GEOS-Chem Newsletter Summer 2011
Dear GEOS-Chem Users,
A lot has happened in the past few months! Therefore, we have decided to bundle all of the news into a Summer 2011 edition.
Bob Yantosca, Michael Long, Melissa Payer, and Matthew Cooper
What's new in the GEOS-Chem community
5th International GEOS-Chem Meeting recap
Harvard University hosted the 5th International GEOS-Chem Meeting (aka IGC5)] from May 2-5, 2011. To view presentations, posters, and working group summaries from IGC5, please see our web page meeting.geos-chem.org.
GEOS-Chem Steering Committee
GCSC elections were held during IGC5 in May 2011. The following members were elected to new terms:
|Daniel Jacob||Model Scientist (re-elected)||2015|
|Dylan Jones||Co-Chair, GEOS-Chem Adjoint and Data Assimilation Working Group and "Transport Czar"||2015|
|Hong Liao||Co-Chair, Chemistry-Climate Working Group||2015|
|Jingqiu Mao||Co-Chair, Oxidants and Chemistry Working Group||2015|
|Loretta Mickley||Co-Chair, Chemistry-Climate Working Group||2013|
|Ray Nassar||Co-chair, Carbon Gases and Organics Working Group||2015|
|Jeffrey Pierce||Co-chair, Aerosols Working Group||2015|
|Noelle Selin||Co-chair, Hg and POPs Working Group||2015|
|Jun Wang||Co-chair, Nested Model Working Group||2015|
The GCSC met in person on Thursday, May 5, 2011 during the IGC5 meeting. Major outcomes of this GCSC meeting were:
- Adoption of a a new benchmarking protocol for evaluating updates made to GEOS-Chem;
- Revision of the guidelines for offering credit to GEOS-Chem developers;
- Addition of a narrative description of GEOS-Chem that GEOS-Chem users can include in journal articles
The GCSC met again on Tuesday, August 2, 2011 via telecon. Please feel free to read the meeting minutes at your convenience.
The next GCSC telecon shall take place on Wednesday, November 9, 2011 at 10:30 AM ET (15:30 GMT). Please mark your calendars! If you have any items for the GCSC, then please bring them to the attention of your Working Group Chairpersons.
Nested Model Working Group
The Regional Air Quality Working group has now been renamed to the Nested Model Working Group. This name change reflects the important role that this working group has in the continued development of the GEOS-Chem nested grid simulations.
GEOS-Chem Support Team
We are happy to announce that Michael Long and Melissa Payer have joined the GEOS-Chem Support Team (GCST) as of June 2011. Please join us in welcoming them to the GEOS-Chem community!
Here are some short bios for Michael & Melissa:
Michael S. Long
- Title: Postdoctoral Fellow
- PhD (2010) U. Virginia Environmental Science
- M.S. (2004) UNC-Wilmington Marine Science
- B.S. (1999) NC State Univ. - Meteorology
- B.S. (1999) NC State Univ. - Environmental Science
- Michael’s research has focused on resolving the physics and chemistry associated with the air-sea interface, marine aerosol production, and multiphase chemical processing. His Master’s thesis investigated the speciation of bioavailable N in the air, stream and surface water, and precipitation in SE North Carolina. His dissertation focused on the production of nascent, unreacted marine aerosol, and assessing their physico-chemical processing in the atmosphere using a fully-implicit multiphase (gas/aerosol/cloud) chemical module coupled to the NCAR Community Atmosphere Model. His work at Harvard will include the development of a grid-independent version of GEOS-Chem for use in the NASA GEOS Data Assimilation System (DAS).
- Title: Scientific Programmer
- Melissa Payer joined the Geos-Chem Support Team as a scientific programmer on June 13, 2011. Melissa received a Master’s degree in Atmospheric Science from SUNY Albany last December and also holds a Bachelor of Science degree in Meteorology from Plymouth State University in Plymouth, NH. Prior to joining our team, Melissa worked as a Chemistry Tutor at Anna Maria College.
We have set up the email@example.com email, which forwards to all GCST members (Bob Yantosca, Matthew Cooper, Michael Long, and Melissa Payer). We ask that you send all G-C support requests and questions to this email address. This will make sure that all of us on the GCST receive your email (so that if one of us cannot respond, someone else will).
