelength. A new file, jv_spec_aod.dat, has now been added to all of the GEOS-Chem v8-03-01 run directories. This file can be edited to contain the optical parameters for the aerosols at the target wavelength. Currently the default jv_spec_aod.dat is set up to scale AOD output from 400nm to 550nm.

For more information, please see the Section 5.4.4 of the GEOS-Chem v8-03-01 User's Guide. This contains information about how to edit jv_spec_aod.dat for other wavelengths.

It is important to note that this capability does not change the scientific results of GEOS-Chem, but is just a new option for the diagnostic output.

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 has been delivered to G-C support team; Slated for inclusion into v8-03-02.
Updated CO2 simulation Ray Nassar Code has been added to GEOS-Chem v8-03-02. Final shakedown testing is has begun.
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 v8-03-02.
Bromine chemistry mechanism Justin Parella Justin Parella's bromine chemistry mechanism is mature. We shall begin the process of including it into GEOS-Chem shortly.

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

GEOS-Chem Support Team

Vacation schedule

Bob Yantosca will be on vacation from June 7-25, 2010. Claire Carouge will be available during this time for GEOS-Chem and GAMAP support issues. Please plan accordingly.

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 Yantosca has improved the error traceback output of the GEOS-Chem column code (i.e. so that if the code dies with an error, it will print out which routine it died in, along with all of the calling routines). Bob has also simplified and cleaned up how the code writes log file output to disk.

An ESMF Gridded Component has been created which calls the GEOS-Chem column chemistry routines. 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. 11:33, 28 May 2010 (EDT)