GEOS-Chem Newsletter February 2010

From Geos-chem
Jump to: navigation, search

Dear GEOS-Chem Users,

Here is your February 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 December 8, 2009. Minutes of this meeting (and past meetings) are available HERE.

Next meeting

The next Steering Committee Telecon shall take place on Tuesday, March 9, 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

Please take a moment to review the website. Please inform the GEOS-Chem Support Team of any new developments such as newly submitted or published papers, personnel changes in your user group, updated research blurbs, etc.

We have recently released GEOS-Chem v8-02-04-beta (see below for more info). Please see Apppendix 8 (Addenda) of the GEOS-Chem user's manual for the latest updates. As a reminder, we typically rewrite the GEOS-Chem user's manual for "public" releases only. For "beta" releases we'll post the relevant info on the Addenda page.

We'd also like to remind everyone to take advantage of the GEOS-Chem search engines. This is the fastest way to search the the GEOS-Chem web, wiki, and manual pages.

GEOS-Chem wiki

The GEOS-Chem wiki has been recently updated to make it much easier to navigate! The Main Page now contains a tabular layout which is able to display more links simultaneously (so that you don't have to scroll as far down the page to find what you want).

New and improved pages

The following new pages have been added to the GEOS-Chem wiki. (Some of these are still "under construction".)

  1. Advection scheme TPCORE
  2. Boundary layer mixing
  3. Carbonaceous aerosols
  4. Cloud convection
  5. Dicarbonyls simulation
  6. Dry deposition
  7. Emissions overview
  8. EPA/NEI05 North American emissions
  9. Global Terrestrial Mercury Model
  10. GMAO GEOS-4
  12. Linoz stratospheric ozone chemistry
  13. MEGAN biogenic emissions
  14. Mean OH lifetime in GEOS-Chem
  15. Mineral dust aerosols
  16. New isoprene scheme
  17. MODIS leaf area indices
  18. Scale factors for anthropogenic emissions
  19. Ship emissions
  20. Soil NOx emissions
  21. TOMAS aerosol microphysics
  22. Volcanic SO2 emissions from Aerocom
  23. Wet deposition

The following existing pages (as well as the various Working Group pages) have been updated to reflect the latest information about GEOS-Chem and related topics:

  1. Aerosol-only simulation
  2. Aerosol thermodynamical equilibrium
  3. Anthropogenic emissions
  4. Biomass burning emissions
  5. Biogenic emissions
  6. Bugs and fixes
  7. Downloading GEOS-Chem source code and data
  8. GEOS-Chem Adjoint
  9. GEOS-Chem v8-02-04
  10. GEOS-Chem v8-03-01
  11. GEOS-Chem versions under development
  12. Machine issues & portability
  13. NOx-Ox-HC-aerosol
  14. Sea salt aerosols
  15. Secondary organic aerosols
  16. Sulfate aerosols
  17. Tagged CO 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 is now released

The GEOS-Chem Support Team is happy to announce the release of GEOS-Chem v8-02-04-beta. This "beta" release includes the following updates:

  1. LINOZ stratospheric ozone chemistry (Dylan Jones group @ U. Toronto)
  2. Updated inventory of volcanic SO2 emissions from AeroCom (J. Fisher)
  3. EPA/NEI2005 regional emissions inventory for North America (P. Le Sager)
  4. Update to near-IR photolysis of HNO4 (J. Mao)
  5. MEGAN v2.1 biogenic emissions (M. Barkley)
  6. Updates and fixes for sea salt aerosols (L. Jaeglé, B. Alexander)

For a complete description of this version (including information about the 1-year benchmarks, resolved issues, unresolved issues, etc.) please see the GEOS-Chem v8-02-04 wiki page.

For instructions on how to download and run GEOS-Chem v8-02-04, please see the Addenda page of the GEOS-Chem online manual.

As always, please inform the GEOS-Chem support team of any bugs/issues that you may encounter with this version.


  1. The technical issues with KPP as described in the Jan 2010 Newsletter are now fixed in v8-02-04
  2. The 1-year benchmarks for v8-02-04 now contain plots which compare model output to aerosol observations.

In the pipeline

The following updates are currently being incorporated into the GEOS-Chem v8-03-01 release.

Item Author(s) Status
Global 1x1.25 model capability Lok Lamsal Now included in GEOS-Chem v8-03-01; awaiting benchmarking & release.
TOMAS aerosol microphysics Peter Adams
Win T.
Dan Westervelt
Jeffrey Pierce
TOMAS validation has been completed by the CMU group. Awaiting final release of GEOS-Chem v8-03-01.
Thanos Nenes
ISORROPIA is now included in GEOS-Chem v8-03-01; awaiting benchmarking and release.
Updated aerosol optics Randall Martin
Colette Heald
New jv_spec.dat files have been received by the G-C support team. These will ship w/ GEOS-Chem v8-03-01.
Modification to SOA formation [Aerosols Working Group]] Included in GEOS-Chem v8-03-01; awaiting benchmarking and release.
Updated Isoprene Chemistry Fabien Paulot
P. Le Sager
Jingqiu Mao
Claire Carouge wrote:
In fact, this scheme is still slightly evolving. Fabien Paulot developed it based on an old version and didn't have the latest updates of the chemistry and photolysis since v8-02-01. And Fabien had tried including several tracers but then judged that they were superfluous. Jingqiu and Fabien are now using a beta version of v8-03-01 and I'm waiting for their feedback before starting re-creating the files for KPP.
Also, we had to add SOA formation from aromatics developed by Daven Henze. This might change the globchem.dat (and also the KPP source code files) for the SOA simulation.
Updated mercury simulation with improved soil model (GTMM) Chris Holmes
Nicole Smith-Downey
Code has been delivered to G-C support team

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.

Also, Harvard and GSFC will collaborate on the construction of a common emissions component that can be shared by both the columnized versions the GEOS-Chem and GMI models. This will also allow easy interchange of GEOS-Chem emissions into GMI and vice-versa.

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. 13:18, 25 February 2010 (EST)