GEOS-Chem Newsletter November 2009
Dear GEOS-Chem Users,
Here is your November 2009 GEOS-Chem Newsletter. Happy Thanksgiving to one and all!
Thank you for your continued support of GEOS-Chem,
Bob Yantosca, Philippe Le Sager, and Claire Carouge
- 1 Au Revoir to Philippe
- 2 GEOS-Chem Model Management and Logistics
- 3 GEOS-Chem Update
- 4 Column Code Update
Au Revoir to Philippe
Philippe Le Sager wrote:
- Dear GC community
- I am starting a new job as a computational scientist at KNMI, the Dutch meteorological institute next month. I will not be part of the GC support team anymore.... so I really wanted to thank y'all.
- In the past three years, I have learned and passed around an incredible amount of atmospheric science and programming knowledge. It has been a great pleasure interacting with so many of you, taking part to so many projects. It is going to feel empty for a while! I will sure bring back with me many friendships and lots of memorable stories (thanks in part to very successful GC meetings).
- Thanks for bringing challenges, sharing tips and knowledge. Thanks for the fun.
- I wish you all the best in your career and beyond,
Please join us in congratulating Philippe on his new position. He will be sorely missed by the GEOS-Chem community.
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:
- Adjoint Model and Data Assimilation Working Group
- Aerosols Working Group
- Carbon Gases and Organics Working Group
- Emissions Working Group
- Oxidants and Chemistry Working Group
- Regional Air Quality Working Group
Status of GEOS-Chem v8-02-04
- LINOZ stratospheric ozone chemistry (Dylan Jones group @ U. Toronto)
- EPA/NEI 2005 emissions (A. van Donkelaar, P. Le Sager)
- Updated inventory of volcanic SO2 emissions from AeroCom (J. Fisher)
- Update to near-IR photolysis of HNO4 (J. Mao)
- Updated MEGAN biogenic emissions (M. Barkley)
- Updates and fixes for sea salt aerosols (L. Jaeglé, B. Alexander)
- Parallel make capability (R. Yantosca)
as well as several minor fixes.
Currently, the GEOS-Chem support team is implementing and validating the new MEGAN biogenic emissions. After this is completed, GEOS-Chem v8-02-04 will be ready for benchmark testing. Because v8-02-04 contains updates that will have an impact on the full-chemistry simulation this necessitates that we must perform 1-year benchmark simulations to try to assess the impact of the individual changes. We anticipate that benchmark testing will commence shortly after Thanksgiving.
Philippe Le Sager (email@example.com) wrote:
- I have made the modifications in the current code to deal with NEI2005, based on the preliminary work of Aaron. I had to rewrite the PBL mixing of the NOx/SOx/NH3 emissions, since these emissions are given distributed into 5 model levels. I had to create several masks for correct overlaps, since the inventory covers both Mexico and Canada.
