Difference between revisions of "GEOS-Chem Newsletter Summer-Fall 2012"

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== GEOS-Chem v9-01-03 is now released! ==
 
== 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 [http://acmg.seas.harvard.edu/geos/doc/man/ Online GEOS-Chem User's Manual] for full downloading and installation instructions!
+
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 [http://acmg.seas.harvard.edu/geos/doc/archive/man.v9-01-03/index.html Online GEOS-Chem User's Manual] for full downloading and installation instructions!
  
 
=== New features in v9-01-03 ===
 
=== New features in v9-01-03 ===
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# Improved sea salt emission & deposition (Lyatt Jaegle, U. Washington)
 
# Improved sea salt emission & deposition (Lyatt Jaegle, U. Washington)
 
# Updated acetone chemistry algorithm (Emily Fischer, Harvard)
 
# Updated acetone chemistry algorithm (Emily Fischer, Harvard)
 +
# GFED3 daily and 3-hourly emissions (Prasad Kasibhatla, Duke)
 
# Improved snow scavenging & washout parameterization (Qiaoqiao Wang, Harvard)
 
# Improved snow scavenging & washout parameterization (Qiaoqiao Wang, Harvard)
 
# Stratospheric chemistry via archived production/loss rates (Lee Murray, Harvard)
 
# Stratospheric chemistry via archived production/loss rates (Lee Murray, Harvard)
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# Historical emissions of SO2, NOx, BC, and POA (Eric Leibensperger, SUNY Plattsburgh)
 
# 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)
 
# 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:
 +
 +
#[[GEOS-Chem_v9-01-03_benchmark_history#Run0_3|'''v9-01-03e (Run0)''']]
 +
#*Tests the new snow scavenging and washout parameterization.
 +
#[[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03o|'''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).
 +
#[[GEOS-Chem_v9-01-03_benchmark_history#Run0|'''v9-01-03-Release (Run0)''']]
 +
#*Code prior to release, with bromine chemistry turned OFF.
 +
#[[GEOS-Chem_v9-01-03_benchmark_history#Run0|'''v9-01-03-Release (Run1)''']]
 +
#* Code prior to release, with bromine chemistry turned ON.
 +
 +
We also performed a 1-year [[Rn-Pb-Be simulation|Rn-Pb-Be benchmark simulation:]]:
 +
 +
#[[GEOS-Chem_v9-01-03_benchmark_history#Rn-Pb-Be_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_v9-01-03_benchmark_history#1-month_benchmarks|'''GEOS-Chem 1-month benchmark simulations''']].
  
 
=== New data directories for v9-01-03 ===
 
=== New data directories for v9-01-03 ===
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# [[GEOS-Chem_v9-01-03#New_data_directories|New data directories for v9-01-03]]
 
# [[GEOS-Chem_v9-01-03#New_data_directories|New data directories for v9-01-03]]
−
# [[http://acmg.seas.harvard.edu/geos/doc/man/chapter_4.html Chapter 4 of the GEOS-Chem User's Guide: Data Directories]]
+
# [http://acmg.seas.harvard.edu/geos/doc/archive/man.v9-01-03/chapter_4.html Chapter 4 of the GEOS-Chem User's Guide: Data Directories]
  
−
=== Updates for Grid-Independence in v9-01-03 ===
+
=== 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
+
Our goal has been to introduce [[Grid-independent GEOS-Chem|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 [http://acmg.seas.harvard.edu/geos/doc/archive/man.v9-01-03/chapter_3.html#3.4 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 grid-independent modifications in GEOS-Chem v9-01-03, please see:
+
For a complete explanation of recent grid-independent modifications in [[GEOS-Chem v9-01-03]], please see:
  
 
#[[Grid-independent_GEOS-Chem#Standardization_of_code_that_was_originally_only_used_with_the_DEVEL.3Dyes_option|Standardization of grid-independent code modifications]]
 
#[[Grid-independent_GEOS-Chem#Standardization_of_code_that_was_originally_only_used_with_the_DEVEL.3Dyes_option|Standardization of grid-independent code modifications]]
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=== Issues now resolved in GEOS-Chem v9-01-03===
 
=== Issues now resolved in GEOS-Chem v9-01-03===
  
−
Please see this [[GEOS-Chem_v9-01-03#Previous_issues_now_resolved_in_v9-01-03|this wiki post]] for a complete list of issues that have now been corrected in GEOS-Chem v9-01-03.
+
Please see this [[GEOS-Chem_v9-01-03#Previous_issues_now_resolved_in_v9-01-03|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 ===
+
=== Outstanding issues not yet resolved in v9-01-03 ===
  
 
Please see this [[GEOS-Chem_v9-01-03#Negative_ship_emissions_caused_by_PARANOX|this wiki post]] for a list of issues that have yet to be resolved.
 
