GEOS-Chem Newsletter January-February 2011
Dear GEOS-Chem Users,
We apologize for getting the latest GEOS-Chem newsletter out so late...so we've combined Jan and Feb into one single issue.
Bob Yantosca and Claire Carouge
- 1 What's new in the GEOS-Chem community
- 2 GEOS-Chem model development update
- 2.1 GEOS-Chem v9-01-01
- 2.2 Important bugs fixed in v9-01-01
- 2.3 v9-01-01 post-release issues
- 2.4 MERRA reanalysis met fields
- 2.5 In the pipeline
- 2.6 Column code update
- 3 GEOS-Chem reference
What's new in the GEOS-Chem community
The 5th International GEOS-Chem Meeting
Harvard University will host the 5th International GEOS-Chem Meeting from May 2-5, 2011. Please mark your calendars!
NOTE: Registration is now closed.
Be sure to check back here for the latest information!
We invite you to read the preliminary meeting agenda (subject to change). To help with your travel plans, please note that:
- An icebreaker social for young scientists will be organized on the evening of Sunday May 1. This will be an opportunity for graduate students and postdocs to meet in a relaxed atmosphere prior to the meeting.
- The first two-and-a-half days of the meeting (Monday May 2 at 8:30 am to Wednesday May 4 at 12 pm) will be devoted to general scientific sessions and should be of broad interest to the atmospheric composition research community.
- The final day of the meeting (Wednesday afternoon to Thursday May 5 at 12:30 pm) will be devoted to working groups and GEOS-Chem community business. This should be of most interest to GEOS-Chem users.
- Thursday afternoon events will include
- The GEOS-Chem steering committee meeting
- A GEOS-Chem model clinic. This will be led by the GEOS-Chem Support Team to initiate new users as well as answer questions from experienced users.
- A GEOS-Chem Adjoint model clinic. This will be led by the GEOS-Chem Adjoint and Data Assimilation Working Group to initiate new users as well as answer questions from experienced users.
The scientific sessions will include a mix of oral and poster presentations. All sessions will be plenary. Due to the nature of the meeting, priority for oral presentations will have to be given to GEOS-Chem users. Poster presentations are open to all and will be scheduled to receive a lot of attention.
We look forward to seeing you in May!
Comings and goings on the GEOS-Chem Support Team
As you know, Claire Carouge has been providing GEOS-Chem support from her location in Canberra since October 2010. Claire will leave the GEOS-Chem Support Team by the end of February in order to start a new position at the University of New South Wales. (Claire will continue to work on special GEOS-Chem projects on an ad-hoc basis, so she'll still be in touch with us.) Please join us in thanking Claire for her dedication and service to the GEOS-Chem user community.
Matthew Cooper, who is working with Randall Martin at Dalhousie University, will join the GEOS-Chem Support Team part-time within the next couple of weeks. Matthew, who will work remotely from Halifax, will assist Bob Yantosca with various model development and support tasks.
Michael Long, a new Harvard hire, will join the GEOS-Chem Support Team in June 2011. Michael has recently finished his PhD at the University of Virginia and has extensive expertise with atmospheric models and the KPP chemical solver.
New and updated wiki pages
For your convenience, we have updated the following wiki pages. We ask that you take a moment and peruse these pages. You may find the exact answer to your question!
- Biofuel emissions
- Dicarbonyls simulation
- Downloading GEOS-Chem source code and data
- GEOS-Chem welcome letter for new users
- GEOS-Chem v9-01-01
- GEOS-Chem v9-01-02
- Secondary organic aerosols
GEOS-Chem Steering Committee
The next GEOS-Chem Steering Committee meeting will take place at Harvard University during the afternoon of May 5, 2011 at the 5th International GEOS-Chem Meeting. The exact meeting time is yet to be determined; we will keep you posted.
We invite you to read the minutes from the January 25th Steering Committee Meeting.
GEOS-Chem Working Groups
We invite all GEOS-Chem users (especially new users) to join a Working Group and sign up for the relevant email list. Working Groups are designed to foster discussion between GEOS-Chem users who are doing research in similar areas.
Each GEOS-Chem user should also post a short description of their project(s) on the relevant Working Group wiki page. Please remove any obsolete projects, add new ones, and review the work planned by other groups. This will allow the Working Group Chairpersons to be informed about the type of research that is being conducted by individual GEOS-Chem users while avoiding duplication of effort.
