Difference between revisions of "GEOS-Chem Newsletter June 2009"

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|Members of the [[Aerosols_overview:_projects_and_developments|Aerosols Working Group]]
|Members of the [[Aerosols Working Group]]

Latest revision as of 18:12, 8 December 2016

Dear GEOS-Chem Users,

Here is the June 2009 GEOS-Chem Newsletter. Happy Summer Solstice!

Bob Yantosca, Philippe Le Sager, and Claire Carouge

GEOS-Chem Update

GEOS-Chem v8-02-02

GEOS-Chem v8-02-02 "beta" has now been released. This version includes:

  • new boundary layer mixing scheme (developed by Jintai Lin)
  • updated Bond emission inventories for BC & OC (prepared by Eric Leibensperger).

This version may be downloaded from:

 ftp ftp.as.harvard.edu
 cd pub/geos-chem/beta_releases
 get GEOS-Chem.v8-02-02-beta.stdrun.tar.gz

NOTE: We are currently working on enabling access to our CVS repository to outside users so that you will be able to obtain the GEOS-Chem source code without having to download a large TAR file. Stay tuned...

GEOS-Chem Steering Committee

The GEOS-Chem Steering Committee held a telecon on June 11, 2009. Click HERE to view the meeting minutes.

Since last April's GEOS-Chem meeting, a number of GEOS-Chem model development priorities that were identified by the Steering Committee and Working Groups have now been implemented into GEOS-Chem:

Item Author(s) Completion Date
Improved BL mixing scheme Jintai Lin Now included in GEOS-Chem v8-02-02; released 08 Jun 2009
BC/OC aerosol emissions from Bond inventory Eric Leibensperger Now included in GEOS-Chem v8-02-02; released 08 Jun 2009
Chemical updates Mat Evans
Fabien Paulot
Jingqiu Mao
Paul Palmer
Updated chemical mechanism and photolysis files
globchem.dat, jv_spec.dat, ratj.d
(see documentation)
Now included in GEOS-Chem v8-02-01; released 26 May 2009
Common model adjoint and documentation Daven Henze
Kumaresh Singh
Monika Kopacz
Code merging session took place June 6-9, 2009 @ Virginia Tech
  • Merged 3 branches of adjoint
  • Forward model now based on v8-02-01 (w/ GEOS-5)
  • Input files cleaned up and standardized
  • New makefiles; code separated into subdirectories
  • New CVS repository @ U. Colorado for code access
  • Some minor cleanup may still be needed (as of June 2009)

At the June 10, 2009 telecon, the GEOS-Chem Steering Committee identified the following remaining model development items as top priorities (here listed in order):

# Development priority Point person(s) Status
1. GEOS-5 ozone columns GC support team Validation is ongoing
2 KPP implementation GC support team
Virginia Tech
In beta testing
3. TOMAS implementation Win Trivitayanurak
GC Support Team
Telecon to discuss implementation
scheduled for June 16th
4. Linoz Dylan Jones and
U. Toronto group
In beta testing @ U. Toronto
5. Updated methane simulation Christopher Pickett-Heaps
Kevin Wecht
Debugging and code cleanup is ongoing
6. Updated CO2 Simulation Ray Nassar  
7. Updated MEGAN emission from terpenes Dylan Millet  
8. COADS ship emissions Chulkyu Lee  
9. Include updated aerosol optics Colette Heald
Randall Martin
and Aerosols Working Group
Randall Martin will create "master list" of optical properties
10. Include aromatic SOA Daven Henze  
11. Archive OH fields from benchmark
for use in off-line simulations
GC support team  

GEOS-Chem Working Groups

A couple of the GEOS-Chem Working Groups have been renamed:

  • "Carbon Gases" and "Organics" has been merged into "Carbon Gases & Organics" (co-chairs Dylan Jones, Dylan Millet)
  • "Regional Modeling" is now "Regional Air Quality" (co-chairs Rokjin Park, Yuxuan Wang)

We ask that each GEOS-Chem user join the Working Group that is most relevant to his/her area of research. The Working Groups are meant to foster communication and information sharing between GEOS-Chem users, as well as to identify priorities for model development to the GEOS-Chem Steering Committee.

For more information about a particular working group, please contact the appropriate Working Group Chairperson(s).

Subscribing to the GEOS-Chem email lists

There are now several GEOS-Chem email lists:

Email list address Intended audience
geos-chem@seas.harvard.edu All GEOS-Chem users and developers
NOTE: This is the email list to which information about
new model versions, bugs & fixes, etc. will be sent
geos-chem-adjoint@seas.harvard.edu Members of the Adjoint Model and Data Assimilation Working Group
geos-chem-aerosols@seas.harvard.edu Members of the Aerosols Working Group
geos-chem-carbon@seas.harvard.edu Members of the Carbon Gases and Organics Working Group
geos-chem-emissions@seas.harvard.edu Members of the Emissions Working Group
geos-chem-oxidants@seas.harvard.edu Members of the Oxidants and Chemistry Working Group
geos-chem-regional@seas.harvard.edu Members of the Regional Air Quality Working Group

To subscribe to any of these lists, please visit the page: https://lists.seas.harvard.edu/mailman/listinfo and then click on the name of the list to which you wish to subscribe. You will be taken to a page where you can specify your email address and a password and then click SUBMIT. You will then receive a confirmation email from the system. Follow the directions in the confirmation email and then you will be added to the list.

PLEASE NOTE: If you wish to send an email to any of the above GEOS-Chem mailing lists, then please be sure to send your email from the same address with which you subscribed to the list. Otherwise your email may bounce back to you. The GEOS-Chem mailing lists are set up to reject emails from non-list members. This is done in order to prevent spam.