Please see this [[GEOS-Chem_v9-01-03#Negative_ship_emissions_caused_by_PARANOX|this wiki post]] for a list of issues that have yet to be resolved.
  
−
== Grid-Independent GEOS-Chem ==
+
=== Installing libraries for GEOS-Chem v9-01-03 ===
  
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We have an ongoing collaboration with [http://gmao.gsfc.nasa.gov 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 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 [http://www.earthsystemmodeling.org ESMF framework]) and to run on many more CPUs than is possible with the current configuration.
+
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.'''''
  
−
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]].
+
To simplify the library installation process, the [[GEOS-Chem Support Team]] has created the <tt>GEOS-Chem-Libraries</tt> installer package.  Detailed instructions about how to download and install netCDF with <tt>GEOS-Chem-Libraries</tt> 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.)
  
−
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.
+
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:
  
−
Here is a list of the issues that Mike found, and the solutions that we implemented:
+
#[[GEOS-5.7.2|GEOS-5.7]] met data files
 +
#[[Olson land map]] (1992) and (2001)
 +
#[[MODIS leaf area indices|MODIS LAI data]]
 +
#[[Dry deposition]] input files
 +
#The <tt>jv_atms.dat</tt> input file for the [[Photolysis mechanism|FAST-J photolysis mechanism]]
 +
#[[Stratospheric chemistry]] input files
  
−
{| border=1 cellspacing=0 cellpadding=5
+
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.   
−
|-bgcolor="#cccccc"
+
−
!width="450px"|Problem
+
−
!width="450px"|Solution
+
−
|-valign="top"
+
−
|'''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. <tt>drydep.table</tt>, <tt>drydep.coef</tt>, <tt>vegtype.global</tt>, <tt>lai*.global</tt>) 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 <tt>input.geos</tt> file that is used to specify GEOS-Chem options was left untouched for the moment.
+
−
|-valign="top"
+
−
|'''Problem:''' The GEOS-Chem dry deposition and soil NOx emissions modules rely on [[Olson land map#Olson 1992 land map|Olson land map (1992)]] data contained in an ASCII file named <tt>vegtype.global</tt>.  A different version of <tt>vegtype.global</tt> is currently required for each different horizontal grid resolution (4&deg; x 5&deg;, 2&deg; x 2.5&deg;, nested-grids).  However, for grid-independent operation, we cannot assume a-priori what the grid definition shall be.
+
−
|'''Solution:''' Bob Yantosca wrote [[Olson_land_map#Modifications_for_the_grid-independent_model|a new land type module]] which reads the Olson land map (1992) data from its native resolution (0.5&deg; x 0.5&deg; ) 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#Olson 2001 land map|Olson land map (2001)]] data at 0.25&deg; x 0.25&deg; resolution.  This modification has already been added to GEOS-Chem v9-01-03.
+
−
|-valign="top"
+
−
|'''Problem:''' The [[MODIS_leaf_area_indices|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 <tt>lai*.global</tt>.  The data in <tt>lai*.global</tt> were indexed by land type in the same order as the land types were listed in <tt>vegtype.global</tt>.  Different versions of <tt>lai*.global</tt> 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&deg; x 1&deg; 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&deg; x 0.666&deg; nested region.
+
−
|'''Solution:''' Bob Yantosca wrote [[Leaf area indices in GEOS-Chem|a new MODIS LAI module]] that reads LAI data at the native resolution of 0.5&deg; x 0.5&deg; (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&deg; x 0.25&deg; resolution (corresponding to the [[Olson land map#Olson 2001 land map|Olson 2001 land map]]).  This modification has already been added to [[GEOS-Chem v9-01-03|v9-01-03]].
+
−
|-valign="top"
+
−
|'''Problem:''' The [[Photolysis mechanism|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 <tt>fast_j.F</tt> and the interpolation to the current day and overwriting of the default O3 columns was done in the lower-level routine <tt>set_prof.F</tt>.  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 <tt>main.F</tt> 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 [[GEOS-Chem v9-01-03|v9-01-03]].
+
−
|-valign="top"
+
−
|'''Problem:''' GEOS-Chem currently assumes a pure Cartesian grid.  Query functions <tt>GET_XMID(I)</tt>, <tt>GET_YMID(J)</tt>, <tt>GET_XEDGE(I)</tt>, <tt>GET_YEDGE(J)</tt> etc. from <tt>grid_mod.F</tt> 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 <tt>grid_mod.F90</tt> and have extended the query functions to accept lon, lat, and level indices, i.e., <tt>GET_XMID(I,J,L)</tt>, <tt>GET_YMID(I,J,L)</tt>, <tt>GET_XEDGE(I,J,L)</tt>, <tt>GET_YEDGE(I,J,L)</tt>.  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 [[Leaf area indices in GEOS-Chem|MODIS leaf area index]] modules, also facilitated the effort to make GEOS-Chem compatible with the [[GEOS-5.7.2]] meteorology.
+
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 ==
 +
 
