GEOS-Chem v7-04-13

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BETA RELEASE November 2007

What's new in this version

Contains everything in v7-04-12, with the following additions:

  1. Offline H2/HD simulation (cf. Lyatt Jaegle et al)
  2. Bug fix in "smvgear.f" -- due to a design flaw, you could have a situation where you could have negative or zero tracer in a box even if the global & local error criteria were satisfied. If this condition is encountered, we now revert to the concentrations at the end of the previous internal timestep, and then reduce the internal timestep and try again until we get convergence.
  3. Bug fix -- replace GEMISNOX w/ module arrays to avoid common block errors in lightning & aircraft NOx emissions
  4. Bug fix -- cap variable tropopause at 200hPa for polar regions (90S-60S and 60N-90N)
  5. Lee Murray's local lightning redistribution of lightning flashes
  6. Minor bug fixes for GCAP and diagnostics

Also note that the Last year of GFED2 biomass emissions is still 2005 in this version. If you want to use the 2006 emissions you will have to edit the source code module "gfed2_biomass_mod.f".

1-Year Benchmarks


The 3 models compared (and their colors on the plots) were:

Color Quantity Plotted Met Type Lightning algorithm Mean OH [molec/cm3]
Red v7-04-12 Run1 GEOS-4 4x5 ancient 11.763
Green v7-04-12 Run2 GEOS-4 4x5 near-land w/ OTD-LIS regional scaling 12.816
Blue v7-04-13 GEOS-4 4x5 updated non-near-land w/ OTD-LIS local scaling 12.147
Black Observations      


  1. v7-04-13-Run uses the same input conditions and emissions as v7-04-12-Run2, except for the updated lightning emissions as described above.

We have archived the files for v7-04-13-geos4-Run into TARBALL (i.e. tar.gz) format to save disk space. To download the TARBALL containing all relevant files, type:

get gcgrid/geos-chem/1yr_benchmarks/v7-04-13/v7-04-13-geos4-Run0.tar.gz

And then to extract the data, type:

tar xvzf v7-04-13-geos4-Run0.tar.gz

The comparison plots will be in located in the output/pdf folder.

Previous issues now resolved in v7-04-13


NOTE: This code was removed from GEOS-Chem v10-01 and higher versions. Emissions in these versions are now regridded by HEMCO.

Mike Barkley wrote:

I think I've found an error in the regrid_1x1_mod.f subroutine (attached in the text file):
There is a do loop over longitude with the upper limit defined as the input latitude (J1) instead what should (?) be the output longitude (I2) - I've indicated where this in the program, Which is correct? We didn't notice this until we were running multi-processor 2x2.5 simulations on different servers.
The bug was:
 ! Non-polar latitudes
 DO J = 2, J2-1    
    DO I = 1, J1
which needs to be replaced by:
 ! Non-polar latitudes
 DO J = 2, J2-1    
    DO I = 1, I1


NOTE: Routine smvgear.F is slated for removal from GEOS-Chem v11-01 once the new FlexChem solver is implemented.

Bob Yantosca wrote

Some of you have reported a weird error in SMVGEAR that causes GEOS-Chem simulations to die unexpectedly. The main symptom of this error is that concentrations of some species (e.g CO) appear to go to zero, while other species (e.g. Ox) seem to reach unphysically high values, all within a single chemistry timestep. Then the simulation dies shortly thereafter.
May Fu and Philippe Le Sager have isolated the cause of the problem. They found that in some instances it is possible (e.g. due to locally low OH) to get into a regime where the first derivative of a species goes very negative during SMVGEAR's internal iteration loop. This then causes the new species concentration to be negative. This can sometimes happen even if the local & global error tolerance checks have passed. Then upon exiting the internal iteration loop, SMVGEAR would automatically reset any negative species concentrations to zero (actually a small positive number like 1e-99). A species with zero concentration can adversely affect other species within the SMVGEAR solver process. Furthermore, sometimes these zero concentrations were propagating out of SMVGEAR and into the STT tracer array, which caused problems in other areas of the code.
May & Philippe implemented a fix into the file "smvgear.f" which does the following: If a negative species concentration value is found during an internal iteration, then we don't set it to zero. We instead reduce the internal iteration timestep and do another iteration (i.e. re-evaluate the Jacobian matrix) to solve for the new species concentration. This process is repeated until SMVGEAR converges onto a non-negative solution. May & Philippe also added an extra error trap to stop the simulation if any negative species concentrations still persist upon exiting the subroutine. So the entire process should now be more robust.
You may download the updated "smvgear.f" file from our anonymous FTP site:
   cd pub/geos-chem/patches/v7-04-12
   get README
   get smvgear.f
Then copy the "smvgear.f" file to your own source code directory and recompile. Please see the README file for more information on how to locate the places in "smvgear.f" that were modified.
This is not really a "bug" but more of a "design flaw" in the original SMVGEAR package.

--Bob Y. 16:59, 7 May 2009 (EDT)