Being a member of the GEOS-Chem community

We would like to encourage all new GEOS-Chem users to take a moment to read our GEOS-Chem welcome letter for new users. (Also, veteran users may want to look at this too for a "refresher"...)

We expect that each GEOS-Chem user will possess at least some familiarity with the following:

  • The Fortran programming language (F77 OK, F90 preferred)
  • IDL (preferred), or other graphics software (e.g. Splus, Matlab)
  • The Unix environment (i.e. commands, file paths, etc.)
  • Unix scripts (not strictly required but is very helpful to know!)

The GEOS-Chem support team cannot provide you with general instruction in programming languages or answer general programming questions. We would like to invite you to view to view the list of tutorials and other relevant resources that are listed on the GEOS-Chem web page at GEOS-Chem Resources Page.

We invite you to read our document on User Resources, Code Development Guidelines, and Debugging Tips.

Each GEOS-Chem user is also expected to adhere to our list of best practices.

We also would like to invite all GEOS-Chem users outside Harvard who have run the 1-month benchmark simulation on their own systems to update the table of GEOS-Chem supported platforms and compilers with your timing information.

And lastly, be sure to read this page about the Features of the GEOS-Chem public wiki, which will describe how you can obtain automatic updates via the RSS feed.

Adjoint Model Update

A successful meeting was held at Virginia Tech to develop a standard version of the GC adjoint merging the capabilities developed by individual groups: participants were Kumaresh Singh, Adrian Sandu, Monika Kopacz, Changshub Shim, and Daven Henze. The result was an integrated adjoint code based on v8-02-01 with GEOS-5 and including updates from the different groups, improved file formats and input files, etc.

GEOS-5 met field reprocessing


As described in the April-May 2009 newsletter, we are reprocessing the entire archive of GEOS-5 met field data. As of June 15, 2009 the following fields have been completed:

  • 2003: December only
  • 2004: entire year
  • 2005: entire year
  • 2006: entire year
  • 2007: thru 2007/06/29
  • 2008: entire year

for each of the following geographic domains:

  • China nested 0.5 x 0.667
  • Global 2 x 2.5
  • Global 4 x 5

Therefore, the only "missing" data as of June 15, 2009 is the remainder of 2007.


(1) As of June 2009, Harvard's filesystem has been modified. The directories on the FTP site

 ftp ftp.as.harvard.edu
 cd pub/geos-chem/data

are now a straight mirror of the internal firewall-protected directories. Any files that are added to the internal directories will be automatically mirrored to the FTP site during the nightly system reboots. This means that the *.tar.gz files are no longer stored on the FTP site.

(2) As of June 16, 2009, the following data is now available for download:

 Nested China
 ftp ftp.as.harvard.edu
 cd pub/geos-chem/data/GEOS_0.5x0.666_CH.d/GEOS_5/YYYY/MM/

 2 x 2.5 Global (except 2006-2007)
 ftp ftp.as.harvard.edu
 cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/YYYY/MM/

 2 x 2.5 Global (2006-2007 only)
 ftp ftp.as.harvard.edu
 cd pub/geos-chem/data/bmy_temp/GEOS_2x2.5.d/GEOS_5/YYYY/MM/
 4 x 5 Global (except 2006-2007)
 ftp ftp.as.harvard.edu
 cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/YYYY/MM/

 4 x 5 Global (2006-2007 only)
 ftp ftp.as.harvard.edu
 cd pub/geos-chem/data/bmy_temp/GEOS_2x2.5.d/GEOS_5/YYYY/MM/

where YYYY/MM/ are the year and month that you wish to download.

As you may have noticed, the 2006 and 2007 reprocessed GEOS-5 met data is placed in a "temporary" directory bmy_temp. These met data have also not been placed in a "temporary" folder in the internal firewall-protected directories (so as to avoid confusion w/ the existing met data).

As soon as all of the met fields for 2006-2007 have been reprocessed then we will move them from the "temporary" directory structure into the normal directory structure. At that point, they will also be mirrored into the "normal" FTP directory structure.

(3) IMPORTANT! At present the OTD/LIS lightning flash redistribution has not been done for years 2006-2007. Therefore, if you run a full-chemistry simulation with 2006 or 2007 reprocessed met fields, the lightning NOx emissions will be incorrect. We will recompute the OTD/LIS lightning flash redistribution at a later date.

ESMF and Column Code Update

We have created a GEOS-Chem column code wiki page. At present the page is still under construction, but content will be added here on a regular basis. Please check back often for the latest information!

The GEOS-Chem column chemistry code has achieved a milestone: the SMVGEAR chemistry solver, as well as its various supporting routines, have been columnized and appear to work properly! Also, the "driver" loop over longitude and latitude has now been parallelized with OpenMP. This will allow us to do longer testing runs (i.e. 1 month instead of 1 day, etc.)

Several of the chemistry routines for aerosol tracers, including sea salt, dust, and carbon/SOA tracers, have been columnized. Work is still progressing to columnize the sulfate tracer chemistry routines.

The challenging part of this work is that several of the "legacy" code routines need to be rewritten in order to separate any input/output from the places where we do computation. Also, several references to some GEOS-Chem modules need to be removed in certain places in the code in order to make the column code more cleanly separatable from the rest of GEOS-Chem. The work is ongoing.

Vacation Schedule

Please note: Claire Carouge will be on vacation from June 17th thru July 5th. Bob and Philippe will be available during this time period; however, we will be a little short-handed during this time so please plan accordingly.

--Bob Y. 14:32, 15 June 2009 (EDT)