GEOS-Chem Newsletter Summer-Fall 2012
We have had a busy summer! We were not able to get out a newsletter in the Summer, so we have denoted this as the Summer-Fall 2012 issue.
The GEOS-Chem Support Team!
- 1 GEOS-Chem v9-01-03 is now released!
- 2 GAMAP v2-16
- 3 GEOS-Chem Steering Committee
- 4 Grid-Independent GEOS-Chem
- 5 GMAO met field update
- 6 GEOS-Chem Adjoint news
- 7 Miscellany
- 8 Addenda Section
GEOS-Chem v9-01-03 is now released!
We are happy to announce the public release of GEOS-Chem v9-01-03 today (September 14, 2012)! We encourage all GEOS-Chem users to update to the new version. Please see our Online GEOS-Chem User's Manual for full downloading and installation instructions!
New features in v9-01-03
For a complete list of all new features and fixes in GEOS-Chem v9-01-03, please see this table.
Some exciting new features include:
- Capability to read data files in netCDF format (GEOS-Chem Support Team)
- Improved sea salt emission & deposition (Lyatt Jaegle, U. Washington)
- Updated acetone chemistry algorithm (Emily Fischer, Harvard)
- GFED3 daily and 3-hourly emissions (Prasad Kasibhatla, Duke)
- Improved snow scavenging & washout parameterization (Qiaoqiao Wang, Harvard)
- Stratospheric chemistry via archived production/loss rates (Lee Murray, Harvard)
- Addition of bromine chemistry into the standard mechanism (Justin Parella, formerly Harvard)
- PARANOX plume model for ship emissions (Geert Vinken, Eindhoven)
- Historical emissions of SO2, NOx, BC, and POA (Eric Leibensperger, SUNY Plattsburgh)
- Updates to facilitate Grid-Independence and interface with the GEOS-5 GCM (GEOS-Chem Support Team)
- Implementation of an improved regridding algorithm (GEOS-Chem Support Team + Prasad Kasibhatla, Duke)
View benchmark results from v9-01-03
Prior to releasing GEOS-Chem v9-01-03, we performed several 1-year benchmarks with full chemistry:
- v9-01-03e (Run0)
- Tests the new snow scavenging and washout parameterization.
- v9-01-03o (Run0):
- This version was not approved by the GCSC, but subjected to further investigation due to a larger effect of bromine chemistry on ozone and OH than reported in Parrella et al. (2012).
- v9-01-03-Release (Run0)
- Code prior to release, with bromine chemistry turned OFF.
- v9-01-03-Release (Run1)
- Code prior to release, with bromine chemistry turned ON.
We also performed a 1-year Rn-Pb-Be benchmark simulation::
- v9-01-03e (Rn-Pb-Be)
- Tests the new snow scavenging and washout parameterization.
You may also view the plots from our GEOS-Chem 1-month benchmark simulations.
New data directories for v9-01-03
We have made available several new data directories containing new emissions and other input files for use with GEOS-Chem v9-01-03. For a complete list of these directories, please see:
Updates for grid-independence in v9-01-03
Our goal has been to introduce grid-independent functionality into GEOS-Chem without destroying any of the existing functionality. We have done this by adding new code in parallel to the existing GEOS-Chem code. The new code is set apart from the existing code by one or more C-preprocessor switches. If the switches are turned on, then the new grid-independent code is invoked; otherwise the new code is not compiled into the executable.
For a complete explanation of recent grid-independent modifications in GEOS-Chem v9-01-03, please see:
- Standardization of grid-independent code modifications
- Additional grid-independent modifications
- Using the DEVEL C-preprocessor switch
- Implementation of derived types
- Modifications to restrict screen and log file output to the root CPU
- Dynamically assiging logical unit numbers for file I/O
Issues now resolved in GEOS-Chem v9-01-03
Please see this this wiki post for a complete list of issues that have now been corrected in GEOS-Chem v9-01-03.
Outstanding issues not yet resolved in v9-01-03
Please see this this wiki post for a list of issues that have yet to be resolved.
Installing libraries for GEOS-Chem v9-01-03
We have added a netCDF I/O capability into GEOS-Chem v9-01-03 to facilitate the Grid-independent GEOS-Chem project, which seeks to integrate GEOS-Chem within the NASA GEOS-5 GCM. Therefore, starting with GEOS-Chem v9-01-03, all GEOS-Chem users must have a netCDF library installation on their systems in order to run GEOS-Chem.
To simplify the library installation process, the GEOS-Chem Support Team has 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. (NOTE: If you are one of several GEOS-Chem users at a single institution, the libraries only have to be built once and then placed in a common directory where all users may access them. Ask your IT staff for help.)
