GEOS-Chem Newsletter Winter 2013

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Dear GEOS-Chem users,

We are happy to bring you the Winter 2013 edition of the GEOS-Chem Newsletter! Please read below to find out the latest goings-on in the GEOS-Chem community.


The GEOS-Chem Support Team

Last call to register for the 6th International GEOS-Chem Meeting!

Daniel Jacob wrote:

Dear colleagues and GEOS-Chem users:
Please take note of the January 31 registration deadline for the 6th International GEOS-Chem Meeting (IGC6) at Harvard University on May 6-9, 2013. Go to the meeting website to register. We expect the meeting to be oversubscribed. You will hear of acceptance in mid-February.
Daniel Jacob

GEOS-Chem Model Scientist

GEOS-Chem Steering Committee

GCSC Meetings

The GEOS-Chem Steering Committee (GCSC) last met on Tuesday January 8th, 2013. We invite you to read the meeting minutes.

The next GCSC telecon will take place on Friday, April 12, 2013 at 10:00 AM ET (14:00 GMT). If you have any items for the Steering Committee, then please bring them to the attention of your Working Group chairpersons.

GCSC Elections

Daniel Jacob wrote:

Dear GEOS-Chem user:
A number of GEOS-Chem Working Group Co-Chair positions on the GEOS-Chem Steering Committee (GCSC) will become available as terms end in May. New co-chairs will be elected at the 6th International GEOS-Chem Meeting. Please let me know if you are interested in serving. Click HERE to learn more about the functions and responsibilities of the GCSC and about the different WGs. We eagerly encourage qualified candidates to apply. We are particularly interested in maintaining the international character of the GCSC.
Daniel Jacob
GEOS-Chem Model Scientist
for the GCSC

GEOS-Chem v9-01-03 was released in September 2012

The current released version of GEOS-Chem is v9-01-03, released in September 2012. If you have not updated to this version, we encourage you to do so at your earliest convenience.

For a complete list of all new features and fixes in GEOS-Chem v9-01-03, please see this table. We also invite you to view the Online GEOS-Chem User's Manual for more information.

Starting with v9-01-03, users must have a netCDF library installation on their systems in order to run GEOS-Chem. To simplify the library installation process, we have created the GEOS-Chem-Libraries installer package. Detailed instructions about how to download and install netCDF with GEOS-Chem-Libraries may be found on our Installing libraries for GEOS-Chem wiki page.

GEOS-Chem v9-02 news


As of this writing (09 Jan 2013), we have completed the following benchmarks for GEOS-Chem v9-02:

We have completed the following benchmarks:

  1. v9-02a: Correction for PBL heights
  2. v9-02b: New soil NOx emissions module + minor bug fixes
  3. v9-02c: Updates for the Hg simulaton: emissions + kinetics
  4. v9-02d: Structural updates for the Grid-Independent GEOS-Chem
  5. v9-02e: Bug fix for regridding of anthro emissions (Streets, NEI2005)

We are still working on the following benchmarks:

  1. The Hg and POPs Working Group is working on a 1-yr Hg simulation, based on v9-02c.
  2. The Nested Model Working Group is performing a 1-yr full-chemistry simulation for the North American Nested Grid with GEOS-5 met (0.5° x 0.666°). They have completed 6 months of the benchmark.

The next set of updates to GEOS-Chem v9-02 shall be chemistry updates, including:

  1. Updating rate constants for consistency with observations
  2. Update to isoprene scheme
  3. Include HO2 uptake onto aerosol
  4. Putting inhibition to N2O5 uptake.

We shall run 1-month and 1-year benchmarks at intermediate points the development in order to better assess how these updates impact the simulation results.

Bugs and fixes

GEOS-Chem v9-02 shall contain fixes for the following bugs and/or technical issues:

  1. Correction for GEOS-5 PBL heights
  2. Bug fixes for tagged CO simulation
  3. Regridding error in NEI2005 emissions
  4. Bug fix for updated CAC emissions
  5. Fixed incorrect loop limits in Br2 emissions code
  6. Bugs in diurnal NOx scaling and biofuel double-counting

Other updates

Please see this table for the complete list of updates that shall be added to GEOS-Chem v9-02. We also invite you to view the list of GEOS-Chem model development priorities, as determined by Steering Committee, with input from the Working Groups.

Grid-Independent GEOS-Chem news

Much of the recent Grid-independent GEOS-Chem (aka GIGC) work has involved restructuring how data flows between routines in the standard GEOS-Chem code. In general, we now make use of derived-type objects to carry data fields instead of referencing arrays from other modules with USE statements. We have been making these types of structural updates concurrently with scientific development in GEOS-Chem in order to avoid the GIGC code from lagging behind the standard GEOS-Chem code.