GEOS-Chem model development update
Re-release of v9-01-01
GEOS-Chem v9-01-01 was re-released on 07 Jun 2011. The re-release fixed several issues that had been noted at IGC5, including:
- Double counting of biofuel emissions over Asia
- Updated annual and monthly CO2 emissions from CDIAC
- Typos in vdiff_mod.f90
- Negative tracer caused by DO_MERRA_CONVECTION
- Omitted code in Hg simulation
- Bug fixes for drydep (ND44) and wetdep (ND17,ND18,ND37,ND38,ND39) diagnostic archival
- Bug fix for time-in-tropopause (ND54) diagnostic
- Only apply wetdep error trap when using MERRA met fields
- Apply washout to the proper fraction of the grid box
- Better representation of aqueous SO2 chemistry
We also performed 1-year benchmark simulations with v9-01-01. For more information, please see out GEOS-Chem v9-01-01 benchmark history wiki page.
New benchmarking protocol
GEOS-Chem Benchmarking Protocol
adopted at the 5th International GEOS-Chem Meeting (May 2011)
Any change to the GEOS–Chem source code will require a dedicated 1-month "full-chemistry" benchmark and a version update code a,b,c... (such as v9–01–02a). These final letter codes are for internal use only and do not represent a version release. The benchmark results will be posted publicly with an email sent to the GEOS–Chem Steering Committee.
The developer will assess the benchmark results by filling out a form (created by Colette Heald and adapted to a wiki page) for all to see. If the developer has any concerns about the benchmark results they will contact the GEOS-Chem Support Team, the relevant GEOS–Chem Working Group Chairs, or Model Scientist Daniel Jacob. GEOS–Chem Steering Committee members can also comment on the benchmark results if they desire.
Once the developer is satisfied, GEOS–Chem Model Scientist Daniel Jacob will quickly review the results and approve the new internal version.
1-year benchmarks for these internal version updates will be conducted only if justifiably requested by the developer or by GEOS–Chem Steering Committee members.
Each new version release (such as v9–01–02) will be subject to a 1-year benchmark to be inspected by the GEOS–Chem Steering Committee before approval (as was done for v9–01–01). Changes will be bundled so that we will have new versions released only every 4 months or so — this has been our rhythm in recent years.
For more information about the standard 1-month and 1-year benchmark simulations, please see our GEOS-Chem Benchmarking web page.
Development of GEOS-Chem v9-01-02 had proceeded significantly prior to IGC5. Many important developments (such as APM, RETRO, GFED3) were added into the source code. However, in light of the new benchmarking protocols, we started the v9-01-02 development process from scratch. We checked out a clean copy of the v9-01-01 “Re-Release” code and used that as our code base.
We have created a GEOS-Chem v9-01-02 benchmark history page on the wiki. On this page you will find a Benchmark Assessment Form for each 1-month benchmark that we have completed.
Please see the list of features that are being added to GEOS-Chem v9-01-02.
Other Important Updates
In addition to the updates listed here, the FAA/AEDT aircraft emissions update (submitted by Steven Barrett et al from MIT) is technically ready to be added into the standard code. However, the FAA has exercised some reservations about making its emission data public. FAA has requested that all manuscripts that reference their emissions be submitted to them for internal review. For the time being, we have decided to postpone adding the FAA/AEDT emissions into GEOS-Chem until further advisement from Steven Barrett.
Barron Henderson, Mat Evans and Jingqiu Mao have approved a list of changes to the standard GEOS-Chem chemistry mechanism based on the new JPL reaction rates. Eloise Marais has submitted the source code and input file modifications to the GCST for inclusion into the standard code. This is currently slated for inclusion into GEOS-Chem v9-01-03.
We are also looking into some as-yet unresolved issues in GEOS-Chem:
- Appparent optimization or parallelization error in ISORROPIA II
- Apparent bug in the LINOZ stratospheric chemistry algorithm
- Inconsistencies when partitioning tracers into species
- Updating the standard chemistry mechanism w/ rxns from JPL 10-6
- Updated acetone chemistry (ocean source & sink)
- Retirement of obsolete GEIA biogenic emissions (necessary for new acetone chemistry)
- OVOC dry deposition
- SOA simulation with semi-volatile POA
- POPs simulation
- Updates to Dicarbonyls simulation
- Tropopsheric bromine chemistry mechanism
GEOS-Chem will form the core of a fully-coupled system interfaced directly into NASA's GEOS GCM. In order for this to happen, the GEOS-Chem standard model will become compliant with the Earth System Model Framework (ESMF). This will allow us to take advantage of Message Passing Interface (MPI) parallelization via ESMF, which has been a long-term goal of the GEOS-Chem development community. MPI parallelization will facilitate GEOS-Chem simulations at extremely fine horizontal resolution, running on 100’s or 1000’s of CPUs.