We realize that the full conversion from binary to netCDF I/O cannot be achieved overnight. We have already converted the following data files to netCDF:
- GEOS-5.7 met data files
- Olson land map (1992) and (2001)
- MODIS LAI data
- Dry deposition input files
- The jv_atms.dat input file for the FAST-J photolysis mechanism
- Stratospheric chemistry input files
As GEOS-Chem development progresses, the list of input files in netCDF format shall grow until eventually all of GEOS-Chem's input files will have been migrated to netCDF format.
At a later time, in conjunction with the Grid-independent GEOS-Chem project, we shall also begin to convert GEOS-Chem's diagnostic outputs to netCDF format. Fortran code for writing netCDF files is necessarily much more wordy than code for reading from netCDF files because one must supply information (aka metadata) about the variables that will constitute each netCDF file. To simplify the coding process for the GEOS-Chem community, Bob Yantosca has included into GEOS-Chem some Perl scripts which will automatically generate the proper Fortran for both writing to and reading from netCDF files.
GAMAP v2-16 is now released! We have made some new modifications specific to GEOS-Chem v9-01-03. We therefore ask you to upgrade to this GAMAP v2-16 as soon as possible.
New features include:
- Support for reading/plotting GEOS-5.7.2 met data
- Improved support for netCDF file I/O
- Updated code for plotting results from GEOS-Chem 1-month benchmarks
- Flexible colorbar scaling with the /CBSCALE option (submitted by Chris Holmes)
- Now can read binary files larger than 2.4 GB in size (submitted by Prasad Kasibhatla)
Please see the online GAMAP manual for detailed information about GAMAP v2-16, including downloading and installation instructions.
GEOS-Chem Steering Committee
Minutes from the last GCSC telecon which was held on Wednesday 23 May 2012 @ 10:00 AM ET (14:00 GMT) are available HERE.
The next scheduled GEOS-Chem Steering Committee telecon will take place at 10AM ET (15:00 GMT) on October 4, 2012. As always, if you have any items for the Steering Committee please be sure to identify them to your Working Group chairpersons.
We have an ongoing collaboration with NASA where we seek to embed GEOS-Chem within the NASA GEOS-5/GCM. In order to do this, the GEOS-Chem Support Team has been working towards making GEOS-Chem grid-independent; that is, to have the ability to accept an arbitrary geospatial grid. This will finally enable GEOS-Chem to utilize MPI parallelization (via the ESMF framework) and to run on many more CPUs than is possible with the current configuration.
The first phase of this project has involved preparing GEOS-Chem for the GEOS-5 GCM interface. We reached an important milestone in June 2012 (the end of Year 1 of the project) when Mike Long and Bob Yantosca traveled to GSFC to install GEOS-Chem within the GEOS-5 GCM. The GEOS-5/GEOS-Chem combination now compiles on the NASA computer system. Further testing and refinement of the GEOS-5/GEOS-Chem interface is ongoing.
Postdoc Christoph Keller is working on a new Grid-Independent Emissions Component, which will be the focus of the upcoming year.
GMAO met field update
As of August 2011, NASA/GMAO has updated the operational GEOS system from GEOS-5.2.0 to GEOS-5.7.2.
- Horizontal resolution: 0.25° lat x 0.3125° lon (i.e. 1/4° x 5/16°)
- Vertical resolution: 72 hybrid layers (identical to the vertical grids used by the GEOS-5.2.0 and MERRA met data products)
- Time resolution: Hourly and 3-hourly data (timestamps very similar to MERRA)
- Input data format: netCDF-4 (as opposed to HDF4-EOS, used for past GMAO data products)
- Output data format: netCDF-3 (instead of flat binary). This will allow the files to be read by IDL routines such as GAMAP.
GEOS-5 FP and GEOS-5 FP-IT
GMAO recently has made further changes to the assimilated meteorology product:
GEOS-5.7.2 met data has been renamed to GEOS-5.8 (aka "GEOS5-FP"). This data comes on a 0.25° x 0.3125° x 72 layer grid, with hourly and 3-hourly time resolution. This is the operational data set, which means that the assimilation system that produces these data data shall evolve to match the state of the science.
The GEOS-5.2.0 met data product has now been turned off. It is replaced with GEOS-5 FP-IT. This data comes on a 0.5° x 0.666 ° x 72 layer grid. This is a frozen data set, which means that the assimilation system that produces these data shall not be modified.
We shall continue developing the 0.25° x 0.3125° nested grid capability in the next version of GEOS-Chem (denoted as GEOS-Chem v9-02), using the operational GEOS-5 "FP" data. This work is ongoing.
GEOS-Chem Adjoint news
Please see the new GEOS-Chem Adjoint v33 wiki page for a complete list of updates pertaining to the current GEOS-Chem adjoint version. This wiki page is updated often, so please check back frequently for the latest news!
Also, any technical questions that you may have pertaining to the adjoint source code may be directed to Nicolas Bousserez, who joined the GEOS-Chem Support Team as GEOS-Chem Adjoint liaison. You may contact Nicolas (and all other Support Team) members by sending an email to email@example.com.