We’ve also streamlined the Earth System Model Framework (ESMF) interface that connects GEOS-Chem to the GEOS-5 GCM. The ESMF interface can now deliver the following information from the GCM to GEOS-Chem:

  1. Size of data arrays on each CPU: (IIPAR, JJPAR, LLPAR)
  2. Size of the entire global grid: (IM_WORLD, JM_WORLD, LM_WORLD)
  3. Corner grid box indices on each CPU (I_LO, I_HI, J_LO, J_HI)
  4. Date and time from the GCM
  5. Level edge pressures from the GCM

We also made sure to bring the ESMF interface up-to-date with the tracers and species introduced by the latest bromine chemistry mechanism.

All of these updates are now reflected on the GIGC wiki pages. Please see:

  1. Grid-Independent GEOS-Chem
  2. Grid-Independent GEOS-Chem: Chemistry Component
  3. Grid-Independent GEOS-Chem: Emissions Component
  4. Derived type objects used by the Grid-Independent GEOS-Chem
  5. Programming techniques used for the Grid-Independent GEOS-Chem

We recently performed a test simulation of GEOS-Chem in our ESMF “Sandbox” environment, which replicates the connection to the GEOS-5 GCM without having to run the full GCM. We demonstrated that GEOS-Chem could be successfully run within the ESMF environment using MPI parallelization.

Christoph Keller is working on the GIGC Emissions Component, which will run independently of the chemistry. The Emissions Component will combine emissions from several inventories, apply the relevant scale factors, regrid the emissions, and pass them to the GIGC Chemistry Component via the ESMF interface. Christoph has been making use of a new data structure to store emissions. He is also handling disk I/O operations separately from the data structure, which is a requirement of the ESMF environment. Please see this presentation for further details.

Still to do:

  1. Modify the GIGC code to read data from ASCII input files (i.e. input.geos, globchem.dat, ratj.d, etc.) on the root CPU, and to broadcast the data to other CPUs. This is necessary in order to prevent all CPUs on the system from performing disk I/O operations simultaneously.
  2. Bring dry deposition into the ESMF interface. Mike Long has been working on this.
  3. Port the updated GEOS-Chem source code back to NASA/GSFC to allow testing of the GEOS-5/GEOS-Chem combined model on NASA machines.

We anticipate to be able to run a GEOS-5 GCM/GEOS-Chem simulation before the IGC6 meeting in May. Stay tuned for results!

GEOS-Chem Adjoint News

GEOS-Chem Adjoint v34 is now the standard version of the GEOS-Chem adjoint model. Please see this table for a list of new features in v34.

Some key improvements:

  1. The adjoint code is now distributed using Git instead of CVS. Users of the adjoint model will need to re-register in order to download the adjoint source code from the new Git repository:
  2. Makefiles were updated to better follow the makefile structure used by the forward model. For more information please see this link.
  3. Implemented GFED3 emissions.

Most of the additions to v34 were technical software updates. The next version of the GEOS-Chem adjoint will have more scientific updates.

Please contact GEOS-Chem Support Team Adjoint Specialist Nicolas Bousserez for specific support requests regarding the GEOS-Chem Adjoint code.

In other news

Here are some other noteworthy news items ...

  1. The GEOS-Chem Support Team (GCST) is currently investigating why full-chemistry simulations done with GEOS-Chem v9-01-03 and GEOS-Chem v9-02 take longer to run than older model versions. Melissa Payer is taking the lead on this effort.

  2. We are continuing to work on the 0.25° x 0.3125° nested grid capability with the GEOS-5 “FP” (formerly known as GEOS-5.7.2) met fields. Sajeev Philip (GCST member, Dalhousie) will be extracting and regridding the met data. We are preparing to have this high-resolution nested grid capability ready for the revamped SEAC4RS mission this fall. The GCST is collaborating with Yuxuan Wang (Tsinghua), Jenny Fisher (Wollongong), Lin Zhang (Peking U.), Patrick Kim (Harvard) and others towards this end.

  3. Jeff Pierce (CSU) recently hired programmer Sal Farina to synchronize the TOMAS aerosol microphysics package with the latest GEOS-Chem code. TOMAS had been integrated into GEOS-Chem v8-03-01, but further TOMAS development lagged behind the standard GEOS-Chem.

  4. Sebastian Eastham (working w/ Steven Barrett @ MIT) has deliverd a new aircraft emissions module (AEIC) to the GCST. This new aircraft emissions package is slated to be added into GEOS-Chem v9-02, along with other emissions updates.

  5. Prasad Kasibhatla (Duke) has prepared GFED3 emissions throughout the end of 2011 (the previous data ended in 2010). The new data are stored on the Harvard server. We plan to standardize support for the extended GFED3 data as part of our "emissions update" to GEOS-Chem v9-02.

  6. Debra Weisenstein (Harvard) and Steven Barrett (MIT) are working on a state-of-the-art OCS simulation for GEOS-Chem.

  7. Colette Heald (MIT) is working with AER Corp. to install the RRTMG radiative transfer model into GEOS-Chem.

  8. We invite you to view the GEOS-Chem board on to see the current tasks that we are working on now. We update this board whenever we complete tasks (cards are archived for future reference).

--Bob Y. 14:57, 9 January 2013 (EST)