GEOS-Chem model development update
GEOS-Chem v9-01-01 was released on 10 Feb 2011. It contains the following major updates and improvements:
- Capability to run with GMAO MERRA met fields (R. Yantosca)
- Improvements to algorithms for convective updraft scavenging and wet deposition (H. Amos, B. Corbitt)
- Updated volcanic SO2 emissions from Aerocom (J. Fisher)
- Allow both washout and rainout to occur when new precipitation forms (Q. Wang)
- Updated lightning parameterization and fix for cloud-top-height algorithm (L. Murray)
GEOS-Chem v9-01-01 is a "public" release. We have totally rewritten the GEOS-Chem Online User's Guide in order to document the new features of v9-01-01. We have added several new sections of text which we feel improve the overall clarity and readability of the Guide. The User's Guide describes:
- How to download and install GEOS-Chem on your system
- How to compile the source code
- How to set up a GEOS-Chem simulation
- How to debug GEOS-Chem effectively
The User's Guide also contains several comprehensive appendices which contain information about the horizontal and vertical grids, met fields, diagnostics, and simulation options used by GEOS-Chem.
Important bugs fixed in v9-01-01
We discovered and fixed several bugs in GEOS-Chem v9-01-01 during the benchmarking process, as listed below. We recommend that all users upgrade to v9-01-01 as soon as possible.
EPA/NEI05 biofuel bug
We discovered that if you select the EPA/NEI05 anthropogenic emissions over North America, GEOS-Chem would use the older Yevich & Logan 2003 biofuel inventory (which does not contain emissions over the continental USA) instead of using biofuel emissions from EPA/NEI99. We corrected this situation in v9-01-01.
For a complete description, please see this post on our EPA/NEI05 wiki page.
Ship emission bugs
Geert Vinken discovered a couple of bugs that affected how GEOS-Chem processed emissions from ship exhaust. We have corrected these issues in v9-01-01. For more information, please see:
Cloud top height bug
Lee Murray discovered a bug that affected how GEOS-Chem was computing the cloud top heights, which in turn impacted the GEOS-Chem lightning NOx emissions algorithm:
When reading in the 3-D met fields from disk, GEOS-Chem determines the model level of the cloud top height (CTH). Since at least GEOS-3, this was accomplished by running a counter from the surface to the model top, increasing the counter by one when a grid box was discovered to contain a positive convective mass flux across its top interface. The counter value was applied as the cloud top level.
K = 1 DO L = 1, LLPAR IF ( CMFMC(I,J,L) > 0d0 ) THEN K = K + 1 ENDIF ENDDO CLDTOPS(I,J) = K
This algorithm neglects the possibility of levels containing no upward mass flux existing beneath a vertical region of convection, which is a common occurrence with the fine tropospheric resolution of GEOS-5 (and MERRA) that contains ~20 levels under 4km. GEOS-5 miscalculates the CTH 84% of the time, versus 1% for GEOS-4.
Long story short: The algorithm should have been counting from the top of the atmosphere downward, we have corrected this issue in GEOS-Chem v9-01-01.
For a full description of the problem, please see this document by Lee Murray. This document also describes the new vertical profiles that are used to place lightning at the proper altitude in GEOS-Chem.
We fixed several other minor issues in GEOS-Chem v9-01-01. For a complete list, please see this wiki post.
v9-01-01 post-release issues
The following bugs were discovered after the release of GEOS-Chem v9-01-01:
Double counting of biofuel emissions over Asia
Claire Carouge pointed out a minor bug in v9-01-01 that makes the GEOS-Chem double-count biofuel emissions over Asia. The fix is just a single line of code.
We have created a software patch containing this fix that you can apply to your existing v9-01-01 code. If you have already downloaded a copy of GEOS-Chem v9-01-01, then you can apply the patch with a Git Pull command:
cd Code.v9-01-01 # or whatever your code directory is named git pull git://git.as.harvard.edu/bmy/GEOS-Chem master
If you have not yet downloaded a copy of GEOS-Chem v9-01-01, then the patch will be applied during the initial download process. For more information, please see Chapter 2.2: Downloading the GEOS-Chem Source Code in the GEOS-Chem Online User's Guide.
Dicarbonyl simulation issues
If you are using the GEOS-Chem dicarbonyls simulation, then you should be aware of some minor bugs that were not caught prior to the v9-01-01 release:
- Out of bounds errors in routines SOAG_LIGGIO_DIFF and SOAM_LIGGIO_DIFF
- NL parameter in jv_mie.h needs to be increased.