 +
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)
  
−
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 GEOS-Chem#Emissions Component|Grid-Independent Emissions Component]], which will occupy most of Year 2.
+
Please see the [http://acmg.seas.harvard.edu/gamap/doc/index.html online GAMAP manual] for detailed information about GAMAP v2-16, including downloading and installation instructions.
  
 
== GEOS-Chem Steering Committee ==
 
== GEOS-Chem Steering Committee ==
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Minutes from the last GCSC telecon which was held on '''Wednesday 23 May 2012 @ 10:00 AM ET (14:00 GMT)''' are available [http://acmg.seas.harvard.edu/geos/word_pdf_docs/steering_cmte/gc_sc_minutes_021512.pdf HERE].
 
Minutes from the last GCSC telecon which was held on '''Wednesday 23 May 2012 @ 10:00 AM ET (14:00 GMT)''' are available [http://acmg.seas.harvard.edu/geos/word_pdf_docs/steering_cmte/gc_sc_minutes_021512.pdf HERE].
  
−
The next scheduled [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html 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 [http://acmg.seas.harvard.edu/geos/geos_working_groups.html Working Group chairpersons].
+
The next scheduled [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html 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 [http://acmg.seas.harvard.edu/geos/geos_working_groups.html Working Group chairpersons].
  
−
== GEOS-5.7.2 met field update ==
+
== Grid-Independent GEOS-Chem ==
 +
 
 +
We have an ongoing collaboration with [http://gmao.gsfc.nasa.gov 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 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 [http://www.earthsystemmodeling.org 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 GEOS-Chem#Emissions Component|Grid-Independent Emissions Component]], which will be the focus of the upcoming year.
 +
 
 +
== GMAO met field update ==
 +
 
 +
=== GEOS-5.7.2 ===
  
−
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:
+
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&deg; lat x 0.3125&deg; lon (i.e. 1/4&deg; x 5/16&deg;)
 
#'''Horizontal resolution:''' 0.25&deg; lat x 0.3125&deg; lon (i.e. 1/4&deg; x 5/16&deg;)
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#'''Output data format:''' netCDF-3 (instead of flat binary).  This will allow the files to be read by IDL routines such as GAMAP.
 
#'''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:
+
=== GEOS-5 FP and GEOS-5 FP-IT ===
  
−
#Global 2&deg; x 2.5&deg;
+
GMAO recently has made further changes to the assimilated meteorology product:
−
#Global 4&deg; x 5&deg;
+
−
#SEA4CRS Nested grid at 0.25&deg; x 0.3125&deg; 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.
+
# <p>GEOS-5.7.2 met data has been renamed to '''GEOS-5.8 (aka "GEOS5-FP")'''.  This data comes on a 0.25&deg; x 0.3125&deg; 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.</p>
 +
#<p>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&deg; x 0.666 &deg; x 72 layer grid. This is a '''frozen data set''', which means that the assimilation system that produces these data shall not be modified.</p>
  
−
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:
+
We shall continue developing the 0.25&deg; x 0.3125&deg; 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.
  