We would like to thank all of the GEOS-Chem user groups who sent us an updated research blurb and list of group members for the GEOS-Chem people and projects page. This information helps us keep an to accurate count of GEOS-Chem users. If you have not submitted an updated research blurb, then please do so at your earliest convenience.
The next GEOS-Chem version shall be denoted GEOS-Chem v9-02. The GEOS-Chem Steering Committee shall review the list of GEOS-Chem model development priorities in order to determine which items will be installed into v9-02. We shall update this information on the GEOS-Chem wiki soon.
(on behalf of Mike Long, Melissa Payer, Matthew Cooper, and Nicolas Bousserez)
14 Sep 2012
--Bob Y. 14:10, 14 September 2012 (EDT)
These items were added to the Summer-Fall 2012 newsletter after the initial publication date (14 Sep 2012):
The GEOS-Chem version immediately following v9-01-03 shall be denoted as v9-02. We have dropped the last two digits (which were the old “beta release” numbers). We now use the new benchmarking procedure adopted at IGC5, which calls for one or more 1-year benchmarks to be performed prior to each GEOS-Chem release. Thus, each new GEOS-Chem release is equivalent to what we used to call a “public” release. Furthermore, intermediate states of the code where we perform a 1-month benchmark are now denoted by alphabetical letters (e.g. v9-02a, v9-02b, etc). Therefore, the old “beta release” numbers are unnecessary, and have now been removed.
Several new features have been proposed for inclusion into v9-02. The GEOS-Chem Steering Committee shall determine the order of inclusion. In addition, updates from the Grid-independent GEOS-Chem development effort shall be synchronized into the standard repository at frequent intervals.
Bob Yantosca has discovered an issue in that may be causing the full-chemistry simulation to take longer to execute than is necessary. An extraneous DO loop over all lons/lats/levels had been placed into routine calcrate.F as part of the bromine chemistry update. But calcrate.F itself is called from within a parallel loop from a higher level routine, making the new DO loop superfluous. Bob has created a fix for this issue which will be bundled with other changes into the first v9-02 1-month benchmark (v9-02a).
Grid Independent GEOS-Chem: Update
As of 28 Sep 2012, Bob Yantosca, Mike Long, and Christoph Keller have been granted access to the NASA/GMAO computer systems. The GEOS-Chem code currently compiles with the GEOS-5 GCM. We shall also focus on integrating the GEOS-Chem dry deposition routines into the GCM interface. Testing is ongoing.
Eric Nielsen (at GMAO) discovered that further modifications (click HERE and HERE) had to be made in order to get GEOS-Chem to compile within the framework of the GEOS-5 GCM. These structural modifications were standardized in GEOS-Chem v9-01-03.
A secondary partner in our Grid-Independent GEOS-Chem project is the Beijing Climate Center (BCC), who wishes to interface the Grid-independent GEOS-Chem into its GCM (which is a version of CAM). Based on Mike Long’s Feb 2012 visit to BCC, a number of technical issues were in GEOS-Chem were corrected and standardized in the v9-01-03 release. Mike visited the BCC again in September 2012, which resulted in a successful implementation of a GEOS-Chem/GCM simulation for CO2. The CO2 simulation is a stepping stone to more complex simulations.
Postdoc Christoph Keller is working on a new Grid-Independent “Emissions Component”, which will occupy most of Year 2 of the project. Much of Christoph’s work involves converting existing bpch files to netCDF and separating file I/O from the rest of the emissions code. The work is ongoing.
Flexible Chemistry with KPP
Mat Evans is spearheading an effort to replace the existing SMVGEAR chemistry solver in GEOS-Chem with a flexible chemistry mechanism using KPP. Instead of using pre-determined chemistry mechanisms (i.e. standard, SOA, dicarbonyls, isoprene), we would allow the user to pick and choose which species to include. KPP would be then compiled with a custom species list each time GEOS-Chem is compiled. We are also investigating how to integrate the flexible chemistry with the Grid-independent GEOS-Chem project, such that it can be used with the GEOS-5 GCM. This project is currently in the planning stage.
Radiative transfer with RRTMG
Colette Heald (MIT) has started a project to integrate AER’s RRTMG radiative transfer model into GEOS-Chem. Collaborators are Matt Alvarado (AER) and Karen Cady-Pereira (AER). AER has downloaded GEOS-Chem v9-01-03 and has started coding the GEOS-Chem/RRTMG interface. The project is ongoing.
Potential issue with TOMAS microphysics
Peter Adams and Dan Westervelt noticed a bug in OH (off by a factor of 10) in the TOMAS aerosol microphysics package based on GEOS-Chem v8-03-01. This bug is apparent when compared to an older (non-standard) version. We are currently investigating.
(on behalf of Mike Long, Melissa Payer, Matthew Cooper, and Nicolas Bousserez)
28 Sep 2012