These bugs will be fixed in the next version, GEOS-Chem v9-01-02.
Also, if you are using trying to run a dicarbonyls simulation with a version of GEOS-Chem prior to v9-01-01, you may encounter this out-of-bounds error in drydep_mod.f.
MERRA reanalysis met fields
The GEOS-Chem Support Team has started the process of modifying GEOS-Chem for use with the MERRA met field product. MERRA is a 30-year reanalysis done with GMAO's GEOS-5.2.0 GCM. For the latest information about MERRA, please the following wiki pages:
The GEOS-Chem Support Team has started to download and regrid the MERRA data for GEOS-Chem. At present we have downloaded the following time periods.
- 1979-2010: entire data period, regridded to 4° x 5° resolution
After a planned storage upgrade we will have the capacity to also store the 2° x 2.5° MERRA data as well.
MERRA data subsetting
Several of you have asked us about how to obtain the "raw" 0.5° x 0.666° MERRA met field data for your own research projects. NASA's GES-DISC department has created a user interface from which you can request "subsetted" data files (i.e. data files that have been trimmed down to a specific geographic region and/or contain a reduced number of data fields). You can then download the subsetted files via FTP file transfer to your own disk space.
For more information, please see the NASA GES-DISC user interface for requesting subsetted MERRA data.
In the pipeline
The following updates will be added into GEOS-Chem following the v9-01-01 release.
|APM aerosol microphysics||Fangqun Yu||APM source code has been merged into GEOS-Chem v9-01-02 and is undergoing final testing at SUNY Albany.|
|GFED3 biomass emissions||Prasad Kasibhatla||Completed and handed over to the G-C support team; slated for inclusion to GEOS-Chem v9-01-02.|
|New soil NOx emissions||Rynda Hudman
|Completed and handed over to the G-C support team; slated for inclusion to GEOS-Chem v9-01-02.|
|Updated stratospheric chemistry from GMI prod/loss rates||Lee Murray||Completed; Awaiting inclusion into v9-01-02|
|Capability to read data files in netCDF format||Lee Murray||Completed; Awaiting inclusion into v9-01-02|
|Add scavenging by snow||Qiaoqiao Wang||Slated for inclusion into GEOS-Chem v9-01-02.|
|Fixes to correct inconsistencies in aerosol diagnostics||Patrick Kim||Slated for inclusion in v9-01-02|
|Bromine chemistry mechanism||Justin Parella||Substantially complete but undergoing further validation.|
|Updated aircraft emissions||Lee Murray||Awaiting handover from MIT; expected ETA late Feb or early Mar 2011|
|Implementation of RETRO Anthropogenic Emissions||Wes Reinhart||Slated for inclusion into v9-01-02 or v9-01-03|
For a complete list of outstanding code updates, please see our GEOS-Chem model development priorities page.
Column code update
An ESMF Gridded Component has been created which calls the GEOS-Chem column chemistry routines. Some key bugs have now been fixed and work to finalize the interface has begun. 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 will be spending 50% of his time towards GEOS-Chem Column Code development and 50% towards GEOS-Chem support tasks.
Be sure to send all new journal article submissions to the GEOS-Chem support team at firstname.lastname@example.org. We will post your papers on the GEOS-Chem Publications page.
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.
Please see the Recent Changes wiki page to see which wiki pages have been updated.
Finally, if you have not already done so, consider signing up for automatic wiki notification. You will be updated whenever someone modifies the GEOS-Chem wiki...you'll never miss a discussion!
Subscribing to the GEOS-Chem email lists
We use several GEOS-Chem email lists to share information among the user community:
To subscribe to any of the GEOS-Chem lists, send an email to:
To unsubscribe from any of the GEOS-Chem lists, send an email to:
where LISTNAME is the name of the intended email list (e.g. geos-chem, geos-chem-adjoint etc.). You can leave the subject and body of the email blank if you wish. You will receive a confirmation email from the system.
NOTE: To prevent spam, the GEOS-Chem email lists will reject mail from unrecognized addresses. When sending an email message to a list, make sure that you send your message from the same email address under which you subscribed to that list. Otherwise your message may not get delivered.
We have set up several GEOS-Chem search engines which will let you search for information in the GEOS-Chem website, wiki, and manual pages.
You can also search the GEOS-Chem wiki by means of the search box in the left column. It is often more efficient to search for a topic rather than to follow links down from the main page.
--Bob Y. 16:25, 20 December 2010 (EST)