−
    #if defined( MERRA )
+
== GEOS-Chem Adjoint news ==
  
−
to  
+
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!
  
−
    #if defined( MERRA ) || defined( GEOS_57 )
+
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 <tt>geos-chem-support@as.harvard.edu</tt>.
  
−
which tells the code to treat GEOS-5.7 in the same way as we already do for MERRA.
+
== Miscellany ==
  
−
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.
+
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 [http://acmg.seas.harvard.edu/geos/ 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.
  
−
Yuxuan Wang and her team at Tsinghua have been working on the nested-grid transport at 0.25&deg; x 0.3125&deg; resolution.
+
The next GEOS-Chem version shall be denoted [[GEOS-Chem v9-02]]. The [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html 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.
  
−
== Transition to netCDF file format ==
+
<br>
 +
----
 +
Bob Yantosca<br>
 +
(on behalf of Mike Long, Melissa Payer, Matthew Cooper, and Nicolas Bousserez)<br>
 +
14 Sep 2012
  
−
One of the necessary steps that we must undertake as we prepare to interface GEOS-Chem with an external GCM (such as the NASA GEOS-5/GCM) is to adopt [http://www.unidata.ucar.edu/software/netcdf/docs/netcdf_format.html netCDF file I/O].  The current [http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 binary punch] format used by GEOS-Chem is incompatible with MPI parallelization in the sense that small chunks of a binary punch file cannot be read simultaneously across CPUs in a distributed memory environment.  Rather, the entire file must be read on each CPU that is executing, thus adding much more file I/O overhead to the system, which in turn negatively impacts model performance and scalability. 
+
--[[User:Bmy|Bob Y.]] 14:10, 14 September 2012 (EDT)
  
−
Starting with [[GEOS-Chem v9-01-03 benchmark history#v9-01-03g|v9-01-03g]], we have added netCDF file I/O capability to GEOS-Chem.  '''''Going forward, all GEOS-Chem users will have to have access to a netCDF library installation on their systems in order to be able to run GEOS-Chem.'''''  Where there are several GEOS-Chem users at a single institution, the libraries only have to be built once (by the IT guru) and then placed in a common directory where all users may access them.  Bob Yantosca and Lee Murray have created [[Installing libraries for GEOS-Chem|a user-friendly netCDF installer]] which should simplify the library build process and also help to standardize the GEOS-Chem compilation sequence.
+
== Addenda Section ==
  
−
We realize the transition to full netCDF I/O cannot be achieved overnight.  The first step shall be to modify GEOS-Chem to be able to read certain netCDF data files from disk.  This has already been done with the following input files:
+
These items were added to the Summer-Fall 2012 newsletter after the initial publication date (14 Sep 2012):
  
−
#[[GEOS-5.7.2]] met data files
+
=== GEOS-Chem v9-02 ===
−
#[[Olson land map]] (1992) and (2001)
+
−
#[[MODIS leaf area indices|MODIS LAI data]]
+
−
#[[Dry deposition]] 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.   
+
The GEOS-Chem version immediately following v9-01-03 shall be denoted as [[GEOS-Chem v9-02|v9-02]].  We have dropped the last two digits (which were the old “beta release” numbers).  We now use [http://acmg.seas.harvard.edu/geos/geos_benchmark.html 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.
  
−
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.
+
[[GEOS-Chem_model_development_priorities|Several new features have been proposed for inclusion into v9-02]].  The [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html 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.
  
−
== De-supporting of GEOS-3 meteorology ==
+
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).
  
−
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.
+
=== Grid Independent GEOS-Chem: Update ===
  
−
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.
+
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.
  
−
== GEOS-Chem Adjoint news ==
+
Eric Nielsen (at GMAO) discovered that further modifications (click [http://wiki.seas.harvard.edu/geos-chem/index.php/Grid-independent_GEOS-Chem#Additional_modifications_that_are_activated_with_the_DEVEL.3Dyes_option HERE] and [http://wiki.seas.harvard.edu/geos-chem/index.php/Grid-independent_GEOS-Chem#Additional_modifications_that_are_activated_with_the_DEVEL.3Dyes_option 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.
  
