GEOS-Chem Newsletter November 2009

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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

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:

GEOS-Chem Update

Status of GEOS-Chem v8-02-04


GEOS-Chem v8-02-04 "beta" will be the next GEOS-Chem release. This version will have the following updates over the previous version v8-02-03:

  • 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.

MEGAN update

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.

EPA/NEI2005 update

Philippe Le Sager ( 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:
    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

    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

    Tracer     nei05   v8-02-03   nei05 - v8-02-03
   ACETol      0.902      0.913       -0.011     Tg C

    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

    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

    Tracer     nei05   v8-02-03   nei05 - v8-02-03
   SO2-an      4.280      4.323       -0.043     Tg S

    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:

LINOZ Update

Dylan Jones ( 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.

Item Author(s) Status
Updated Isoprene Chemistry Fabien Poulot
P. Le Sager
Jingqiu Mao
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.
Thanos Nenes
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.
Dan Westervelt
Peter Adams
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)