GEOS-Chem Newsletter October 2009

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Dear GEOS-Chem Users,

Here is your October 2009 GEOS-Chem Newsletter! Happy autumn to one and all!

Thank you for your continued support of GEOS-Chem!

Bob Yantosca, Philippe Le Sager, and Claire Carouge

GEOS-Chem Model Management and Logistics

GEOS-Chem Steering Committee

The next Steering Committee Telecon shall take place on Tuesday, December 8, 2009 at 10:30 EST.

NOTE: After some discussion, the Steering Committee has decided to keep its telecons private. If you have any concerns to bring up for discussion, please contact your Working Group Chairperson.

Minutes from previous telecons are available HERE.

GEOS-Chem Working Groups

We ask that each GEOS-Chem user join the Working Group that is most relevant to his/her area of research. For more information about a particular working group, please contact the appropriate Working Group Chairperson(s).

The Working Group Wiki pages are constantly being updated! Please be sure to check them often for the latest news:

Offering co-authorship to GEOS-Chem code developers

Daniel Jacob wrote:

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. To facilitate this good practice, we list recent developments for which a co-authorship offer is encouraged if these developments contributed substantively to the work. The list is updated by the GEOS–Chem Steering Committee every three months. As new developments meld into the code mainstream they are moved to the GEOS–Chem Code Development History list and can be adequately credited by citation. We encourage regular reading of GEOS–Chem publications to keep up with recent model applications and developments.
Questions about co-authorships or GEOS-Chem literature should be directed to the relevant Working Group Chair or Model Scientist.

GEOS-Chem Update

Release of GEOS-Chem v8-02-03

GEOS-Chem v8-02-03 "beta" is now officially released! This version contains the following important updates:

For instructions on how to download the code and required input files, please see Appendix 8.2 of the GEOS-Chem User's Manual.

Technical notes:

  1. KPP/Rosenbrock is now the default chemical solver option. You can choose to revert to the previous SMVGEAR chemical solver in by simply setting a switch in the input.geos file at runtime. Philippe Le Sager has created a wiki page for the KPP chemical solver, which goes into more detail about how to compile and run GEOS-Chem with the various KPP options.
    1. The KPP implementation in GEOS-Chem v8-02-03 is not compatible with the older IFORT 9.1 compiler. We do not anticipate fixing this anytime soon, as IFORT 9.1 is an obsolete compiler version.
  2. The code structure of GEOS-Chem v-02-03 has been partitioned into subdirectories. This was done in order to allow GEOS-Chem to incorporate various several 3rd-party code packages (e.g. KPP, TOMAS, APM, etc.) cleanly.
  3. As a result of the code restructuring, the Makefiles have been completely rewritten. You must now have the GNU Make utility installed on your system. (Most of you probably already have GNU Make as part of your default Linux/Ubuntu/Fedora etc. installation.) Please follow this link for more information.
  4. Compiler notes:
    1. GEOS-Chem no longer supports the SGI/MIPS compiler. This was the compiler used on the ancient SGI/Origin and SGI/Power Challenge platforms.
    2. GEOS-Chem no longer supports the HP/COMPAQ compiler. This was the compiler used on the now obsolete HP-UX systems.
    3. The new GEOS-Chem Makefile Structure has not yet been tested with the IBM XLF compiler. If anyone is willing to be a beta-tester for this compiler, please contact the GEOS-Chem support team.
    4. At present, the issue with the IFORT 11 compiler has not yet been resolved.


A new version (v3-07) of the TESTRUN package for compiling and running GEOS-Chem simulations is now available for download!

TESTRUN v3-07 has been modified to be compatible with the new code structure of GEOS-Chem v8-02-03. It is also compatible with older versions of GEOS-Chem.

One new feature of TESTRUN v3-07 is the ability to compile GEOS-Chem directly without having to submit to a queue. For some configurations this makes compilation much easier!

GAMAP v2-13

A new version of GAMAP is now available for download! This version (v2-13) standardizes several fixes as well as user-supplied functionality. Here is a summary of some of the new features:

  • User-defined colortable in MYCT
  • New routine to retrieve an air number density for GEOS-Chem
  • New routine to recursively convert binary punch (bpch) files into netCDF format
  • New updates to TVMAP, TVPLOT, and CTM_PLOTDIFF
  • Many other minor fixes

The GAMAP website and user manual have been updated. Please see:

GAMAP manual (and link to download)
GAMAP on the GEOS-Chem wiki
GAMAP search engine

In the Pipeline

The following updates are slated to be incorporated into GEOS-Chem very soon:

Item Author(s) Status
Linoz stratospheric O3 chemistry Dylan Jones' group @ U. Toronto Code has been incorporated into GEOS-Chem v8-02-04; undergoing final shakedown testing @ U. Toronto.
Volcanic emissions of SO2 from Aerocom Jenny Fisher (Harvard) Will be included in GEOS-Chem v8-02-04.
Global Terrestrial Mercury Model Nicole Downey (UT Austin) Implementation and beta-testing is being done by Claire Carouge. Slated for inclusion into GEOS-Chem v8-02-04.
TOMAS aerosol Microphysics Peter Adams' group @ CMU Beta testing for GEOS-5 is ongiong. Waiting on final code submission from CMU group.
Soil NOx emissions updates Neil Moore (formerly Dalhousie U.)
Rynda Hudman (U. Berkeley)
Implementation and beta-testing is currently being done.
MEGAN updates for isoprene Mike Barkley (U. Edinburgh) Beta-testing is being done by Eloise Marais (Harvard U.)
Minor chemical rxn rate updates Jingqiu Mao (Harvard) Will be included in GEOS-Chem v8-02-04.
EPA/NEI 2005 emissions Philippe Le Sager (Harvard) Beta-testing is ongoing.

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. The GEOS-Chem support team held a telecon with NASA in early October. Several of the implementation details were discussed. Based on our feedback, NASA will create an interface code that will link the GEOS-Chem column code with the GEOS-5 CTM. More information to follow...

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. 12:24, 26 October 2009 (EDT)