−
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!
+
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 [[GEOS-Chem v9-01-03|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.
  
−
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 <tt>geos-chem-support@as.harvard.edu</tt>.
+
Postdoc Christoph Keller is working on a new [[Grid-independent GEOS-Chem#Emissions Component|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.
  
−
== GAMAP v2-16 ==
+
=== Flexible Chemistry with KPP ===
  
−
We plan on releasing the next [http://acmg.seas.harvard.edu/gamap/ GAMAP] version (v2-16) when [[GEOS-Chem v9-01-03]] is officially released.  GAMAP v2-16 will contain the following new features:
+
Mat Evans is spearheading an effort to replace the existing SMVGEAR chemistry solver in GEOS-Chem with a [https://docs.google.com/document/d/1p-n-m5SIpRecXjVBIU9EsZU3wHZSj93zr2UoaEIrARQ/edit 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.
  
−
#Support for reading/plotting [[GEOS-5.7.2]] met data
+
=== Radiative transfer with RRTMG ===
−
#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)
+
  
−
This release shall standardize several fixes that had been made to the GAMAP source code over the past year.  We shall also update the [http://acmg.seas.harvard.edu/gamap/doc/index.html GAMAP manual] to remove outdated information.
+
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.
  
−
== Miscellany ==
+
=== Potential issue with TOMAS microphysics ===
  
−
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 [http://acmg.seas.harvard.edu/geos/ 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!
+
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.
  
−
--<br>
+
<br>
 +
----
 
Bob Yantosca<br>
 
Bob Yantosca<br>
−
(with input from Mike Long, Melissa Payer, and Matthew Cooper)<br>
+
(on behalf of Mike Long, Melissa Payer, Matthew Cooper, and Nicolas Bousserez)<br>
−
21 May 2012
+
28 Sep 2012
−
 
+
−
--[[User:Bmy|Bob Y.]] 16:34, 21 May 2012 (EDT)
+

Latest revision as of 14:07, 19 June 2019

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. GFED3 daily and 3-hourly emissions (Prasad Kasibhatla, Duke)
  5. Improved snow scavenging & washout parameterization (Qiaoqiao Wang, Harvard)
  6. Stratospheric chemistry via archived production/loss rates (Lee Murray, Harvard)
  7. Addition of bromine chemistry into the standard mechanism (Justin Parella, formerly Harvard)
  8. PARANOX plume model for ship emissions (Geert Vinken, Eindhoven)
  9. Historical emissions of SO2, NOx, BC, and POA (Eric Leibensperger, SUNY Plattsburgh)
  10. Updates to facilitate Grid-Independence and interface with the GEOS-5 GCM (GEOS-Chem Support Team)
  11. 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:

  1. v9-01-03e (Run0)
    • Tests the new snow scavenging and washout parameterization.
  2. 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).
  3. v9-01-03-Release (Run0)
    • Code prior to release, with bromine chemistry turned OFF.
  4. 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::

  1. 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:

  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 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:

  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 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:

  1. GEOS-5.7 met data files
  2. Olson land map (1992) and (2001)
  3. MODIS LAI data
  4. Dry deposition input files
  5. The jv_atms.dat input file for the FAST-J photolysis mechanism
  6. 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

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:

  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)

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.

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; 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

GEOS-5.7.2

As of August 2011, NASA/GMAO has updated the operational GEOS system from GEOS-5.2.0 to GEOS-5.7.2.

  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.

GEOS-5 FP and GEOS-5 FP-IT

GMAO recently has made further changes to the assimilated meteorology product:

  1. 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.

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

Miscellany

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.


Bob Yantosca
(on behalf of Mike Long, Melissa Payer, Matthew Cooper, and Nicolas Bousserez)
14 Sep 2012

--Bob Y. 14:10, 14 September 2012 (EDT)

Addenda Section

These items were added to the Summer-Fall 2012 newsletter after the initial publication date (14 Sep 2012):

GEOS-Chem v9-02

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.


Bob Yantosca
(on behalf of Mike Long, Melissa Payer, Matthew Cooper, and Nicolas Bousserez)
28 Sep 2012

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