- I made a one month run and simply run the benchmark comparison with the last version of the code. The main difference is in CO (note that the reference v8-02-03 uses Rynda correction to EPA99 for CO and NOx). Here are the emissions totals that change:
ANTHROPOGENIC Tracer nei05 v8-02-03 nei05 - v8-02-03 ===================================================== NOx 1.957 1.927 0.029 Tg N CO 31.460 28.455 3.005 Tg ALK4 1.392 1.966 -0.573 Tg C ACET 0.054 0.065 -0.012 Tg C MEK 0.045 0.047 -0.002 Tg C PRPE 0.591 0.667 -0.076 Tg C C3H8 1.720 1.853 -0.133 Tg C C2H6 1.054 1.142 -0.087 Tg C SO2 4.280 4.323 -0.043 Tg S SO4 0.090 0.096 -0.006 Tg S BIOFUELS Tracer nei05 v8-02-03 nei05 - v8-02-03 ===================================================== NOx 0.188 0.186 0.002 Tg N CO 14.707 14.547 0.160 Tg ALK4 0.064 0.063 0.001 Tg C ACET 0.021 0.021 0.000 Tg C MEK 0.111 0.110 0.001 Tg C ALD2 0.055 0.054 0.001 Tg C PRPE 0.531 0.525 0.006 Tg C C3H8 0.078 0.077 0.001 Tg C CH2O 0.101 0.100 0.001 Tg C2H6 0.173 0.171 0.002 Tg C ACETONE SINKS Tracer nei05 v8-02-03 nei05 - v8-02-03 ===================================================== ACETol 0.902 0.913 -0.011 Tg C CO SOURCES Tracer nei05 v8-02-03 nei05 - v8-02-03 ===================================================== COanth 31.460 28.455 3.005 Tg CObf 14.707 14.547 0.160 Tg NOx SOURCES Tracer nei05 v8-02-03 nei05 - v8-02-03 ===================================================== NOx-an 1.957 1.927 0.029 Tg N NOx-bf 0.188 0.186 0.002 Tg N SO2 SOURCES Tracer nei05 v8-02-03 nei05 - v8-02-03 ===================================================== SO2-an 4.280 4.323 -0.043 Tg S SO4 SOURCES Tracer nei05 v8-02-03 nei05 - v8-02-03 ===================================================== SO4-an 0.090 0.096 -0.006 Tg S
- I put all the plots into pdf files here: ftp://ftp.as.harvard.edu/pub/exchange/phs/nei2005_benchmark
Dylan Jones (firstname.lastname@example.org) wrote:
- Testing [the Linoz code in GEOS-Chem v8-02-04] was more difficult that I thought. I began by trying to compare the output of v8-02-04 with our previous runs with v8-02-01. I accounted for the changes in the transport_mod.f and I tried to undo the changes in when the diagnostics are archived in v8-02-04, but I was still getting large differences between v8-02-04 and v8-02-01. I finally gave up on this since I may have made a mistake in reverting to the old way of doing the diagnostics in v8-02-04. In the end I took the new linoz code from v8-02-04 and used it in v8-02-01. I ran two GEOS-5 full chemistry simulations for 2007 and the output were consistent over the full year.
- I think that it is safe to release [Linoz in v8-02-04]. However, we should acknowledge that it was [only] tested in v8-02-01, since I was not able to assess the quality of the output in v8-02-04.
Parallel make capability
Also, the GEOS-Chem Support Team have made some additional changes to the GEOS-Chem Makefile Structure such that the executable can be built using more than one processor. Tests have shown that building the executable on 4 processors reduces the compile time from approximately 8 minutes to approximately 3 minutes. More information about this will be posted shortly!
In the Pipeline
The following updates are slated to be incorporated into GEOS-Chem after the GEOS-Chem v8-02-04 release.
|Updated Isoprene Chemistry||Fabien Poulot
P. Le Sager
|In beta testing. The GEOS-Chem KPP source code is currently being recompiled for the new isoprene mechanism. Slated for inclusion into GEOS-Chem v8-03-01.|
|ISORROPIA II||Havala Pye
|G-C support team is awaiting delivery of code. Probably will go into GEOS-Chem v8-03-01.|
|Global Terrestrial Mercury Model||Nicole Downey||Implementation and beta-testing is being done by Claire Carouge. Slated for inclusion into GEOS-Chem v8-03-01, along with the most-recent mercury chemistry mechanism.|
|TOMAS aerosol Microphysics||Win T.
|Final shakedown testing & benchmarking is now being done @ CMU. Slated for inclusion into GEOS-Chem v8-03-01.|
|Soil NOx emissions updates||Neil Moore (formerly Dalhousie U.)
Rynda Hudman (U. Berkeley)
|Implementation and beta-testing is currently being done.|
|Updated aerosol optics||Randall Martin, Colette Heald||Updates have been received by the G-C support team. Slated for inclusion into GEOS-Chem v8-03-01.|
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 has created the beginnings of the GEOS-Chem emissions component (i.e. the code that will be used to read emissions data from disk, apply scale factors, and send it to the column chemistry component).
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. 14:54, 24 November 2009 (EST)