It is a priority of our implementation strategy to complete this project without disabling or significantly disrupting ongoing research utilizing the stand-alone GEOS-Chem. We believe that this is possible; but it won't be seamless. In anticipation of merging ESMF compatibility into the standard GEOS-Chem model, we will soon need to add several source-code modifications (aimed at cleaning up legacy code and making specific portions of the code FORTRAN 90/95 compliant) into our main Git repository. These source-code updates will likely affect code development norms, and will have to be reflected in any changes or developments submitted by the community.
Our efforts to develop the Grid-Independent GEOS-Chem will be assisted by:
- Removing legacy code from the current GEOS-Chem. In many cases, legacy code prevents the implementation of MPI parallelization.
- Encouraging GEOS-Chem developers to avoid using legacy coding constructs (i.e. don’t use COMMON blocks, EQUIVALENCE, BLOCK DATA, or other obsolete statements).
- Encouraging GEOS-Chem developers to submit updates via Git. This makes it easier to ingest source code updates into the repository. Otherwise, the merge must be done manually, which takes longer and is prone to error.
- Encouraging GEOS-Chem developers to adhere to the GEOS-Chem Style Guide.
Flexible chemistry mechanism
We plan on improving the chemistry mechanism input in GEOS-Chem so that a user can select an arbitrary set of species and reactions to be solved for. This will remove some of the obsolete legacy code from GEOS-Chem. We are currently in the planning stages.
Met field update
GEOS-5.7.2 data product
In Summer 2011, NASA/GMAO plans to make a major upgrade to its near real time (NRT) GEOS-5 data production system. Designated as GEOS-5.7.2, the new system includes many scientific improvements to the dynamics, physics, and the analysis. These improvements improve the quality of all GEOS-5 products. Additionally, a few major engineering changes are also present in the new system, including:
- the horizontal spatial resolution is increased to 1/4° lat x 5/16° lon
- file format is changed from the current HDF-4 to netCDF-4/HDF-5
- temporal frequency of 3-D products is changed from 6 hr to 3 hr
- temporal frequency of most 2-D products is changed from 3 hr to 1 hr
- new variables are added such as ocean and aerosols fields
- The groupings of variables in the GEOS-5.7.2 file collections are considerably different from those of the current GEOS-5.2.0
For more information, please follow these links:
- GEOS-5.7.2 file specification document, Version 1.2 (04 Aug 2011)
- GEOS-5.7.2 upgrade page
- GEOS-5.7.2 page on the GEOS-Chem wiki
- List of GEOS-5.7.2 met fields used for GEOS-Chem
- Definitions of individual fields in the GEOS-5.7.2 data
GEOS-5.2.0 data product
The current GEOS-5 data product, aka GEOS-5.2.0, (at 0.5° x 0.666° resolution) will be produced concurrently with GEOS-5.7.2 for approximately two months. After this time, the GEOS-5.2.0 data stream will be turned off and only GEOS-5.7.2 data shall be produced going forward.
Please note: Presently, the Harvard data server (ftp.as.harvard.edu) contains GEOS-5 met data thru July 31, 2010 regridded to the following GEOS-Chem resolutions:
- 4° x 5°
- 2° x 2.5°
- 0.5° x 0.666° nested China
- 0.5° x 0.666° nested North America
You may download data for August 1, 2010 and onwards from the Dalhousie data server (rain.ucis.dal.ca). In addition, the Dalhousie server contains met data for the 0.5° x 0.666° Europe nested grid.
MERRA data product
The MERRA data product is still being produced. We have currently processed the 30-year data archive (1979-2010) for GEOS-Chem to 4° x 5° resolution. Matthew Cooper (Dalhousie U.) is working on regridding MERRA to 2° x 2.5° resolution.
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.
We invite you to consult our Credits and References web page for you are unsure how to give credit to GEOS-Chem developers.
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 email lists to share information among the GEOS-Chem user community:
- We send information about new GEOS-Chem releases, bug fixes, and other notices of importance to the the GEOS-Chem "general" email list (firstname.lastname@example.org)
- Each GEOS-Chem Working Group uses its own email list to exchange information between group members.
We invite you to join the Working Group that is most appropriate to your research, and to subscribe to the relevant email list. Consider joining more than one Working Group (and email list) if your research spans several topics.
For complete instructions on how to subscribe to (or unsubscribe from) the GEOS-Chem email lists, please see our Subscribing to the GEOS-Chem email lists wiki page.
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. 15:02, 4 August 2011 (EDT)