GEOS-Chem Newsletter Summer-Fall 2012

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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.

Happy Modeling,

The GEOS-Chem Support Team!

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:

  1. Capability to read data files in netCDF format (GEOS-Chem Support Team)
  2. Improved sea salt emission & deposition (Lyatt Jaegle, U. Washington)
  3. Updated acetone chemistry algorithm (Emily Fischer, Harvard)
  4. Improved snow scavenging & washout parameterization (Qiaoqiao Wang, Harvard)
  5. Stratospheric chemistry via archived production/loss rates (Lee Murray, Harvard)
  6. Addition of bromine chemistry into the standard mechanism (Justin Parella, formerly Harvard)
  7. PARANOX plume model for ship emissions (Geert Vinken, Eindhoven)
  8. Historical emissions of SO2, NOx, BC, and POA (Eric Leibensperger, SUNY Plattsburgh)
  9. Updates to facilitate Grid-Independence and interface with the GEOS-5 GCM (GEOS-Chem Support Team)
  10. Implementation of an improved regridding algorithm (GEOS-Chem Support Team + Prasad Kasibhatla, Duke)

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:

  1. New data directories for v9-01-03
  2. [Chapter 4 of the GEOS-Chem User's Guide: Data Directories]

Updates for Grid-Independence in v9-01-03

Our goal has been to introduce the Grid-Independent functionality without destroying any of the existing GEOS-Chem functionality. We have done this by mostly 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. This allows us

For a complete explanation of grid-independent modifications in GEOS-Chem v9-01-03, please see:

  1. Standardization of grid-independent code modifications
  2. Additional grid-independent modifications
  3. Using the DEVEL C-preprocessor switch
  4. Implementation of derived types
  5. Modifications to restrict screen and log file output to the root CPU
  6. 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 GEOS-Chem v9-01-03

Please see this this wiki post for a list of issues that have yet to be resolved.

Grid-Independent GEOS-Chem

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, or able to accept an arbitrary horizontal grid definition. 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 GCM interface. To date, Mike Long and Bob Yantosca have made significant progress towards this goal. Much of this work involved replacing legacy code based on Fortran-77 (i.e. common blocks, etc) with modern Fortran-90 code. We have already added many of these source code modifications to the standard GEOS-Chem repository for 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). In February 2012, Mike Long visited the BCC in order to test the interface that links GEOS-Chem to the BCC/GCM. This exercise proved to be very fruitful, and Mike identified a number of technical issues that needed to be resolved immediately. These issues would have also prevented the Grid-Independent GEOS-Chem from interfacing effectively with the NASA GEOS-5/GCM. We therefore made it a priority to correct each of these issues as soon as possible.

Here is a list of the issues that Mike found, and the solutions that we implemented:

Problem Solution
Problem: The BCC/GCM cannot read data from ASCII input files. Several of GEOS-Chem's legacy codes (dry deposition, leaf area index, etc) read from ASCII files. Because the BCC/GCM runs with MPI parallelization, each CPU would have to read the ASCII input files independently, which would adversely impact scalability. Solution: We converted several of GEOS-Chem's data files (e.g. drydep.table, drydep.coef, vegtype.global, lai*.global) from ASCII to netCDF. We introduced the capability to read netCDF data (based on Bob Yantosca's NcdfUtilities package) into GEOS-Chem v9-01-03. The input.geos file that is used to specify GEOS-Chem options was left untouched for the moment.
Problem: The GEOS-Chem dry deposition and soil NOx emissions modules rely on Olson land map (1992) data contained in an ASCII file named vegtype.global. A different version of vegtype.global is currently required for each different horizontal grid resolution (4° x 5°, 2° x 2.5°, nested-grids). However, for grid-independent operation, we cannot assume a-priori what the grid definition shall be. Solution: Bob Yantosca wrote a new land type module which reads the Olson land map (1992) data from its native resolution (0.5° x 0.5° ) in netCDF format and regrids it to the current GEOS-Chem resolution. The existing arrays used by the GEOS-Chem dry deposition and soil NOx emissions code are populated in the exact same manner as before. Also, the user now has the option to switch to the Olson land map (2001) data at 0.25° x 0.25° resolution. This modification has already been added to GEOS-Chem v9-01-03.
Problem: The MODIS leaf area index (LAI) data were being read from several different sources. The Dry deposition and Soil NOx emissions routines were reading MODIS LAI data from ASCII files named lai*.global. The data in lai*.global were indexed by land type in the same order as the land types were listed in vegtype.global. Different versions of lai*.global had to be created for each horizontal grid. On the other hand, the MEGAN biogenic emissions module was reading MODIS LAI data from binary punch files at 1° x 1° native resolution, which were then regridded to the current horizontal resolution. Finally, the nested-grid simulations were reading from a separate set of LAI data files that were created for each at 0.5° x 0.666° nested region. Solution: Bob Yantosca wrote a new MODIS LAI module that reads LAI data at the native resolution of 0.5° x 0.5° (in netCDF format) and regrids to the current horizontal grid. The LAI arrays used by GEOS-Chem are populated in exactly the same manner as before. Thus, all LAI data now used by GEOS-Chem now comes from the same source at the same resolution. Also, the user has the option of switching to the MODIS LAI data at 0.25° x 0.25° resolution (corresponding to the Olson 2001 land map). This modification has already been added to v9-01-03.
Problem: The FAST-J photolysis module uses a default overhead ozone climatology that is overwritten with TOMS/SBUV ozone values (for the months and latitudes where TOMS data exists). Monthly TOMS/SBUV data is read from disk directly in the driver routine fast_j.F and the interpolation to the current day and overwriting of the default O3 columns was done in the lower-level routine set_prof.F. However, when GEOS-Chem is interfaced with a GCM, it will need to use the overhead O3 columns that is generated by the GCM. Also, when we interface GEOS-Chem to the GCM, file I/O operations will not be allowed to be performed at that level in the code. Solution: We now pass the overhead O3 columns as an input to the FAST-J photolysis module. A new routine in main.F is used to determine if the default overhead O3 climatology needs to be overwritten with TOMS/SBUV O3. The resultant overhead O3 is then passed as an argument directly to the FAST-J module. FAST-J will also be able to directly accept overhead O3 columns from a GCM. This modification has already been added to v9-01-03.
Problem: GEOS-Chem currently assumes a pure Cartesian grid. Query functions GET_XMID(I), GET_YMID(J), GET_XEDGE(I), GET_YEDGE(J) etc. from grid_mod.F are used to return longitude and latitude information at grid box centers and edges. However, in the future we may not be able to assume that GEOS-Chem will always be running with a regular Cartesian grid. Solution: We have introduced a new module grid_mod.F90 and have extended the query functions to accept lon, lat, and level indices, i.e., GET_XMID(I,J,L), GET_YMID(I,J,L), GET_XEDGE(I,J,L), GET_YEDGE(I,J,L). This will leave room for future expansion in case GEOS-Chem ever should use a non-regular horizontal grid.

It should be noted that several of these modifications, in particular new Olson land map and MODIS leaf area index modules, also facilitated the effort to make GEOS-Chem compatible with the GEOS-5.7.2 meteorology.

We have currently reached the end of Year 1 of the Grid-independent GEOS-Chem project. At the end of May 2012, we shall deliver the first GEOS-Chem module to NASA for inclusion into the GEOS-5/GCM. This will be our Chemistry Component (i.e. GEOS-Chem's chemical mechanism solver, photolysis, and dry deposition routines). Postdoc Christoph Keller is working on a new Grid-Independent Emissions Component, which will occupy most of Year 2.

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 in the Sept-Oct time frame. We will keep you posted. As always, if you have any items for the Steering Committee please be sure to identify them to your Working Group chairpersons.

GEOS-5.7.2 met field update

NASA/GMAO has updated the operational GEOS system from GEOS-5.2.0 to GEOS-5.7.2. Here is a quick summary of the new GEOS-5.7.2 data product:

  1. Horizontal resolution: 0.25° lat x 0.3125° lon (i.e. 1/4° x 5/16°)
  2. Vertical resolution: 72 hybrid layers (identical to the vertical grids used by the GEOS-5.2.0 and MERRA met data products)
  3. Time resolution: Hourly and 3-hourly data (timestamps very similar to MERRA)
  4. Input data format: netCDF-4 (as opposed to HDF4-EOS, used for past GMAO data products)
  5. Output data format: netCDF-3 (instead of flat binary). This will allow the files to be read by IDL routines such as GAMAP.

We plan to store the GEOS-5.7.2 following data at Harvard (which will be downloadable by the community). Data will be processed for Aug 2011-onward. Priority will be given to these grids:

  1. Global 2° x 2.5°
  2. Global 4° x 5°
  3. SEA4CRS Nested grid at 0.25° x 0.3125° resolution

The large size of the nested data files makes disk storage an issue. At present, we plan on giving priority to the SEA4CRS nested grid.

We have added several structural modifications for GEOS-5.7.2 met into GEOS-Chem v9-01-03. Because the structure of the GEOS-5.7.2 met data is very similar to MERRA, many of the modifications simply involved simply extending C-preprocessor statements such as:

   #if defined( MERRA )

to

   #if defined( MERRA ) || defined( GEOS_57 )

which tells the code to treat GEOS-5.7 in the same way as we already do for MERRA.

Patrick Kim has done some initial benchmarking of GEOS-Chem driven with the GEOS-5.7.2 met product and have compared the results to GEOS-5.2 and MERRA. His findings are included in the separate document entitled SEAC4RS_Update.pdf which I have distributed along with this report. The GEOS-5.7.2 moist fields seem to be significantly different as compared to MERRA. We are still investigating.

Yuxuan Wang and her team at Tsinghua have been working on the nested-grid transport at 0.25° x 0.3125° resolution.


De-supporting of GEOS-3 meteorology

All support for GEOS-3 met data has now been officially removed from GEOS-Chem. GEOS-3 is now several versions behind the current GMAO met data product, and is obsolete.

We shall still keep the archive of GEOS-3 met data at both Harvard and Dalhousie in case there are users who still wish to access this data.

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 recently 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 geos-chem-support@as.harvard.edu.

GAMAP v2-16

We plan on releasing the next GAMAP version (v2-16) when GEOS-Chem v9-01-03 is officially released. GAMAP v2-16 will contain the following new features:

  1. Support for reading/plotting GEOS-5.7.2 met data
  2. Improved support for netCDF file I/O
  3. Updated code for plotting results from GEOS-Chem 1-month benchmarks
  4. Flexible colorbar scaling with the /CBSCALE option (submitted by Chris Holmes)
  5. Now can read binary files larger than 2.4 GB in size (submitted by Prasad Kasibhatla)

This release shall standardize several fixes that had been made to the GAMAP source code over the past year. We shall also update the GAMAP manual to remove outdated information.

Miscellany

We would like to each GEOS-Chem user group to take a moment to review the research blurb and list of group members on the GEOS-Chem people and projects page. Also, we apologize if you sent us updates that were not posted on the website. As you can see from all of the news above, it has been a busy few months for us on the GEOS-Chem Support Team!

--
Bob Yantosca
(with input from Mike Long, Melissa Payer, and Matthew Cooper)
21 May 2012

--Bob Y. 16:34, 21 May 2012 (EDT)